Finding the Optimal Regimen for Mycobacterium Abscessus Treatment (FORMaT)
Phase: PHASE2
Conditions: Pulmonary Disease Due to Mycobacteria (Diagnosis)
Sponsor: The University of Queensland

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
i 
 
A multi-centre, randomised, multi-arm, adaptive platform trial in 
people with or without cystic fibrosis Finding the Optimal 
Regimen for Mycobacterium abscessus Treatment (FORMaT) 
MASTER PROTOCOL 
Protocol Version 
Version 4.1 
Protocol Date 
20 February 2024 
Protocol Number  
FORMaT001 
Funding 
 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
EudraCT Number 
2020-000050-10 
EU-CT Number 
2023-506575-99-00-EU CT 
Sponsor 
Contact  
The University of Queensland 
FORMaTtrial@uq.edu.au 
 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
ii 
TABLE OF CONTENTS 
1.1 
SYNOPSIS ................................................................................................................................................... 2 
1.2 
PROTOCOL STRUCTURE .............................................................................................................................. 4 
1.3 
FORMAT MASTER PROTOCOL................................................................................................................... 5 
1.3.1 FORMaT Appendices and Supplements ................................................................................................ 5 
2.1 
MICROBIOLOGY OF MABS ........................................................................................................................ 7 
2.2 
EPIDEMIOLOGY .......................................................................................................................................... 7 
2.2.1 High-risk Patient Populations ............................................................................................................... 7 
2.3 
CLINICAL PRESENTATION AND DIAGNOSTIC CHALLENGES ...................................................................... 8 
2.4 
TREATMENT REGIMENS GUIDELINES AND CHALLENGES .......................................................................... 8 
2.5 
HEALTH RELATED QUALITY OF LIFE ........................................................................................................ 8 
2.6 
THE PATIENT VOICE .................................................................................................................................. 9 
2.7 
GENERATING EVIDENCE USING A RANDOMISED PLATFORM TRIAL DESIGN ............................................ 9 
2.8 
SUMMARY ................................................................................................................................................ 10 
3.1 
PRIMARY OBJECTIVE ............................................................................................................................... 10 
3.2 
SECONDARY OBJECTIVES ........................................................................................................................ 10 
4.1 
ELIGIBILITY CRITERIA ............................................................................................................................. 10 
4.2 
INTERVENTION PROGRAM ELIGIBILITY (APPENDIX A) ........................................................................... 11 
4.2.1 Intervention Program Inclusion Criteria ............................................................................................. 11 
4.2.2 Intervention Program Exclusion Criteria ............................................................................................ 12 
4.3 
OBSERVATIONAL COHORT (APPENDIX B) ............................................................................................... 12 
4.3.1 Observational Cohort Inclusion Criteria ............................................................................................ 12 
4.3.2 Observational Cohort Exclusion Criteria............................................................................................ 12 
4.4 
ADDITIONAL ELIGIBILITY CRITERIA........................................................................................................ 13 
4.5 
TRIAL SETTING AND PARTICIPATING REGIONS ........................................................................................ 13 
4.6 
TRIAL ENDPOINTS .................................................................................................................................... 13 
5.1 
SITE INITIATION ....................................................................................................................................... 14 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
iii 
5.2 
TRIAL DURATION ..................................................................................................................................... 14 
5.3 
RECRUITMENT OF POTENTIAL PARTICIPANTS ......................................................................................... 14 
5.4 
INFORMED CONSENT................................................................................................................................ 14 
5.4.1 Consent to the FORMaT Master Protocol ........................................................................................... 14 
5.4.2 Consent to Specific Appendix Intervention Program(s), Observation, Discovery Sub-Studies and 
Integrated studies ............................................................................................................................................ 15 
5.5 
CORE TRIAL PROCEDURES ....................................................................................................................... 15 
5.5.1 Respiratory Samples for Microbiology Assessment ............................................................................. 18 
5.5.2 Whole Genome Sequencing ................................................................................................................. 19 
5.5.3 Chest Computed Tomography ............................................................................................................. 19 
5.5.4 Spirometry ........................................................................................................................................... 19 
5.5.5 Physical Examination and Vital Signs ................................................................................................. 19 
5.5.6 Six Minute Walk Test ........................................................................................................................... 20 
5.5.7 Medication Review............................................................................................................................... 20 
5.6 
QUALITY ASSURANCE (QA) .................................................................................................................... 20 
5.6.1 Microbiology and DNA Extraction QA ............................................................................................... 20 
5.7 
NOTES ON SPECIFIC TRIAL VISITS ........................................................................................................... 21 
5.7.1 Screening ............................................................................................................................................. 21 
5.7.2 Time Point Start treatment (TPST) ...................................................................................................... 21 
5.7.3 Time Point Final (TPF) ....................................................................................................................... 21 
5.7.4 Early Withdrawal Visit ........................................................................................................................ 21 
5.7.5 Unscheduled Visit ................................................................................................................................ 21 
5.8 
SAFETY MONITORING .............................................................................................................................. 22 
5.8.1 Definition of Adverse Events ............................................................................................................... 22 
5.8.2 Attribution of Adverse Events in the FORMaT Trial ........................................................................... 22 
5.8.3 Definition of Serious Adverse Events .................................................................................................. 22 
5.8.4 Reporting of Safety Events ................................................................................................................... 23 
5.8.5 Coding of Adverse Events for Analysis ................................................................................................ 24 
5.8.6 Toxicology Thresholds ......................................................................................................................... 24 
5.9 
PARTICIPANT WITHDRAWAL AND DISCONTINUATION OF TREATMENT .................................................. 24 
5.9.1 Withdrawal of Consent ........................................................................................................................ 24 
5.9.2 Discontinuation of Treatment .............................................................................................................. 24 
5.10 
DATA MANAGEMENT............................................................................................................................... 28 
5.10.1 Data Collection, Entry and Storage .................................................................................................... 28 
5.10.2 Data Storage and Retention ................................................................................................................. 29 
6.1 
BAYESIAN ANALYSIS AND BAYESIAN ADAPTIVE RANDOMISATION (BAR) ........................................... 29 
6.2 
RANDOMISATION ..................................................................................................................................... 30 
6.2.1 Blinding of Treatment Allocation ........................................................................................................ 30 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
iv 
6.3 
MINIMISATION ......................................................................................................................................... 30 
6.4 
ADDING AND STOPPING INTERVENTIONS ................................................................................................ 31 
6.5 
SEAMLESS PHASE II TO PHASE III............................................................................................................ 31 
6.6 
SIMULATIONS AND STATISTICAL POWER ................................................................................................ 32 
6.7 
GENERAL ANALYSIS PRINCIPLES ............................................................................................................ 32 
7.1 
OVERVIEW ............................................................................................................................................... 32 
7.2 
TRIAL STEERING COMMITTEE ................................................................................................................. 32 
7.3 
INDEPENDENT DATA SAFETY MONITORING BOARD ............................................................................... 32 
7.4 
TRIAL MANAGEMENT COMMITTEE ......................................................................................................... 34 
7.5 
FORMAT PHARMACOVIGILANCE TEAM .................................................................................................. 34 
7.6 
DRUG AND INTERVENTION SELECTION COMMITTEE (DISC) .................................................................. 35 
7.7 
CONSUMER ADVISORY GROUP (CAG) .................................................................................................... 35 
7.8 
MONITORING ........................................................................................................................................... 35 
8.1 
RESEARCH ETHICS APPROVAL AND SITE-SPECIFIC GOVERNANCE ......................................................... 35 
8.1.1 FORMaT Master Protocol and Trial Document Amendments ............................................................ 36 
8.1.2 Protocol Deviations ............................................................................................................................. 36 
8.2 
CONFIDENTIALITY ................................................................................................................................... 37 
8.3 
SITE REIMBURSEMENT ............................................................................................................................. 37 
8.4 
DATA SHARING ........................................................................................................................................ 37 
8.5 
PUBLICATION POLICY .............................................................................................................................. 37 
 
 
 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
v 
TABLE OF TABLES 
Table 1 Special Considerations for Core Trial Procedures and Schedule .................................................................. 16 
Table 2 Core Trial Procedures and Schedule ............................................................................................................. 17 
Table 3: Safety critical monitoring thresholds ............................................................................................................ 25 
 
TABLE OF FIGURES 
Figure 1 Design of the FORMaT Master Protocol and Appendices ............................................................................. 4 
Figure 2 FORMaT participant flow diagram ................................................................................................................ 6 
Figure 3 Participant enrolment into the FORMaT trial. ............................................................................................. 11 
 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
vi 
ABBREVIATIONS  
 
ADL 
 
 
Activities of Daily Living 
AE 
 
 
Adverse Event 
AFB 
 
 
Acid-Fast Bacilli 
ATS 
 
 
American Thoracic Society 
BAL 
 
 
Bronchoalveolar Lavage 
BAR 
 
 
Bayesian Adaptive Randomisation 
BCM  
 
Biased Coin Minimisation 
CAG  
 
Consumer Advisory Group 
CF 
 
 
Cystic Fibrosis 
CFTR  
 
Cystic Fibrosis Transmembrane Conductance Regulator 
CI 
 
 
Chief Investigator 
CRF 
 
 
Case Report Form 
CT 
 
 
Computed Tomography 
CTCAE 
 
Common Terminology Criteria for Adverse Events 
DISC  
 
Drug and Intervention Selection Committee 
DNA  
 
Deoxyribonucleic Acid 
eCRF  
 
electronic Case Report Form 
eISF 
 
 
electronic Investigator Site File 
eTMF  
 
electronic Trial Master File 
FDA 
 
 
Food and Drug Administration 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
GCP 
 
 
Good Clinical Practice 
GDPR  
 
General Data Protection Regulation 
GLI 
 
 
Global Lung Initiative 
HRCT  
 
High-Resolution Computed Tomography 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
vii 
HREC  
 
Human Research Ethics Committee 
IA 
 
 
Inhaled Amikacin 
ICH-GCP  
 
International Council for Harmonisation Good Clinical Practice Guidelines 
ICMJE  
 
International Committee of Medical Journal Editors 
iDSMB  
 
Independent Data Safety Monitoring Board 
IEC 
 
 
Independent Ethics Committee 
IRB 
 
 
Independent Review Board 
ISO 
 
 
International Organization for Standardization 
IV 
 
 
Intravenous 
IVA 
 
 
Intravenous Amikacin 
LAI 
 
 
Liposomal Amikacin for Inhalation 
LLN 
 
 
Lower Limit of Normal 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
MBS  
 
Medicare Benefits Scheme 
MCRI  
 
Murdoch Children’s Research Institute 
MoOP  
 
Manual of Operating Procedures 
MRL  
 
Mycobacterial Reference Laboratory 
NTM  
 
Non-Tuberculous Mycobacteria 
PBS 
 
 
Pharmaceutical Benefits Scheme 
PI 
 
 
Principal Investigator 
PICF  
 
Participant Information and Consent Form 
PK 
 
 
Pharmacokinetics 
QA 
 
 
Quality Assurance 
QoL 
 
 
Quality of Life 
R-Con  
 
Randomisation – Consolidation 
RCT 
 
 
Randomised Control Trial 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
viii 
REDCap 
 
Research Electronic Data Capture 
REMAP-CAP  
Randomised, Embedded, Multifactorial Adaptive Platform trial for Community-
Acquired Pneumonia  
R-PI/IC 
 
Randomisation – Prolonged Intensive or Immediate Consolidation 
rRNA  
 
ribosomal ribonucleic acid 
R-SI 
 
 
Randomisation – Short Intensive  
SAEs  
 
Serious Adverse Events 
SAHMRI 
 
South Australian Health and Medical Research Institute 
SIV 
 
 
Site Initiation Visit 
SOP 
 
 
Standard Operating Procedure 
SSI 
 
 
Significant Safety Issues 
SUSAR 
 
Suspected Unexpected Serious Adverse Reaction 
TB 
 
 
Tuberculosis 
TDM  
 
Therapeutic Drug Monitoring 
TMC  
 
Trial Management Committee 
TPF 
 
 
Time Point Final 
TPST  
 
Time Point Start Treatment 
TSC 
 
 
Trial Steering Committee 
ULN 
 
 
Upper Limit of Normal 
USMs  
 
Urgent Safety Matters 
UQ 
 
 
University of Queensland 
WGS  
 
Whole Genome Sequencing 
6MWD 
 
Six-minute walk distance  
6MWT  
 
Six-minute walk test  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
1 
PRINCIPAL INVESTIGATORS STATEMENT 
 
I confirm that I have read the FORMaT Master Protocol Version 4.1, dated 20th February 2024. As the Principal 
Investigator, I understand it, and I agree to adhere to the study conduct requirements and agree to conduct this protocol 
in accordance with International Conference on Harmonization Good Clinical Practice E6 (ICH-GCP), the 
Declaration of Helsinki, the United States (US) Food and Drug Administration (FDA), and local regulations and 
guidelines.  I agree to report all information or data in accordance with the protocol, and in particular I agree to report 
any serious adverse events.  I will accept the monitors’, auditors’ and regulatory inspectors’ oversight of the study.  
I will promptly submit the protocol to the applicable ethical review board as required. 
 
………………………………………………………………………………………………...... 
Principal Investigator Signature 
 
………………………………………………………………………………………………….. 
Principal Investigator Name 
 
………………………………………………………………………………………………….. 
Date (dd/mmm/yyyy) 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
2 
1 
INTRODUCTION 
1.1 
SYNOPSIS 
Background: Mycobacteria in the Mycobacterium abscessus group (MABS) are a species of non-tuberculous 
mycobacteria (NTM) found in water and soil habitats that exhibit high levels of intrinsic multi-drug resistance (1).  
NTM includes more than 160 species that are recognised opportunistic human pathogens, with chronic pulmonary 
infections the most common clinical presentation.  Individuals with underlying inflammatory lung diseases are more 
susceptible to MABS pulmonary disease (MABS-PD), but MABS also affects patients with no underlying condition.  
MABS-PD can result in significant morbidity, increased healthcare utilisation, accelerated lung function decline, 
impaired quality of life (QoL) (2), more challenging lung transplantation (3), and increased mortality (2).  Of 
particular concern is the increasing prevalence of pulmonary infections occurring worldwide in patients with 
bronchiectasis and cystic fibrosis (CF), with prevalence between 5 to 20% (2, 4, 5).  There is real evidence of this in 
Queensland, Australia (where the infection is notifiable) with the prevalence increasing from 0.85/100,000 in 2001 
to 2.35/100,000 in 2016, where now over 100 cases are reported annually, clearly illustrating the emerging threat of 
this infection.  While the increasing prevalence might be reflective of enhanced surveillance and improved 
microbiological detection (6-8) (9) the reasons for this changing epidemiology are poorly understood (2, 4, 10, 11). 
Treatment regimens for MABS are highly variable, not evidence-based and involve complex, expensive, and often 
poorly tolerated drug combinations for prolonged periods (>12 months).  Some individuals will have positive cultures 
that clear spontaneously, some will initially have positive cultures without obvious MABS-PD but go on to develop 
disease at a later stage, and some may present with established MABS-PD.  MABS-PD can be associated with a rapid 
decline in health status, and there is evidence that successfully clearing infection is associated with better health 
outcomes (12, 13).  However, toxicity, poor tolerance and the prolonged and complex nature of therapy may increase 
the reluctance of clinicians to initiate treatment and for patients to accept it.  A recent systematic review and meta-
analysis revealed that such treatment regimens are often ineffective and may even worsen QoL (14).  The costs and 
treatment burden of NTM infection are high, and highest for MABS-PD, estimated at $AUD12-28,000/month (15) 
highlighting the need to assess the healthcare costs and cost-effectiveness of therapies to inform health policy around 
NTM.  Pathogen, host, and treatment factors all likely play a role in clinical and microbiological outcomes. 
 
Aims: 
1. To build an iterative, standing, platform trial with innovative and adaptive properties to evaluate combinations 
of therapies for patients with MABS-PD.  Initially this will test therapies that are currently used and 
recommended in published international consensus guidelines and are the basis for the current treatment 
guidelines for MABS-PD.  Once the best combinations have been established the platform described in the 
Master Protocol will have the capacity to add new treatments and to eliminate therapies because of futility as 
they either lack efficacy or cause unacceptable toxicity.  The data obtained as part of the trial will be used to plan 
for new waves of the platform trial using novel therapeutic approaches that may be tested against the previously 
determined optimal approaches, thus leading in an iterative fashion to improving microbiological clearance and 
health outcomes associated with MABS-PD. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
3 
2. To use the opportunities afforded by the clinical trial platform to establish discovery studies to: 
i. 
Understand the effects of MABS-PD and therapeutic interventions on health-related quality of life and 
determine the cost effectiveness of proposed therapy combinations; 
ii. 
 To develop strategies for optimising drug dosing using robust pharmacokinetics; 
iii. 
 Understand susceptibility to MABS-PD and develop biomarkers of clinical disease, disease progression 
and response to therapy; 
iv. 
 Investigate the genomics of human MABS strains and antibiotic resistance genes and impact of 
therapeutic interventions. 
3. To investigate the use of registries to facilitate the long-term monitoring of patient outcomes from MABS-PD 
and treatment. 
 
Methodology: Entry into the Finding the Optimal Regimen for Mycobacterium abscessus Treatment (FORMaT) 
trial can occur at two different levels; 
1 - participants of any age from their first MABS isolate and not receiving current MABS therapy are eligible to enrol 
in the Observational Cohort and; 
2 - participants of any age meeting the American Thoracic Society (ATS) criteria for the diagnosis of MABS-PD and 
are untreated for MABS-PD at the time of starting intensive therapy are eligible to enrol in the Intervention Program.  
Participants initially enrolled into the Observational Cohort who go on to meet the ATS criteria for MABS-PD can 
transition to the Intervention Program at any time.  Intervention Program participants will be randomised to receive 
MABS-PD therapy combinations and additional outcomes will be assessed. 
Participants in both the Observational Cohort and Intervention Programs will contribute the same core data, thus 
providing the opportunity to examine what happens to both treated and untreated patients with positive cultures 
longitudinally as well as the transition to MABS-PD.   
 
Primary Outcome 
The primary outcome of the Intervention Program is microbiological clearance of MABS with good tolerance of the 
interventions. 
Definition of MABS clearance at final outcome: 
Negative MABS cultures from four consecutive sputum samples with one of those sputum specimens collected four 
weeks after the completion of consolidation therapy, or a MABS negative Bronchoalveolar Lavage (BAL) collected 
four weeks after completion of consolidation. 
Definition of tolerance: 
Tolerance is based on the Common Terminology Criteria for Adverse Events (CTCAE version 5.0).  Only adverse 
events that are attributed as either “possibly-“, “probably-“, or “definitely-“ related to study drug will be assessed in 
the determination of tolerance.  “Good” tolerance is defined as no adverse events occurring or only adverse events 
coded as CTCAE grades 1 and 2. “Poor” tolerance is defined as any adverse events attributed as possibly-, probably-
, or definitely-related to study drug coded as CTCAE grades 3, 4, or 5. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
4 
 
The Intervention Program within the FORMaT platform will adopt an adaptive design with Bayesian Adaptive 
Randomisation (BAR) when there is randomisation across three or more interventions and may also include interim 
rules for dropping or adding treatment arms. BAR allows the randomisation probabilities to each of the interventions 
to be updated during the trial to enable more participants to be randomised to more promising interventions. The 
probabilities of allocation to each intervention are based on the posterior probability of the intervention being superior 
to the control (16). The approach used will carry forward the most promising arms that achieve a minimum level of 
efficacy with acceptable toxicity. If a treatment is carried forward until the end it will be tested against the 
control/reference group and recommended if the test statistic is above a certain threshold. The Intervention Program 
will consist of treatment modules specified in Appendix A starting with sequential Phase II trials, including a 
randomised intensive treatment phase, and a randomised consolidation treatment phase. In the future, interventions 
reaching a probability threshold of demonstrating success at the end of the Phase II trial will have the potential to 
seamlessly continue to recruit to a Phase III study to enable the Phase II data to be utilised as part of a Phase III study, 
thus reducing the resources required to achieve high quality evidence on which to base treatments.  
The FORMaT Master Protocol describes the adaptive platform trial to evaluate microbiological, functional, 
radiological, and quality of life outcomes of interventions utilised in the treatment of MABS-PD, in combination 
with the Observational Cohort. 
 
1.2 
PROTOCOL STRUCTURE 
The FORMaT trial is designed as a standing iterative, platform trial with innovative and adaptive properties.  This is 
reflected in the multi component structure of the FORMaT Protocol outlined in Figure 1.  The framework for the 
FORMaT trial is established within the FORMaT Master Protocol.  The Intervention Program(s), the Observational 
Cohort, Discovery, Registry Linkage studies, Health Economics and General Statistical Principles are described in 
specific Appendices. 
 
 
Figure 1 Design of the FORMaT Master Protocol and Appendices
Finding the Optimal Regimen for Mycobacterium Abscessus Treatment (FORMaT)
MASTER PROTOCOL
APPENDIX A
INTERVENTION
PROGRAMS
APPENDIX D
REGISTRY
LINKAGE
STUDIES
APPENDIX B
OBSERVATIONAL
COHORT
APPENDIX C
DISCOVERY
STUDIES
APPENDIX E
HEALTH
ECONOMICS
APPENDIX F
GENERAL
STATISTICAL
PRINCIPLES

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
5 
1.3 
FORMAT MASTER PROTOCOL 
The FORMaT Master Protocol outlines the core structure, procedures, and processes of the FORMaT trial.  The 
information described in the FORMaT Master Protocol applies to all participants regardless of if they are receiving 
intervention treatment for MABS-PD or are enrolled in the Observational Cohort, unless otherwise stated. 
The Master Protocol has the following structure: 
• 
The background and rationale for determining the optimal treatment regimens for MABS-PD. 
• 
The overarching objectives of the FORMaT trial (including both the Intervention Program and the 
Observational Cohort). 
• 
The design of the FORMaT trial including the two-level approach to assessing eligibility into the trial, the 
trial endpoints and the general statistical principles to be used in the analysis of the trial. 
• 
The conduct of the FORMaT trial detailing recruitment methods and consent processes, the core trial 
timepoints and procedures, safety monitoring processes and data management procedures. 
• 
Details of The FORMaT trial oversight, ethical and administrative considerations. 
 
1.3.1 
FORMAT APPENDICES AND SUPPLEMENTS 
The FORMaT Appendices describe in detail the information specific to the Appendices and the sub-studies and 
integrated studies nested within them. As such, appendix specific information is not described within the FORMaT 
Master Protocol but rather the Master Protocol sets the framework within which the Appendices exist.  As the trial 
progresses, new interventions and methodologies can be added to the FORMaT trial through the addition of a new 
appendix.  Conversely, as interventions and methodologies are found to be futile the corresponding studies in the 
appendix can be removed.  It is not anticipated that these changes will affect the framework of the Master Protocol.  
Any changes to appendix specific studies require ethics approval. 
The FORMaT Supplements are additional documents that expand the scope of the relevant appendices.  They provide 
additional detail and information to supplement the specific appendix they are linked to.  Changes to supplements do 
not require ethical approval as they are not a part of the Master Protocol or appendices but are an additional document 
to elaborate on the specific components contained within an appendix.  FORMaT Appendices are structured as 
follows: 
• 
Each appendix has a theme: for example, Appendix A for Interventions, Appendix B for Observation, 
Appendix C for Discovery studies, Appendix D for Registry Interactions, Appendix E for Health Economics, 
and Appendix F for General Statistical Principles. 
• 
Appendix A describes the details for the Intervention Programs of the FORMaT Trial including intensive 
and consolidation interventions (Figure 2).  For example, Appendix A1 describes the first of such 
Intervention Programs and if new interventions are added to either the intensive or consolidation phases these 
would be added in new Appendices A2, A3 etc.  Data from previous programs using the same intervention 
combinations may be incorporated in the analysis of a new program.  Thus, data from Appendix A1 could 
be combined with data from Appendix A2 for example. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
6 
• 
Within some of the Appendices are nested studies that have been designed to investigate specific objective(s). 
The components described within each appendix are variable and dependant on the nature of the appendix and the 
studies nested within it.  Overall, FORMaT Appendices will contain the following components: 
• 
The overall objective specific to that appendix. 
• 
Where relevant, information about the features of the interventions or the study to be investigated. 
• 
Appendix specific eligibility criteria. 
• 
Appendix specific consent requirements. 
• 
Appendix specific procedures and safety measures to be assessed. 
• 
Appendix specific statistical methods and simulations where relevant. 
 
Figure 2 FORMaT participant flow diagram 
Eligibility into the Intervention Program or Observational Cohort is determined at Screening.  For the first iteration 
of the Intervention Program, there will be up to three randomisations between Screening and the Final Outcome Visit.  
Symbols (▲✢) indicate possible randomisation points (see the relevant appendix for further information on 
randomisation). 
 
 
+ve
Observation Cohort
Final Outcomes
Screening and Eligibility
Short
Intensive
A
Short
Intensive
B
Short
Intensive
C
Future
Intensive
Arms
-ve
Consolidation b
Consolidation a
Future Consolidation Arms
▲
★
✢
Final Outcomes
Physician
Directed
Consolidation b
Consolidation a
Future Consolidation Arms
✢
Screening
Consolidation b
Consolidation a
Future Consolidation Arms
✢
Prolonged
Intensive
Therapy
BAL / Sputum Samples Taken
Consolidation b
Consolidation a
Future Consolidation Arms
✢
BAL / Sputum Samples Taken
Future
Novel
Therapy /
Placebo
⬢

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
7 
2 
BACKGROUND 
2.1 
MICROBIOLOGY OF MABS 
Of the many pathogenic NTM species, MABS are recognised as causing the most serious pulmonary infections, 
associated with the greatest problems of antibiotic resistance, toxicity and treatment failure (12, 17).  MABS are 
currently divided into 3 subspecies: M. abscessus subspecies abscessus (M. a. abscessus), subs. massiliense (M. a. 
massiliense) and subs. bolletii (M. a. bolletii).  While there is variation in the prevalence of the subspecies in different 
populations, M. a. abscessus is the most common overall (45-68%), followed M. a. massiliense (20-55%) and M. a. 
bolletii (8-25%) (18-20).  Progression of MABS-PD due to the different subspecies (21) appears to be similar, 
although treatment outcomes vary significantly and are partially explained by differential antimicrobial susceptibility 
to macrolide antibiotics.  MABS are intrinsically drug resistant to multiple classes of antibiotics and they can also 
acquire antibiotic resistance genes to macrolides and aminoglycosides, leading to clearance rates of ≈50% following 
intensive therapy (19, 22, 23).  After apparently successful treatment, relapse or recurrences with new strains occur 
in 15-33% of patients (19).  Nevertheless, macrolides provide the therapeutic backbone of guideline-based MABS 
treatment (1, 4).  Furthermore, they are the only antibiotic class where there is some correlation between in vitro 
susceptibility data and clinical response (14).  Macrolide resistance in MABS is either constitutive or inducible (20).  
The less common, constitutive resistance may be acquired during macrolide therapy and results from mutations in 
the 23S rRNA gene (rrl).  Inducible macrolide resistance is related to the MABS ribosomal methyl transferase gene, 
erm(41).  Such isolates appear susceptible at day 3 following infection, but resistant by day 14 using prolonged 
incubation drug susceptibility testing.  M. a. massiliense has a truncated and dysfunctional erm(41) gene, thus making 
it more susceptible to macrolides, whereas M. a. abscessus and M. a. bolletii usually, but not invariably, have 
inducible resistance (20).  It is not surprising then that microbiological cure rates of MABS-PD appear partly related 
to macrolide resistance with clearance rates up to 88% in those with macrolide susceptible isolates, and only 36% in 
the setting of inducible macrolide resistance (19).  Molecular detection of the subspecies, including identifying the 
erm(41) and rrl genes is important in understanding treatment response, and potentially targeting novel treatment 
approaches. 
 
2.2 
EPIDEMIOLOGY 
NTM can cause both asymptomatic and symptomatic infections in humans (1).  Pathogenic strains of MABS have 
been isolated from potable water, and MABS infections are more prevalent in coastal areas and regions with humid 
tropical climates (12, 24, 25).  While most infections are thought to be acquired from environment aerosols (26), in 
patients with CF there is evidence supporting the emergence of worldwide dominant clones (of increased virulence) 
that may be capable of patient-to-patient transmission (18). 
 
2.2.1 
HIGH-RISK PATIENT POPULATIONS 
CF is an autosomal recessive condition caused by mutations in the CF transmembrane conductance regulator (CFTR) 
gene.  Mortality and morbidity of CF patients are predominantly related to chronic suppurative lung disease (27).  CF 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
8 
is a risk factor for MABS-PD (and NTM more broadly) and even carrier status of disease-causing mutation in CFTR 
(24) may also increase risk.  Other structural lung diseases, bronchiectasis, chronic obstructive pulmonary disease, 
previous mycobacterial disease (including Tuberculosis (TB) and NTM), severe gastro-oesophageal reflux and 
immunosuppression (where dissemination can occur) (11) also increase risk of infection.  The age range of CF and 
non-CF affected patients with MABS-PD overlap, with non-CF patients generally being older than those with CF 
(>55 vs <30 years) (24). 
 
2.3 
CLINICAL PRESENTATION AND DIAGNOSTIC CHALLENGES 
Due to their ubiquitous nature, the clinical significance of positive MABS cultures in respiratory specimens can be 
challenging.  It may appear transiently in sputum cultures, persistently colonise the lower airways or progress to 
MABS-PD.  The radiological and clinical features of underlying chronic respiratory disorders overlap considerably 
with changes attributable to MABS-PD making diagnosis and treatment decisions difficult and care is required to 
follow the ATS criteria in making the diagnosis of MABS-PD.  Inclusion into the intervention program(s) will require 
meeting all the ATS criteria including both microbiological and clinical criteria. 
 
2.4 
TREATMENT REGIMENS GUIDELINES AND CHALLENGES 
MABS treatment outcomes differ according to the etiologic organism.  Recurrence rates for infection are high, despite 
successful treatment completion (28) but these approaches have not been evaluated in any trials.  Differing treatment 
outcomes present multiple therapeutic challenges in the treatment of MABS.  In recognition of these challenges, the 
ATS and the United States CF Foundation/European CF Society have published guidelines on NTM pulmonary 
disease (1, 4).  In agreement with the latest Cochrane Review (29), they note there are no drug regimens of proven or 
predictable efficacy for treating MABS.  Therefore, the guidelines are based on expert opinion only and in practice 
the treatments vary considerably (30).  Suggested regimens include an intensive phase of 4-12 weeks (based on 
microbiological response) of intravenous (IV) antibiotics (usually amikacin, cefoxitin or imipenem + tigecycline) 
plus an oral macrolide.  This is followed by consolidation therapy that includes oral drugs (usually a macrolide, plus 
others based on antibiograms, tolerability and experience) and an inhaled IV formulation of amikacin for 3 to >12 
months.  Dosing by individual pharmacokinetic (PK) data and therapeutic drug monitoring (TDM) may lead to 
optimal drug levels at infection sites and better treatment outcomes, although measuring levels within the lower 
airways frequently and non-invasively is challenging.  Few PK studies involving antibiotics for NTM have been 
performed and few assays are currently available.  Inhaled antibiotics have the potential advantages of achieving 
higher airway concentrations, while reducing the risk of systemic toxicity. 
 
2.5 
HEALTH RELATED QUALITY OF LIFE 
A recent systematic review and meta-analysis revealed that MABS treatments are often ineffective and may even 
worsen QoL (14).  The review strongly recommended that “clinical, functional and QoL parameters should be given 
more emphasis in the evaluation of treatment outcomes” and that “better applications of current antibiotics are 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
9 
urgently needed” (14, 30).  In addition, the costs and the treatment burden of NTM infection are high, and highest 
for MABS-PD; estimated at $AUD12-28,000/month (15), highlighting the need to assess the healthcare costs and 
cost-effectiveness of therapies to inform health policy around NTM.  Pathogen, host and treatment factors are all 
likely to play a role in clinical and microbiological outcomes.  Consequently, there is an urgent need for evidence to 
support treatment decision-making for patients with MABS lung infection. 
 
2.6 
THE PATIENT VOICE 
In October 2015, the Food and Drug Administration (FDA) held a public meeting on NTM infection with patients 
and carers with the key theme to emerge (31) being the need for better, less toxic treatment with lower therapeutic 
burden.  Participants also prioritised “validating and using tools to measure QoL and developing disease specific 
activity and severity assessment tools” (32).  In January 2017, The James Lind Alliance released their top 10 research 
priorities for people with CF developed by CF patients, their families, and healthcare providers.  The third top priority 
was “What is the best treatment for NTM, including when to start and what medication?” (33).  Patients and 
healthcare providers are asking for evidence to guide the best approaches to manage this challenging infection. 
A consumer representative is a member of the FORMaT Trial Steering Committee and will be involved in the ongoing 
oversight of the trial.  In addition, the FORMaT consumer advisory group will enable a range of consumers to 
participate in the review of the protocol, trial development plans and consumer materials.  The consumer group will 
be able to provide their views and advice which will then be taken on board by the investigators and trial management 
team. 
 
2.7 
GENERATING EVIDENCE USING A RANDOMISED PLATFORM TRIAL 
DESIGN 
Platform trials using Bayesian statistical models, provide the opportunity to efficiently investigate multiple treatments 
for difficult-to-treat infections (e.g. multi-drug resistant TB (34)) requiring complex drug regimens in a 
heterogeneous population and can provide an iterative resource facilitating the translation of findings to improve 
clinical outcomes (35-37).  New adaptive trial approaches are now recognised and accepted by regulatory authorities, 
including the FDA.  Such trials are now being used in infectious diseases (38)  and TB (34), complex chronic diseases 
(36) and rare oncology conditions (39).  MABS-PD is a serious but relatively rare problem which can benefit from 
such methodology.  FORMaT provides a common platform that will enable a broad enrolment of patients who both 
do and do not have cystic fibrosis and across all ages that enables generalisability but also maintains the ability to 
examine the heterogeneity of treatment responses across specific subgroups, while also enabling a comparison with 
non-treated patients through an Observational Cohort who are followed up simultaneously.  The ability to examine 
novel therapeutic approaches using a common platform, along with the option to seamlessly move from phase II to 
phase III if warranted, also reduces the resources and the time required to deliver evidence-based treatments to 
patients who need it compared with conducting a series of independent trials. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
10 
2.8 
SUMMARY 
There is no evidence currently to guide therapy for MABS-PD, a complex and increasing health problem.  The 
FORMaT trial seeks to provide answers to key questions by healthcare providers and patients on the timing and 
nature of treatments for the growing number of people infected with MABS, as well as the potential to model the 
progression of this condition in both treated and untreated patients.  Furthermore, the trial will provide a platform for 
improving health outcomes for MABS patients and build a solid foundation for future testing of new therapeutics in 
the treatment of MABS. 
 
3 
OBJECTIVES 
3.1 
PRIMARY OBJECTIVE 
To determine the optimal therapy for the treatment of patients with MABS-PD. 
 
3.2 
SECONDARY OBJECTIVES 
1. To investigate the optimal approaches to antibiotic dosing and therapeutic drug monitoring. 
2. To investigate the health-related quality of life and cost effectiveness of proposed therapy combinations. 
3. To examine changes in clinical markers such as chest imaging and lung function to predict the onset of 
MABS-PD and response to therapies. 
4. To develop biomarkers to predict the onset of MABS-PD and response to therapies. 
5. To understand susceptibility to infection with MABS associated with the development of MABS-PD and host 
immune responses to infection and with treatment. 
6. To characterise the genomics of human MABS strains and antibiotic resistance genes in patients in the 
observation and intervention studies. 
 
4 
TRIAL DESIGN 
4.1 
ELIGIBILITY CRITERIA 
Eligibility criteria for the FORMaT trial can be applied at two levels: 
1. Eligibility into the Intervention Program, or; 
2. Eligibility into the Observational Cohort. 
Potential participants can only be enrolled in either the Intervention Program or the Observational Cohort at any one 
time.  Provided the eligibility criteria are met, potential participants may either: 
1. Enrol directly into the Intervention Program, or; 
2. Enrol into the Observational Cohort and transition into the Intervention Program once they satisfy the 
inclusion criteria for this program which can occur at any time during the trial (see Figure 3). 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
11 
 
 
Figure 3 Participant enrolment into the FORMaT trial. 
Eligibility into the FORMaT trial will be assessed at screening. Observational Cohort participants who go on to meet 
the Intervention Program eligibility criteria can transition from the Observational Cohort to the Intervention Program. 
 
4.2 
INTERVENTION PROGRAM ELIGIBILITY (APPENDIX A) 
Potential participants are eligible for the Intervention Program (Appendix A) if the criteria below are met.  Eligible 
participants with mixed NTM infections (slow growers + MABS) or with recurrence of MABS infection following 
completion of previous treatment  will be eligible if they meet the inclusion and exclusion criteria listed below.  For 
eligible participants with mixed NTM infections additional therapy combinations are available as detailed in the 
relevant appendices. 
 
4.2.1 
INTERVENTION PROGRAM INCLUSION CRITERIA 
1. 
Positive MABS-PD diagnosis meeting all three American Thoracic Society clinical, radiological and 
microbiological diagnostic criteria for MABS-PD. Defined as: 
a. 
Clinical: Pulmonary symptoms and exclusion of other diagnoses. 
b. 
Radiological: Nodular or cavitary opacities on chest radiograph or a chest high-resolution computed 
tomography (HRCT) scan showing multifocal bronchiectasis with multiple small nodules. 
c. 
Microbiological: MABS positive culture results from at least two separate expectorated sputum 
samples. 
or 
Positive culture results from at least one bronchial wash or lavage. 
 
or 
FORMAT
Eligibility Criteria
Assessed
Intervention
Program
Observational
Cohort

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
12 
Transbronchial or other lung biopsy with mycobacterial histopathologic features (granulomatous 
inflammation or acid-fast bacilli (AFB)) and positive culture for NTM or biopsy showing 
mycobacterial histopathologic features (granulomatous inflammation or AFB) and one or more sputum 
or bronchial washes that are culture positive for NTM. 
Screening samples must be collected within the timeframes stated in the relevant appendix. 
2. 
Male or female participants of any age. 
3. 
Participant has not received treatment for MABS-PD in the 12 months preceding assessment of eligibility 
or as specified in the relevant appendix (this includes drugs prescribed for the treatment of other 
mycobacteria and/or other indications that may have activity against MABS, as specified in the FORMaT 
Prohibited Drug List Standard Operating Procedure (SOP)). 
4. 
Informed consent signed by participant or parent/legal guardian if participant is under 18 years of age. 
5. 
Ability to comply with study visits, therapies and study procedures as judged by the site investigator. 
 
4.2.2 
INTERVENTION PROGRAM EXCLUSION CRITERIA 
• 
Participants receiving current treatment for MABS (this includes drugs prescribed for the treatment of other 
mycobacteria and/or other indications that may have activity against MABS, as specified in the FORMaT 
Prohibited Drug List SOP), except for participants taking azithromycin as part of routine treatment for CF or 
chronic infection-related pulmonary disease, or as specified in the relevant appendix. 
• 
Participants who have a QTc interval of >500 milliseconds (QT interval corrected based on Fridericia 
method). 
• 
Participants who are pregnant or planning to continue breast feeding. 
• 
Known hypersensitivity to any of the therapies for which no alternative option(s) have been provided. 
 
4.3 
OBSERVATIONAL COHORT (APPENDIX B) 
4.3.1 
OBSERVATIONAL COHORT INCLUSION CRITERIA 
To be eligible to participate in the Observational Cohort the following criteria must be met: 
1. Male and female participants of any age with at least one positive respiratory culture for MABS. 
2. Informed consent signed by participant or parent/legal guardian if participant is under 18 years of age. 
3. Ability to comply with study visits and study procedures as judged by the site investigator. 
 
4.3.2 
OBSERVATIONAL COHORT EXCLUSION CRITERIA 
Potential participants will be ineligible to participate in the Observational Cohort if any of the following criterion are 
met: 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
13 
• 
Receiving active treatment for MABS within the previous 12 months (this includes drugs prescribed for the 
treatment of other mycobacteria and/or other indications that may have activity against MABS, as specified 
in the FORMaT Prohibited Drug List SOP, except for participants taking azithromycin as part of routine 
treatment for CF or chronic infection-related pulmonary disease). 
 
4.4 
ADDITIONAL ELIGIBILITY CRITERIA 
Mixed NTM infections 
Participants who have cultured slow growing NTM of the same species two or more times in the 24 months prior to 
screening, with one of those cultures within the 6 months prior to screening, will be considered to have mixed NTM 
infection at the time of screening.  The participants must meet all other inclusion criteria and no exclusion criteria to 
be eligible for participation.  Ethambutol may be used in addition to trial therapies to cover mixed NTM infections 
considered to require treatment by their clinician. 
Appendix specific sub-studies and integrated studies  
Appendix specific sub-studies and integrated studies may have additional eligibility criteria which are described in 
each of the relevant appendices. 
 
4.5 
TRIAL SETTING AND PARTICIPATING REGIONS 
The trial will be conducted in multiple regions and trial sites.  There is no limit to the number of countries or 
participating sites.  A list of participating countries and sites are available on the FORMaT trial website 
(www.formattrial.com) and the clinical trial registries and will be updated as required. 
Race and Ethnicity 
Race and ethnicity will be collected as part of the demographic information for each participant. This information 
may be used to determine whether there are any potentially clinically significant racial and/or ethnic differences in 
the effects of any trial interventions. 
 
4.6 
TRIAL ENDPOINTS 
The primary outcome for the FORMaT Trial (Appendix A Intervention Program) is MABS clearance from 
respiratory samples with treatment tolerance.  MABS clearance is defined as negative MABS cultures from four 
consecutive sputum samples with one of those sputum specimens collected four weeks after the completion of 
consolidation therapy or a MABS negative Bronchoalveolar Lavage (BAL) collected four weeks after completion of 
consolidation therapy. 
The Common Terminology Criteria for Adverse Events (CTCAE) Version 5.0 will be applied for the coding of all 
adverse events (AEs) and serious adverse events (SAEs) that occur during the FORMaT trial that are categorised as 
“possibly-”, “probably-,” or “definitely-” related to study medications and/or interactions between study medications 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
14 
and concomitant medications.  “Good” tolerance will be defined as no adverse events occurring or only adverse 
events coded CTCAE grades 1 or 2. “Poor” tolerance will be defined as any adverse events coded as CTCAE grades 
3, 4, or 5. 
The primary outcome of the FORMaT Trial will be assessed as per the relevant appendices. 
 
5 
TRIAL CONDUCT 
5.1 
SITE INITIATION 
The FORMaT Trial is a multicentre, international clinical trial and the initiation of the FORMaT Master Protocol 
(including the Appendices) will be staggered across trial sites.  This staggered approach will allow the FORMaT 
Trial Management Team to closely examine the effectiveness of the FORMaT Trial Master Protocol.  Any changes 
required to improve the trial processes can be shared and implemented in other trial sites prior to site initiation.  The 
FORMaT Trial will open in Australia, and as feasible expand to other countries including centres in Europe, the 
United Kingdom, the Asia Pacific Region, Canada and North and South America.  Site activation and initiation will 
be performed in accordance with the FORMaT Site Initiation and Activation SOP. 
 
5.2 
TRIAL DURATION 
The FORMaT Master Protocol describes a standing platform trial with an innovative design tailored to the clinical 
setting that will enable new therapies to be tested as they become available.  As such, there is no specific limit to the 
duration of the FORMaT trial while there is clinical need for the trial except for logistic issues which include trial 
funding.  A detailed outline of the trial timeline for participants is described in the relevant appendix. 
 
5.3 
RECRUITMENT OF POTENTIAL PARTICIPANTS 
Potential participants will be identified at study sites by the treating physician.  Once identified, potential participants 
or their parent/guardian will be approached by the FORMaT Trial site-specific research team or treating physician to 
discuss the FORMaT trial and provided with the FORMaT Participant or Parent/Guardian Information and Consent 
Forms (PICFs).  The FORMaT Trial site-specific research team members will allow participants and/or their 
parent/guardian adequate time to read the PICFs and an opportunity to ask any trial related questions and to have 
these questions answered to the satisfaction of the potential participant or their parent/guardian. 
 
5.4 
INFORMED CONSENT 
5.4.1 
CONSENT TO THE FORMAT MASTER PROTOCOL 
In accordance with the International Council for Harmonisation Good Clinical Practice Guidelines (ICH-GCP) and/or 
the Declaration of Helsinki, consent to the FORMaT Master Protocol will be obtained by the FORMaT trial site-
specific research team prior to any study related procedures being performed or study data being collected.  All 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
15 
participants, regardless of whether they are enrolled in the Observational or Intervention Program are required to 
consent to the FORMaT Master Protocol.  If the participant is under 18 years of age or unable to provide consent 
(due to severe cognitive impairment, an intellectual disability, or a mental illness, including patients with dementia) 
then informed consent will be obtained from the participant’s parent/legal guardian in accordance with FDA guidance 
(40).  Where it is expected that the subject population will not understand English, the written participant information 
and consent forms will be translated into the anticipated specific language that will be understood in accordance with 
FDA guidance (40).  Participants who are enrolled and are under 18 years of age who turn 18 during the study period 
will require re-consent on the adult consent form.  Telephone consent, re-consent, and re-consent via email will be 
acceptable (using the informed consent checklist outlined in the FORMaT Trial Site Manual of Operating Procedures 
(MoOP)) when face-to-face consent is not possible. 
The FORMaT Master Protocol consent form is required to be signed and dated by the individual providing consent 
or the participant’s parent/guardian where appropriate.  A copy of the signed consent form will be given to the 
participant or their parent/guardian for their records with the original signed consent form(s) stored at the site in the 
participant’s medical record and a copy of the signed consent form(s) stored in the participant’s study file.  Any 
Independent Review Board (IRB) / Independent Ethics Committee (IEC) / Human Research Ethics Committee (HREC) 
approved changes to the trial Master Protocol that affect the participant’s rights and/or safety will require the 
participant’s reconsent. 
 
5.4.2 
CONSENT 
TO 
SPECIFIC 
APPENDIX 
INTERVENTION 
PROGRAM(S), 
OBSERVATION, DISCOVERY SUB-STUDIES AND INTEGRATED STUDIES 
If a participant meets the eligibility criteria for the FORMaT Appendices and/or specific sub-studies and integrated 
studies, additional appendix specific consent will be required in accordance with the procedures detailed above in 
section 5.4.1.  Appendix specific consent requirements are detailed in the appendices.  If additional sub-studies and/or 
integrated studies are added or removed from an appendix, or any changes are made to the appendix specific sub-
studies and/or integrated studies, IRB/IEC/HREC approval for these changes will be sought.  Reconsent will be 
required for additional trial specific procedures and changes that affect the participant’s rights and/or safety. 
 
5.5 
CORE TRIAL PROCEDURES 
Table 1 lists the special considerations that are applicable to Table 2 Core Trial Procedures and Schedule.  Scheduling 
of core trial procedures (including collection time points) are detailed in Table 2 and in the Schedule of Assessment 
Tables in the relevant appendix. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
16 
Table 1 Special Considerations for Core Trial Procedures and Schedule 
Symbol 
Definition 
A 
Trial phases relate to various stages of treatment, participant cohorts and/or FORMaT substudies as outlined in the relevant appendices. 
B 
Start of trial phase, Interim and End of trial phase visits are required for FORMaT participants as per the Schedule of Assessments in the relevant appendices. 
C 
Participant reconsent is required with IRB/ IEC/HREC approved changes to the protocol that affect participants’ rights and/or safety and/or if a child turns 18 
years old during the trial and must reconsent as an adult participant. 
D 
MABS-PD status reviewed in accordance with the ATS criteria as per the Schedule of Assessments in the relevant appendices. 
E 
Respiratory Samples are required to be collected for FORMaT participants as per the Schedule of Assessments in the relevant appendices. 
F 
Participants unable to produce a sputum sample (expectorated or induced) to be marked as unproductive on the CRF. 
G 
If participants are unable to provide the minimum requested sputum samples as per the Schedule of Assessments in the relevant appendices, then a BAL sample 
is to be collected. 
H 
Adult participants require height to be recorded once only during the study (ideally at the Screening Visit). 
I 
Adult participants do not require weight to be measured at every visit. 
J 
Chest CT Scan at early withdrawal visit will only be requested if clinically indicated. 
K 
Safety/Toxicology Monitoring assessments are to be performed as per the Schedule of Assessments in the relevant appendices. 
L 
Specific Health Related Quality of Life questionnaires are required to be completed by FORMaT participants as per the Schedule of Assessments in the relevant 
appendices. 
M 
Six-minute walk test to be performed in participants ≥ 18 years of age only. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
17 
Table 2 Core Trial Procedures and Schedule 
Assessments 
Screening Visit 
Start of Trial 
Phase A 
Interim Visit(s) 
End of Trial 
Phase A 
Final Outcome 
Early 
Withdrawal Visit 
Clinic Visit 
✓ 
✓B 
✓B 
✓B 
✓ 
✓ 
Informed Consent C 
✓ 
 
 
 
 
 
Review Eligibility 
✓ 
 
 
 
 
 
MABS-PD Status 
✓ 
 
✓D 
 
✓D 
✓D 
Randomisation 
 
✓ 
 
 
 
 
Medication Review 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Respiratory Sample 
✓ 
 
✓E/F/G 
✓E/F/G 
✓E/F/G  
✓E/F 
Height H and Weight I 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Spirometry 
✓ 
 
✓ 
✓ 
✓ 
✓ 
Chest Computed Tomography 
✓ 
 
 
 
✓ 
✓J 
Physical Examination 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Safety/Toxicology Monitoring K 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Health Related Quality of Life 
Questionnaires L 
✓ 
 
✓ 
✓ 
✓ 
✓ 
Costs Questionnaire 
✓ 
 
✓ 
✓ 
✓ 
✓ 
Six-minute walk test M 
✓ 
 
✓ 
 
✓ 
✓ 
  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
18 
5.5.1 
RESPIRATORY SAMPLES FOR MICROBIOLOGY ASSESSMENT 
Respiratory samples are to be collected for participants enrolled in either the Observational Cohort or the Intervention 
Program.  The respiratory samples will be collected as per the relevant appendix. 
Collection of respiratory sample(s) for the identification of MABS at screening may not be required if recent 
sample(s) have been provided by the participant, (within the specified time frames prior to screening stated in the 
relevant appendix) have been stored and are available as per the local laboratory guidelines (standard of care) to 
identify and diagnose MABS.  If the screening sample has been stored, then the sample will be analysed 
retrospectively once consent to participate in the FORMaT trial is given. 
All respiratory samples collected for MABS identification are to be sent to local pathology as per local guidelines. 
Acceptable methods for collecting a respiratory sample for the microbiological assessment of MABS include: 
 
5.5.1.1 
Expectorated Sputum 
Participants able to expectorate sputum are required to provide a 1ml expectorated sputum sample in a specimen jar 
or separate specimen jars if multiple samples are obtained.  Specimen jar(s) are to be labelled and sputum samples 
processed in accordance with site specific pathology requirements for the detection of MABS. 
 
5.5.1.2 
Induced Sputum 
Sputum induction is indicated for participants incapable of expectorating sputum.  Prior to sputum induction a 
bronchodilator can be administered to minimise bronchospasm.  Sputum induction should be conducted as per local 
guidelines. 
 
5.5.1.3 
Bronchoalveolar Lavage (BAL) 
A BAL is indicated if an expectorated or induced sputum sample is unobtainable.  Where possible, a six-lobe lavage 
should be collected.  If six-lobe lavage is not feasible, a minimum two-lobe lavage from the area most affected on 
chest CT scan should be collected.  All BAL samples are to be processed in accordance with site specific procedures. 
 
5.5.1.4 
Lung/Airway Biopsy 
Lung/airway biopsy is only acceptable for the initial MABS diagnosis, but not as a routine method for MABS 
microbiological assessment throughout the trial. 
Please note, cough swabs are not an acceptable respiratory sampling technique for the FORMaT Trial. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
19 
5.5.2 
WHOLE GENOME SEQUENCING 
All MABS-positive isolates cultured from the respiratory samples collected in the FORMaT Trial will be stored and 
deoxyribonucleic acid (DNA) extracted according to FORMaT DNA Extraction SOP.  The extracted DNA from all 
samples will undergo whole genome sequencing (WGS) according to the FORMaT WGS SOP and/or local laboratory 
standard procedures). The genetic data generated from the WGS of MABS DNA will be stored by the approved 
collaborator in a mycobacterial genomic library. 
 
5.5.3 
CHEST COMPUTED TOMOGRAPHY 
Chest CT will be performed at screening and at final outcome.  If at screening a recent chest CT scan has already 
been performed (within 6 months of screening), as part of the standard of care diagnosis of MABS an additional chest 
CT will not be required.  Any additional chest CT scans performed for clinical purposes at other time points while 
the participant is enrolled in the FORMaT Trial will also be collected as an outcome measure.  Once consent is 
provided for the FORMaT trial these images will be accessed from the participant’s medical records and included in 
trial analysis. 
The site and scanner specific protocols for chest CTs as well as the evaluation of trial CTs are described in the relevant 
appendix.  The site and scanner specific protocols are recommended to be used to perform the core trial chest CT 
scans where feasible at sites that are certified and trained to use the site and scanner specific protocols. 
 
5.5.4 
SPIROMETRY 
Spirometry will be measured in all participants from three years of age in accordance with the American Thoracic 
Society and European Respiratory Society standards (41) and according to the appendix specific schedule of 
assessments where possible. The multi-ethnic global lung initiative (GLI) reference values for all spirometry indices 
will be applied to participants 3-95 years of age (42). 
 
5.5.5 
PHYSICAL EXAMINATION AND VITAL SIGNS 
A physical examination of all body systems and vital signs will be completed in accordance with appendix specific 
schedule of assessments (where possible) and with assessment of any adverse event(s).  A physical examination is to 
be completed by a site investigator or delegate.  The physical examination includes a review of the following systems: 
head/neck/thyroid, eyes/ears/nose/throat, respiratory, cardiovascular, lymph nodes, abdomen, skin, musculoskeletal 
and neurological systems.  Breast, anorectal, and genital examinations will be performed only when medically 
indicated.  After screening, any new clinically significant abnormal findings in physical examinations will be reported 
as adverse events (AEs), see section 5.8. 
Vital signs include blood pressure (systolic and diastolic), temperature, pulse rate and respiration rate will be assessed 
following a 5-minute rest in the seated or supine position. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
20 
5.5.6 
SIX MINUTE WALK TEST 
There are several modalities available for the objective evaluation of functional exercise capacity.  The 6-minute 
walk test (6MWT) is a clinical exercise test that is tolerated by those with chronic respiratory disease and is reflective 
of activities of daily living.  This test measures the distance that a patient can quickly walk on a flat, hard surface in 
a period of 6 minutes (6-minute walk distance (6MWD)).  The strongest indication for the 6MWT is to measure 
response to medical interventions in patients with moderate to severe heart or lung disease.  Most 6MWTs will be 
performed before and after an intervention to determine whether the patient has experienced a clinically significant 
improvement.  The change in 6MWD is expressed as an absolute value. 
The 6MWT is to be conducted in adult participants only and performed according to the protocol in the ATS 
Statement: Guidelines for the Six-Minute Walk Test and/or local standard clinical practice guidelines (43).  The ATS 
guideline includes absolute contraindications, relative contraindications and precautions to completing the test. 
 
5.5.7 
MEDICATION REVIEW 
Current medication use including both prescription, over-the counter medication, herbal remedies and preparations 
will be recorded from time of consent until final outcome visit as per the schedule of assessments in the relevant 
appendix.  Trade drug names, start and stop dates, dose, route, and indications for use should be recorded in the 
relevant Case Report Form (CRF). 
 
5.6 
QUALITY ASSURANCE (QA) 
The FORMaT trial will be conducted in accordance with the current approved Master Protocol and Appendices.  To 
improve Master Protocol adherence as well as ensure complete data entry, the following QA procedures will be 
implemented: 
1. A FORMaT trial start-up meeting for research coordinators and site investigators prior to the submission of 
ethical approval and any other required approvals. 
2. A Site Initiation Visit (SIV) once the FORMaT site has obtained ethics and any other required approvals, but 
prior to participant recruitment. 
3. A CRF Completion Guide detailing all the data to be collected in the CRFs/electronic CRFs (eCRFs). 
4. Regular and timely validation of entered data, queries and corrections by the FORMaT Trial Management Team. 
5. Trial monitoring (onsite, remote, central, and/or local) as described in Section 7.7 Monitoring and according to 
the FORMaT Monitoring SOP and Monitoring Plan. 
 
5.6.1 
MICROBIOLOGY AND DNA EXTRACTION QA 
Microbiology is of key importance and samples are processed in each of the participating countries in the local 
mycobacterial reference laboratories (MRLs). The FORMaT trial management team will work collaboratively with 
each MRL to ensure standard approaches for sample processing are followed where feasible.  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
21 
 
5.7 
NOTES ON SPECIFIC TRIAL VISITS 
The timepoint definitions outlined below are overarching concepts that are applicable to each of the intervention 
studies described within the relevant appendices. 
5.7.1 
SCREENING  
Screening is a window of time between the Date of Consent and the date of first randomisation in which a 
participant’s eligibility into the trial is assessed and screening assessment data is collected according to the schedule 
of assessments in the relevant Appendices.   
 
5.7.2 
TIME POINT START TREATMENT (TPST) 
Participants in the Intervention program(s) will commence on the treatment arm allocated by randomisation.  Time 
Point Start Treatment (TPST) is defined as the date the participant undergoes the randomisation allocating a treatment 
arm. Each separate randomisation will have its own TPST as defined in the relevant appendix. 
 
5.7.3 
TIME POINT FINAL (TPF) 
Participants will be reviewed at the end of each trial phase (Time Point Final (TPF)) and assessments will be 
performed as per the appendix specific schedule of assessments.  Each treatment phase that follows a randomisation 
will have its own separate TPF as defined in the relevant appendix. 
 
5.7.4 
EARLY WITHDRAWAL VISIT 
Participants who are withdrawn or who withdraw from the trial will be asked to attend an Early Withdrawal Visit.  
Where practical, all efforts should be made for the participants to complete the early withdrawal trial procedures 
detailed in the appendix specific schedule of assessments.  Where possible, if there are any ongoing AEs these should 
be followed and monitored in accordance with the FORMaT Master Protocol irrespective of withdrawal from study. 
 
5.7.5 
UNSCHEDULED VISIT 
Study visits that are conducted in addition to those listed in the appendix specific assessment schedule are known as 
Unscheduled Visits.  If the Investigator deems that a participant should attend the study site to follow up an AE, 
repeat laboratory testing or any other study-related reason, then this visit should be documented in the FORMaT 
Research Electronic Data Capture (REDCap) database via the Unscheduled Visit CRF. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
22 
5.8 
SAFETY MONITORING  
Occurrence of AEs due to the underlying MABS infection and treatments used are well recognised and expected 
during the FORMaT trial.  As such, AE monitoring procedures outlined in the relevant appendices will be 
implemented for participants enrolled in the Intervention Program or Observational Cohort. Toxicology monitoring 
procedures will be implemented for Intervention Program participants.  
 
5.8.1 
DEFINITION OF ADVERSE EVENTS 
An AE is any untoward medical occurrence in a clinical investigation of a participant enrolled in FORMaT who 
may or may not be treated with an investigational product. 
The Investigator will probe, via discussion with the participant, for the occurrence of AEs during each participant 
visit and record the information in the participant’s medical record or source documents.  AEs will be recorded in the 
AE or SAE eCRF.  AEs will be described by duration (start and stop dates), severity, outcome, treatment, and 
relationship to study medication (where relevant), or if unrelated, the cause. 
AEs will be collected from the time of informed consent until the final study visit. 
All AEs will be reviewed by the FORMaT trial Pharmacovigilance Team and coded in accordance with the CTCAE 
version 5.  For any AE that is unable to be categorised in accordance with the CTCAE, the independent data safety 
monitoring board (iDSMB) will be required to review and categorise the AE. 
 
5.8.2 
ATTRIBUTION OF ADVERSE EVENTS IN THE FORMAT TRIAL 
The relationship, or attribution, of an AE to the trial therapies will be determined by the Investigator.  The relationship 
of the AE to the investigational product should be coded according to the following definitions: 
Unrelated: The adverse event is clearly not related to the investigational product. 
Unlikely: The adverse event is doubtfully related to the investigational product. 
Possibly: The adverse event may be related to the investigational product. 
Probably: The adverse event is likely related to the investigational product. 
Definitely: The adverse event is clearly related to the investigational product. 
 
5.8.3 
DEFINITION OF SERIOUS ADVERSE EVENTS 
SAEs will be defined as any untoward medical occurrence that: 
1. Results in death. 
2. Is considered life threatening (i.e., in the view of the Investigator the adverse experience places the participant 
at immediate risk of death from the reaction, as it occurred; it does not include a reaction that, had it occurred 
in a more severe form, might have caused death). 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
23 
3. Requires hospital admission or prolongation of an existing hospitalisation. 
4. Results in persistent or significant disability/incapacity (i.e., a substantial disruption of a person’s ability to 
conduct normal life functions). 
5. Is a congenital anomaly/birth defect. 
6. Is an important medical event (i.e., when based upon appropriate medical judgment, the adverse experience 
may jeopardise the participant and may require medical or surgical intervention to prevent one of the above 
listed outcomes). 
 
5.8.4 
REPORTING OF SAFETY EVENTS 
Study sites will document all SAEs that occur after informed consent is obtained until the final study visit in an SAE 
Report (whether or not related to study treatment).  All SAEs will be reported to the FORMaT Trial Management 
Team within 24 hours of becoming aware of the event.  Exclusions to the expedited SAE reporting include: 
1. Infective exacerbation of an underlying lung condition requiring hospitalisation or home intravenous 
antibiotic treatment does not require expedited reporting to the FORMaT Trial Management Team; 
2. Any planned and/or elective hospital admissions does not require expedited reporting; 
3. Any planned and/or elective medical procedures does not require expedited reporting. 
The site will complete and submit an initial SAE report form via the FORMaT trial database.  Any follow up 
information about the SAE is to be reported on an SAE follow up report form and submitted in the FORMaT trial 
database as soon as relevant information is available. 
All SAEs will be reviewed by the FORMaT trial Pharmacovigilance Team and coded in accordance with the CTCAE 
version 5.  For any SAE that is unable to be categorised in accordance with the CTCAE, the iDSMB will be required 
to review and categorise the SAE. 
Suspected unexpected serious adverse reactions (SUSARs) will be reported on the SAE form via the FORMaT Trial 
database.  Urgent safety measures (USMs) and significant safety issues (SSIs) will be reported via email to the FORMaT 
Trial Management Team and submitted in the FORMaT trial database (if the USM or SSI is also an SAE).  USMs, SSIs, 
and SUSARs are to be reported by the FORMaT Trial Management Team and/or the local site investigator to the relevant 
regulatory bodies within their required timeframes. 
The FORMaT Trial Management Team, as the Sponsor delegate, will notify the Sponsor of all SUSARs, USMs and 
SSIs as required and submit an Annual Safety Report to the Sponsor.  Site investigators are required to report all AEs 
that are related to study intervention(s) and/or interaction with study intervention(s) within 2 weeks of becoming 
aware of the event.  All other AEs and laboratory abnormalities that are not related to study intervention(s) or 
interactions with study intervention(s) are to be reported to the FORMaT Trial Management by the end of specified 
TPF outlined in the relevant appendix. 
Refer to FORMaT Safety Monitoring and Reporting SOP for detailed procedure(s) for safety reporting. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
24 
5.8.5 
CODING OF ADVERSE EVENTS FOR ANALYSIS 
CTCAE, version 5.0 will be applied for the database coding of all AEs including SAEs but only those categorised as 
at least “possibly”, “probably”, or “definitely” related to study medications and/or interactions between study 
medications and concomitant medications will be used to assess tolerance.  Coding for analysis will be completed by 
the FORMaT Pharmacovigilance Team.  Refer to section 4.6 for the definition of tolerance. Coding and grading is 
performed in accordance with the FORMaT Coding and Grading Work Instruction.  
If an AE is unable to be coded and/or graded by the pharmacovigilance team or if coding/grading cannot be agreed 
upon, the iDSMB will be consulted to assess and code and/or grade the AE. 
 
5.8.6 
TOXICOLOGY THRESHOLDS 
Toxicology monitoring will use the thresholds that match the grading from CTCAE, Version 5.0 as described in 
Table 3 and toxicity monitoring procedures for trial interventions will be as specified in the relevant intervention 
appendix. New interventions will require a separate toxicity monitoring plan including any requirements for central 
laboratory testing of samples. 
 
5.9 
PARTICIPANT WITHDRAWAL AND DISCONTINUATION OF TREATMENT 
5.9.1 
WITHDRAWAL OF CONSENT 
All participants are free to withdraw from the study at any time, with or without a specified reason and without 
prejudice.  Where possible, the participant or the participant’s parent/legal guardian is required to sign the withdrawal 
of consent form, formally documenting the withdrawal process including the reason for withdrawal if they choose to 
provide this information.  In the event of a participant withdrawing from the trial, an early withdrawal visit should 
be completed within the specified window of time from withdrawal if the participant is agreeable.  If for any reason 
the participant is unable to complete the early withdrawal visit this should be noted on the Study Completion eCRF.   
 
5.9.2 
DISCONTINUATION OF TREATMENT 
Participants enrolled in the Intervention Program can discontinue treatment at any time during the trial if: 
• 
The participant is no longer able to comply with the FORMaT Master Protocol and relevant appendix, 
including completing required study assessments for safety requirements. 
• 
The site investigator believes that treatment is no longer in the participant’s best interests (due to safety or 
tolerance concerns). 
• 
The participant no longer wants to continue treatment. 
Participants discontinuing treatment prematurely but who do not withdraw consent or assent will be encouraged to 
continue with the trial according to the specific appendix intervention study and schedule of assessments in 
accordance with the relevant appendices with the final outcome respiratory sampling assessments to be prioritised. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
25 
Table 3: Safety critical monitoring thresholds 
Investigations 
Grade 
CTCAE Term 
1 
2 
3 
4 
5 
Alanine 
aminotransferase 
increased 
>ULN - 3.0 x ULN if 
baseline was normal, or; 
1.5 – 3.0 x baseline if 
baseline was abnormal.  
>3.0 - 5.0 x ULN if baseline 
was normal, or; 
>3.0 - 5.0 x baseline if 
baseline was abnormal. 
>5.0 - 20.0 x ULN if 
baseline was normal, or; 
>5.0 - 20.0 x baseline if 
baseline was abnormal. 
>20.0 x ULN if baseline 
was normal, or; 
>20.0 x baseline if baseline 
was abnormal. 
- 
Definition: A finding based on laboratory test results that indicate an increase in the level of alanine aminotransferase (ALT or SGPT) in the blood specimen.  
Anaemia 
 
Haemoglobin (Hgb) <LLN 
- 10.0 g/dL; <LLN – 6.2 
mmol/L; <LLN – 100 g/L. 
Hgb <10.0 – 8.0 g/ dL; <6.2 
– 4.9 mmol/L; <100 - 80 
g/L. 
Hgb 
<8.0 
g/ 
dL;  
<4.9 mmol/L; < 80 g/L; 
transfusion indicated. 
Life-threatening 
consequences; 
urgent 
intervention indicated.  
Death 
Definition: A disorder characterized by a reduction in the amount of haemoglobin in 100 ml of blood. Signs and symptoms of anaemia may include pallor of the 
skin and mucous membranes, shortness of breath, palpitations of the heart, soft systolic murmurs, lethargy, and fatigability.  
Aspartate aminotransferase 
increased 
>ULN - 3.0 x ULN if 
baseline was normal, or; 
1.5 – 3.0 x baseline if 
baseline was abnormal. 
>3.0 - 5.0 x ULN if baseline 
was normal, or; 
>3.0 – 5.0 x baseline if 
baseline was abnormal. 
>5.0 - 20.0 x ULN if 
baseline was normal, or; 
>5.0 – 20.0 x baseline if 
baseline was abnormal. 
>20.0 x ULN if baseline 
was normal, or; 
>20.0 x baseline if baseline 
was abnormal. 
- 
Definition: A finding based on laboratory test results that indicate an increase in the level of aspartate aminotransferase (AST or SGOT) in the blood specimen. 
Blood bilirubin increased 
>ULN - 1.5 x ULN if 
baseline was normal, or; 
>1.0 – 1.5 x baseline if 
baseline was abnormal.  
>1.5 - 3.0 x ULN if baseline 
was normal, or; 
>1.5 – 3.0 x baseline if 
baseline was abnormal.  
>3.0 – 10.0 x ULN if 
baseline was normal, or; 
>3.0 – 10.0 x baseline if 
baseline was abnormal. 
>10.0 x ULN if baseline 
was normal, or; 
>10.0 x baseline if baseline 
was abnormal. 
- 
Definition: A finding based on laboratory test results that indicate an abnormally high level of bilirubin in the blood. Excess bilirubin is associated with jaundice. 
Electrocardiogram 
QT 
corrected interval prolonged 
Average QTc 450 - 480 ms 
Average QTc 481 - 500 ms 
Average QTc >= 501 ms; 
>60 
ms 
change 
from 
baseline.  
Torsade 
de 
pointes; 
polymorphic 
ventricular 
tachycardia; 
signs/symptoms of serious 
arrhythmia. 
- 
Definition: A disorder characterised by Electrocardiogram T wave amplitude changes.  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
26 
Investigations 
Grade 
CTCAE Term 
1 
2 
3 
4 
5 
Hearing impaired 
Adults enrolled on a 
Monitoring Program (on a 
1, 2, 4, 3, 6, and 8 kHz 
audiogram): Threshold 
shift of 15 - 25 dB 
averaged at 2 contiguous 
test frequencies in at least 
one ear; 
Adults not enrolled on a 
Monitoring Program: 
Subjective change in 
hearing in the absence of 
documented hearing loss; 
Pediatric (on a 1, 2, 3, 4, 6, 
and 8 kHz audiogram): 
Threshold shift >20 dB 
hearing loss (HL) (i.e., 25 
dB HL or greater); 
sensorineural hearing loss 
(SNHL) above 4 kHz (i.e., 
6 or 8 kHz) in at least one 
ear. 
Adults enrolled on a 
Monitoring Program (on a 
1, 2, 3, 4, 6, and 8 kHz 
audiogram): Threshold 
shift of >25 dB averaged at 
2 contiguous test 
frequencies in at least one 
ear; 
Adults not enrolled on a 
Monitoring Program: 
Hearing loss with hearing 
aid or intervention not 
indicated; limiting 
instrumental ADL; 
Pediatric (on a 1, 2, 3, 4, 6, 
and 8 kHz audiogram): 
Threshold shift >20 dB at 4 
kHz in at least one ear. 
Adults enrolled on a 
Monitoring Program (on a 
1, 2, 3, 4, 6, and 8 kHz 
audiogram): Threshold 
shift of >25 dB averaged at 
3 contiguous test 
frequencies in at least one 
ear; therapeutic 
intervention indicated; 
Adults not enrolled on a 
Monitoring Program: 
Hearing loss with hearing 
aid or intervention 
indicated; limiting self care 
ADL; 
Pediatric (on a 1, 2, 3, 4, 6, 
and 8 kHz audiogram): 
Hearing loss sufficient to 
indicate therapeutic 
intervention, including 
hearing aids; threshold shift 
>20 dB at 2 to < 4 kHz in 
at least one ear. 
Adults: Decrease in hearing 
to profound bilateral loss 
(absolute threshold >80 dB 
HL at 2 kHz and above); 
nonservicable hearing. 
Pediatric: Audiologic 
indication for cochlear 
implant; > 40 dB HL (i.e., 
45 dB HL or more); SNHL 
at 2 kHz and above. 
- 
Definition: A disorder characterized by partial or complete loss of the ability to detect or understand sounds resulting from damage to ear structures 
Leukocytosis 
- 
- 
>100,000/mm3 
Clinical manifestations of 
leucostasis; 
urgent 
intervention indicated. 
- 
Definition: A disorder characterised by laboratory results that indicate an increased number of white blood cells in the blood.  
Lymphocyte count decreased 
<LLN - 800/mm3; 
 <LLN - 0.8 x 109/L 
<800 – 500/mm3;  
<0.8 - 0.5 x 109/L 
<500 – 200/mm3;  
<0.5 - 0.2 x 109/L 
< 200/mm3;  
< 0.2 x 109/L 
- 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
27 
Investigations 
Grade 
CTCAE Term 
1 
2 
3 
4 
5 
Definition: A finding based on laboratory test results that indicate a decrease in the number of lymphocytes in a blood specimen. 
Neutrophil count decreased 
<LLN - 1500/mm3; 
<LLN - 1.5 x 109/L 
<1500 - 1000/mm3; 
<1.5 - 1.0 x 109/L 
<1000 - 500/mm3; 
<1.0 - 0.5 x 109/L 
<500/mm3;  
< 0.5 x 109/L 
- 
Definition: A finding based on laboratory test results that indicate a decrease in the number of neutrophils in a blood specimen. 
Platelet count decreased 
<LLN 
- 
75,000/ 
mm3; 
<LLN - 75.0 x 109/L 
<75,000 - 50,000/ mm3; 
<75.0 - 50.0 x 109/L 
<50,000 - 25,000/ mm3; 
<50.0 - 25.0 x 109/L 
<25,000/ mm3;  
<25.0 x 109/L 
- 
Definition: A finding based on laboratory test results that indicate a decrease in the levels of pancreatic enzymes in a biological specimen. 
Tinnitus 
Mild symptoms; 
intervention not indicated. 
Moderate symptoms; 
limiting instrumental ADL. 
Severe symptoms; limiting 
self care ADL. 
- 
- 
Definition: A disorder characterised by noise in the ears, such as ringing, buzzing, roaring or clicking. 
Vertigo 
Mild symptoms. 
Moderate 
symptoms; 
limited instrumental ADL. 
Severe symptoms; limiting 
self care ADL. 
 
- 
- 
Definition: A disorder characterised by a sensation as if the external world were revolving around the patient (objective vertigo) or as if he himself were 
revolving in space (subjective vertigo).  
Vestibular Disorder 
- 
Symptomatic; limiting 
instrumental ADL. 
Severe symptoms; limiting 
self care ADL. 
- 
- 
Definition: A disorder characterised by dizziness, imbalance, nausea and vision problems.  
White blood cell decreased 
<LLN - 3000/ mm3; 
<LLN – 3.0 x 109/L 
<3000 - 2000/ mm3; 
<3.0 – 2.0 x 109/L 
<2000 - 1000/ mm3; 
<2.0 – 1.0 x 109/L 
<1000/ mm3; 
<1.0 x 109/L 
- 
Definition: A finding based on laboratory test results that indicate a decrease in the number of white blood cells in a blood specimen. 
Adapted from CTCAE, version 5.0

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
28 
5.10 DATA MANAGEMENT 
5.10.1 DATA COLLECTION, ENTRY AND STORAGE 
Trial data will be collected from various sources including, but not limited to, medical records, participant 
questionnaires, output from lab results, study assessments, correspondence and CT scans.  These documents and any 
documents where data is first recorded for a participant will form the source documents.  FORMaT trial site staff will 
be trained in the collection of the required data during the site initiation visit and data collection instructions will be 
stored in the site’s electronic Investigator Site File (eISF). 
The site investigators are responsible for ensuring the accuracy, completeness, legibility, and timeliness of all trial 
data reported.  All source documents are to be viewable in a neat, legible manner to ensure accurate interpretation of 
data.  The site investigators will maintain adequate case histories of trial participants, including source 
documentation.  
Sites will enter the data required for the trial directly into an eCRF located in a study specific Research Electronic 
Data Capture (REDCap) FORMaT database.  Data for the eCRF will be obtained directly from the medical record or 
source documents. 
Due to the adaptive design of the trial all data is to be entered within 14 days from the specified TPF as defined 
in the relevant appendix unless otherwise stated (e.g. expedited AE/SAE reporting)  Data cleaning will be 
performed at regular intervals for the trial to ensure that the data are cleaned and ready for interim analyses. 
The REDCap FORMaT database will be hosted on Murdoch Children’s Research Institute (MCRI) infrastructure 
and is subject to the same security and backup regimen as other systems at the MCRI (e.g. the network file servers).  
Data is backed up nightly to a local backup server, with a monthly backup taken to tape and stored offsite.  All data 
transmissions between users and the REDCap server are encrypted.  Regular data quality checks, such as automatic 
range checks, will be performed to identify data that appear inconsistent, incomplete, or inaccurate. 
Access to REDCap is managed by the system administrator.  The permissions granted to each user within each 
REDCap project is controlled by and is the responsibility of the FORMaT trial management team.  REDCap has 
functionality that makes adding and removing users and managing user permissions straightforward.  REDCap 
maintains an audit trail of data created/updated/deleted that is accessible to project users that are granted permission 
to view it. 
The SiteDocs Portal is an online tool hosted by TrialDocs Clinical Research Document Management and The 
University of Queensland (UQ) that is compliant with FDA requirements and General Data Protection Regulation 
(GDPR) which will securely host and track all key trial documents for the FORMaT Trial, including the electronic 
Trial Master File (eTMF).  SiteDocs includes features such as version control, document protection, temporary 
remote monitoring access, alerts, archiving and a full audit trail of data and users. 
Trial sites will have individual secure access to their site’s eISF via SiteDocs, where protocols, templates, trial 
documents and correspondence will be hosted.  Sites will be able to collaborate with the Sponsor and/or their delegate 
to upload site-specific clinical trial documents or deidentified participant documents to their eISF, receive 
notifications of changes and easily access the most up-to-date document versions. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
29 
Trial sites will have access to their own separate site-specific Portal for SiteDocs where they can upload and manage 
identifiable source documents.  Sites will be responsible for granting access to their site-specific Portal, including 
temporary access to external monitors. 
 
5.10.2 DATA STORAGE AND RETENTION 
Each site is required to maintain source documents for a minimum of 15 years post completion of the trial.  If site 
specific requirements or relevant legislation dictate data retention for periods longer than 15 years, trial sites will be 
required to adhere to these requirements. 
 
6 
STATISTICAL ANALYSIS PRINCIPLES 
This section of the Master Protocol provides an outline and summary of the general statistical methods and principles 
used for FORMaT.  The detailed statistical methods and sample size simulations relevant to each of the Intervention 
Programs and discovery studies are outlined in the relevant appendix. 
 
6.1 
BAYESIAN ANALYSIS AND BAYESIAN ADAPTIVE RANDOMISATION (BAR) 
Interim monitoring for the Intervention Program in the FORMaT trial will use a Bayesian analysis approach (44).  
This approach will calculate the (posterior) probability of an intervention being found to be superior to the reference 
arm during the trial.  As new data is generated the probability will be updated.  This updating will occur at the time 
of the meetings of the iDSMB, who will have access to blinded and unblinded data and will ask the Trial Steering 
Committee (TSC) to ratify the updated blinded probabilities.  Initially there are no plans to stop any arms of the study 
arms due to superiority, but such rules may be established as the trial continues and will be detailed in the relevant 
appendices.  The iDSMB may however make a recommendation to the TSC about stopping current interventions if 
they show poor promise or futility.  Stopping rules will be defined to guide the use of the posterior probabilities. 
Adaptive randomisation allows intervention arm allocation ratios to be adapted based on interim analyses undertaken 
during the trial to favour the intervention arm with the highest posterior probability of success (45).  This approach 
can lead to increased efficiency of the trial and reduce patient exposures to less promising or more toxic therapies 
compared with non-adaptive randomisation.  In the FORMaT trial, BAR will be used for updating allocation 
probabilities in randomisations when there are more than two interventions being compared at any one of the 
randomisation stages.  BAR will be implemented after every 60 participants have been randomised so that there is 
sufficient information available to determine the adaptation.  Success of an intervention (and hence the adaptations) 
will be determined by the primary outcome; microbiological clearance with tolerability (refer to sections 1.1 Synopsis 
and 4.6 Trial Endpoints for definitions of clearance and tolerance). 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
30 
6.2 
RANDOMISATION 
6.2.1 
BLINDING OF TREATMENT ALLOCATION 
The FORMaT trial may include placebo controlled double blind randomised interventions in the future, but the initial 
Intervention Program detailed in Appendix A1 is randomised and open label. 
Each stage of the FORMaT intervention program(s) requires randomisation and is detailed in the relevant appendix. 
The allocated treatment must start on the same day as the randomisation where feasible, or as soon as possible after 
the randomisation has been performed. Any delays to starting an allocated treatment after randomisation has occurred 
must be reported to the FORMaT Trial Management Team. 
 
6.3 
MINIMISATION 
To ensure balance between arms in important patient characteristics, randomisation at the different stages of the trial 
will use minimisation with a random element.  Minimisation is a dynamic randomisation approach used in clinical 
trials to balance allocation to treatment arms with respect to a number of important stratification factors.  In 
minimisation, the first participant is allocated to their treatment arm at random.  Subsequent participants are assigned 
to a treatment arm by first selecting the preferred arm that would best improve the balance of participants across the 
arms based on the stratification variables of interest in terms of the numerical difference in the sample size in each 
of the treatment arms across all of the stratification factors (46, 47).  The preferred arm is then selected with a 
probability of 0.7, with rest of the probability split between the alternative arms. 
Following updating the randomisation allocations through BAR, minimisation will be conducted using Biased Coin 
Minimisation (BCM) (48).  Under this method, the same methodology as standard minimisation will be used to 
determine the preferred intervention, but the randomisation probabilities will be altered to reflect the minimisation 
probabilities and the updated allocation ratios from the BAR as detailed in Han et al (48). 
Randomisation will be conducted electronically through the trial database following completion of all the specific 
required data entry by the study team at each site.  Participants will be randomised according to the stratification 
criteria described below using to the weights specified for each factor: 
1.  Macrolide resistance*: Yes or no (weight = 50% in randomisations 1 and 2 (Randomisation-Short Intensive 
(R-SI) and Randomisation-Prolonged Intensive or Immediate Consolidation (R-PI/IC), respectively), 25% 
in randomisation 3 (Randomisation-Consolidation (R-Con))). 
Any of these measurement methods are acceptable for defining macrolide resistance (in order of preference): 
a. Inducible at 14 days or constitutive at 3 days, and/or; 
b. Erm(41) status: Functional or dysfunctional, and/or; 
c. MABS subspecies: M. a. abscessus & M. a. bolletii combined or M. a. massiliense. 
2. Age: <12 years, 12-30 years and >30 years of age (weight = 20%). 
3. Sex: Male or Female (weight = 7.5%). 
4. Location: Asia Pacific as one stratum (includes Australia, New Zealand, Singapore and other Asian Pacific 
countries), United Kingdom and Republic of Ireland as one stratum, Europe as another stratum (includes 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
31 
Denmark, France, Netherlands), and Canada and the Americas as one stratum (weight = 7.5%). Parts of the 
world not listed above can be added into the regions based on closest proximity to the regions longitudinally. 
5. Cystic Fibrosis Status: Yes or no (weight = 7.5%). 
6. Mixed NTM infections at enrolment: Yes or no (weight =7.5%). 
7. MABS positive culture (at initial randomisation to intensive therapy (R-SI) and for R-PI/IC all participants 
will have a positive culture, so this factor will not be required. However, it will be required for R-Con): Yes 
or no (weight = 25%). 
 
6.4 
ADDING AND STOPPING INTERVENTIONS 
New interventions, which may include new therapeutics or new timelines either during the intensive or consolidation 
phase, may be added as a treatment arm either for the intensive or for the consolidation phase as determined by the 
trial Drug and Intervention Selection committee (DISC) with approval of the TSC.  No new therapies will be added 
until at least 60 subjects have completed the trial phase associated with the proposed new intervention. 
Interventions may be stopped early due to a lack of benefit at interim analyses.  Interim analyses will be conducted 
after every 60 participants have completed the trial phase.  The statistical team, acting in confidence, will present the 
results from such analyses only to the iDSMB who will provide guidance around stopping particular interventions.  
Pre-defined triggers for stopping an intervention will be specified for both intensive and consolidation interventions 
separately, and for the combination of intensive and consolidation.  If a single intervention, or combination of 
interventions, has less than a 0.01 posterior probability of being an optimal intervention in that phase then that 
intervention will be regarded as inferior and should be recommended to be discontinued. 
For new interventions in the future, if an intervention has a high posterior probability (to be pre-specified prior to the 
new intervention being added) of being an optimal therapy this invention will be considered as superior, in which 
case the iDSMB might recommend that the randomisation stage be stopped for superiority.  Stopping rules for 
superiority will be detailed in the relevant section of the appendices.  Following the iDSMB meeting, the 
recommendations from the iDSMB will be notified to the Trial Management Committee (TMC) and TSC.  The TSC 
will consider the recommendations and make a decision regarding the potential to stop the randomisation stage for 
superiority.  If any interventions are stopped, the TMC will have the responsibility of developing a public disclosure 
as is practical through presentation of results and publications. 
 
6.5 
SEAMLESS PHASE II TO PHASE III 
The FORMaT platform trial provides a resource to enable promising therapies to be more rapidly evaluated and has 
the potential to facilitate seamless transition from Phase II to a Phase III study.  Initially the platform will support a 
phase II study, but new interventions being evaluated in the future may be considered for the potential to move 
seamlessly from this Phase II study to a Phase III (49).  The principles guiding this move will include planning for 
the potential of Phase III in the design of the Phase II study and with agreement between the Platform trial team and 
sponsors of the new therapy around management and access to data.  The move to a Phase III trial will be guided by 
a pre-defined threshold for the probability of a successful intervention during phase III, which would need to be 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
32 
established in planning the Phase II trial and agreed to by regulatory authorities for pivotal studies.  If a seamless 
transition to Phase III is considered feasible, the TMC along with the trial statistics team will provide the iDSMB 
and TSC with a Phase III proposal, and if this is approved by the iDSMB and TSC then further recruitment to the 
target number determined would be undertaken. 
 
6.6 
SIMULATIONS AND STATISTICAL POWER 
The design (including stopping rules) and sample size of each intervention program will be informed by simulations 
using Monte Carlo methods to give a range of power according to different scenarios and taking into account the 
probabilities of variable responses to intensive and/or consolidation interventions.  Simulations will be updated with 
the addition of any new interventions.  The details of these simulations can be found in the relevant appendix. 
 
6.7 
GENERAL ANALYSIS PRINCIPLES 
The analyses will be conducted according to the statistical analysis methods described in the relevant appendices, 
statistical principles appendix and the statistical analysis plan. 
 
7 
STUDY OVERSIGHT 
7.1 
OVERVIEW 
The FORMaT Trial will have several committees established to provide oversight of the FORMaT Trial. 
 
7.2 
TRIAL STEERING COMMITTEE 
The TSC is the executive decision-making group and provides overall supervision of the FORMaT trial.  The Terms 
of Reference (available on request) outlines the roles and responsibilities of the TSC members.  Membership to the 
TSC will consist of independent and non-independent members from a variety of backgrounds including clinical and 
statistical as well as a member from the general community.  The Chair of the TSC will be independent of the 
FORMaT Trial. 
 
7.3 
INDEPENDENT DATA SAFETY MONITORING BOARD 
The iDSMB will review interim analyses, monitor for effectiveness and safety, along with trial conduct.  They will 
meet prior to the commencement of the trial at least annually and at the time of interim analysis after every 60 
participants have completed each stage of the trial.  The iDSMB will provide advice to the TSC and the Trial 
Management Committee (TMC).  The iDSMB Charter (available on request) outlines the roles and responsibilities 
of the iDSMB members.  Membership to the iDSMB will consist of clinicians and statisticians who are independent 
of the FORMaT Trial. 
The iDSMB will be responsible for defining its deliberative processes, including event triggers that would call for an 
unscheduled review and voting procedures prior to initiating any data review.  The iDSMB will be responsible for 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
33 
maintaining the confidentiality of its internal discussions and activities as well as the contents of reports provided to 
it. 
The iDSMB will review each version of the FORMaT Master Protocol (including any new or updated appendices). 
During the trial, the iDSMB will review cumulative study data to evaluate safety, study conduct, and scientific 
validity and integrity of the trial. As part of this responsibility, iDSMB members must be satisfied that the timeliness, 
completeness, and accuracy of the data submitted to them for review are sufficient for evaluation of the safety and 
welfare of study participants.  The iDSMB will also assess the performance of overall study operations and any other 
relevant issues, as necessary. 
Items to be reviewed by the iDSMB may include: 
• 
Interim/cumulative data for evidence of study-related AEs. 
• 
Interim/cumulative data for evidence of efficacy and futility according to pre-established statistical 
guidelines. 
• 
Data quality, completeness and timeliness. 
• 
Performance of individual centres/countries. 
• 
Adequacy of compliance with goals for recruitment and retention, including those related to the participation 
of women and minorities. 
• 
Adherence to the protocol. 
• 
Factors that might affect the study outcome or compromise the confidentiality of the trial data (such as 
protocol deviations, unmasking, etc.). 
• 
Factors external to the study such as scientific or therapeutic developments that may impact participant safety 
or the ethics of the study. 
• 
AEs that are unable to be categorised by the FORMaT Pharmacovigilance Team in accordance with the 
CTCAE. 
The iDSMB will conclude each review with their recommendations to the TSC and the FORMaT Chief Investigator 
(CI) as to whether the study should continue without change, be modified, or terminated.  Recommendations 
regarding modification of the design and conduct of the study could include: 
• 
Modifications of the Master Protocol (including appendices) based upon the review of the safety data. 
• 
Suspension or early termination of the study or of one or more study arms because of serious concerns about 
subjects’ safety, inadequate performance or rate of enrolment. 
• 
Suspension or early termination of the study or of one or more study arms because study objectives have 
been obtained according to pre-established statistical guidelines. 
• 
Corrective actions regarding a study centre whose performance appears unsatisfactory or suspicious. 
Confidentiality must always be maintained during all phases of iDSMB review and deliberations. 
Meeting sessions can be either open or closed at the request of the iDSMB Chair or may involve periods of each. The 
lead investigators of FORMaT can attend the open session along with other investigators as requested. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
34 
The closed session will only include the iDSMB members who have voting rights and they will formulate 
recommendations regarding the study to the TSC.  The FORMaT CI may be invited to the closed session to present 
an update of the trial but will not be present for any other agenda items. 
Reports will be provided to iDSMB that include an open report and a closed report.  Reports for the iDSMB will be 
prepared by the Clinical Epidemiology and Biostatistics Unit at MCRI. 
Open reports will include information on the study conduct such as accrual data, demographics and baseline 
characteristics, site performance and protocol compliance and quality control issues along with general toxicity and 
safety data presented across the study as a whole with no reference to treatment arm. 
Closed reports will include the same data as the open reports as well as data on efficacy outcomes at the time of each 
interim analysis (every 60 patients in randomisation levels with more than two interventions) and will be presented 
by (masked) treatment arm. 
Reports from the iDSMB will provide details of any items that require urgent action as well as any 
recommendations made by the iDSMB and will be provided to the FORMaT CI and the TSC and notified to other 
participating organisations as well as to the IRB/IEC/HRECs involved. 
 
7.4 
TRIAL MANAGEMENT COMMITTEE 
The Trial Management Committee (TMC) is responsible for reviewing the day-to-day management of the trial and 
assist the FORMaT project team with any issues that arise during the study, as well as provide advice to the TSC and 
iDSMB where relevant. The TMC will include the FORMaT Trial CI, the Senior Trial Project Managers, appropriate 
representatives across all the key areas (Statistics, Database, Pharmacovigilance, Drug and Intervention Selection 
Committee (DISC), and Microbiology), and a representative from each participating country or region.  To facilitate 
and ensure adequate communication across the large number of team members and a wide geographic spread, 
information from the TMC may be shared on the FORMaT trial website and SiteDocs.  The TMC will report to the 
TSC.  Day-to-day management will be overseen by the FORMaT CI, the senior trial project managers and the core 
trial clinical lead physicians.  A Terms of Reference (available on request) outlines the roles and responsibilities of 
the TMC. 
 
7.5 
FORMAT PHARMACOVIGILANCE TEAM 
All AEs and SAEs will be reviewed by the FORMaT Pharmacovigilance Team and coded in accordance with the 
CTCAE, version 5.0. Members of the FORMaT Pharmacovigilance Team include: 
• 
Senior Clinical Pharmacist (Lead). 
• 
Non-independent senior paediatric physician. 
• 
Non-independent senior adult physician. 
• 
FORMaT Trial database representative (if required). 
• 
Statistician (If required). 
For further detail refer to the Pharmacovigilance Team Terms of Reference (available on request). 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
35 
7.6 
DRUG AND INTERVENTION SELECTION COMMITTEE (DISC) 
The DISC includes the DISC chair, FORMaT CI, FORMaT Trial Management Team, a representative from each 
participating country and experts external to the trial. The role of the DISC includes assessment of new intervention 
or therapies to be considered for inclusion in a new Intervention Program. The DISC will provide a report supported 
by the Statistical Analysis Team and reviewed by the trial management team, for consideration by the TSC and if 
approved will lead to a new therapy program being included.  For further detail refer to the DISC Terms of Reference 
(available on request). 
 
7.7 
CONSUMER ADVISORY GROUP (CAG) 
The purpose of the FORMaT consumer advisory group (CAG) is to provide a consumer and community perspective 
to various aspects of the FORMaT trial. This includes advice on participant facing documents such as consent forms, 
future research plans including proposals for new treatments to be added to the study, grant applications requesting 
funding support for the study, and lay summaries of the study and any study results. Members of the CAG may also 
be invited to join various trial committee meetings to provide their perspective. 
 
7.8 
MONITORING 
The Sponsor and its delegates will have overall responsibility for monitoring.  An SIV will occur prior to sites 
commencing the recruitment of trial participants.  The purpose of the SIV is to train site investigators and local study 
coordinators with regards to the Master Protocol, the Appendices, data entry, management of trial documentation, 
and safety monitoring and reporting.  The site will be activated once the SIV has been presented and all the essential 
documentation from the local site has been collected according to FORMaT Site Initiation and Activation SOP.  
Monitoring visits will ensure that the study is being conducted according to good clinical practice (GCP), the Master 
Protocol and relevant appendices, that study participants’ safety, rights and well-being are being protected and that 
data entry is accurate and verifiable from source documentation.  These will be conducted via central, remote, local 
or on-site monitoring.  Visits may be conducted either face-to-face or through on-site electronic facilities, at intervals 
specified in the FORMaT Trial Monitoring SOP and Trial Monitoring Plan.  The FORMaT trial will accommodate 
any requests to be audited by ethical, regulatory and/or other relevant authorities. 
 
8 
ETHICAL AND ADMINISTRATIVE CONSIDERATIONS 
The trial will be conducted according to the Declaration of Helsinki, the International Conference on 
Harmonization - Good Clinical Practice E6 (ICH-GCP) and with the laws and regulations of the country in which 
the research is conducted, whichever represents the greater protection of the individual. 
 
8.1 
RESEARCH ETHICS APPROVAL AND SITE-SPECIFIC GOVERNANCE 
Prior to trial initiation the FORMaT Master Protocol, appendices, information sheets and consent forms, trial 
questionnaires and any other patient facing material will be reviewed and approved by the relevant IRB/IEC/HREC 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
36 
for each participating country and/or site.  Approved delegates will keep the IRB/IEC/HREC informed as to the 
progress of the trial and comply with annual reporting requirements. 
The IRB/IEC/HREC must approve any revisions to FORMaT trial documents and be informed of any serious and/or 
unexpected AEs occurring during the trial as required and of any new information that may adversely affect the safety 
of the participants or the conduct of the trial.  Reporting requirements are to be adhered to in accordance with local 
IRB/IEC/HREC and additional site-specific requirements. 
 
8.1.1 
FORMAT MASTER PROTOCOL AND TRIAL DOCUMENT AMENDMENTS 
Any amendments to the approved IRB/IEC/HREC FORMaT trial documents may not be initiated without prior 
written IRB/IEC/HREC approval except when necessary to eliminate immediate hazards to the participants.   
Amendments will be submitted in writing to relevant IRB/IEC/HRECs and written approval will be obtained before 
the updated version is implemented. 
 
8.1.2 
PROTOCOL DEVIATIONS 
A protocol deviation occurs when there is any deviation from the study procedures or treatment plans as specified in 
the IRB/IEB/HREC approved protocol.  Examples of protocol deviations may include non-compliance with GCP, 
study visits outside of set windows and missing assessments outlined in the protocol.  Participants enrolled in the 
intervention cohort where protocol deviations have occurred involving modifications to the study drug regimen are 
able to continue to be enrolled and assessed for the remainder of the study. 
Protocol deviations may be minor or major. Minor protocol deviations do not carry significant ethical or 
administrative consequences.  Major protocol deviations are those that affect participant’s rights, safety or wellbeing 
and/or accuracy and reliability of the study data. An example of a minor protocol deviation is visit non-compliance 
(i.e. study visit and assessments are conducted outside of the required timeframe, or a procedure is missed) and there 
are no participant safety concerns. 
Examples of major protocol deviations include: 
a. Randomisation of an ineligible participant. 
b. Visit non-compliance (e.g., study visit and assessments are conducted outside of the required timeframe, or 
visit or assessment is missed) and there are participant safety concerns. 
c. Dispensing or dosing error of IMP. 
d. Not reporting SAEs. 
When a major protocol deviation occurs, it will be discussed with the site investigator(s) and site PI and a Protocol 
Deviation Form detailing the deviation will be generated.  This form, outlining the major protocol deviation, will be 
signed by the site investigator.  A copy of the form will be filed in the investigator site file and details of the deviation 
will be entered onto the study database. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
37 
8.1.2.1 
Reporting Requirements 
Minor protocol deviations do not need to be reported to the lead IRB/IEB/HREC at the time they occur. All minor 
deviations must be recorded in the protocol deviation log and reported to the Sponsor (if applicable). 
Major protocol deviations may need to be reported to the lead IRB/IEC/HREC and to the Sponsor (if applicable) as 
per local requirements and a protocol deviation form detailing the event completed.  The protocol deviation CRF is 
to be completed, signed by the site investigator, and entered in the database. 
All protocol deviations (major or minor) must be recorded in a protocol deviation log and reported as per local ethical 
and regulatory requirements. 
 
8.2 
CONFIDENTIALITY 
The Investigator must ensure that a participant’s anonymity will be respected throughout the study and that their 
identities are protected from unauthorised parties.  A participant’s privacy and confidentiality will be maintained by 
the assignment of a unique identification number.  On CRFs and other documents submitted to review committees 
and the Sponsor participants will not be identified by their names, rather their unique identification number.  These 
numbers will be used to collect, store and report participant information, including in the trial database.  The local 
site should keep a Subject Identification Log showing codes, names and dates of birth of the participants.  
Confidentiality and protection of data will be maintained according to local regulatory requirements.  All information 
disclosed or obtained during the trial is confidential.  The site PI and any person under his/her authority must maintain 
this confidentiality and must not disclose the information to any third party without the prior written approval of the 
CI. 
 
8.3 
SITE REIMBURSEMENT 
Sites will be reimbursed according to each participating site’s contract.  Please see the relevant appendix for further 
information. 
 
8.4 
DATA SHARING 
All de-identified raw data measured during the trial will be made available on request to relevant regulatory authorities, 
recognised academic institutions and clinical teams.  Deidentified, aggregated data sets will be hosted on an approved 
public research data platform. Data requests must be made in writing with a proposal for data usage to the CI.  Upon 
the approval for data sharing by the CI, the requester will be required to sign a data agreement.    
 
8.5 
PUBLICATION POLICY 
The results of this trial (positive, negative and/or inconclusive) will be published and/or presented at scientific 
meetings.  The preparation and submission for publication of manuscripts containing the trial results shall only be 
done if prior consent is obtained by the CI.  Any manuscript requests can be submitted to the FORMaT Trial 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
38 
Management Team.  Authorship will be granted according to the recommendations from the International Committee 
of Medical Journal Editors (ICMJE)(50).

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
39 
REFERENCES 
1. 
Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, et al. An official ATS/IDSA 
statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit 
Care Med. 2007;175(4):367-416. 
2. 
Lee MR, Sheng WH, Hung CC, Yu CJ, Lee LN, Hsueh PR. Mycobacterium abscessus Complex Infections 
in Humans. Emerg Infect Dis. 2015;21(9):1638-46. 
3. 
Smibert O, Snell GI, Bills H, Westall GP, Morrissey CO. Mycobacterium abscessus Complex - a Particular 
Challenge in the Setting of Lung Transplantation. Expert Rev Anti Infect Ther. 2016;14(3):325-33. 
4. 
Floto RA, Olivier KN, Saiman L, Daley CL, Herrmann JL, Nick JA, et al. US Cystic Fibrosis Foundation 
and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous 
mycobacteria in individuals with cystic fibrosis: executive summary. Thorax. 2016;71(1):88-90. 
5. 
Park IK, Olivier KN. Nontuberculous mycobacteria in cystic fibrosis and non-cystic fibrosis bronchiectasis. 
Semin Respir Crit Care Med. 2015;36(2):217-24. 
6. 
Olivier KN, Weber DJ, Wallace RJ, Jr., Faiz AR, Lee JH, Zhang Y, et al. Nontuberculous mycobacteria. I: 
multicenter prevalence study in cystic fibrosis. Am J Respir Crit Care Med. 2003;167(6):828-34. 
7. 
Catherinot E, Roux AL, Vibet MA, Bellis G, Lemonnier L, Le Roux E, et al. Inhaled therapies, azithromycin 
and Mycobacterium abscessus in cystic fibrosis patients. Eur Respir J. 2013;41(5):1101-6. 
8. 
Bange, Böttger. Improved Decontamination Method for Recovering Mycobacteria from Patients with Cystic 
Fibrosis. European Journal of Clinical Microbiology and Infectious Diseases. 2002;21(7):546-8. 
9. 
Ferroni A, Sermet-Gaudelus I, Bourgeois ML, Pierre-Audigier C, Offredo C, Rottman M, et al. Measurement 
of Immunoglobulin G against Mycobacterial Antigen A60 in Patients with Cystic Fibrosis and Lung 
Infection Due to Mycobacterium abscessus. Clinical Infectious Diseases. 2005;40(1):58-66. 
10. 
Stout JE, Floto RA. Treatment of Mycobacterium abscessus: all macrolides are equal, but perhaps some are 
more equal than others. Am J Respir Crit Care Med. 2012;186(9):822-3. 
11. 
Prevots DR, Marras TK. Epidemiology of human pulmonary infection with nontuberculous mycobacteria: a 
review. Clin Chest Med. 2015;36(1):13-34. 
12. 
Esther CR, Jr., Esserman DA, Gilligan P, Kerr A, Noone PG. Chronic Mycobacterium abscessus infection 
and lung function decline in cystic fibrosis. J Cyst Fibros. 2010;9(2):117-23. 
13. 
Park HY, Jeong BH, Chon HR, Jeon K, Daley CL, Koh WJ. Lung Function Decline According to Clinical 
Course in Nontuberculous Mycobacterial Lung Disease. Chest. 2016;150(6):1222-32. 
14. 
Diel R, Ringshausen F, Richter E, Welker L, Schmitz J, Nienhaus A. Microbiological and Clinical Outcomes 
of Treating Non-Mycobacterium Avium Complex Nontuberculous Mycobacterial Pulmonary Disease: A 
Systematic Review and Meta-Analysis. Chest. 2017;152(1):120-42. 
15. 
Thomson R, Donnan E, Unwin S. Nontuberculous Mycobacterial Lung Disease. Time to Get a Grip! Ann 
Am Thorac Soc. 2015;12(10):1425-7. 
16. 
Wason JM, Trippa L. A comparison of Bayesian adaptive randomization and multi-stage designs for multi-
arm clinical trials. Stat Med. 2014;33(13):2206-21. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
40 
17. 
Qvist T, Taylor-Robinson D, Waldmann E, Olesen HV, Hansen CR, Mathiesen IH, et al. Comparing the 
harmful effects of nontuberculous mycobacteria and Gram negative bacteria on lung function in patients with 
cystic fibrosis. Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society. 
2016;15(3):380-5. 
18. 
Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, et al. Emergence and spread 
of a human-transmissible multidrug-resistant nontuberculous mycobacterium. Science. 2016;354(6313):751-
7. 
19. 
Koh WJ, Jeong BH, Kim SY, Jeon K, Park KU, Jhun BW, et al. Mycobacterial Characteristics and Treatment 
Outcomes in Mycobacterium abscessus Lung Disease. Clin Infect Dis. 2017;64(3):309-16. 
20. 
Rubio M, March F, Garrigo M, Moreno C, Espanol M, Coll P. Inducible and Acquired Clarithromycin 
Resistance in the Mycobacterium abscessus Complex. PLoS One. 2015;10(10):e0140166. 
21. 
Park J, Cho J, Lee CH, Han SK, Yim JJ. Progression and Treatment Outcomes of Lung Disease Caused by 
Mycobacterium abscessus and Mycobacterium massiliense. Clin Infect Dis. 2017;64(3):301-8. 
22. 
Lyu J, Jang HJ, Song JW, Choi CM, Oh YM, Lee SD, et al. Outcomes in patients with Mycobacterium 
abscessus pulmonary disease treated with long-term injectable drugs. Respir Med. 2011;105(5):781-7. 
23. 
Jarand J, Levin A, Zhang L, Huitt G, Mitchell JD, Daley CL. Clinical and microbiologic outcomes in patients 
receiving treatment for Mycobacterium abscessus pulmonary disease. Clin Infect Dis. 2011;52(5):565-71. 
24. 
Aksamit TR, Philley JV, Griffith DE. Nontuberculous mycobacterial (NTM) lung disease: the top ten 
essentials. Respir Med. 2014;108(3):417-25. 
25. 
Sherrard LJ, Tay GT, Butler CA, Wood ME, Yerkovich S, Ramsay KA, et al. Tropical Australia is a potential 
reservoir of non-tuberculous mycobacteria in cystic fibrosis. Eur Respir J. 2017;49(5). 
26. 
Thomson R, Tolson C, Carter R, Coulter C, Huygens F, Hargreaves M. Isolation of nontuberculous 
mycobacteria (NTM) from household water and shower aerosols in patients with pulmonary disease caused 
by NTM. J Clin Microbiol. 2013;51(9):3006-11. 
27. 
Doring G, Flume P, Heijerman H, Elborn JS, Consensus Study G. Treatment of lung infection in patients 
with cystic fibrosis: current and future strategies. J Cyst Fibros. 2012;11(6):461-79. 
28. 
Lyu J, Kim B-J, Kim B-J, Song JW, Choi C-M, Oh Y-M, et al. A shorter treatment duration may be sufficient 
for patients with Mycobacterium massiliense lung disease than with Mycobacterium abscessus lung disease. 
Respiratory Medicine. 2014;108(11):1706-12. 
29. 
Waters V, Ratjen F. Antibiotic treatment for nontuberculous mycobacteria lung infection in people with 
cystic fibrosis. Cochrane Database Syst Rev. 2020;6:CD010004. 
30. 
Novosad SA, Beekmann SE, Polgreen PM, Mackey K, Winthrop KL, Team MaS. Treatment of 
Mycobacterium abscessus Infection. Emerg Infect Dis. 2016;22(3):511-4. 
31. 
Centre for Drug Evaluation and Research US Food and Druig Administration. Non-tuberculous 
mycobacterial lung infection. Food and Drug Administration (FDA); 2016 April 2016. 
32. 
Henkle E, Aksamit T, Barker A, Daley CL, Griffith D, Leitman P, et al. Patient-Centered Research Priorities 
for Pulmonary Nontuberculous Mycobacteria (NTM) Infection. An NTM Research Consortium Workshop 
Report. Ann Am Thorac Soc. 2016;13(9):S379-84. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
41 
33. 
Rowbotham NJ, Smith S, Leighton PA, Rayner OC, Gathercole K, Elliott ZC, et al. The top 10 research 
priorities in cystic fibrosis developed by a partnership between people with CF and healthcare providers. 
Thorax. 2017. 
34. 
Cellamare M, Milstein M, Ventz S, Baudin E, Trippa L, Mitnick CD. Bayesian adaptive randomization in a 
clinical trial to identify new regimens for MDR-TB: the endTB trial. Int J Tuberc Lung Dis. 2016;20(12):8-
12. 
35. 
Berry SM, Connor JT, Lewis RJ. The platform trial: an efficient strategy for evaluating multiple treatments. 
JAMA. 2015;313(16):1619-20. 
36. 
Bhatt DL, Mehta C. Adaptive Designs for Clinical Trials. N Engl J Med. 2016;375(1):65-74. 
37. 
Davies GR, Phillips PP, Jaki T. Adaptive clinical trials in tuberculosis: applications, challenges and solutions. 
Int J Tuberc Lung Dis. 2015;19(6):626-34. 
38. 
Angus DC, Berry S, Lewis RJ, Al-Beidh F, Arabi Y, van Bentum-Puijk W, et al. The REMAP-CAP 
(Randomized Embedded Multifactorial Adaptive Platform for Community-acquired Pneumonia) Study. 
Rationale and Design. Ann Am Thorac Soc. 2020;17(7):879-91. 
39. 
Fountzilas E, Tsimberidou AM. Overview of precision oncology trials: challenges and opportunities. Expert 
Review of Clinical Pharmacology. 2018;11(8):797-804. 
40. 
Informed Consent Information Sheet Guidance for IRBs, Clinical Investigators, and Sponsors. In: 
Administration USDoHaHSFaD, editor. 2014. 
41. 
Miller MR, Hankinson J, Brusasco V, Burgos F, Casaburi R, Coates A, et al. Standardisation of spirometry. 
Eur Respir J. 2005;26(2):319-38. 
42. 
Quanjer PH, Stanojevic S, Cole TJ, Baur X, Hall GL, Culver BH, et al. Multi-ethnic reference values for 
spirometry for the 3-95-yr age range: the global lung function 2012 equations. Eur Respir J. 2012;40(6):1324-
43. 
43. 
Laboratories ATSCoPSfCPF. ATS statement: guidelines for the six-minute walk test. Am J Respir Crit Care 
Med. 2002;166(1):111-7. 
44. 
Smith CL, Jin Y, Raddad E, McNearney TA, Ni X, Monteith D, et al. Applications of Bayesian statistical 
methodology to clinical trial design: A case study of a phase 2 trial with an interim futility assessment in 
patients with knee osteoarthritis. Pharm Stat. 2019;18(1):39-53. 
45. 
Park JJ, Thorlund K, Mills EJ. Critical concepts in adaptive clinical trials. Clin Epidemiol. 2018;10:343-51. 
46. 
Taves DR. Minimization: a new method of assigning patients to treatment and control groups. Clin 
Pharmacol Ther. 1974;15(5):443-53. 
47. 
Pocock SJ, Simon R. Sequential treatment assignment with balancing for prognostic factors in the controlled 
clinical trial. Biometrics. 1975;31(1):103-15. 
48. 
Han B, Enas NH, McEntegart D. Randomization by minimization for unbalanced treatment allocation. Stat 
Med. 2009;28(27):3329-46. 
49. 
Cuffe RL, Lawrence D, Stone A, Vandemeulebroecke M. When is a seamless study desirable? Case studies 
from different pharmaceutical sponsors. Pharm Stat. 2014;13(4):229-37. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
Master Protocol Version 4.1 Date 20 February 2024  
42 
50. 
Defining the Role of Authors and Contributors International Committee of Medical Journal Editors;  
[Available from: https://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-
role-of-authors-and-contributors.html. 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
i 
 
APPENDIX A1- INTERVENTION PROGRAM 
Combined Intensive and Consolidation Therapies 
Appendix 
A1 
– 
Intervention 
Program 
Version 1.1 
Appendix Date 
20 February 2024 
Protocol Number  
FORMaT001 
Funding 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
EudraCT Number 
2020-000050-10 
EU-CT Number 
2023-506575-99-00-EU CT 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS ...................................................................................................................... II 
TABLE OF TABLES ............................................................................................................................ V 
TABLE OF FIGURES .......................................................................................................................... V 
ABBREVIATIONS ............................................................................................................................... VI 
APPENDIX A: INTERVENTION PROGRAM .................................................................................. 9 
APPENDIX A1 – COMBINED INTENSIVE AND CONSOLIDATION MODULE .................... 10 
1 
INTRODUCTION ......................................................................................................................... 14 
2 
OBJECTIVES ................................................................................................................................ 14 
2.1 
PRIMARY OBJECTIVES ........................................................................................................................... 14 
2.2 
SECONDARY OBJECTIVES ...................................................................................................................... 15 
2.3 
EXPLORATORY OBJECTIVES .................................................................................................................. 15 
3 
DESIGN .......................................................................................................................................... 15 
4 
ELIGIBILITY CRITERIA .......................................................................................................... 17 
4.1 
INCLUSION CRITERIA ............................................................................................................................. 17 
4.2 
EXCLUSION CRITERIA ............................................................................................................................ 18 
4.3 
ADDITIONAL CRITERIA .......................................................................................................................... 19 
4.3.1 Mixed NTM infections........................................................................................................................ 19 
4.3.2 Co-enrolment with other trials .......................................................................................................... 19 
5 
ACCEPTABLE METHODS OF CONTRACEPTION ............................................................. 19 
6 
TRIAL CONDUCT ....................................................................................................................... 20 
6.1 
INFORMED CONSENT.............................................................................................................................. 20 
6.2 
PREGNANCY INFORMATION CONSENT ................................................................................................... 20 
6.3 
METHODS OF ASSIGNING PARTICIPANTS TO TREATMENT ARMS .......................................................... 20 
7 
INTERVENTION PROGRAM PROCEDURES AND SAFETY MONITORING ................ 21 
7.1 
SERUM/URINE PREGNANCY TEST .......................................................................................................... 21 
7.2 
CHEST CT SCAN .................................................................................................................................... 21 
7.3 
RESPIRATORY SAMPLING ....................................................................................................................... 21 
7.4 
AUDIOGRAM .......................................................................................................................................... 21 
7.5 
VESTIBULAR MONITORING .................................................................................................................... 22 
7.5.1 Dynamic Visual Acuity Testing (DVA) .............................................................................................. 22 
7.5.2 Head Impulse Testing (HIT) .............................................................................................................. 22 
7.5.3 Romberg on Foam Test ...................................................................................................................... 22 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
iii 
7.6 
PHYSICAL EXAMINATION ...................................................................................................................... 22 
7.7 
ELECTROCARDIOGRAM (ECG) .............................................................................................................. 22 
7.8 
SIX-MINUTE WALK TEST ........................................................................................................................ 23 
7.9 
BLOOD SAMPLING.................................................................................................................................. 23 
7.10 
STUDY MEDICATION REVIEW ................................................................................................................ 23 
7.11 
AMIKACIN ADMINISTRATION AND MONITORING .................................................................................. 23 
7.11.1 Nebuliser Type FOR IA ..................................................................................................................... 23 
7.11.2 Amikacin Therapeutic Drug Monitoring ........................................................................................... 24 
7.12 
HEALTH RELATED QUALITY OF LIFE AND UTILITY MEASURES............................................................ 24 
7.12.1 Cystic Fibrosis Questionnaire-Revised (CFQ-R) .............................................................................. 24 
7.12.2 EQ-5D-5L .......................................................................................................................................... 25 
7.12.3 EQ-5D-Y ............................................................................................................................................ 25 
7.12.4 St. George Respiratory Questionnaire (SGRQ) ................................................................................. 25 
7.12.5 Short Form- 36 Health Survey ........................................................................................................... 25 
7.12.6 Pediatric Quality of Life Inventory (PedsQL™) ............................................................................... 25 
7.12.7 Child Health Utility 9D (CHU9D) .................................................................................................... 26 
7.13 
MABS CLEARANCE FOLLOW-UP QUESTIONNAIRE ............................................................................... 26 
8 
SITE REIMBURSEMENT ........................................................................................................... 26 
9 
INTENSIVE THERAPY NESTED STUDIES ........................................................................... 27 
9.1 
NESTED STUDY A1.1: SHORT INTENSIVE THERAPY ................................................................. 27 
9.1.1 Primary Objective .............................................................................................................................. 27 
9.2 
NESTED STUDY A1.2: DURATION OF INTENSIVE THERAPY FOR PATIENTS WITH ONGOING 
POSITIVE MABS CULTURES AFTER 4 WEEKS OF INTENSIVE THERAPY. ............................................................. 32 
9.2.1 Introduction ....................................................................................................................................... 32 
9.2.2 Eligibility Criteria ............................................................................................................................. 32 
9.2.3 Objectives .......................................................................................................................................... 32 
9.2.4 Statistical Analysis ............................................................................................................................. 33 
9.3 
INTENSIVE THERAPY DOSING REGIMEN ................................................................................................ 34 
9.3.1 Drug Supply, Storage and Distribution during Intensive Therapy .................................................... 41 
9.3.2 Options for Reducing Nausea During Intensive Therapy .................................................................. 41 
10 NESTED STUDY A1.3: CONSOLIDATION THERAPY ........................................................ 42 
10.1 
INTRODUCTION ...................................................................................................................................... 42 
10.2 
OBJECTIVES ........................................................................................................................................... 42 
10.2.1 Primary Objective .............................................................................................................................. 42 
10.2.2 Secondary Objectives......................................................................................................................... 43 
10.3 
ELIGIBILITY CRITERIA ........................................................................................................................... 43 
10.4 
STATISTICAL ANALYSIS ......................................................................................................................... 43 
10.5 
CONSOLIDATION THERAPY DOSING REGIMEN ...................................................................................... 44 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
iv 
10.5.1 Drug Supply, Storage and Distribution during Consolidation Therapy ............................................ 49 
10.5.2 Drug Compliance during Consolidation Therapy ............................................................................. 49 
11 SCHEDULE OF ASSESSMENTS ............................................................................................... 50 
12 RANDOMISATION ...................................................................................................................... 57 
13 APPLICABLE DISCOVERY STUDIES AND REGISTRY LINKAGE FOR APPENDIX A158 
14 REFERENCES .............................................................................................................................. 59 
 
 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
v 
TABLE OF TABLES 
Table 1 Intensive therapy dosing regimen for Intensive Arm A in adults .................................................................. 35 
Table 2 Intensive therapy dosing regimen for Intensive Arm B in adults .................................................................. 36 
Table 3 Intensive therapy dosing regimen for Intensive Arm C in adults .................................................................. 37 
Table 4 Intensive therapy dosing regimen for Intensive Arm A in paediatrics .......................................................... 38 
Table 5 Intensive therapy dosing regimen for Intensive Arm B in paediatrics .......................................................... 39 
Table 6 Intensive therapy dosing regimen for Intensive Arm C in paediatrics .......................................................... 40 
Table 7 Consolidation therapy dosing regimen for Consolidation Arm a in adults ................................................... 45 
Table 8 Consolidation therapy dosing regimen for Consolidation Arm b in adults ................................................... 46 
Table 9 Consolidation therapy dosing regimen for Consolidation Arm a in paediatrics ............................................ 47 
Table 10 Consolidation therapy dosing regimen for Consolidation Arm b in paediatrics ......................................... 48 
Table 11 Special considerations for Schedule of Assessments .................................................................................. 50 
Table 12 Schedule of Assessments for Intervention Program Participants: Intensive Therapy ................................. 52 
Table 13 Schedule of Assessments for Intervention Program Participants: Prolonged Intensive Therapy ................ 54 
Table 14 Schedule of Assessments for Consolidation Therapy and Final Outcome .................................................. 56 
 
TABLE OF FIGURES 
Figure 1 Flow Diagram for Appendix A1, Intervention Program .............................................................................. 17 
 
 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
vi 
ABBREVIATIONS  
 
AE 
 
 
Adverse Event 
AFB 
 
 
Acid-Fast Bacilli 
ATS 
 
 
American Thoracic Society 
AUC 
 
 
Area Under the Curve 
BAL 
 
 
Bronchoalveolar Lavage 
BAR 
 
 
Bayesian Adaptive Randomisation 
BTS 
 
 
British Thoracic Society 
CEACS 
 
Cost-effectiveness acceptability curves 
CF 
 
 
Cystic Fibrosis 
CFQ-R  
 
Cystic Fibrosis Questionnaire-Revised 
CHU9D 
 
Child Health Utility 9D 
Cmax  
 
Maximum serum concentration 
Cmin  
 
Minimum serum concentration 
CRF 
 
 
Case Report Form 
CT 
 
 
Computed Tomography 
CTCAE 
 
Common Terminology Criteria for Adverse Events 
DVA 
 
 
Dynamic Visual Acuity 
ECG 
 
 
Electrocardiogram 
eCRF  
 
electronic Case Report Form 
FEV1  
 
Forced Expiratory Volume in one second 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
HIT 
 
 
Head Impulse Test  
HRCT  
 
High-Resolution Computed Tomography 
HRQoL 
 
Health Related Quality of Life 
IA 
 
 
Inhaled Amikacin 
ICD 
 
 
International Statistical Classification of Diseases 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
vii 
ICERS  
 
Incremental cost-effectiveness ratios 
IV 
 
 
Intravenous 
IVA 
 
 
Intravenous Amikacin 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
MAC  
 
Mycobacterium avium Complex 
MARS-5 
 
5-item Medication Adherence Rating Scale 
MIC 
 
 
Minimum Inhibitory Concentration 
MoOP  
 
Manual of Operating Procedures 
MPR 
 
 
Medication Possession Ratio 
NMB  
 
Net Monetary Benefit 
NTM  
 
Non-Tuberculous Mycobacteria 
PedsQL™ 
 
Pediatric Quality of Life Inventory  
QALY  
 
Quality-Life Adjusted Years 
QoL 
 
 
Quality of Life 
RCT 
 
 
Randomised Control Trial 
REDCap 
 
Research Electronic Data Capture 
R-Con  
 
Randomisation – Consolidation  
R-PI/IC  
 
Randomisation – Prolonged Intensive/Immediate Consolidation 
R-SI 
 
 
Randomisation – Short Intensive  
SAE 
 
 
Serious Adverse Event 
SAP 
 
 
Statistical Analysis Plan 
SF-36  
 
Short form-36 
SGRQ  
 
St George Respiratory Questionnaire 
SOP 
 
 
Standard Operating Procedure 
TDM  
 
Therapeutic Drug Monitoring 
TPF 
 
 
Time Point Final 
TPF-PI  
 
Time Point Final – Prolonged Intensive 

Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
viii 
TPF-SI  
 
Time Point Final – Short Intensive  
TPF-WK12 
 
Time Point Final – at Week 12 Visit 
TPST  
 
Time Point Start Treatment 
TPST-Con 
 
Time Point Start Treatment – Consolidation  
TPST-SI 
 
Time Point Start Treatment – Short Intensive  
VAS 
 
 
Visual Analogue Scale 
vHIT 
 
 
Video Head Impulse Test 
VOR 
 
 
Vestibulo-ocular Reflex 
WTP   
 
Willingness To Pay 
6MWD  
 
Six Minute Walk Distance 
6MWT  
 
Six Minute Walk Test 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
9 
APPENDIX A: INTERVENTION PROGRAM 
Appendix A contains the Intervention Program modules, with new modules created as interventions are added to 
either intensive or consolidation phases of the trial.  They are numbered sequentially, A1, A2, A3 etc, with Appendix 
A1 describing the first iteration of the Intervention Program.  The relevant detailed statistical methods and simulations 
for each Intervention Program module will be described in Appendix F: General Statistical Principles.  Separate 
consent procedures may be required for each appendix.  Of note, in some cases data collected as part of one appendix 
may be incorporated in the analysis of another appendix, if collected to address the same objective.  If this occurs, it 
will be detailed in the relevant appendices.  Should an intervention arm be dropped, or a new intervention arm added 
either to intensive therapy or consolidation therapy this will require a new appendix and a new statistical analysis 
plan. 
Each program in Appendix A will stipulate which of the Discovery studies and Registry linkages is applicable. The 
Intervention Program modules in Appendix A will include the following: 
• 
A description of the primary and secondary objectives. 
• 
A description of the intervention trial design including any specific inclusion or exclusion criteria specific to 
the Intervention Program modules. 
• 
A description of the interventions and dosing. 
• 
The methods for assigning treatment arms to the Intervention Program participants. 
• 
Consent requirements. 
• 
Specific Intervention Program trial procedures, monitoring and safety requirements and schedule of 
assessments. 
• 
A description of relevant nested studies. 
• 
A description of cost effectiveness methodology and analysis as appropriate will be detailed in Appendix E: 
Health Economics. 
• 
A description of statistical analyses and simulations will be detailed in Appendix F: General Statistical 
Principles. 
• 
The Discovery studies applicable to the module (if relevant). 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
10 
APPENDIX A1 – COMBINED INTENSIVE AND CONSOLIDATION MODULE 
Appendix A1 describes the initial Mycobacterium abscessus Pulmonary Disease (MABS-PD) intervention platform 
for the FORMaT trial.  Within Appendix A1 there are intensive and consolidation therapy nested studies which are 
governed by the trial design and conduct described below.  
FORMaT Appendix A1 Summary 
Treatment 
combinations: 
Intensive therapy arms: 
Arm A  
Arm B  
Arm C  
 
1. IV amikacin, and; 
1. Inhaled amikacin, and; 
1. IV amikacin, and; 
 
2. IV tigecycline, and; 
2. IV tigecycline, and; 
2. IV tigecycline, and; 
 
3. IV imipenem or IV 
cefoxitin, and; 
3. IV imipenem or IV 
cefoxitin, and; 
3. IV imipenem or IV 
cefoxitin, and; 
 
4. Oral azithromycin or 
oral clarithromycin, and; 
4. Oral azithromycin or 
oral clarithromycin, and; 
4. Oral azithromycin or 
oral clarithromycin. 
 
5. Oral clofazimine. 
5. Oral clofazimine. 
 
 
Consolidation therapy arms: 
 
Arm a  
Arm b  
 
1. Oral clofazimine, and; 
2. Oral azithromycin or clarithromycin, 
and; 
3. In combination with one to three of the 
following oral antibiotics: 
• 
Linezolid, 
• 
Trimethoprim / sulfamethoxazole 
(co-trimoxazole), 
• 
Bedaquiline, 
• 
Rifabutin. 
• 
Doxycycline 
• 
Moxifloxacin 
1. 
Inhaled amikacin 
2. 
Oral clofazimine, and 
3. 
Oral azithromycin or clarithromycin, 
and; 
4. 
In combination with one to three of the 
following oral antibiotics: 
• 
Linezolid, 
• 
Trimethoprim / sulfamethoxazole 
(co-trimoxazole), 
• 
Bedaquiline, 
• 
Rifabutin. 
• 
Doxycycline 
• 
Moxifloxacin 
 
 
 
 
 
 
 
 
A mixed Non-Tuberculous Mycobacteria (NTM) infection (slow grower + Mycobacterium 
abscessus (MABS)) can include the use of ethambutol in either/both the intensive or 
consolidation phase/s of treatment. 
Appendix 
A1-
specific eligibility: 
Inclusion and exclusion criteria as per Master Protocol section 4.1 and below. 
Appendix 
A1-
specific inclusions: 
1. Positive MABS-PD diagnosis meeting all three American Thoracic Society (ATS) 
clinical, radiological and microbiological diagnostic criteria for MABS-PD.  Defined as; 
Clinical: Pulmonary symptoms and exclusion of other diagnoses. 
Radiological: Nodular or cavitary opacities on chest radiograph or a chest high-
resolution computed tomography (HRCT) scan showing multifocal bronchiectasis with 
multiple small nodules. 
Microbiological: MABS positive culture results from at least two separate expectorated 
sputum samples. 
or; 
Positive culture results from at least one bronchial wash or lavage. 
or; 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
11 
FORMaT Appendix A1 Summary 
Transbronchial or other lung biopsy with mycobacterial histopathologic features 
(granulomatous inflammation or acid-fast bacilli (AFB)) and positive culture for NTM 
or biopsy showing mycobacterial histopathologic features (granulomatous inflammation 
or AFB) and one or more sputum or bronchial washes that are culture positive for NTM. 
2. Male or female participants of any age. 
3. Informed consent signed by participant or parent/legal guardian if participant is under 
18 years of age.  For those participating in both the intensive and consolidation modules 
a combined consent form may be used. 
4. Participant has not received MABS-PD treatment in the 12 months preceding assessment 
of eligibility (this includes drugs prescribed for treatment of other mycobacteria and/or 
other indications that may have activity against MABS as specified in FORMaT 
Prohibited Drug List SOP). 
5. Ability to comply with study visits, therapies and study procedures as judged by the site 
investigator. 
Appendix 
A1-
specific 
exclusions: 
1. Participants receiving current treatment for MABS within the previous 12 months (this 
includes drugs prescribed for treatment of other mycobacteria and/or other indications 
that may have activity against MABS, as specified in FORMaT Prohibited Drug List 
SOP), except for participants taking azithromycin as part of routine treatment for Cystic 
Fibrosis (CF) or chronic infection-related pulmonary disease). 
2. Positive pregnancy test at screening or any time during the FORMaT trial for females 
of childbearing potential. 
3. Breast-feeding. 
4. An unwillingness to comply with the acceptable methods of contraception defined in the 
relevant section of Appendix A1. 
5. QTc>500 milliseconds (QT interval to be corrected based on Fridericia method). 
6. Known hypersensitivity to any of the therapies for which no alternative option(s) have 
been provided. 
Target recruitment: 300 participants 
Outcome 
measures: 
Primary outcome: MABS clearance from respiratory sample(s) with tolerance at the Final 
Outcome. 
Secondary outcomes: 
1. Probability of MABS clearance at Final Outcome irrespective of toxicity according to 
participant’s treatment pathway. 
2. Safety of treatment combinations, including changes in microbiological resistance. 
3. Change in FEV1 z-score at Final Outcome compared with Screening in participants who 
do and do not clear MABS at Final Outcome. 
4. Phenotype of the structural abnormalities of chest CTs and changes in chest CT scores 
between Screening and Final Outcome between participants who clear or do not clear 
MABS at Final Outcome. 
5. Predictive value of structural abnormalities on Screening CT scans for sputum 
conversion and for progression of structural changes in relation to treatment. 
6. Change in 6-minute walk distance (6MWD) for adult participants from Screening to 
Final Outcome according to treatment pathway and in participants who do and do not 
clear MABS at Final Outcome. 
7. Change in HRQoL for participants from Screening to Final Outcome according to 
treatment pathway and in participants who do and do not clear MABS at Final Outcome. 
8. Cost effectiveness of the treatment combinations across intensive and consolidation 
phases of the trial. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
12 
FORMaT Appendix A1 Summary 
9. Causes for early withdrawal from MABS-PD treatment due to reasons other than poor 
tolerance as defined in the primary objectives. 
Exploratory outcomes: 
1. Participant’s MABS clearance status 12 months after Final Outcome.  
 
Timepoints: 
Screening: 
Up to Minus 42 days from Date of Randomisation-Short 
Intensive (R-SI). 
Time Point Start Treatment-
Short Intensive (TPST-SI): 
R-SI. 
Time Point Final (TPF): 
End of treatment plus four weeks off-treatment (Final 
Outcome Visit date). 
Nested studies 
Intensive Therapy Modules: 
Nested study A1.1: 
Nested study A1.2: 
Type of Short intensive Therapy 
Duration of intensive therapy for patients completing short 
intensive treatment with ongoing positive MABS cultures 
collected at 4 weeks and randomised to either a further 6 
weeks intensive therapy or immediate consolidation. 
Consolidation Therapy Module: 
Nested study A1.3: 
The use of oral therapy only or oral therapy and inhaled 
amikacin for consolidation therapy. 
 
Intensive Therapy Module Nested Studies 
Nested study A1.1: Type of Short Intensive Therapy 
Timepoints: 
Screening: 
Up to Minus 42 days from Date of R-SI. 
TPST-SI: 
R-SI 
Time Point Final-Short 
Intensive (TPF-SI)*: 
Date of Randomisation Prolonged Intensive or Immediate 
Consolidation (R-PI/IC) minus 1 day for those allocated 
prolonged intensive or Randomisation-Consolidation (R-
Con) minus 1 day for those allocated to immediate 
consolidation.  
*The most accurate method of determining TPF for this trial phase is calculating the time immediately 
preceding randomisation to the next treatment phase i.e. date of next randomisation minus 1 day. 
Nested study A1.2: Duration of intensive therapy for patients with ongoing positive MABS cultures 
Timepoints: 
Screening: 
TPST-SI: 
Up to Minus 42 days from R-SI. 
Date of R-SI 
 
TPF-PI* 
or 
TPF-WK12: 
Date of R-Con minus 1 day (for those allocated to prolonged intensive) 
or Week 12 visit date (for those allocated to immediate consolidation). 
 
*The most accurate method of determining TPF for this trial phase is calculating the time immediately 
preceding randomisation to the next treatment phase i.e. date of next randomisation minus 1 day. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
13 
Consolidation Therapy Module Nested Study 
 
Nested study A1.3: Use of oral therapy +/- inhaled amikacin for consolidation therapy 
Timepoints: 
Time Point Start Treatment-
Consolidation (TPST-Con): 
Date of R-Con 
TPF: 
End of treatment plus 4 weeks off treatment (Final 
Outcome Visit date). 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
14 
1 INTRODUCTION 
The probability of microbiological clearance with acceptable toxicity for treatment combinations tested in FORMaT, 
inclusive of both Appendix A1 intensive and Appendix A1 consolidation for patients with Mycobacterium abscessus 
pulmonary disease (MABS-PD) will be determined. 
The probability of microbiological clearance with acceptable toxicity of treatment combinations will also be 
examined in different patient subpopulations (CF and non-CF, those infected with different MABS subspecies (M. 
a. abscessus/ M. a. bolletii [inducible macrolide resistance] and M. a. massiliense) and those with constitutive 
macrolide resistance and those with mixed NTM infections). 
The best therapy combinations may then form the control arms for new intervention studies which can be added as 
new arms within Appendix A. 
Sites may undertake both intensive and consolidation modules or if they are unable to conduct the intensive therapy 
module, then they can partner with a FORMaT site that is able to manage the intensive therapy module, and only 
undertake the consolidation module themselves. Sites that are unable to undertake the intensive therapy module 
themselves and are unable to partner with a site that is able to manage the intensive therapy module, can choose to 
only undertake the consolidation module (see Appendix A2 for detailed information). 
 
2 OBJECTIVES 
2.1 
PRIMARY OBJECTIVES 
The primary objective for Appendix A1 is to determine the optimal treatment for MABS-PD. Optimal treatment is 
defined by MABS clearance from respiratory samples with tolerance at 56 weeks (denoted Final Outcome) for 
participants who received short intensive therapy or at 62 weeks (denoted Final Outcome) for participants who 
received prolonged intensive therapy. 
Definition of tolerance: 
Tolerance is based on the Common Terminology Criteria for Adverse Events (CTCAE version 5.0). Only adverse 
events that are attributed as either “possibly”, “probably”, or “definitely” related to study drug will be assessed in the 
determination of tolerance.  “Good” tolerance is defined as no adverse events occurring or only adverse events coded 
as CTCAE grades 1 and 2. “Poor” tolerance is defined as any adverse events attributed as possibly, probably, or 
definitely related to study drug coded as CTCAE grades 3, 4, or 5. 
MABS clearance at final outcome will be defined as: 
Negative MABS cultures from four consecutive sputum samples with one of those sputum specimens collected four 
weeks after the completion of consolidation therapy (either week 56 or 62, depending on treatment arm 
randomisation). Or, a MABS negative Bronchoalveolar Lavage (BAL) collected four weeks after completion of 
consolidation (either week 56 or 62, depending on treatment arm randomisation). 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
15 
 
2.2 
SECONDARY OBJECTIVES 
1. To examine the probability of microbiological clearance at Final Outcome (irrespective of toxicity) for 
participants according to treatment path. 
2. To describe the safety of the treatment combinations in patients with MABS. 
3. To examine the change in Forced Expiratory Volume in one second (FEV1) z-score at Final Outcome compared 
with Screening in patients who do and who do not clear MABS at Final Outcome. 
4. To phenotype the structural abnormalities of chest Computed Tomography (CT)s of MABS patients and examine 
changes in chest CT scores (bronchiectasis, trapped air, % disease) between Screening and Final Outcome 
between those who clear and those who do not clear MABS at Final Outcome. 
5. To examine the predictive value of structural abnormalities on Screening CTs for sputum conversion and for 
progression of structural changes in relation to therapy. 
6. To examine change in 6MWD for adult participants from Screening to Final Outcome according to treatment 
pathway and in participants who do and do not clear MABS at Final Outcome. 
7. To examine the change in Health-Related Quality of Life (HRQoL) for participants with CF (using the Cystic 
Fibrosis Questionnaire-Revised (CFQ-R)) at Final Outcome compared with Screening according to treatment path 
and in those that do and those that do not clear MABS at Final Outcome. 
8. To examine general HRQoL at Final Outcome compared with Screening according to treatment path and in those 
who do and who do not clear MABS at Final Outcome. 
9. To examine the cost effectiveness of the proposed treatment combinations across both intensive and consolidation 
phases of the trial. 
10. To examine causes for early withdrawal from MABS-PD treatment due to reasons other than poor tolerance as 
defined in the primary objectives. 
2.3 
EXPLORATORY OBJECTIVES 
• 
To examine MABS clearance status at twelve (12) months after Final Outcome. 
3 DESIGN 
Appendix A1 describes the intensive and consolidation modules (Figure A1.1) and will test therapies that are 
currently used and are the basis for the current treatment guidelines. 
The intensive and consolidation modules function as nested studies within the trial. 
Sites that are unable to participate in intensive therapy (nested A1 studies A1.1 and A1.2) but are able to undertake 
consolidation (nested study A1.3) may still be included as a trial site and partner with other trial sites that are able to 
undertake intensive therapy to facilitate trial participation (see FORMaT Shared Trial Sites SOP for further 
information on management of shared trial sites). 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
16 
Intensive Therapy Module 
Appendix A1.1: Short Intensive Therapy: 
A1.1.1: Use of Inhaled Amikacin (IA) During Intensive Therapy to Replace Intravenous 
Amikacin (IVA) in the Treatment of MABS-PD. 
A1.1.2: The Use of Additional Clofazimine to Standard Intravenous Therapies during 
Intensive Therapy in the Treatment of MABS-PD. 
Appendix A1.2: Duration of Intensive Therapy for Patients with Ongoing Positive MABS cultures after 
completing 4 weeks vs 10 weeks of Intensive Therapy. 
Consolidation Therapy Module 
Appendix A1.3: The use of oral therapy only or oral therapy and inhaled amikacin for Consolidation 
Therapy.  Note, participants recruited as part of Appendix A2 will also be included in the analysis of the 
objectives of this nested study. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
17 
 
Figure 1 Flow Diagram for Appendix A1, Intervention Program Eligibility into the Intervention Program is 
determined at screening. At Randomisation-Short Intensive (R-SI) (▲); participants are randomised between the 
different intensive therapy arms (Intensive A, Intensive B and Intensive C) for a period of 6 weeks. At the end of 
intensive therapy, it will be determined if participants are still MABS positive, or MABS negative (cleared). 
Randomisation-Prolonged Intensive or Immediate Consolidation (R-PI/IC) (★) will ONLY be for participants who 
are still MABS positive based on respiratory samples taken at 4 weeks and will allocate participants to either 1) 
continue intensive therapy or 2) immediately commence consolidation therapy. Randomisation-Consolidation (R-
Con) (✢) allocates participants to the consolidation therapy arms either at week 6 (for those allocated to immediate 
consolidation) or at week 12 (for those allocated to prolonged intensive therapy). Refer to Appendix A2 for 
information regarding Consolidation Only intervention program module where participants receive physician 
directed intensive therapy prior to enrolment into Consolidation Only program. 
 
4 ELIGIBILITY CRITERIA 
Participants are eligible for Appendix A1 if the following criteria are met: 
4.1 
INCLUSION CRITERIA  
1. Positive MABS-PD diagnosis meeting all three American Thoracic Society clinical, radiological and 
microbiological diagnostic criteria for MABS-PD.  Defined as: 
 
Clinical: Pulmonary symptoms and exclusion of other diagnoses. 
 
Radiological: Nodular or cavitary opacities on chest radiograph or a chest high-resolution computed 
tomography (HRCT) scan showing multifocal bronchiectasis with multiple small nodules. 
 
Microbiological: MABS positive culture results from at least two separate expectorated sputum samples. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
18 
or 
Positive culture results from at least one bronchial wash or lavage. 
or 
Transbronchial or other lung biopsy with mycobacterial histopathologic features (granulomatous 
inflammation or acid-fast bacilli, (AFB))) and positive culture for NTM or biopsy showing 
mycobacterial histopathologic features (granulomatous inflammation or AFB) and one or more sputum 
or bronchial washes that are culture positive for NTM. 
2. Male or female participants of any age. 
3. Informed consent signed by participant or parent/legal guardian if participant is under 18 years of age.  For 
those participating in both the intensive and consolidation modules at the same site a combined consent may 
be used.  For those sites only participating in the consolidation module, a specific consolidation consent may 
be required.  
4. Participant has not received MABS-PD treatment in the 12 months preceding assessment of eligibility (this 
includes drugs prescribed for the treatment of other mycobacteria and/or other indications that may have 
activity against MABS, as specified in FORMaT Prohibited Drug List SOP). 
5. Ability to comply with study visits, therapies and study procedures as judged by the site investigator. 
 
4.2 
EXCLUSION CRITERIA 
• 
Participants receiving treatment for MABS within the previous 12 months (this includes drugs prescribed for 
treatment of other mycobacteria and/or other indications that may have activity against MABS, as specified in 
FORMaT Prohibited Drug List SOP), except for participants taking azithromycin as part of routine treatment for 
CF or chronic infection-related pulmonary disease. 
• 
Positive pregnancy test at any time during the FORMaT trial for females of childbearing potential.  
• 
Breast-feeding. 
• 
An unwillingness to comply with the acceptable methods of contraception, as described in Section 5 of this 
appendix. 
• 
Participants with a QTc interval >500 milliseconds (QT interval corrected based on Fridericia method). 
• 
Known hypersensitivity to any of the therapies for which no alternative option(s) have been provided.  This 
includes: 
o Amikacin, 
o Tigecycline, 
o Macrolide antibiotics, and 
o Clofazimine. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
19 
4.3 
ADDITIONAL CRITERIA 
4.3.1 
MIXED NTM INFECTIONS 
Participants who have cultured slow growing NTM of the same species two or more times in the 24 months prior to 
screening, with one of those cultures within the 6 months prior to screening will be considered to have mixed NTM 
infection at the time of screening.  If the participant meets all other inclusion criteria and no exclusion criteria they 
will be eligible for participation.  Ethambutol may be used in addition to trial therapies to cover mixed infections 
considered to require treatment by their clinician. 
4.3.2 
CO-ENROLMENT WITH OTHER TRIALS  
Co-enrolment is not permitted when there is a potential interaction between trial interventions, any compromise to 
the validity of either trial or impact on participants’ rights and/or safety.  However, co-enrolment may be permitted 
in the instance where all trials that the participant is enrolled or to be enrolled in have mutually agreed to the co-
enrolment arrangement. 
 
5 ACCEPTABLE METHODS OF CONTRACEPTION 
The effects of some drugs used during the Intervention Program on the unborn child and on the newborn baby are 
not known.  Because of this, it is important that participants are not pregnant or breast-feeding and do not become 
pregnant during the course of the research project. 
It is therefore important that highly effective birth control is used while in this study.  Site investigators should discuss 
effective methods of contraception with participants.  Both male and female participants are to use effective 
contraception, used correctly with every act of sexual intercourse, from at least 14 days before the first dose of 
MABS-PD therapy, during the course of the trial and for a period of 90 days after the last dose of MABS-PD therapy.  
Acceptable methods of contraception for participants enrolled in Appendix A1 include: 
1) Male vasectomy 6 months or more previously, with a documented negative post-vasectomy semen analysis 
for sperm. 
2) Female bilateral tubal ligation performed at least 6 months previously. 
3) Female continuous use of an intrauterine device (non-hormone releasing or hormone releasing) for at least 
90 days before the first dose of MABS-PD therapy. 
4) Female combined (estrogen and progestogen-containing) or progestogen-only oral, injected, implanted or 
vaginal hormonal contraception associated with inhibition of ovulation. 
The barrier contraception methods listed below are not acceptable and are only to be used in special circumstances 
where the investigator determines that barrier contraception is appropriate. 
1) Male and female condom with spermicide (either as a single product if commercially available and/or as 
allowed according to local regulations; otherwise condom and spermicide as separate products). 
2) Male condom with female diaphragm, cervical cap, or vaginal sponge, each with spermicide. 
For female participants using birth control pills 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
20 
The use of birth control pills for contraception must be discussed and approved by the local site investigator at the 
start of each phase of the trial and when any changes in therapy occur, as some therapies used during the trial may 
interact with the effectiveness of birth control pills.  Birth control pills should be in successful use from at least 60 
days before the first dose of MABS-PD therapy (unless otherwise noted) and until 90 days following the last dose of 
MABS-PD therapy. 
Female participants who change their method of contraception to birth control pills during the trial must continue to 
use a second form of approved contraception for at least 60 days after starting the use of birth control pills. 
For female participants using hormonal injected, implanted or vaginal contraception 
Injected, implanted or vaginal hormonal contraception should be used successfully from at least 60 days before the 
first dose of MABS-PD therapy (unless otherwise noted) and until 90 days following the last dose of MABS-PD 
therapy. 
 
6 TRIAL CONDUCT 
6.1 
INFORMED CONSENT 
In addition to providing consent to the FORMaT Master Protocol, participants enrolling in the Intervention Program 
are required to sign and date the relevant Appendix A1 consent.  Consent to Appendix A1 includes consent to all 
Appendix A1 nested studies.  Consent will be obtained from participants or their parent/guardian in accordance with 
the policies described in section 5.4 of the FORMaT Master Protocol. 
6.2 
PREGNANCY INFORMATION CONSENT 
If a FORMaT trial participant becomes pregnant or is the biological father of a child conceived while enrolled in this 
Intervention Program the site investigators are requested to provide the participant with the FORMaT pregnancy 
information and consent form.  The FORMaT pregnancy and consent form requests to follow the participant and the 
child for 12 months after conception.  Please refer to FORMaT Safety Monitoring and Reporting SOP for further 
detail for safety monitoring and reporting of pregnancies and pregnancy outcomes in female trial participants or 
female partners who are pregnant to male participants in the Intervention Program. 
6.3 
METHODS OF ASSIGNING PARTICIPANTS TO TREATMENT ARMS 
Participants will be randomised into different treatment arms for both the intensive and consolidation phase of 
treatment as described in the Master Protocol section 6.2 using the randomisation technique minimisation, initially 
in a 1:1:1 ratio for R-SI and 1:1 ratio for R-PI and R-Con.  As described in the Master Protocol, all randomisations 
will be conducted via Research Electronic Data Capture (REDCap) at each FORMaT trial site.  At each stage, study 
staff will enter the subject demographic data and the stratification factors (see section 6.3 in the Master Protocol) into 
REDCap, which will then inform them of the participant’s treatment allocation for that stage. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
21 
Following interim analysis, after 60 participants have completed 6 weeks of intensive therapy, if appropriate, 
Bayesian Adaptive Randomisation (BAR) will be implemented for R-SI to implement the allocation probabilities 
which will be used until the data support either early stopping for futility, or a maximum sample size is attained.  
Refer to Appendix F: General Statistical Principles for detailed information regarding randomisation and statistical 
principles for Appendix A1. 
 
7 INTERVENTION PROGRAM PROCEDURES AND SAFETY MONITORING  
In addition to the core trial procedures described in the Master Protocol, participants enrolled in the Intervention 
Program are required to undertake procedures and regular toxicology monitoring.  The type of toxicology monitoring 
procedure required will be determined by the treatment arm the participant is allocated to, and in accordance with 
the schedule of assessments outlined in tables 12 to 14.  Toxicology thresholds will be defined in accordance with 
CTCAE criteria as outlined in the Master Protocol, section 5.9.2.  The outcome of all the assessments below will be 
documented in the corresponding Case Report Form (CRF) and entered into REDCap. 
7.1 
SERUM/URINE PREGNANCY TEST 
All female participants of childbearing potential are required to undergo regular pregnancy testing while enrolled in 
the Intervention Program.  Childbearing potential is defined as a premenopausal female capable of becoming 
pregnant, and includes females on oral, injectable, or mechanical contraception; females who are single and females 
whose male partners have been vasectomised or are using mechanical contraception (1).  A serum pregnancy test 
will be performed at screening and at the final study visit (either week 56 or 62 depending on treatment arm 
allocation) and if applicable, at the early withdrawal visit.  A urine β-hCG test or serum pregnancy is acceptable for 
regular pregnancy monitoring from day 1 in accordance with the schedule of assessments outlined in tables 12 to 14.  
Both urine and serum pregnancy tests are to be performed in accordance with site specific procedures. 
7.2 
CHEST CT SCAN 
The chest CT scan for screening is to be performed ideally within the three months prior to screening for Intervention 
Program participants (maximum of six months earlier). 
7.3 
RESPIRATORY SAMPLING 
For screening a minimum of 2 sputum samples (with at least 1 collected within 6 months prior to screening and other 
samples collected within 12 months prior to screening) or 1 BAL collected within 6 months prior to screening is 
required for Intervention Program participants.  Tables 12 to 14 outline the minimum respiratory sample collection 
timepoints during the trial; however, monthly sputum sample collections are recommended. 
7.4 
AUDIOGRAM 
To monitor aminoglycoside induced ototoxicity, regular audiometry assessments will be undertaken in accordance 
with the schedule of assessments outlined in tables 12 to 14.  The battery of assessments to be completed should 
comply with the site-specific requirements. Assessments can be conducted in either a hospital or community setting. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
22 
7.5 
VESTIBULAR MONITORING 
Vestibular toxicity monitoring will document any vestibular symptoms (motion-induced oscillopsia, postural 
instability and gait unsteadiness) associated with prolonged aminoglycoside use.  Assessments will take place in 
accordance with the schedule of assessments outlined in tables 12 to 14.  Testing can be completed either by the 
treating physician or a physiotherapist.  Additional vestibular monitoring may be required if deemed necessary by 
the Site investigator.   
7.5.1 
DYNAMIC VISUAL ACUITY TESTING (DVA) 
Ask the patient to read a visual acuity chart (e.g., Snellen) while sitting still at recommended distance.  This result is 
their static visual acuity.  Repeat task while oscillating the patient’s head horizontally or vertically at 1 to 2 Hz.  An 
abnormal DVA is defined as loss of at least three lines of visual acuity compared with static condition (horizontal 
and/or vertical). 
7.5.2 
HEAD IMPULSE TESTING (HIT) 
Stand in front of the seated patient, facing them, and ask the patient to focus on a target directly in front of them.  
Briskly rotate the patient’s head horizontally approximately 10 to 20° amplitude, watching the patient’s eyes closely.  
In normal subjects, the patient’s eyes remain still as they remain on target.  However, in a patient with impaired 
vestibulo-ocular reflex (VOR), the patient’s eyes drift off the target and require a corrective ‘catch-up’ saccade to re-
fixate on the target and stabilise vision.  This catch-up saccade is a small amplitude horizontal eye movement in the 
opposite direction of the head turn and should occur with every head impulse (repeatable). 
If available, Video Head Impulse Test (vHIT) is recommended as this has a higher sensitivity than the traditional 
bedside head impulse test at detecting impaired VOR.  M=The main benefits include detecting covert (hidden) catch 
up saccades and peer review. 
7.5.3 
ROMBERG ON FOAM TEST 
On a foam surface, ask the participant to stand still with two feet together.  The participant should be able to stand 
steady with their eyes open.  If the participant is not able to perform this task, ask them to separate their feet to 
minimal distance that allows them to do so.  Repeat the task this time with their eyes closed.  Record if the participant 
falls (positive Romberg test) or does not (negative Romberg test). 
Document vestibular test results and any further actions (if results indicate significant vestibular impairment) in the 
CRF. 
7.6 
PHYSICAL EXAMINATION 
The physical examination will be performed in accordance with the procedures outlined in the FORMaT Master 
Protocol, section 5.5.5. in accordance with the schedule of assessments outlined in tables 12 to 14. 
7.7 
ELECTROCARDIOGRAM (ECG) 
A standard 12 lead ECG will be performed in accordance with the relevant tables and site-specific procedures after 
the participant has been supine for at least 5 minutes.  A site investigator will interpret, sign and date the ECG.  The 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
23 
QTc interval and the clinical interpretation will be recorded in the electronic case report form (eCRF) and ECGs will 
be required to be scanned and stored in the CRF.  The QT interval at Screening is to be corrected using the Fridericia 
method.  For any subsequent QTc intervals which are ‘abnormal’ the Fridericia method is to be used to confirm the 
QTc value. 
7.8 
SIX-MINUTE WALK TEST 
A 6-minute walk test (6MWT) will be performed in adult participants only, at the time points outlined in tables 12 
to 14 if the testing is available at the trial site.  The 6MWT will be performed according to the protocol in the ATS 
Statement: Guidelines for the Six Minute Walk Test (2) and/or local standard procedures.  Results of the 6MWT will 
be recorded in the relevant eCRF in the FORMaT database by the end of the Final Outcome visit. 
7.9 
BLOOD SAMPLING 
Blood samples will be collected in accordance with tables 12 to 14.  Liver function, full blood count and chemistry 
and renal function tests (refer to FORMaT Monitoring Blood Parameters SOP for specific blood parameters to be 
measured) are to be performed in accordance with the local pathology requirements.  All relevant de-identified blood 
pathology reports are to be uploaded in the appropriate eCRFs in the FORMaT database by the end of the Week 6, 
Week 12 and Final Outcome Visits.  Any blood abnormalities that meet Adverse Event (AE) or Serious Adverse 
Event (SAE) criteria are to be reported as an AE/SAE within the specified timeframes. 
7.10 STUDY MEDICATION REVIEW 
Participant adherence to MABS-PD treatment in the intervention cohort will be measured via two indirect methods.  
Self-reported adherence will be assessed using a questionnaire, the 5-item Medication Adherence Rating Scale 
(MARS-5)(3, 4) at the timepoints outlined in tables 12 to 14 and results recorded in the Medication Adherence 
Questionnaire CRF.  Data from pharmacy prescription refill records and prescription claims databases will be 
obtained (where possible) and used to calculate the refill adherence measure, Medication Possession Ratio (MPR) 
(5-8). 
7.11 AMIKACIN ADMINISTRATION AND MONITORING 
7.11.1 NEBULISER TYPE FOR IA 
Amikacin for injection preparation (not liposomal amikacin) is to be used for inhalation in participants randomised 
to inhaled amikacin. A low preservative preparation, if available, is advised to reduce the risks of bronchospasm.  
The brand of amikacin preparation, if known, is to be recorded in the study drug CRF.  Five hundred milligrams of 
amikacin should be administered according to local standard practices.  Prior to administration the patient should 
receive a bronchodilator, for example salbutamol, to reduce the risk of coughing and bronchospasm.  This can be 
given nebulised or by metered dose inhaler.  Amikacin for injection may only be mixed with sodium chloride 0.9%.  
It must not be nebulised as a mixture with other nebulised drugs (e.g. salbutamol, dornase alfa or other nebulised 
antibiotics). 
High efficiency nebulisers are required to nebulise amikacin (IV formulation).  A suitable nebuliser with a filter 
attachment (e.g., SideStream Plus with filter attachment, or Pari LC Plus with filter attachment) are to be used to 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
24 
prevent environmental deposition of nebulised antibiotics and to reduce the risk of developing antibiotic resistant 
organisms.  Air flow of 6-10 L/min is required to achieve effective nebulisation of amikacin. 
7.11.2 AMIKACIN THERAPEUTIC DRUG MONITORING 
TDM of intravenous amikacin will be required to reduce and monitor toxicity.  There is currently variation across 
trial sites surrounding amikacin TDM methods.  To reflect this, acceptable amikacin TDM strategies that can be used 
in this trial include; 
1) Trough amikacin levels (independent of minimum inhibitory concentration (MIC) using nomogram for next 
dose); 
2) Maximum serum concentration (Cmax)/MIC target; 
3) Area under the curve (AUC) target; 
4) Cmax/MIC and minimum serum concentration (Cmin); 
5) AUC/MIC and Cmin. 
The chosen amikacin TDM strategy used must be recorded in the CRF and adhered to consistently for that participant. 
For subjects randomised to Intensive Therapy Arm B, an amikacin level should be collected at week one, 90 minutes 
(range 60 to 120 minutes) post completion of the inhaled dose.  The time of starting and completing the inhaled 
therapy and time of blood collection should be documented.  No adjustment of the inhaled amikacin dose should be 
undertaken. 
7.12 HEALTH RELATED QUALITY OF LIFE AND UTILITY MEASURES 
HRQoL will be assessed in all participants (where possible) according to the schedule of assessments in the relevant 
appendix.  The questionnaires are required to be completed prior to any clinical assessment and are dependent on the 
participant’s age and whether they have CF.  The age appropriate HRQoL questionnaire issued to the participant at 
the start of the study will continue to be used throughout the study even if the participant progresses to a different 
age range.  HRQoL questionnaires will be made available to study sites.  All questionnaires will be made available 
in English or if available the local language version will be sourced.  Questionnaires can be completed by the 
participant and/or their parent/carer via an online link to the questionnaire(s) on the trial database or if unable to 
access the electronic form these may be completed using a paper-based questionnaire.  Responses from paper-based 
questionnaires are to be entered into the trial database by trial site staff. 
7.12.1 CYSTIC FIBROSIS QUESTIONNAIRE-REVISED (CFQ-R) 
The CFQ-R has been developed specifically for use in people with CF.  This questionnaire measures the impact of 
CF on overall health, daily life, perceived well-being and symptoms.  Age-appropriate questionnaires have been 
developed; CFQ-R teen/adult for adolescents and adults 14 years of age and older, the CFQ-R child for those 6-13 
years of age, and the CFQ-R parent for the parents of those aged 6-13. 
In children ≤16 years of age, the CFQ-R should be administered after the PedsQL™. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
25 
7.12.2 EQ-5D-5L 
The EQ-5D-5L questionnaire is a standardised measure of health status in adults 18 years of age and older.  This 
questionnaire can be applied as a generic measure of health for clinical and economic appraisal, including the 
calculation of quality-life adjusted years (QALYs).  The EQ-5D-5L measures five dimensions: 
1. Mobility; 
2. Self-care; 
3. Usual activities; 
4. Pain/discomfort; 
5. Anxiety/depression. 
Each dimension has five possible answers: no problems, slight problems, moderate problems, severe problems and 
extreme problems.  The respondent is asked to indicate his/her health state by selecting the most appropriate statement 
from a list. 
7.12.3 EQ-5D-Y 
The EQ-5D-Y is the child friendly version of the EQ-5D-5L questionnaire.  The EQ-5D-Y has been developed for 
use in children 8 to 17 years of age.  The dimensions and the visual analogue scale (VAS) measured are the same as 
the EQ-5D-5L questionnaire, but with child friendly wording.  For children 4 to 7 years of age the proxy 1 version 
of the EQ-5D-Y can be utilised allowing the respondent (parent/carer) to evaluate participants quality of life (QoL) 
from respondents’ own view. 
7.12.4 ST. GEORGE RESPIRATORY QUESTIONNAIRE (SGRQ) 
The SGRQ is to be completed by all non-CF participants 18 years of age and older. The SGRQ is a supervised self-
administered 50-item questionnaire measuring health status across three domains: symptoms, activity and impacts 
(psycho-social) in people with airway obstruction. 
7.12.5 SHORT FORM- 36 HEALTH SURVEY 
The SF-36 health survey is a self-reported questionnaire applicable in all participants 16 years and older.  Covering 
eight health concepts the SF-36 health survey is a generic outcome measure designed to examine a person’s perceived 
health status. 
7.12.6 PEDIATRIC QUALITY OF LIFE INVENTORY (PEDSQL™) 
The PedsQL™ child health questionnaire is a non-preference-based measure to assess HRQoL for children and 
adolescents from 2 years up to 16 years of age.  Children less than 16 years of age at screening will continue to use 
the PedsQLTM up until the end of the trial, rather than change to using the SF-36 if they turn 16 years of age during 
the study. 
Developmentally appropriate child self-report questionnaires are available (ages 5-7, 8-12, 13-18) together with 
parent/carer proxy-reports (ages 2-4, 5-7, 8-12 and 13-18).  If feasible, the PedsQL™ should be completed before 
the respondents complete any other health data forms and before they see their physician or healthcare provider. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
26 
Parents/carers, children (aged 8-12) and young people (aged >12 years) may self-administer the PedsQL™ after the 
FORMaT site researcher has provided instructions.  If it is determined by the FORMaT site researcher that the child, 
young person or parent/carer is unable to self-administer the PedsQL™ the questionnaire should be administered, 
word for word by the FORMaT site researcher.  If the child has difficulty understanding the age appropriate 
PedsQL™ the preceding age questionnaire may be used.  The parent and the child must complete the questionnaires 
independently of each other and in accordance with the PedsQL™ administration guidelines (available via hyperlink 
or refer to relevant section in FORMaT Trial Site Manual of Operating Procedures (MoOP)). 
7.12.7 CHILD HEALTH UTILITY 9D (CHU9D) 
The CHU9D is a generic preference-based measure of paediatric HRQoL for use in children 7 to 17 years of age.  
The use of a descriptive system and a set of preference weights allows for the calculation of quality adjusted life 
years (QALYs) for use in economic evaluation. 
7.13 MABS CLEARANCE FOLLOW-UP QUESTIONNAIRE 
Site investigators will be requested to complete a follow up questionnaire for eligible intervention participants to 
assess microbiological clearance of MABS at 12 months after final outcome. 
 
8 SITE REIMBURSEMENT 
For participants enrolled in Appendix A1, trial sites will be reimbursed on a per participant basis at each of the 
following time points;  
1. Screening; 
2. End of intensive; 
3. End of consolidation; 
4. Final study visit. 
Sites will be reimbursed according to their contract. Payments will be paid for each time point once the data is entered 
into the trial database and all queries finalised. Invoices should be prepared at a minimum of every 6 months. 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
27 
9 INTENSIVE THERAPY NESTED STUDIES 
9.1 
NESTED STUDY A1.1: SHORT INTENSIVE THERAPY 
9.1.1 
PRIMARY OBJECTIVE 
To compare the efficacy of intensive therapies on microbiological clearance of MABS with good tolerance at end of 
short intensive.  Respiratory samples will be collected at 4 weeks to allow microbiological outcomes to be available 
at end of short intensive and tolerance will be assessed at the end of short intensive.  Treatment will continue up until 
the end of short intensive (6 weeks).  Specifically, the effects of inhaled amikacin (IA) versus intravenous amikacin 
(IVA) will be examined (A1.1.1) and the efficacy of additional oral clofazimine to standard intravenous therapy will 
be examined (A1.1.2). 
Investigation of the efficacy of intensive therapy on microbiological clearance with acceptable toxicity of treatment 
combinations will also be examined in different patient subpopulations (CF and non-CF, those infected with different 
MABS subspecies M. a. abscessus/ M. a. bolletii [inducible macrolide resistance] and M. a. massiliense) and those 
with constitutive macrolide resistance). 
MABS clearance at the end of the short intensive therapy will be defined as negative MABS cultures from all 3 
sputum samples or from one BAL sample collected at week 4. 
 
Additional studies nested within Appendix A1.1 are: 
A1.1.1: Use of IA During Intensive Therapy to Replace IVA in the Treatment of MABS-PD; 
A1.1.2: The use of Additional Clofazimine to Standard IV Therapies During Intensive Therapy in the 
Treatment of MABS-PD. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
28 
9.1.1.1. 
Study A1.1.1: Use of Inhaled Amikacin (IA) During Intensive Therapy to Replace 
Intravenous Amikacin (IVA) in the Treatment of MABS-PD 
Introduction 
Amikacin is an aminoglycoside recommended in guideline-based therapy for the treatment of MABS-PD.  It can be 
administered either intravenously or nebulised for inhalation (using the IV formulation).  Inhaled aminoglycosides 
have the potential advantages of achieving higher airway concentrations, while reducing the risk of systemic toxicity.  
However, amikacin for inhalation is not currently available commercially for the indication of treating MABS and 
clinicians have used an “off-label” IV form of amikacin (delivered via a nebuliser).  A Phase II Randomised Control 
Trial (RCT) (9) of amikacin liposome inhalation suspension (Arikayce) sponsored by Insmed Inc., investigated the 
safety and efficacy of Arikayce to treat NTM infection (36% MABS) in addition to highly variable multi-drug therapy 
in 89 patients with (19%) and without (81%) CF in patients who had failed to clear infection using their current 
treatment.  The trial did not meet the primary endpoint of decreased mycobacterial load, but the treatment group had 
a higher proportion of subjects with >1 negative sputum (32% vs 9%, p=0.006) and improved 6- minute walk 
distance, suggesting a potential benefit from adding Arikayce to consolidation therapy.  Arikayce has now been 
approved for the treatment of patients infected with Mycobacterium avium complex (MAC) who do not respond to 
conventional treatment.  This trial highlighted the difficulties and inefficiencies of undertaking conventional clinical 
trials using the “one population, one drug, one disease” in a disease where there are relatively small patient numbers, 
a heterogeneous population and complex, inconsistent drug combinations.  These factors greatly limit the clinical 
information obtained and contribute to making conventional trials in this patient population difficult to interpret.  
This contrasts with innovative platform trials, which have advantages for efficiently evaluating multiple treatment 
combinations (e.g. multi-drug resistant TB (10)) requiring complex drug regimens in a heterogeneous population. 
Eligibility Criteria 
No additional eligibility criteria are required for participation in A1.1.1 from those described in Appendix A1, Section 
4. 
Objectives 
Primary Objective 
To compare the microbiological clearance of MABS from respiratory samples collected at 4 weeks with good 
tolerability assessed at the end of short intensive therapy between the use of IA (Arm B) and the use of IVA (Arm 
A) given during intensive phase. 
Secondary Objectives 
1. Microbiological clearance at 4 weeks (irrespective of toxicity) with use of IA (Arm B) compared with use of 
IVA (Arm A) in different patient subpopulations (CF and non-CF, those infected with different MABS 
subspecies M. a. abscessus/ M. a. bolletii [inducible macrolide resistance] and M. a. massiliense and those 
with constitutive macrolide resistance).  
2. Safety of using IA to replace IVA in the short intensive therapy phase. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
29 
3. Change in FEV1 z-score at end of short intensive therapy versus at Screening  with use of IA (Arm B) 
compared with use of IVA (Arm A). 
4. Change in HRQoL (CFQ-R) for participants at end of short intensive therapy versus at Screening with use 
of IA (Arm B) compared with use of IVA (Arm A). 
5. To examine general HRQoL between Screening and end of short intensive therapy in participants with use 
of IA (Arm B) compared with use of IVA (Arm A). 
6. To examine the cost effectiveness of IA compared with IVA during short intensive therapy. 
7. To examine causes for early withdrawal from MABS-PD treatment due to reasons other than poor tolerance 
as defined in the primary objectives with use of IA (Arm B) compared with use of IVA (Arm A). 
Statistical Analysis 
Details of the simulations (sample size calculation) for Appendix A1 are outlined in Section 6 of the Master Protocol 
and the relevant section of Appendix F: General Statistical Principles and the Statistical Analysis Plan (SAP). 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
30 
9.1.1.2. 
Study A1.1.2: The Use of Additional Clofazimine to Standard Intravenous 
Therapies During Intensive Therapy in the Treatment of MABS-PD 
Introduction 
Clofazimine is approved for use in leprosy.  It has recognised antibacterial and anti-inflammatory effects in the 
management of leprosy and has been used to treat erythema nodosum related to leprosy.  There is no current clinical 
trial evidence to support the use of clofazimine in the treatment of MABS-PD.  Clofazimine use has however 
increased clinically, potentially driven by the difficulty in achieving microbiological clearance and reports of in vitro 
synergy between combinations of clofazimine and amikacin (11, 12). 
Eligibility Criteria 
No additional eligibility criteria are required for participation in nested study A1.1.2 from those described in 
Appendix A1, Eligibility Criteria. 
Objectives 
Primary Objective 
To compare the microbiological clearance of MABS from respiratory samples collected at 4 weeks with good 
tolerability assessed at the end of short intensive therapy between standard IV therapy without clofazimine (Arm C) 
and with clofazimine (Arm A) given during intensive phase. 
Secondary Objectives 
1. 
Microbiological clearance from respiratory samples collected at 4 weeks with acceptable toxicity of intensive 
therapy at the end of short intensive therapy without (Arm C) and with the addition of clofazimine (Arm A) 
to standard IV treatment will be examined in different patient subpopulations (CF and non-CF, those infected 
with different MABS subspecies M. a. abscessus/ M. a. bolletii [inducible macrolide resistance] and M. a. 
massiliense) and those with constitutive macrolide resistance). 
2. 
Microbiological clearance (irrespective of toxicity) at 4 weeks without (Arm C) and with the addition of 
clofazimine (Arm A) to standard IV treatment. 
3. 
Microbiological clearance (irrespective of toxicity) at 4 weeks without (Arm C) and with the addition of 
clofazimine (Arm A) to standard IV treatment will be examined in different patient subpopulations (CF and 
non-CF, those infected with different MABS subspecies M. a. abscessus/ M. a. bolletii [inducible macrolide 
resistance] and M. a. massiliense) and those with constitutive macrolide resistance). 
4. 
Safety of treatment without (Arm C) and with the addition of clofazimine (Arm A) in the short intensive 
therapy phase. 
5. 
Change in FEV1 z-score between Screening and end of short intensive therapy in participants treated without 
(Arm C) and with the addition of clofazimine (Arm A). 
6. 
Changes in HRQoL (CFQ-R) for participants with CF between Screening and end of short intensive therapy 
in participants treated without (Arm C) and with the addition of clofazimine (Arm A). 
7. 
To examine general HRQoL between Screening and end of short intensive therapy in participants treated 
without (Arm C) and with the addition of clofazimine (Arm A). 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
31 
8. 
To examine the cost effectiveness of treatment without (Arm C) and with the addition of clofazimine (Arm 
A) during short intensive therapy in addition to standard IV treatment. 
9. 
To examine causes for early withdrawal from MABS-PD treatment due to reasons other than poor tolerance 
as defined in the primary objectives without (Arm C) and with the addition of clofazimine (Arm A) to 
standard IV treatment. 
Statistical Analysis 
Details of the sample size calculation for this study are presented in Section 6.0 of the Master Protocol and the 
relevant section of Appendix F: General Statistical Principles and in the SAP.

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
32 
9.2 
NESTED STUDY A1.2: DURATION OF INTENSIVE THERAPY FOR PATIENTS 
WITH ONGOING POSITIVE MABS CULTURES AFTER 4 WEEKS OF 
INTENSIVE THERAPY. 
9.2.1 
INTRODUCTION 
Current published guidelines for the treatment of MABS-PD (13-15) are based on expert opinion, and in practice 
treatments vary considerably (16).  Suggested regimens include an intensive phase of 4-12 weeks of IV antibiotics 
with duration based on clinical and microbiological response.  Whether extending the length of intensive therapy 
improves microbiological clearance of MABS is not known but the strategy is used clinically in patients with ongoing 
positive cultures.  Toxicity and costs are thought to be related to length of treatment and need to be balanced against 
the potential for better microbiological outcomes. 
9.2.2 
ELIGIBILITY CRITERIA 
Participants are required to have completed 6 weeks of intensive therapy and will have at least one out of 3 sputum 
cultures or one BAL culture positive for MABS collected at week 4 (± 3 days). 
No other additional eligibility criteria are required for participation in nested study A1.2 from those described in 
Section 4 of Appendix A1. 
9.2.3 
OBJECTIVES 
9.2.3.1. 
Primary Objective 
To compare the microbiological clearance from samples collected at 10 weeks with good tolerability between those 
who are allocated to prolonged intensive therapy and those allocated to immediate consolidation following short 
intensive therapy. 
MABS clearance, assessed at the end of prolonged intensive therapy (for those allocated to prolonged intensive) or 
at 12 weeks (for those allocated to immediate consolidation) will be defined as negative MABS cultures from all 3 
sputum samples or from one BAL sample collected at 10 weeks. 
9.2.3.2. 
Secondary Objectives 
1. To compare microbiological clearance from samples collected at 10 weeks (irrespective of toxicity) in 
prolonged intensive therapy compared with short intensive and immediate consolidation therapy in patients 
who had MABS positive cultures from samples collected at 4 weeks. 
2. Safety of prolonged intensive therapy compared with short intensive + immediate consolidation therapy. 
3. Change in FEV1 z-score between Screening and end of prolonged intensive therapy or 12 weeks in 
participants that received prolonged intensive compared with short intensive and immediate consolidation 
who had MABS positive cultures from samples collected  at 4 weeks. 
4. Change in FEV1 z-score between Screening and end of prolonged intensive therapy or 12 weeks between 
those participants still culture positive for MABS at 10 weeks compared with those who have cleared MABS 
at 10 weeks. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
33 
5. Change in 6MWD between Screening and end of prolonged intensive therapy or 12 weeks in adult 
participants who receive prolonged intensive compared with short intensive and immediate consolidation 
therapy who had MABS positive cultures from samples collected at 4 weeks. 
6. Change in HRQoL (CFQ-R) for participants with CF between Screening and end of prolonged intensive 
therapy or 12 weeks in participants who received prolonged intensive compared with short intensive and 
immediate consolidation therapy who had MABS positive cultures from samples collected at 4 weeks.  
7. Changes in general HRQoL in prolonged intensive therapy compared with short intensive and immediate 
consolidation therapy in patients who had MABS positive cultures at 4 weeks. 
8. Change in CT scan parameters (bronchiectasis, mucus plugging, airway wall thickening, --atelectasis, % 
disease and air trapping), between Screening and end of prolonged intensive therapy (for those allocated to 
prolonged intensive) or 12 weeks (for those allocated to immediate consolidation) taking into account 
microbiological clearance based on samples collected at 4 and at 10 weeks. 
9. To examine the cost effectiveness of prolonged intensive compared with short intensive and immediate 
consolidation for those who remain MABS positive based on samples collected at 4 weeks. 
10. To examine causes for early withdrawal from MABS-PD treatment due to reasons other than poor tolerance 
as defined in the primary objectives in prolonged intensive compared with short intensive and immediate 
consolidation in patients who had MABS positive cultures based on samples collected at 4 weeks. 
 
9.2.4 
STATISTICAL ANALYSIS  
Details of the sample size calculation for this study are presented in Section 6.0 of the Master Protocol and the 
relevant section of Appendix F: General Statistical Principles and in the SAP.  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
34 
9.3 
INTENSIVE THERAPY DOSING REGIMEN 
At R-SI, participants will be randomised to one of three treatment arms during the intensive phase and will receive 
drug therapy in accordance with the dosing tables below.  Drug therapy, administration and duration is dependent on 
the treatment arm (Intensive A, Intensive B, Intensive C) the participant is randomised to.  Drug dosing is based on 
the participants age (<18 or ≥18 years of age).  The start and end points of each drug therapy, the dose of each drug 
therapy used, any changes in dosing and all concomitant medications used will be required to be entered into the 
CRF. 
There are currently three proposed treatment arms in the intensive therapy phase.  Randomisation – Short Intensive 
dictates the drug therapy that participants will be randomised to.  Treatment Arm A is the reference arm (i.e., control). 
 
Intensive Arm A 
Intensive Arm B 
Intensive Arm C 
1. IV amikacin, and; 
1. Inhaled amikacin, and; 
1. IV amikacin, and; 
2. IV tigecycline, and; 
2. IV tigecycline, and; 
2. IV tigecycline, and; 
3. IV imipenem/cilastatin or IV 
cefoxitin, and; 
3. IV imipenem/cilastatin or IV 
cefoxitin, and; 
3. IV imipenem/cilastatin or IV 
cefoxitin, and; 
4. Oral 
azithromycin 
or 
oral 
clarithromycin, and; 
4. Oral 
azithromycin 
or 
oral 
clarithromycin, and; 
4. Oral 
azithromycin 
or 
oral 
clarithromycin. 
5. Oral clofazimine. 
5. Oral clofazimine. 
 
 
For participants with confirmed mixed NTM infections (slow growers + MABS), ethambutol can be added to the 
treatment arms (in accordance with the dosing tables below) if required by the treating physician. 
The intensive therapy dosing regimen tables outlined below are separated by age (adult, paediatric) and by intensive 
treatment arm (Arm A, Arm B, Arm C).  The recommended doses and frequencies are a guideline and participant 
dosing must also take into account clinical judgement and relevant prescribing information. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
35 
Table 1 Intensive therapy dosing regimen for Intensive Arm A in adults 
Intensive Arm A: Adult Dosing A 
Drug 
Recommended Dose (per dose) 
Frequency 
IV amikacin 
15mg/kg 
 
OR 
 
Once daily 
 
20-25mg/kg 
Thrice weekly 
Dosing will be made in accordance with British Thoracic Society (BTS) guidelines (13) and is dependent on the physiology, 
site and therapeutic drug monitoring (TDM) outcomes of each participant.  In overweight participants use the ideal body 
weight calculator or in cases of extremes of actual body weight where body weight is greater than 20% above ideal use the 
adjusted body weight calculator available in the MoOP.  To determine ideal body weight for amputees, refer to for the table 
in the MoOP describing the percentage of total weight contributed by individual body parts. 
IV tigecycline 
25mg increasing by 5mg every two 
doses until either 50mg reached or until 
patient is unable to tolerate. 
Twice daily or same total daily dose 
over a 24-hour infusion 
IV imipenem/cilastatin  
IV imipenem/cilastatin is preferred but if 
not tolerated, use IV cefoxitin. 
≥50kg 
1g (dose based on imipenem 
component) 
 
Twice – four times daily infused over 
1-4 hours as tolerated 
 
<50kg 
15 – 25mg/kg (dose based on 
imipenem component).  Maximum 1g. 
 
Twice – four times daily infused over 
1-4 hours as tolerated 
IV cefoxitin 
Cefoxitin only for use if 
imipenem/cilastatin not tolerated. 
2 – 4g 
Thrice daily infused over 1-4 hours as 
tolerated, or same total daily dose 
over a 24-hour infusion. 
Oral azithromycin 
250 – 500mg 
Once daily 
 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Once daily 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
Oral clofazimine 
100 – 300mg 
Once daily 
 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg  
(rounded to account for tablet strength) 
OR 
Once daily 
25mg/kg  
(rounded to account for tablet strength) 
Thrice weekly 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
36 
Table 2 Intensive therapy dosing regimen for Intensive Arm B in adults 
Intensive Arm B: Adult Dosing A 
Drug 
Recommended Dose (per dose) 
Frequency 
Inhaled amikacin (IA) 
(IV formulation) 
500mg 
Twice daily 
IV tigecycline 
25mg increasing by 5mg every two 
doses until either 50mg reached or until 
patient is unable to tolerate. 
Twice daily or same total daily dose 
over a 24-hour infusion 
IV imipenem/cilastatin  
IV imipenem/cilastatin is preferred but if 
not tolerated, use IV cefoxitin. 
≥50kg 
1g (dose based on imipenem 
component) 
 
Twice – four times daily infused over 
1-4 hours as tolerated 
 
<50kg 
15 – 25mg/kg (dose based on imipenem 
component).  Maximum 1g. 
 
Twice – four times daily infused over 
1-4 hours as tolerated 
IV cefoxitin 
Cefoxitin only for use if 
imipenem/cilastatin not tolerated. 
2 – 4g 
Thrice daily infused over 1-4 hours as 
tolerated, or same total daily dose over 
a 24-hour infusion. 
Oral azithromycin 
250 – 500mg 
Once daily 
 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Once daily 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
Oral clofazimine 
100 – 300mg 
Once daily 
 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg  
(round to account for tablet strength) 
OR 
Once daily 
25mg/kg  
(round to account for tablet strength) 
Thrice weekly 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
37 
Table 3 Intensive therapy dosing regimen for Intensive Arm C in adults 
Intensive Arm C: Adult Dosing A 
Drug 
 Recommended Dose (per dose) 
Frequency  
IV amikacin 
15 mg/kg 
 
OR 
 
Once daily 
 
20-25mg/kg 
Thrice weekly 
Dosing will be made in accordance with British Thoracic Society (BTS) guidelines (13) and is dependent on the physiology, 
site and therapeutic drug monitoring (TDM) outcomes of each participant.  In overweight participants use the ideal body 
weight calculator or in cases of extremes of actual body weight where body weight is greater than 20% above ideal use the 
adjusted body weight calculator available in the MoOP.  To determine ideal body weight for amputees, refer to for the table 
in the MoOP describing the percentage of total weight contributed by individual body parts. 
IV tigecycline 
25mg increasing by 5mg every two 
doses until either 50mg reached or until 
patient is unable to tolerate. 
Twice daily or same total daily dose 
over a 24-hour infusion 
IV imipenem/cilastatin 
≥50kg  
1g (dose based on imipenem 
component) 
 
Twice – four times daily infused over 
1-4 hours as tolerated 
 
IV imipenem/cilastatin is preferred but if 
not tolerated, use IV cefoxitin. 
<50kg 
15 – 25mg/kg (dose based on imipenem 
component).  Maximum 1g. 
 
Twice – four times daily infused over 
1-4 hours as tolerated 
IV cefoxitin 
Cefoxitin only for use if 
imipenem/cilastatin not tolerated. 
2 – 4g 
Thrice daily infused over 1-4 hours as 
tolerated, or same total daily dose over 
a 24-hour infusion. 
Oral azithromycin 
 
250 – 500mg 
Once daily 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Once daily 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg  
(round to account for tablet strength) 
OR 
Once daily 
25mg/kg  
(round to account for tablet strength) 
Thrice weekly 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
38 
Table 4 Intensive therapy dosing regimen for Intensive Arm A in paediatrics 
Intensive Arm A: Paediatric Dosing A 
Drug 
 Recommended Dose  
(per dose) 
Frequency 
IV amikacin 
15-30mg/kg,  
max 1500mg initial dose 
Once daily 
 
Dosing will be made in accordance with BTS guidelines (13) and is dependent on the physiology, site and TDM outcomes 
of each participant. In obese participants, use the ideal body weight calculator or in cases of extremes of actual body weight 
where body weight is greater than 20% above ideal body weight use the adjusted body weight calculator available in the 
MoOP. To determine ideal body weight or adjusted body weight for amputees, refer to for the table in the MoOP describing 
the percentage of total weight contributed by individual body parts. 
IV tigecycline 
(ages ≥8 years) 
Day 1: 
(50% of optimal dose) 
0.6mg/kg, max 25mg 
Twice daily (12 hourly) 
Day 2: 
(75% of optimal dose) 
0.6mg/kg, max 25mg 
In the morning 
1.2mg/kg, max 50mg 
At night 
Day 3: 
(100% of optimal dose) 
1.2mg/kg, max 50mg 
Twice daily (12 hourly) 
IV imipenem/cilastatin 
IV imipenem/cilastatin is 
preferred but if not 
tolerated, use IV cefoxitin. 
Day 1-2 
15 - 25mg/kg, max 1g 
(dose based on imipenem 
component) 
Twice daily (12 hourly) 
Day 3 
15 - 25mg/kg, max 1g 
(dose based on imipenem 
component) 
Four times daily (reduce to 3 
times daily if not tolerated) 
(6 or 8 hourly) 
IV cefoxitin 
Only for use if imipenem/cilastatin not tolerated. 
40mg/kg, max 2g 
Four times daily (6 hourly) 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if 
azithromycin not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
Oral clofazimine 
Dosing may be rounded to account for capsule strength. 
<40kg 
3-5mg/kg, max 100mg 
Once daily 
≥40kg 
100mg 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg 
(round to account for tablet 
strength) 
Once daily 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
39 
Table 5 Intensive therapy dosing regimen for Intensive Arm B in paediatrics 
Intensive Arm B: Paediatric Dosing A 
Drug 
 Recommended Dose  
(per dose) 
Frequency 
Inhaled amikacin (IA) (IV formulation) 
 
500mg 
Twice daily 
IV tigecycline 
(ages ≥8 years) 
Day 1: 
(50% of optimal dose) 
0.6mg/kg, max 25mg 
Twice daily (12 hourly) 
Day 2: 
(75% of optimal dose) 
0.6mg/kg, max 25mg 
In the morning 
1.2mg/kg, max 50mg 
At night 
Day 3: 
(100% of optimal dose) 
1.2mg/kg, max 50mg 
Twice daily (12 hourly) 
IV imipenem/cilastatin 
IV imipenem/cilastatin is 
preferred but if not 
tolerated, use IV cefoxitin. 
Day 1-2 
15 - 25mg/kg, max 1g. 
(dose based on imipenem 
component) 
Twice daily (12 hourly) 
Day 3 
15 - 25mg/kg, max 1g 
(dose based on imipenem 
component) 
Four times daily (reduce to 3 
times daily if not tolerated) 
(6 or 8 hourly) 
IV cefoxitin 
Only for use if imipenem/cilastatin not tolerated. 
40mg/kg, max 2g 
Four times daily (6 hourly) 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if azithromycin 
not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
Oral clofazimine 
Dosing may be rounded to account for capsules strength. 
<40kg 
3-5mg/kg, max 100mg 
Once daily 
≥40kg 
100mg 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg 
(round to account for tablet 
strength) 
Once daily 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
40 
Table 6 Intensive therapy dosing regimen for Intensive Arm C in paediatrics 
 
Intensive Arm C: Paediatric Dosing A 
Drug 
Recommended Dose  
(per dose) 
Frequency 
IV amikacin 
 
15-30mg/kg,  
max 1500mg initial dose 
Once daily 
Dosing will be made in accordance with BTS guidelines (13) and is dependent on the physiology, site and TDM outcomes 
of each participant. In obese participants, use the ideal body weight calculator or in cases of extremes of actual body weight 
where body weight is greater than 20% above ideal body weight use the adjusted body weight calculator available in the 
MoOP. To determine ideal body weight or adjusted body weight for amputees, refer to for the table in the MoOP describing 
the percentage of total weight contributed by individual body parts. 
IV tigecycline 
(ages ≥8 years) 
Day 1: 
(50% of optimal dose) 
0.6mg/kg, max 25mg 
Twice daily (12 hourly) 
Day 2: 
(75% of optimal dose) 
0.6mg/kg, max 25mg 
In the morning 
1.2mg/kg, max 50mg 
At night 
Day 3: 
(100% of optimal dose) 
1.2mg/kg, max 50mg 
Twice daily (12 hourly) 
IV imipenem/cilastatin 
IV imipenem/cilastatin is 
preferred but if not tolerated, 
use IV cefoxitin. 
Day 1-2 
15 - 25mg/kg, max 1g. 
(dose based on imipenem 
component) 
Twice daily (12 hourly) 
Day 3 
15 - 25mg/kg, max 1g 
(dose based on imipenem 
component) 
Four times daily (reduce to 
3 times daily if not 
tolerated) 
(6 or 8 hourly) 
IV cefoxitin 
Only for use if imipenem/cilastatin not tolerated. 
40mg/kg, max 2g 
Four times daily (6 hourly) 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if azithromycin 
not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg  
(round to account for tablet 
strength) 
Once daily 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
41 
9.3.1 
DRUG SUPPLY, STORAGE AND DISTRIBUTION DURING INTENSIVE THERAPY 
Supply, distribution and storage of drugs will be the responsibility of the site coming from site/institution pharmacy 
stocks as per standard of care and in accordance with site specific guidelines and requirements. 
 
9.3.2 
OPTIONS FOR REDUCING NAUSEA DURING INTENSIVE THERAPY 
Titration of dosing for imipenem and tigecycline is described in tables 1 to 6.  Imipenem should also be given over 
2-3 hours (where possible) to reduce nausea.  Suggested pharmacological treatment options that could be considered 
to manage nausea are provided in the FORMaT Trial Site MoOP. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
42 
10 NESTED STUDY A1.3: CONSOLIDATION THERAPY 
10.1 INTRODUCTION 
Currently, the guidelines for consolidation therapy (13) suggest that patients with isolates that are sensitive to 
macrolides or that have inducible resistance should be managed with a combination of between one and three oral 
antibiotics based on drug susceptibility of the isolate and tolerance in combination with IA.  Those with isolates that 
have constitutive resistance should use a combination of between two and four oral drugs based on susceptibility and 
tolerance in combination with IA.  In addition, guidelines suggest that patients with isolates that have amikacin 
resistance could substitute IA for an alternative oral antibiotic.  It is suggested that treatment should continue for 12 
months after culture conversion. 
There is currently no evidence for any of these guidelines.  IA is costly and requires time and effort for maintenance 
of hygienic practice and drug delivery.  Furthermore, adherence to inhaled therapies over the longer term is variable 
(17-19).  This study will examine the effects of IA in addition to the oral only thus providing some evidence regarding 
the use of additional IA during consolidation.  The timing of consolidation therapy is only 46 weeks for this trial.  
Microbiological clearance will be determined from culture of respiratory samples (sputum (expectorated or induced)) 
collected at least one week apart or BAL as follows: 
Participants who continue to produce sputum samples during the consolidation phase are requested to provide 
additional sputum samples monthly.  Three consecutive sputum samples will be collected at least one week apart 
over the last 6 weeks of consolidation therapy.  A final sputum sample collected four weeks after cessation of 
consolidation therapy will together determine the final outcome of microbiological clearance.  All four samples will 
need to be clear to determine clearance. 
For participants who continue to have positive sputum cultures at the end of consolidation, a gap in therapy to 
complete final outcomes may not be required if ongoing treatment is clinically required as microbiological clearance 
will not have occurred. 
Participants  must cease treatment for 4 weeks at the end of consolidation prior to  the final outcome measures to 
enable assessment of microbiological clearance without antibiotic suppression. 
For participants who are unproductive of sputum and/or induced sputum during the consolidation phase, or who 
become unproductive of sputum and/or induced sputum during the course of consolidation therapy,  a BAL is to be 
performed at final outcome (4 weeks after completing consolidation therapy). 
10.2 OBJECTIVES 
10.2.1 PRIMARY OBJECTIVE 
To compare the microbiological clearance with good tolerability of MABS between those allocated to consolidation 
therapy with oral treatment and those allocated to consolidation therapy with oral treatment and additional IA at Final 
Outcome. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
43 
10.2.2 SECONDARY OBJECTIVES 
1. To compare microbiological clearance (irrespective of toxicity) at Final Outcome between those allocated to 
consolidation therapy with oral treatment and those allocated to consolidation therapy with oral treatment 
and additional IA taking into account microbiological status at the start of consolidation. 
2. Difference in safety between those allocated to consolidation therapy with oral treatment and those allocated 
to consolidation therapy with oral therapy and additional IA. 
3. Change in FEV1 z-score between start of consolidation therapy and Final Outcome between those allocated 
to consolidation therapy with oral treatment and those allocated to consolidation therapy with oral therapy 
and additional IA taking into account microbiological clearance at Final Outcome. 
4. Change in 6MWD between Week 12 of the trial and Final Outcome between adult participants allocated to 
consolidation therapy with oral treatment and those allocated to consolidation therapy with oral therapy and 
additional IA taking into account microbiological clearance at Final Outcome. 
5. Change in CT scan parameters (bronchiectasis, mucus plugging, airway wall thickening, atelectasis, % 
disease and air trapping), between 12 weeks and Final Outcome taking into account microbiological 
clearance at start of consolidation therapy between those allocated to consolidation therapy with oral 
treatment and those allocated to consolidation therapy with oral therapy and additional IA. 
6. Changes in HRQoL (CFQ-R) for participants with CF between start of consolidation therapy and Final 
Outcome between those allocated to consolidation therapy with oral treatment and those allocated to 
consolidation therapy with oral therapy and additional IA. 
7. To examine general HRQoL between start of consolidation therapy and Final Outcome in adults (CF and 
non-CF) between those allocated to consolidation therapy with oral treatment and those allocated to 
consolidation therapy with oral therapy and additional IA. 
8. To compare the cost effectiveness of consolidation between those allocated to consolidation therapy with 
oral treatment and those allocated to consolidation therapy with oral therapy and additional IA. 
9. To examine causes for early withdrawal from MABS-PD treatment due to reasons other than poor tolerance 
as defined in the primary objectives between those allocated to consolidation therapy with oral treatment and 
those allocated to consolidation therapy with oral therapy and additional IA. 
 
10.3 ELIGIBILITY CRITERIA 
Participants who have been randomised to intensive therapy in Appendix A1 and have either completed intensive 
therapy or who are unable to complete Intensive therapy due to a lack of tolerance.  
. 
10.4 STATISTICAL ANALYSIS 
Details of the sample size calculation for this study are presented in Section 6.0 of the Master Protocol and the 
relevant section of Appendix F: General Statistical Principles and in the SAP. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
44 
10.5 CONSOLIDATION THERAPY DOSING REGIMEN 
Following R-Con, participants will receive consolidation treatment in accordance with the dosing tables below. Drug 
therapy, administration and duration is dependent on the treatment arm (Consolidation Arm a and Consolidation Arm 
b), age, and/or weight of the participant.  The start and end points of each drug therapy, the dose of each drug therapy 
used, any changes in dosing, and all concomitant medications used will be required to be entered into the CRF. 
There are currently two proposed treatment arms that participants will be randomised to during consolidation therapy. 
 
Consolidation Arm a 
Consolidation Arm b 
1. Oral clofazimine, and; 
1. Inhaled amikacin 
2. Oral azithromycin or oral clarithromycin, and; 
2. Oral clofazimine, and; 
 
3. Oral azithromycin or oral clarithromycin, and; 
 In combination with one to three of the following oral 
antibiotics: 
 In combination with one to three of the following oral 
antibiotics: 
• 
Oral linezolid, 
• 
Oral linezolid, 
• 
Oral trimethoprim / sulfamethoxazole, 
• 
Oral trimethoprim / sulfamethoxazole, 
• 
Oral bedaquiline, 
• 
Oral bedaquiline, 
• 
Oral rifabutin, 
• 
Oral doxycycline, 
• 
Oral moxifloxacin. 
• 
Oral rifabutin, 
• 
Oral doxycycline, 
• 
Oral moxifloxacin. 
 
For participants with confirmed mixed NTM infections (slow growers + MABS), ethambutol can be added to the 
treatment arms (in accordance with the dosing tables below) if required by the treating physician. 
The consolidation therapy dosing regimen tables outlined below are separated by age (adult, paediatric) and by 
consolidation treatment arm (Arm a and Arm b). The recommended doses and frequencies are a guideline and 
participant dosing must also take into account clinical judgement and relevant prescribing information.  
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
45 
Table 7 Consolidation therapy dosing regimen for Consolidation Arm a in adults 
Consolidation Arm a: Adult DosingA 
Drug 
 Recommended Dose (per dose) 
Frequency  
Oral clofazimine 
100 – 300mg 
Once daily 
Oral azithromycin  
250 – 500mg 
OR 
500mg  
Once daily 
 
Thrice weekly 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Thrice weekly 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
600mg 
Once daily 
Oral trimethoprim with 
sulfamethoxazole  
160mg/800mg 
Twice daily 
Oral bedaquiline  
(Weighing at least 30kg) 
First 2 weeks 400mg 
Once daily 
For remaining 22 weeks 200mg 
Max duration 6 months 
Thrice weekly 
At least 48 hours between doses 
Oral rifabutin 
5mg/kg, max 450mg 
Once daily 
Oral doxycycline 
100mg 
Once daily 
Oral moxifloxacin 
400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg 
(round to account for tablet strength) 
OR 
Once daily 
25mg/kg 
(round to account for tablet strength) 
Thrice weekly 
 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
46 
Table 8 Consolidation therapy dosing regimen for Consolidation Arm b in adults 
Consolidation Arm b: Adult Dosing A 
Drug 
 Recommended Dose (per dose) 
Frequency  
Inhaled amikacin (IA) 
(IV formulation) 
500mg 
Twice daily 
Oral clofazimine 
100 – 300mg 
Once daily 
Oral azithromycin 
250 – 500mg 
OR 
500mg 
Once daily 
 
Thrice weekly 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Thrice weekly 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
600mg 
Once daily 
Oral trimethoprim with 
sulfamethoxazole 
160mg/800mg  
Twice daily 
Oral bedaquiline 
(Weighing at least 30kg) 
First 2 weeks 400mg 
Once daily 
For remaining 22 weeks 200mg 
Max duration 6 months 
Thrice weekly 
At least 48 hours between doses 
Oral rifabutin 
5mg/kg, max 450mg 
Once daily 
Oral doxycycline 
100mg 
Once daily 
Oral moxifloxacin 
400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg  
(round to account for tablet strength) 
OR 
Once daily 
25mg/kg  
(round to account for tablet strength) 
Thrice weekly 
 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
47 
Table 9 Consolidation therapy dosing regimen for Consolidation Arm a in paediatrics 
Consolidation Arm a: Paediatric Dosing A 
Drug 
Recommended Dose  
(per dose) 
Frequency 
Oral clofazimine 
Dosing may be rounded to account for capsules. 
<40kg 
3-5mg/kg, max 100mg 
Once daily 
≥40kg 
100mg 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if azithromycin 
not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
1 month – 9 years 
10mg/kg, max 450mg 
Twice daily 
10 – 12 years 
10mg/kg, max 600mg 
Daily 
>12 years 
600mg 
Daily 
Oral trimethoprim with sulfamethoxazole  
5mg/kg trimethoprim 
max 160mg trimethoprim 
Twice daily 
Oral bedaquiline 
(age ≥5 years) 
Weeks 1 and 2 
≥15kg - <20kg 
160mg 
Once daily 
≥20kg - <30kg 
200mg 
≥30kg 
400mg 
Weeks 3-24 - Max Duration 6 Months 
≥15kg - <20kg 
80mg 
Thrice weekly. 
At least 48 hours between 
doses 
≥20kg - <30kg 
100mg 
≥30kg 
200mg 
Oral rifabutin 
5mg/kg, max 300mg 
Once daily 
Oral doxycycline 
(ages ≥8 years) 
2mg/kg, max 100mg 
Once daily 
Oral moxifloxacin  
Dosing may be rounded to account for capsules. 
10-15mg/kg, max 400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg 
(round to account for tablet 
strength) 
Once daily 
 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
48 
Table 10 Consolidation therapy dosing regimen for Consolidation Arm b in paediatrics 
Consolidation Arm b: Paediatric Dosing A 
Drug 
Recommended Dose  
(per dose) 
Frequency 
Inhaled amikacin (IA) 
(IV formulation) 
500mg 
Twice daily 
Oral clofazimine 
Dosing may be rounded to account for capsules. 
<40kg 
3-5mg/kg, max 100mg 
Once daily 
≥40kg 
100mg 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if azithromycin 
not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
1 month – 9 years 
10mg/kg, max 450mg 
Twice daily 
10 – 12 years 
10mg/kg, max 600mg 
Daily 
>12 years 
600mg 
Daily 
Oral trimethoprim with sulfamethoxazole  
5mg/kg trimethoprim 
max 160mg trimethoprim 
Twice daily 
Oral bedaquiline 
(age ≥5 years) 
Weeks 1 and 2 
≥15kg - <20kg 
160mg 
Once daily 
≥20kg - <30kg 
200mg 
≥30kg 
400mg 
Weeks 3-24 - Max Duration 6 Months 
≥15kg - <20kg 
80mg 
Thrice weekly. 
At least 48 hours between 
doses 
≥20kg - <30kg 
100mg 
≥30kg 
200mg 
Oral rifabutin 
5mg/kg, max 300mg 
Once daily 
Oral doxycycline 
(ages ≥8 years) 
2mg/kg, max 100mg 
Once daily 
Oral moxifloxacin  
Dosing may be rounded to account for capsules. 
10-15mg/kg, max 400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg 
(round to account for tablet 
strength) 
Once daily 
 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information.  
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
49 
10.5.1 DRUG SUPPLY, STORAGE AND DISTRIBUTION DURING CONSOLIDATION 
THERAPY 
Supply, distribution and storage of drugs will be the responsibility of the site coming from site/institution pharmacy 
stocks as per standard of care and made in accordance with site-specific guidelines and requirements. 
10.5.2 DRUG COMPLIANCE DURING CONSOLIDATION THERAPY 
The procedures for distribution of consolidation therapy are site dependent.  Drug compliance during consolidation 
therapy will be captured from pharmacy records of drugs dispensed to the participant while enrolled in FORMaT 
Appendix A1. 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
50 
11 SCHEDULE OF ASSESSMENTS 
Table 11 lists the special considerations that are applicable to all Schedule of Assessment tables.  Table 11 must be 
used in conjunction with Tables 12 to 14.  Tables 12 to 14 show the schedules of assessment tables for participants 
enrolled in Appendix A1.  Table 12 shows the schedule of assessments for all participants from Screening to end of 
Week 6, Table 13 shows the schedule of assessments from Week 7 to Week 12 for participants randomised to 
Prolonged Intensive and Table 14 shows the schedule of assessments for all participants during the Consolidation 
therapy phase and at the Final Outcome.  Acceptable study visit windows are also outlined in tables 12 to 14. 
Table 11 Special considerations for Schedule of Assessments 
Symbol Definition 
A 
Participant reconsent is required with IRB/ IED/HREC approved changes to the protocol that affect the 
participants rights and/or safety and/or if a child turns 18 years old during the trial and must reconsent 
as an adult participant. 
B 
Visits may be conducted while an inpatient or at home if participant is receiving home-based care. 
C 
To be eligible to enrol in the Intervention Program, the participant is required to have either two (2) 
MABS-positive sputum samples or one (1) MABS-positive BAL sample.  Refer to section 7.3 for further 
information.  
D 
To determine MABS clearance following four (4) weeks of intensive therapy, three sputum samples or 
one BAL sample are required to be collected in Week 4 (±3 days) to ensure results are available by week 
6 of intensive therapy to inform randomisation. 
E 
Adult height is to be recorded once (preferably at the screening visit).  Paediatric height must be 
measured at least every six weeks. 
F 
Only required if the screening assessments were reviewed more than two (2) weeks earlier than Day 1. 
G 
Refer to section 7.2 for eligibility criteria for the screening visit chest CT. 
H 
Only required in female participants of childbearing potential.  A serum pregnancy test is required at 
screening and final study visit.  A urine or serum pregnancy test is acceptable at all other times. 
I 
Screening audiology and screening vestibular assessment can be performed if a participant has 
commenced intensive therapy but must be performed within three (3) days of first receiving treatment. 
J 
QT interval at screening is to be corrected using the Fridericia method. Any subsequent abnormal QTc 
intervals are to be confirmed using the Fridericia method. 
K 
Six-minute walk test to be performed in participants ≥18 years of age only. 
L 
Plasma levels post inhaled amikacin are to be collected 90 minutes post dose (range 60 to 120 minutes).  
Please record inhaled amikacin start and stop times.  
M 
IV Amikacin Therapeutic Drug Monitoring to be completed within 48 hours of dosing according to site 
protocol. 
N 
The EQ-5D-5L is to be administered to participants ≥18 years of age whereas the EQ-5D-Y is to be 
administered to participants 8 to 17 years of age.  The EQ-5D-Y Proxy is to be administered to 
parents/carers of participants 4 to 7 years of age. 
O 
The SF-36 is to be administered to participants ≥16 years of age at time of Screening.  For participants 
aged <16 years at Screening, the PedsQLTM is to be used for entire duration of trial. 
P 
The PedsQL™ is only to be assessed in participants <16 years of age at time of Screening.  If both the 
PedsQL™ and the CFQ-R are administered where possible, the PedsQL™ should be administered prior 
to the CFQ-R. 
Q 
The CFQ-R is only to be completed in participants with CF.  The age appropriate CFQ-R assessment 
should be selected; CFQ-R adult/teen (≥14 years of age), CFQ-R child (6 to 13 years of age) and CFQ-
R parent (parent/carer of participant 6 to 13 years of age). 
R 
The Child Health Utility is only to be assessed in participants 7 to 17 years of age. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
51 
S 
The SGRQ is only to be assessed in non-CF participants 18 years of age and older. 
T 
Costs questionnaire only required for participants that are randomised to immediate consolidation.  
U 
MARS-5 is only to be completed in participants in the intervention cohort on outpatient based MABS-
PD treatment. 
V 
Week 12 chest CT scan is optional and requires participant to consent to FORMaT Sub-Study C3: 
Imaging.  The site must have approval to conduct this additional scan, be certified to perform the scan 
using the scanner specific protocol and the participant must provide additional consent. 
W 
To determine MABS clearance following ten (10) weeks of intensive therapy, three sputum samples or 
one BAL sample are required to be collected in Week 10 (±3 days). 
X 
Participants unable to produce a sputum sample (expectorated or induced) to be marked as unproductive 
on the CRF. 
Y 
Participants who have produced sputum samples during Weeks 18, 28, and 38 are requested to provide 
three additional sputum samples collected at least one week apart nearer to the end of Weeks 52.  For 
participants who were unproductive (intermittent or continual) during Weeks 18, 28, 38 and 52, a BAL 
sample is to be collected during Week 56. 
Z 
Clinic visit and some assessments at Week 10 can be completed at any time between Week 10 and Week 
12.  
1 
Chest CT scan at early withdrawal visit will only be requested if clinically indicated. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
52 
Table 12 Schedule of Assessments for Intervention Program Participants: Intensive Therapy (Screening and first six weeks of intensive therapy) 
ASSESSMENT 
SCREENING 
VISIT 
INTENSIVE THERAPY 
Week 1 - Week 6 
Day 0 
Day 1 
Week 1 
Week 2 
Week 3 
Week 4 
Week 5 
Week 6 
-42 Days 
 +24 hours 
+3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
Informed consent for Appendix A1A 
✓ 
 
 
 
 
 
 
 
Clinic visit B 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Review eligibility 
✓ 
 
 
 
 
 
 
 
Randomisation 
 
✓ 
 
 
 
 
 
✓ 
Adverse event monitoring 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Respiratory 
sample 
Sputum (expectorated or induced) or; 
✓C 
 
 
 
 
✓ 
x3D 
 
 
BAL 
✓C 
 
 
 
 
✓D 
 
 
Height E and Weight 
✓ 
 
 
 
 
 
 
✓ 
Medication Review 
✓ 
✓F 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Spirometry 
✓ 
 
 
 
 
 
 
✓ 
Chest CT 
✓G 
 
 
 
 
 
 
 
Pregnancy Test and Breastfeeding Status H 
✓ 
✓ 
 
✓ 
 
✓ 
 
✓ 
Audiogram 
✓I 
 
 
 
 
✓ 
 
 
Vestibular Monitoring 
✓I 
 
 
 
 
✓ 
 
 
ECG J 
✓ 
 
 
✓ 
 
 
 
✓ 
6-minute walk test K 
✓ 
 
 
 
 
 
 
 
Blood collection: 
 
 
 
 
 
 
 
 
1. Chemistry and Renal Function 
✓ 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
2. Liver Function Tests 
✓ 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
3. Full Blood Count 
✓ 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Physical examination 
✓ 
✓F 
 
 
 
 
 
✓ 
Amikacin 
monitoring 
Therapeutic Drug Monitoring, or; 
 
✓M 
Arm A & C 
 
✓ 
Arm A & C 
 
 
 
✓ 
Arm A & C 
Post dose levels L 
 
 
✓ 
Arm B only 
 
 
 
 
 
Health-related quality of life questionnaires: 
 
 
 
 
 
 
 
 
1. EQ-5D-5L or -Y N 
✓ 
 
 
 
 
 
 
✓ 
2. SF36  O 
✓ 
 
 
 
 
 
 
✓ 
3. PedsQL™ P 
✓ 
 
 
 
 
 
 
✓ 
4. CFQ-R Q 
✓ 
 
 
 
 
 
 
✓ 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
53 
ASSESSMENT 
SCREENING 
VISIT 
INTENSIVE THERAPY 
Week 1 - Week 6 
Day 0 
Day 1 
Week 1 
Week 2 
Week 3 
Week 4 
Week 5 
Week 6 
-42 Days 
 +24 hours 
+3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
5. Child Health Utility 9D R 
✓ 
 
 
 
 
 
 
✓ 
6. SGRQ S 
✓ 
 
 
 
 
 
 
✓ 
Costs Questionnaire 
✓ 
 
 
 
 
 
 
✓ 
Medication Adherence Questionnaire U 
 
 
 
 
 
 
 
✓ 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
54 
Table 13 Schedule of Assessments for Intervention Program Participants: Prolonged Intensive Therapy(Total of 12 weeks of intensive therapy) 
ASSESSMENT 
PROLONGED INTENSIVE THERAPY  
Week 7- Week 12 
Week 7 
Week 8 
Week 9 
Week 10 
Week 11 
Week 12 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
Clinic visit B 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Randomisation 
 
 
 
 
 
✓ 
Adverse event monitoring 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Respiratory 
sample 
Sputum (expectorated or induced) or; 
 
 
 
✓ 
x3W 
 
 
BAL 
 
 
 
✓W 
 
 
Height E and Weight 
 
 
 
 
 
✓ 
Medication Review 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Spirometry 
 
 
 
 
 
✓ 
Chest CT 
 
 
 
 
 
Optional V 
Pregnancy Test and Breastfeeding Status H 
 
 
✓ 
 
 
✓ 
Audiogram 
 
✓ 
 
 
 
✓ 
Vestibular Monitoring 
 
✓ 
 
 
 
✓ 
ECGJ 
 
 
 
 
 
✓ 
6-minute walk test K 
 
 
 
 
 
✓ 
Blood collection: 
 
 
 
 
 
 
7. Chemistry and Renal Function 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
8. Liver Function Tests 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
9. Full Blood Count 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Physical examination 
 
 
 
 
 
✓ 
Amikacin Therapeutic Drug Monitoring 
 
 
 
 
 
✓ 
Arm A & C 
Health-related quality of life questionnaires: 
 
 
 
 
 
 
10. EQ-5D-5L or -Y N 
 
 
 
 
 
✓ 
11. SF36  O 
 
 
 
 
 
✓ 
12. PedsQL™  P 
 
 
 
 
 
✓ 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
55 
ASSESSMENT 
PROLONGED INTENSIVE THERAPY  
Week 7- Week 12 
Week 7 
Week 8 
Week 9 
Week 10 
Week 11 
Week 12 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
±3 Days 
13. CFQ-R Q 
 
 
 
 
 
✓ 
14. Child Health Utility 9D R 
 
 
 
 
 
✓ 
15. SGRQ S 
 
 
 
 
 
✓ 
Costs Questionnaire 
 
 
 
 
 
✓ 
Medication Adherence Questionnaire U 
 
 
 
 
 
✓ 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
56 
Table 14 Schedule of Assessments for Consolidation Therapy and Final Outcome 
ASSESSMENT 
CONSOLIDATION THERAPY 
FINAL 
STUDY 
VISIT 
Early 
Withdrawal 
Visit 
Immediate consolidation 
After completing six weeks (short) intensive therapy 
Delayed consolidation 
After completing 12 weeks (prolonged) intensive 
therapy 
Week 
10 
Week 
12 
Week 
18 
Week 
28 
Week 
38 
End of 
consolidatio
n (Week 52) 
Week 18 
Week 28 
Week 38 
End of 
consolidatio
n (Week 58) 
+4 weeks post 
End of 
consolidation 
+30 days 
±3 days 
±3 days 
±30 days 
±30 days 
±30 days 
+5 days 
±30 days 
±30 days 
±30 days 
+5 days 
+14 days 
 
Clinic visit B 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Adverse event monitoring 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Respiratory 
sample 
Sputum (expectorated or induced) 
or; 
✓ 
x3W 
 
✓X 
✓X 
✓X 
✓X 
✓X 
✓X 
✓X 
✓X 
✓Y 
✓ 
Broncho-alveolar lavage (BAL) 
✓W 
 
Height E and Weight 
✓Z 
✓ 
 
✓ 
 
✓ 
 
✓ 
 
✓ 
✓ 
✓ 
Medication Review 
✓Z 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Spirometry 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
Chest CT 
 
Optional V 
 
 
 
 
 
 
 
 
✓ 
✓1 
Pregnancy Test and Breastfeeding Status H 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Audiogram 
 
✓ 
 
✓ 
 
 
 
✓ 
 
 
✓ 
✓ 
Vestibular Monitoring 
 
✓ 
 
✓ 
 
 
 
✓ 
 
 
✓ 
✓ 
ECG J 
 
✓ 
 
✓ 
 
 
 
✓ 
 
 
✓ 
✓ 
6-minute walk test K 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
Blood collections: 
 
 
 
 
 
 
 
 
 
 
 
 
1. 
Chemistry and Renal Function 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
2. 
Liver Function Tests 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
3. 
Full Blood Count 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Physical examination 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
Health-related quality of life questionnaires: 
 
 
 
 
 
 
 
 
 
 
 
 
4. 
EQ-5D-5L or -Y N 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
5. 
SF-36 O 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
6. 
PedsQL™  P 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
7. 
CFQ-R Q 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
8. 
Child Health Utility 9D R  
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
9. 
SGRQ S 
 
✓ 
 
 
 
 
 
 
 
 
✓ 
✓ 
Costs Questionnaire 
 
✓ 
 
✓ 
 
 
 
✓ 
 
 
✓ 
✓ 
Medication Adherence Questionnaire U 
 
✓ 
 
✓ 
 
✓ 
 
✓ 
 
✓ 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
57 
12 RANDOMISATION 
There will be three stages of randomisation in the Intervention Program Appendix A, dictating the treatment the 
participant will receive: 
Randomisation to Short Intensive (R-SI): The first randomisation will be at the start of the intensive phase, with all 
participants randomised between the different intensive therapy arms according to the study specific Appendix. 
Randomisation to Prolonged Intensive or Immediate Consolidation (R-PI/IC): The second randomisation will 
ONLY be for participants who are still MABS positive at the end of short intensive therapy (based on respiratory 
sampling collected at 4 weeks) and are able to continue with intensive therapy.  Randomisation will occur at the end 
of short intensive therapy and will allocate participants to either; 
Continue intensive therapy which will be followed by consolidation (participants remain on the same 
intensive therapy drug regimen if randomised to prolonged intensive therapy),  
or immediately commence consolidation therapy. 
Randomisation to Consolidation (R-Con): This randomisation will allocate participants to the consolidation therapy 
arms.  Each randomisation will function as a ‘quasi-separate’ trial (as described in the relevant sections of Appendix 
A), as well as being considered in combination (intensive + consolidation).  Randomisation at each level will be 
conducted using the method of minimisation (described in the relevant sections of the Master Protocol and Appendix 
F: General Statistical Principles).  Each randomisation level will be planned to enable flexibility via pre-planned 
adaptations as described above. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
58 
13 APPLICABLE DISCOVERY STUDIES AND REGISTRY LINKAGE FOR 
APPENDIX A1 
Intervention Program participants may be eligible to enrol in the following FORMaT Sub-Studies and Integrated 
Studies: 
1) Appendix C Discovery 
i. 
C1: Pharmacokinetics 
i) C1.1 Steady state pharmacokinetics of Amikacin 
ii) C1.2 Microsampling and non-blood matrix validation for amikacin TDM 
iii) C1.3 Pharmacokinetics of MABS-PD therapies 
iv) C1.4 Pharmacokinetics of CFTR modulator therapy in persons with CF on MABS therapy 
ii. 
C2: Immune factors and biomarkers 
i) C2.1 Macrophage function 
ii) C2.2 Mitochondrial stress 
iii) C2.3 T-cell function  
iv) C2.4 Gene expression  
v) C2.5 Serology 
iii. 
C3: Imaging 
2) Appendix D Registry Linkage 
i. 
D1: Australian cystic fibrosis data registry 
3) Appendix E Health Economics 
i. 
E1: Cost effectiveness and Resource utilisation 
Please see the relevant sections of the applicable appendix for further information, including additional eligibility 
criteria. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
59 
14 REFERENCES 
1. 
Food US, Drug A. Guideline for the study and evaluation of gender differences in the clinical evaluation of 
drugs; notice. Fed Regist. 1993;58(139):39406-16. 
2. 
Laboratories ATSCoPSfCPF. ATS statement: guidelines for the six-minute walk test. Am J Respir Crit Care 
Med. 2002;166(1):111-7. 
3. 
Kwan YH, Weng SD, Loh DHF, Phang JK, Oo LJY, Blalock DV, et al. Measurement Properties of Existing 
Patient-Reported Outcome Measures on Medication Adherence: Systematic Review. J Med Internet Res. 
2020;22(10):e19179. 
4. 
Chan AHY, Horne R, Hankins M, Chisari C. The Medication Adherence Report Scale: A measurement tool 
for eliciting patients' reports of nonadherence. Br J Clin Pharmacol. 2020;86(7):1281-8. 
5. 
Lam WY, Fresco P. Medication Adherence Measures: An Overview. Biomed Res Int. 2015;2015:217047. 
6. 
Vrijens B, Urquhart J. Methods for measuring, enhancing, and accounting for medication adherence in 
clinical trials. Clin Pharmacol Ther. 2014;95(6):617-26. 
7. 
Farmer KC. Methods for measuring and monitoring medication regimen adherence in clinical trials and 
clinical practice. Clin Ther. 1999;21(6):1074-90; discussion 3. 
8. 
Al-Hassany L, Kloosterboer SM, Dierckx B, Koch BC. Assessing methods of measuring medication 
adherence in chronically ill children-a narrative review. Patient Prefer Adherence. 2019;13:1175-89. 
9. 
Olivier KN, Griffith DE, Eagle G, McGinnis Ii JP, Micioni L, Liu K, et al. Randomized Trial of Liposomal 
Amikacin for Inhalation in Nontuberculous Mycobacterial Lung Disease. Am J Respir Crit Care Med. 2016. 
10. 
Prevots DR, Marras TK. Epidemiology of human pulmonary infection with nontuberculous mycobacteria: a 
review. Clin Chest Med. 2015;36(1):13-34. 
11. 
van Ingen J, Totten SE, Helstrom NK, Heifets LB, Boeree MJ, Daley CL. <em>In Vitro</em> Synergy 
between Clofazimine and Amikacin in Treatment of Nontuberculous Mycobacterial Disease. Antimicrobial 
Agents and Chemotherapy. 2012;56(12):6324-7. 
12. 
Shen G-H, Wu B-D, Hu S-T, Lin C-F, Wu K-M, Chen J-H. High efficacy of clofazimine and its synergistic 
effect with amikacin against rapidly growing mycobacteria. International Journal of Antimicrobial Agents. 
2010;35(4):400-4. 
13. 
Haworth CS, Banks J, Capstick T, Fisher AJ, Gorsuch T, Laurenson IF, et al. British Thoracic Society 
guidelines for the management of non-tuberculous mycobacterial pulmonary disease (NTM-PD). Thorax. 
2017;72(Suppl 2). 
14. 
Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, et al. An official ATS/IDSA 
statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit 
Care Med. 2007;175(4):367-416. 
15. 
Floto RA, Olivier KN, Saiman L, Daley CL, Herrmann JL, Nick JA, et al. US Cystic Fibrosis Foundation 
and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous 
mycobacteria in individuals with cystic fibrosis: executive summary. Thorax. 2016;71(1):88-90. 
16. 
Novosad SA, Beekmann SE, Polgreen PM, Mackey K, Winthrop KL, Team MaS. Treatment of 
Mycobacterium abscessus Infection. Emerg Infect Dis. 2016;22(3):511-4. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A1 
Appendix A1-Intervention Program Version 1.1  Date 20 February 2024 
60 
17. 
Harrison MJ, McCarthy M, Fleming C, Hickey C, Shortt C, Eustace JA, et al. Inhaled versus nebulised 
tobramycin: A real world comparison in adult cystic fibrosis (CF). Journal of Cystic Fibrosis. 
2014;13(6):692-8. 
18. 
Nasr SZ, Chou W, Villa KF, Chang E, Broder MS. Adherence to dornase alfa treatment among commercially 
insured patients with cystic fibrosis. Journal of Medical Economics. 2013;16(6):801-8. 
19. 
Bakker EM, Volpi S, Salonini E, van Der Wiel-Kooij EC, Sintnicolaas CJJCM, Hop WCJ, et al. Improved 
treatment response to dornase alfa in cystic fibrosis patients using controlled inhalation. European 
Respiratory Journal. 2011;38(6):1328-35. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date 20 February 2024 
i 
 
APPENDIX A2 - INTERVENTION PROGRAM 
 Consolidation Only Therapy 
Appendix A2 – Intervention 
Program (Consolidation Only 
Therapy) 
Version 1.1 
Appendix Date 
 20 February 2024 
Protocol Number  
FORMaT001 
Funding 
 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
EudraCT Number 
2020-000050-10 
EU-CT Number 
2023-506575-99-00-EU CT 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date 20 February 2024 
ii 
TABLE OF CONTENTS 
 
TABLE OF CONTENTS ........................................................................................................................................ 2 
TABLE OF TABLES .............................................................................................................................................. 4 
TABLE OF FIGURES ............................................................................................................................................ 4 
ABBREVIATIONS .................................................................................................................................................. 5 
APPENDIX A: INTERVENTION PROGRAM ................................................................................................... 1 
APPENDIX A2 CONSOLIDATION ONLY THERAPY .................................................................................... 2 
 
INTRODUCTION ........................................................................................................................................... 5 
 
OBJECTIVES .................................................................................................................................................. 6 
 
PRIMARY OBJECTIVE ................................................................................................................................. 6 
 
SECONDARY OBJECTIVES .......................................................................................................................... 6 
 
EXPLORATORY OBJECTIVES ...................................................................................................................... 7 
 
DESIGN ............................................................................................................................................................ 7 
 
ELIGIBILITY CRITERIA ............................................................................................................................. 8 
 
INCLUSION CRITERIA ................................................................................................................................. 8 
 
EXCLUSION CRITERIA ................................................................................................................................ 9 
 
ADDITIONAL CRITERIA .............................................................................................................................. 9 
 Mixed NTM infections............................................................................................................................ 9 
 Co-enrolment with other trials .............................................................................................................. 9 
 
ACCEPTABLE METHODS OF CONTRACEPTION................................................................................ 9 
 
TRIAL CONDUCT ....................................................................................................................................... 10 
 
INFORMED CONSENT................................................................................................................................ 10 
 
PREGNANCY INFORMATION CONSENT ..................................................................................................... 11 
 
METHODS OF ASSIGNING PARTICIPANTS TO TREATMENT ARMS ............................................................ 11 
 
CONSOLIDATION ONLY PROGRAM PROCEDURES AND SAFETY MONITORING ................. 11 
 
SERUM/URINE PREGNANCY TEST ............................................................................................................ 11 
 
CHEST CT SCAN ....................................................................................................................................... 12 
 
RESPIRATORY SAMPLING ......................................................................................................................... 12 
 
AUDIOGRAM ............................................................................................................................................ 12 
 
VESTIBULAR MONITORING ...................................................................................................................... 12 
 Dynamic Visual Acuity Testing (DVA) ................................................................................................ 12 
 Head Impulse Testing (HIT) ................................................................................................................ 12 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date 20 February 2024 
iii 
 Romberg on Foam Test ........................................................................................................................ 13 
 
PHYSICAL EXAMINATION: INTERVENTION .............................................................................................. 13 
 
ELECTROCARDIOGRAM (ECG) ................................................................................................................ 13 
 
SIX MINUTE WALK TEST ........................................................................................................................... 13 
 
BLOOD SAMPLING.................................................................................................................................... 13 
 
STUDY MEDICATION REVIEW .................................................................................................................. 14 
 
HEALTH RELATED QUALITY OF LIFE AND UTILITY MEASURES.............................................................. 14 
 Cystic Fibrosis Questionnaire-Revised ............................................................................................... 14 
 EQ-5D-5L ............................................................................................................................................ 14 
 EQ-5D-Y .............................................................................................................................................. 15 
 St. George Respiratory Questionnaire (SGRQ) ................................................................................... 15 
 Short Form- 36 Health Survey ............................................................................................................. 15 
 Pediatric Quality of Life Inventory ...................................................................................................... 15 
 Child Health Utility 9D (CHU9D) ...................................................................................................... 15 
 
MABS CLEARANCE FOLLOW-UP QUESTIONNAIRE ................................................................................. 16 
 
SITE REIMBURSEMENT ........................................................................................................................... 16 
 
CONSOLIDATION ONLY THERAPY DOSING REGIMENS .............................................................. 17 
 DRUG SUPPLY, STORAGE AND DISTRIBUTION DURING CONSOLIDATION THERAPY ...... 22 
 
DRUG COMPLIANCE DURING CONSOLIDATION THERAPY ....................................................................... 22 
 AMIKACIN GUIDELINES .......................................................................................................................... 22 
 
NEBULISER TYPE FOR IA ......................................................................................................................... 22 
 
THERAPEUTIC DRUG MONITORING FOR IA ............................................................................................. 22 
 SCHEDULE OF ASSESSMENTS ............................................................................................................... 23 
 STATISTICAL ANALYSIS AND SIMULATIONS FOR APPENDIX A2 ............................................. 27 
 
RANDOMISATION ..................................................................................................................................... 27 
 APPLICABLE DISCOVERY STUDIES AND REGISTRY LINKAGE FOR APPENDIX A2 ............ 27 
 REFERENCES .............................................................................................................................................. 28 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date 20 February 2024 
iv 
TABLE OF TABLES 
Table 1 Consolidation Only therapy dosing regimen for Consolidation Arm a in adults .......................................... 18 
Table 2 Consolidation Only therapy dosing regimen for Consolidation Arm b in adults .......................................... 19 
Table 3 Consolidation Only therapy dosing regimen for Consolidation Arm a in paediatrics ................................... 20 
Table 4 Consolidation Only therapy dosing regimen for Consolidation Arm b in paediatrics .................................. 21 
Table 5 Special considerations for Schedule of Assessments .................................................................................... 23 
Table 6 Schedule of Assessments for Intervention Program Participants: Consolidation Only Therapy  ................. 25 
 
TABLE OF FIGURES 
Figure 1 Flow Diagram for Appendix A2: Consolidation Only Therapy program ...................................................... 8 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date 20 February 2024 
v 
ABBREVIATIONS  
 
AE 
 
 
Adverse Event 
AFB 
 
 
Acid-Fast Bacilli 
BAL 
 
 
Bronchoalveolar Lavage 
BAR 
 
 
Bayesian Adaptive Randomisation 
CEAC  
 
Cost-Effectiveness Acceptability Curves 
CF 
 
 
Cystic Fibrosis 
CFQ-R  
 
Cystic Fibrosis Questionnaire-Revised 
CHU9D 
 
Child Health Utility 9D 
CRF 
 
 
Case Report Form 
CT 
 
 
Computed Tomography 
CTCAE 
 
Common Terminology Criteria for Adverse Events 
DVA 
 
 
Dynamic Visual Acuity 
ECG 
 
 
Electrocardiogram 
eCRF  
 
electronic Case Report Form 
FEV1  
 
Forced Expiratory Volume in one second 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
HIT 
 
 
Head Impulse Test  
HRCT  
 
High-Resolution Computed Tomography 
HRQoL 
 
Health Related Quality of Life 
IA 
 
 
Inhaled Amikacin 
ICD-10  
 
International Statistical Classification of Diseases 
ICER  
 
Incremental Cost-Effectiveness Ratio 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
MARS-5 
 
5-item Medication Adherence Rating Scale 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date 20 February 2024 
vi 
MoOP  
 
Manual of Operating Procedures 
MPM  
 
Medication Possession Ratio 
NMP 
 
 
Net Monetary Benefit 
NTM  
 
Non-Tuberculous Mycobacteria 
PedsQL™ 
 
Pediatric Quality of Life Inventory 
QALY  
 
Quality-Life Adjusted Years 
QoL 
 
 
Quality of Life 
REDCap 
 
Research Electronic Data Capture 
R-Con  
 
Randomisation – Consolidation  
SAE 
 
 
Serious Adverse Event 
SAP 
 
 
Statistical Analysis Plan 
SF-36  
 
Short form-36 
SGRQ  
 
St George Respiratory Questionnaire 
SOP 
 
 
Standard Operating Procedure 
TDM  
 
Therapeutic Drug Monitoring 
TPF 
 
 
Time Point Final 
TPS 
 
 
Time Point Screening 
TPST-Con 
 
Time Point Start Treatment - Consolidation 
VAS 
 
 
Visual Analogue Scale 
vHIT 
 
 
Video Head Impulse Test 
VOR 
 
 
Vestibulo-ocular Reflex 
WT 
 
 
Willingness to Pay 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
1 
APPENDIX A: INTERVENTION PROGRAM 
Appendix A contains the Intervention Program modules, with new modules created as interventions are added to 
either intensive or consolidation phases of the trial.  They are numbered sequentially, A1, A2, A3 etc, with Appendix 
A1 describing the first iteration of the Intervention Program.  The relevant detailed statistical methods and simulations 
for each Intervention Program module will be described in Appendix F: General Statistical Principles.  Separate 
consent procedures may be required for each appendix.  Of note, in some cases data collected as part of one appendix 
may be incorporated in the analysis of another appendix, if collected to address the same objective. If this occurs, it 
will be detailed in the relevant appendices.  Should an intervention arm be dropped or a new intervention arm added 
either to intensive therapy or consolidation therapy this will require a new appendix and a new statistical analysis 
plan. 
Each program in Appendix A will stipulate which of the Discovery studies and Registry linkages is applicable. The 
Intervention program modules in Appendix A will include the following: 
• 
A description of the primary and secondary objectives. 
• 
A description of the intervention trial design including any specific inclusion or exclusion criteria specific to 
the Intervention program modules. 
• 
A description of the interventions and dosing. 
• 
The methods for assigning treatment arms to the intervention program participants. 
• 
Consent requirements. 
• 
Specific intervention program trial procedures, monitoring and safety requirements and schedule of 
assessments. 
• 
A description of relevant nested studies. 
• 
A description of cost effectiveness methodology and analysis as appropriate will be detailed in Appendix E: 
Health Economics. 
• 
A description of statistical analyses and simulations will be detailed in Appendix F: Statistical Principles. 
• 
The Discovery studies applicable to the module (if relevant). 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
2 
APPENDIX A2 CONSOLIDATION ONLY THERAPY 
Appendix A2 describes the MABS-PD consolidation only intervention platform for the FORMaT Trial.  This 
Appendix applies to sites that are unable to undertake the FORMaT intensive therapy module themselves and are 
also unable to partner with a site that is able to manage the FORMaT intensive therapy phase. Such sites can 
choose to undertake the FORMaT Consolidation Only therapy module after any physician led intensive therapy.  
Note, the data collected as part of this Appendix will be combined with data from Appendix A1.3 to address the 
objectives stated in Appendix A1.3. 
FORMaT Appendix A2 Summary 
Treatment 
combinations 
Consolidation therapy arms only listed in Appendix A2. 
Reference: 
Consolidation arm a 
Experimental:  
Consolidation arm b 
 
A mixed NTM infection (slow grower + MABS) can include the use of ethambutol in the 
consolidation phase of treatment.  
Appendix 
A2-
specific eligibility: 
Inclusion and exclusion criteria as per Master Protocol section 4.1 and below. 
Appendix 
A2-
specific inclusions: 
1. Positive MABS-PD diagnosis meeting all three American Thoracic Society clinical, 
radiological and microbiological diagnostic criteria for MABS-PD at the time of starting 
physician-directed intensive therapy defined as; 
a. Clinical: Pulmonary symptoms and exclusion of other diagnoses. 
b. Radiological: Nodular or cavitary opacities on chest radiograph or a chest high-
resolution computed tomography (HRCT) scan showing multifocal bronchiectasis 
with multiple small nodules. 
c. Microbiological: MABS positive culture results from at least two separate 
expectorated sputum samples. 
or; 
Positive culture results from at least one bronchial wash or bronchoalveolar lavage 
(BAL). 
or; 
Transbronchial or other lung biopsy with mycobacterial histopathologic features 
(granulomatous inflammation or acid-fast bacilli (AFB) and positive culture for 
NTM or biopsy showing mycobacterial histopathologic features (granulomatous 
inflammation or AFB) and one or more sputum or bronchial washes that are culture 
positive for NTM. 
2. Male or female participants of any age. 
3. Informed consent for consolidation therapy signed by participant or parent/legal 
guardian if participant is under 18 years of age. 
4. Participant has not received MABS-PD treatment in the 12 months prior to receiving 
the physician-directed intensive therapy (this includes drugs prescribed for the treatment 
of other mycobacteria and/or other indications that may have activity against MABS, as 
specified in FORMaT Standard Operating Procedure (SOP) 14). 
5. Ability to comply with study visits, therapies and study procedures as judged by the site 
investigator. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
3 
6. For randomisation the participant must provide respiratory samples (three sputums 
(expectorated or induced) or one BAL, two (2) weeks before completing the physician-
directed intensive therapy and have culture results available for randomisation.  
Appendix 
A2-
specific exclusions: 
Participants receiving current treatment for MABS within the previous 12 months prior to 
commencing physician-directed intensive therapy (this includes drugs prescribed for the 
treatment of other mycobacteria and/or other indications that may have activity against 
MABS, as specified in FORMaT Prohibited Drug List SOP, except for participants taking 
azithromycin as part of routine treatment for cystic fibrosis (CF) or chronic infection-related 
pulmonary disease. 
1. Positive pregnancy test at any time during the FORMaT trial for females of childbearing 
potential. 
2. Breast-feeding. 
3. An unwillingness to comply with the acceptable methods of contraception defined in 
the Appendix A2 Section 5. 
4. QTc> 500 milliseconds (QT interval to be corrected based on Fredericia method) 
5. Known hypersensitivity to any of the therapies for which no alternative option(s) have 
been provided. This includes: 
a. Amikacin, 
b. Macrolide antibiotics, and 
c. Clofazimine. 
Target recruitment: 
300 participants across the combination of Appendix A1 and Appendix A2 
Outcome measures: 
Primary outcome: MABS clearance from respiratory sample(s) with tolerance at Final 
Outcome. 
Secondary outcomes: 
1. Probability of MABS clearance at Final Outcome irrespective of toxicity according to 
participant’s treatment pathway. 
2. Safety of oral versus oral plus inhaled treatment, including changes in microbiological 
resistance.  
3. Change in FEV1 z-score between Screening and Final Outcome between participants 
allocated to oral consolidation treatment versus oral treatment and additional IA taking 
into account MABS clearance at Final Outcome. 
4. Changes in chest CT parameters between 6 weeks and Final Outcome taking into 
account MABS clearance at Final Outcome between participants allocated to oral 
consolidation treatment versus oral treatment and additional IA. 
5. Change in 6-minute walk distance (6MWD) from Screening to Final Outcome between 
participants allocated to oral consolidation treatment versus oral treatment and 
additional IA.  
6. Change in HRQoL for participants from Screening to Final Outcome between 
participants allocated to oral consolidation treatment versus oral treatment and 
additional IA. 
7. Cost effectiveness of consolidation treatment between participants allocated to oral 
consolidation treatment versus oral treatment and additional IA. 
8. Examine causes for early withdrawal from MABS-PD treatment due to reasons other 
than poor tolerance as defined in the primary objectives. 
Exploratory Outcomes: 
1. Participant’s MABS clearance status 12 months after Final Outcome.  
Timepoints: 
Screening: 
From the Date of consent to the Date of 
Randomisation-Consolidation (R-Con). 
Time Point Start Treatment-
Consolidation (TPST-Con): 
Randomisation-Consolidation (R-Con). 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
4 
Time Point Final (TPF): 
End of 46 weeks of treatment plus 4 weeks 
off treatment (Final Outcome Visit date). 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
5 
 
INTRODUCTION 
Currently, the guidelines for consolidation therapy (1) suggest that patients with isolates that are sensitive to 
macrolides or that have inducible resistance should be managed with a combination of between one and three oral 
antibiotics based on drug susceptibility of the isolate and tolerance in combination with inhaled amikacin (IA).  Those 
with isolates that have constitutive resistance should use a combination of between two and four oral drugs based on 
susceptibility and tolerance in combination with IA.  In addition, guidelines suggest that patients with isolates that 
have amikacin resistance could substitute IA for an alternative oral antibiotic.  It is suggested that treatment should 
continue for 12 months after culture conversion. 
There is currently no evidence for any of these guidelines.  IA is costly and requires time and effort for maintenance 
of hygienic practice and drug delivery.  Furthermore, adherence to inhaled therapies over the longer term is variable 
(2-4).  This study will examine the effects of adding IA to oral treatment thus providing some evidence regarding the 
use of IA during consolidation therapy.  The timing of consolidation therapy is only 46 weeks for this trial and 
patients are free to continue treatments after completion of the trial.  Microbiological clearance will be determined 
from culture of respiratory samples (sputum (expectorated or induced) or BAL) collected at least one week apart as 
follows: 
1. Participants who continue to produce sputum samples during the consolidation only therapy phase are 
requested to provide additional sputum samples (preferably monthly).  Three consecutive sputum samples 
will be collected at least one week apart over the last 6 weeks of consolidation and a final sputum sample 
collected four weeks after cessation of consolidation therapy.  These samples will together determine the 
final outcome microbiological clearance.  All four samples will need to be clear to confirm clearance. 
2. For participants who continue to have positive sputum cultures at the end of 46 weeks of consolidation, a 
gap in therapy to final outcome visit may not be required if ongoing treatment is clinically indicated as 
microbiological clearance will not have occurred. 
3. Participants who have negative cultures on treatment at end of consolidation will need to cease treatment for 
4 weeks to enable assessment of microbiological clearance without antibiotic suppression at the final 
outcome visit. 
4. For participants who are unproductive of sputum during the consolidation phase, or who become 
unproductive of sputum during the course of consolidation therapy, a BAL is to be performed at final 
outcome (4 weeks after completing consolidation). 
Sites that are unable to undertake the intensive therapy module themselves and are also unable to partner with a site 
that is able to manage the intensive therapy phase, can choose to only undertake the Consolidation Only therapy 
module. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
6 
 
OBJECTIVES 
 
PRIMARY OBJECTIVE 
The objective of Appendix A2 is to enable more rapid comparison of the microbiological clearance of MABS with 
good tolerability between those allocated to consolidation therapy with oral treatment and those allocated to 
consolidation therapy with oral treatment and additional IA at Final Outcome (46 weeks of consolidation therapy 
plus 4 weeks off treatment) by recruiting eligible participants from sites that are unable to undertake Appendix A1 
intensive therapy.  The data collected as part of this appendix (A2) will be combined with the data from Appendix 
A1.3 to address the same primary (and secondary) objectives as stated in Appendix A1.3 and in A2. 
Definition of tolerance: 
Tolerance is based on the Common Terminology Criteria for Adverse Events (CTCAE version 5.0). Only adverse 
events that are attributed as either “possibly”, “probably”, or “definitely” related to study drug will be assessed in the 
determination of tolerance.  “Good” tolerance is defined as no adverse events occurring or only adverse events coded 
as CTCAE grades 1 and 2. “Poor” tolerance is defined as any adverse events attributed as possibly, probably, or 
definitely related to study drug coded as CTCAE grades 3, 4, or 5. 
MABS clearance at Final Outcome will be defined as: 
Negative MABS cultures from four consecutive sputum samples with one of those sputum specimens collected four 
weeks after the completion of consolidation therapy (at Final Outcome) or, a MABS negative BAL collected four 
weeks after completion of consolidation (at Final Outcome). 
 
SECONDARY OBJECTIVES 
As stated above, the data collected in this Appendix will contribute to the assessment of the secondary objectives 
stated in Appendix A1.3, namely: 
1. To compare microbiological clearance (irrespective of toxicity) at completion of consolidation therapy 
between those allocated to consolidation therapy with oral treatment and those allocated to oral treatment 
with addition of IA at Final Outcome. 
2. Differences in safety between those allocated to consolidation therapy with oral treatment and those allocated 
to oral treatment with addition of IA. 
3. Change in forced expiratory volume in one second (FEV1) z-score between Screening and Final Outcome 
between those allocated to consolidation therapy with oral treatment and those allocated to oral treatment 
with addition of IA taking into account microbiological clearance at end of physician led intensive therapy. 
4. Change in computed tomography (CT) scan parameters (bronchiectasis, mucus plugging, airway wall 
thickening, atelectasis, % disease and air trapping), between 6 weeks and at Final Outcome taking into 
account microbiological clearance at end of physician led intensive therapy between those allocated to 
consolidation therapy with oral treatment and those allocated to oral treatment with addition of IA. 
5. Change in 6-minute walk distance (6MWD) between Screening and Final Outcome between those allocated 
to consolidation therapy with oral treatment and those allocated to oral treatment with addition of IA. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
7 
6. Changes in health-related quality of life (HRQoL) (Cystic Fibrosis Questionnaire-Revised (CFQ-R)) for 
participants with CF between Screening and Final Outcome in those allocated to consolidation therapy with 
oral treatment and those allocated to oral treatment with addition of IA. 
7. To examine general HRQoL between Screening and Final Outcome between those allocated to consolidation 
therapy with oral treatment and those allocated to oral treatment with addition of IA. 
8. To compare the cost effectiveness of consolidation between those allocated to consolidation therapy with 
oral treatment and those allocated to oral treatment with addition of IA. 
9. Examine causes for early withdrawal from MABS-PD treatment due to reasons other than poor tolerance as 
defined in the primary objectives between those allocated to consolidation therapy with oral treatment and 
those allocated to oral treatment with addition of IA at Final Outcome. 
 
EXPLORATORY OBJECTIVES 
The data collected in this Appendix will contribute to the assessment of the exploratory objective stated in Appendix 
A1.3, namely: 
• 
To examine MABS clearance status at 12 months after Final Outcome. 
 
 
DESIGN 
Appendix A2 describes the consolidation only module and will test therapies that are currently used and are the 
basis for the current treatment guidelines (Figure A2.1).
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
8 
Figure 1 Flow Diagram for Appendix A2: Consolidation Only Therapy program Eligibility into the 
consolidation only therapy program is determined at screening. Randomisation-Consolidation (R-Con)(✢) allocates 
participants to the consolidation therapy arms depending on MABS status at 2 weeks prior to entry into Consolidation 
Only therapy module. 
 
 
ELIGIBILITY CRITERIA 
Participants are eligible for Appendix A2 if the following criteria are met in addition to those outlined in section 4.2 
in the FORMaT Master Protocol: 
 
INCLUSION CRITERIA  
1. Positive MABS-PD diagnosis meeting all three American Thoracic Society clinical, radiological and 
microbiological diagnostic criteria for MABS-PD prior to starting physician directed intensive therapy for 
MABS eradication. Defined as: 
• 
Clinical: Pulmonary symptoms and exclusion of other diagnoses. 
• 
Radiological: Nodular or cavitary opacities on chest radiograph or a chest high-resolution computed 
tomography (HRCT) scan showing multifocal bronchiectasis with multiple small nodules. 
• 
Microbiological: MABS positive culture results from at least two separate expectorated sputum samples. 
or 
Positive culture results from at least one bronchial wash or lavage. 
or 
Transbronchial or other lung biopsy with mycobacterial histopathologic features (granulomatous 
inflammation or acid-fast bacilli, AFB) and positive culture for NTM or biopsy showing mycobacterial 
histopathologic features (granulomatous inflammation or AFB) and one or more sputum or bronchial 
washes that are culture positive for NTM. 
2. Male or female participants of any age. 
3. Informed consent signed by participant or parent/legal guardian if participant is under 18 years of age.  For 
those participating in the consolidation only therapy Appendix A2, a specific consolidation only therapy 
consent is required. 
4. Participant has not received MABS-PD treatment in the 12 months preceding any physician-directed 
intensive therapy (this includes drugs prescribed for the treatment of other mycobacteria and/or other 
indications that may have activity against MABS, as specified in FORMaT Prohibited Drug List SOP. 
5. Ability to comply with study visits, therapies and study procedures as judged by the site investigator. 
6. Participant must provide respiratory samples (three sputums (expectorated or induced) or one BAL) two (2) 
weeks before completing the physician-directed intensive therapy and have culture results available for the 
randomisation.  If participant has not received any physician-directed intensive therapy the screening 
respiratory samples may be used for the randomisation. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
9 
 
EXCLUSION CRITERIA 
• 
Participants receiving current treatment for MABS within the previous 12 months of commencing physician-
directed therapy (this includes drugs prescribed for treatment of other mycobacteria and/or other indications that 
may have activity against MABS, as specified in FORMaT Prohibited Drug List SOP, except for participants 
taking azithromycin as part of routine treatment for CF or chronic infection-related pulmonary disease. 
• 
Positive pregnancy test at any time during the FORMaT trial for females of childbearing potential.  
• 
Breast-feeding. 
• 
An unwillingness to comply with the acceptable methods of contraception, as described in Section 5. 
• 
Participants with a QTc interval >500 milliseconds (QT interval corrected based on Fridericia method).  
• 
Known hypersensitivity to any of the therapies for which no alternative option(s) have been provided. This 
includes: 
o Amikacin, 
o Macrolide antibiotics, and  
o Clofazimine. 
 
ADDITIONAL CRITERIA 
 
MIXED NTM INFECTIONS 
Participants who have cultured slow growing NTM of the same species two or more times in the 24 months prior to 
screening, with one of those cultures within the 6 months prior to screening, will be considered to have mixed NTM 
infection.  If the participants meet all other inclusion criteria and no exclusion criteria they will be eligible for 
participation.  Ethambutol may be used in addition to trial therapies to cover mixed NTM infections considered to 
require treatment by their clinician.   
 
CO-ENROLMENT WITH OTHER TRIALS  
Co-enrolment is not permitted when there is a potential interaction between trial interventions, any compromise to 
the validity of either trial or impact on participants’ rights and/or safety.  However, co-enrolment may be permitted 
in the instance where all trials that the participant is enrolled or to be enrolled in have mutually agreed to the co-
enrolment arrangement. 
 
 
ACCEPTABLE METHODS OF CONTRACEPTION 
The effects of some drugs used during the Intervention Program on the unborn child and on the newborn baby are 
not known.  Because of this, it is important that participants are not pregnant or breast-feeding and do not become 
pregnant during the course of the research project. 
It is therefore important that birth control is used while in this study. Site investigators should discuss effective 
methods of contraception with participants. Both male and female participants are to use effective contraception, 
used correctly with every act of sexual intercourse, from at least 14 days before the first dose of MABS-PD therapy, 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
10 
during the course of the trial and for a period of 90 days after the last dose of MABS-PD therapy. Acceptable methods 
of contraception for participants enrolled in Appendix A2 include: 
1) Male vasectomy 6 months or more previously, with a documented negative post-vasectomy semen analysis 
for sperm. 
2) Female bilateral tubal ligation performed at least 6 months previously. 
3) Female continuous use of an intrauterine device (non-hormone releasing or hormone releasing) for at least 
90 days before the first dose of MABS-PD therapy. 
4) Female combined (estrogen and progestogen-containing) or progestogen-only oral, injected, implanted or 
vaginal hormonal contraception associated with inhibition of ovulation. 
The barrier contraception methods listed below are not acceptable and are only to be used in special circumstances 
where the investigator determines that barrier contraception is appropriate. 
1) Male and female condom with spermicide (either as a single product if commercially available and/or as 
allowed according to local regulations; otherwise condom and spermicide as separate products). 
2) Male condom with female diaphragm, cervical cap, or vaginal sponge, each with spermicide. 
For female participants using birth control pills 
The use of birth control pills for contraception must be discussed and approved by the local site investigator at the 
start of each phase of the trial and when any changes in therapy occur as, some therapies used during the trial may 
interact with the effectiveness of birth control pills. Birth control pills should be in successful use from at least 60 
days before the first dose of MABS-PD therapy (unless otherwise noted) and until 90 days following the last dose of 
MABS-PD therapy. 
Female participants who change their method of contraception to birth control pills during the trial must continue to 
use a second form of approved contraception for at least 60 days after starting the use of birth control pills. 
For female participants using hormonal injected, implanted or vaginal contraception 
Injected, implanted or vaginal hormonal contraception should be used successfully from at least 60 days before the 
first dose of MABS-PD therapy (unless otherwise noted) and until 90 days following the last dose of MABS-PD 
therapy. 
 
 
TRIAL CONDUCT 
 
INFORMED CONSENT 
In addition to providing consent to the FORMaT Master Protocol, participants enrolling in the intervention program 
are required to sign and date the relevant Appendix A2 consent.  Consent will be obtained from participants or their 
parent/guardian in accordance with the policies described in section 5.4 of the FORMaT Master Protocol. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
11 
 
PREGNANCY INFORMATION CONSENT 
If a FORMaT trial participant becomes pregnant or is the biological father of a child conceived while enrolled in this 
intervention program the site investigators are requested to provide the participant with the FORMaT pregnancy 
information and consent form.  The FORMaT pregnancy and consent form requests to follow the participant and the 
child for 12 months after conception.  Please refer to FORMaT Safety and Monitoring Plan SOP for further detail 
for safety monitoring and reporting of pregnancies and pregnancy outcomes in female trial participants or female 
partners who are pregnant to male participants in the intervention program. 
 
METHODS OF ASSIGNING PARTICIPANTS TO TREATMENT ARMS 
Participants will be randomised into different treatment arms for the consolidation only phase of treatment as 
described in Appendix A2, Section 131 and Master Protocol section 6 using the randomisation technique 
minimisation in a 1:1 ratio.  As described in the Master Protocol, all randomisations will be conducted via Research 
Electronic Data Capture (REDCap) at each FORMaT trial site.  Study staff will enter the subject demographic data 
and the stratification factors (see section 6.3 in the Master Protocol) into REDCap, which will then inform them of 
the participant’s treatment allocation. 
 
 
CONSOLIDATION ONLY PROGRAM PROCEDURES AND SAFETY 
MONITORING 
In addition to the core trial procedures described in the Master Protocol, participants enrolled in the Intervention 
program are required to undertake procedures and regular toxicology monitoring. The type of toxicology monitoring 
procedure required will be determined by the treatment arm the participant is allocated to, and in accordance with 
the schedule of assessments outlined in Table 6.  Toxicology thresholds will be defined in accordance with CTCAE 
criteria as outlined in the Master Protocol, section 5.8.6.  The outcome of all the assessments below are to be 
documented in the corresponding case report form (CRF) and entered into REDCap. 
 
SERUM/URINE PREGNANCY TEST 
All female participants of childbearing potential are required to undergo regular pregnancy testing while enrolled in 
the intervention program.  Childbearing potential is defined as a premenopausal female capable of becoming 
pregnant, and includes females on oral, injectable, or mechanical contraception; females who are single and females 
whose male partners have been vasectomised or were using mechanical contraception (5).  A serum pregnancy test 
will be performed at screening and at the final study visit and if applicable, at the early termination visit.  A urine β-
hCG test or serum pregnancy is acceptable for regular pregnancy monitoring from day 1 in accordance with the 
schedule of assessments outlined in Table 6.  Both urine and serum pregnancy tests are to be performed in accordance 
with site specific procedures. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
12 
 
CHEST CT SCAN 
The chest CT scan for screening is be ordered ideally within three months (up to maximum of six months) prior to 
commencement of physician-directed intensive therapy or screening if participant has not received any intensive 
therapy.  Table 5 outlines the time points for when a chest CT scan is to be performed. 
 
RESPIRATORY SAMPLING 
For screening a minimum of 2 sputum samples (with at least 1 collected within 6 months prior to screening and other 
samples collected within 12 months prior to screening) or 1 BAL collected within 6 months prior to commencing 
physician-directed intensive therapy will be required to assess eligibility according to the Appendix A2 eligibility 
criteria.  For randomisation, respiratory samples (three sputums (expectorated or induced) or one BAL) are to be 
collected ideally two (2) weeks prior to completing physician-directed intensive therapy with culture results available 
for randomisation. For participants who have not undergone any intensive therapy, the screening respiratory samples 
may be used for randomisation.  Table 6 outlines the minimum respiratory sample collection timepoints; however, 
monthly sputum sample collections are recommended. 
 
AUDIOGRAM 
To monitor aminoglycoside and/or azithromycin induced ototoxicity, regular audiometry assessments will be 
undertaken in accordance with the schedule of assessments outlined in Table 6.  The battery of assessments to be 
completed should comply with the site-specific requirements.  Assessments can be conducted in either a hospital or 
community setting. 
 
VESTIBULAR MONITORING 
Vestibular toxicity monitoring will document any vestibular symptoms (motion-induced oscillopsia, postural 
instability and gait unsteadiness) associated with prolonged aminoglycoside use.  Assessments will take place in 
accordance with the schedule of assessments outlined in Table 6.  Testing can be completed either by the treating 
clinician. 
Additional specific vestibular monitoring may be required if deemed necessary by the site investigator, see below. 
 
DYNAMIC VISUAL ACUITY TESTING (DVA) 
Ask the patient to read a visual acuity chart (e.g. Snellen) while sitting still at recommend distance. This result is the 
static visual acuity. Repeat task while oscillating the patient’s head horizontally or vertically at 1 to 2 Hz. An 
abnormal DVA is defined as loss of at least three lines of visual acuity compared with static condition (horizontal 
and/or vertical). 
 
HEAD IMPULSE TESTING (HIT) 
Stand in front of the seated patient, facing them, and ask the patient to focus on a target directly in front of them.  
Briskly rotate the patient’s head horizontally approximately 10 to 20° amplitude, watching the patient’s eyes closely. 
In normal subjects, the patient’s eyes remain still as they remain on target.  However, in a patient with impaired 
vestibulo-ocular reflex (VOR), the patient’s eyes drift off the target and require a corrective ‘catch-up’ saccade to re-

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
13 
fixate on the target and stabilise vision.  This catch-up saccade is a small amplitude horizontal eye movement in the 
opposite direction of the head turn and should occur with every head impulse (repeatable). 
If available, Video Head Impulse Test (vHIT) is recommended as this has a higher sensitivity than the traditional 
bedside head impulse test at detecting impaired VOR.  M=The main benefits include detecting covert (hidden) catch 
up saccades and peer review. 
 
ROMBERG ON FOAM TEST 
On a foam surface, ask the participant to stand still with two feet together. The participant should be able to stand 
steady with their eyes open. If the participant is not able to perform this task, ask them to separate their feet to minimal 
distance that allows them to do so. Repeat the task this time with their eyes closed. Record if the participant falls 
(positive Romberg test) or does not (negative Romberg test). 
Document vestibular test results and any further actions (if results indicate significant vestibular impairment) in the 
CRF. 
 
PHYSICAL EXAMINATION: INTERVENTION 
The physical examination will be performed in accordance with the procedures outlined in the FORMaT Master 
Protocol, section 5.5.5 in accordance with the schedule of assessments outlined in Table 6. 
 
ELECTROCARDIOGRAM (ECG) 
A standard 12 lead ECG will be performed in accordance with the relevant tables and site-specific procedures after 
the participant has been supine for at least 5 minutes.  The site investigator will interpret, sign and date the ECG.  
The QTc interval and the clinical interpretation will be recorded in the eCRF and ECGs will be required to be scanned 
and stored in the eCRF.  The QT interval at Screening is to be corrected using the Fridericia method.  For any 
subsequent QTc intervals which are ‘abnormal’ the Fridericia method is to be used to confirm the QTc value. 
 
SIX MINUTE WALK TEST 
A 6-minute walk test (6MWT) will be performed in adult participants only at the time points outlined in Table 6 if 
the testing is available at the trial site.  The 6MWT will be performed according to the protocol in the ATS Statement: 
Guidelines for the Six Minute Walk Test (6) and/or local standard procedures.  Results of walk test will be recorded 
in the relevant eCRF in the FORMaT database by the end of the Final Outcome visit.  
 
BLOOD SAMPLING 
Blood samples will be collected in accordance with Table 6.  Liver function, full blood count and chemistry and renal 
function tests (refer to FORMaT Monitoring Blood Parameters SOP for specific blood parameters to be measured) 
are to be performed in accordance with the local pathology requirements.  All relevant de-identified blood pathology 
reports are to be uploaded in the appropriate eCRFs in the FORMaT database by the end of the Final Study Visit.  
Any blood abnormalities that meet adverse event (AE) or serious adverse event (SAE) criteria are to be reported as 
an AE/SAE within the specified timeframes. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
14 
 STUDY MEDICATION REVIEW 
Participant adherence to MABS-PD treatment will be measured via two indirect methods.  Self-reported adherence 
will be assessed using a validated questionnaire, the 5-item Medication Adherence Rating Scale (MARS-5)(7, 8) at 
the timepoints outlined in Table 6 and results recorded in the Medication Adherence Questionnaire CRF.  Data from 
pharmacy prescription refill records and prescription claims databases will be obtained (where possible) and used to 
calculate the refill adherence measure, Medication Possession Ratio (MPR) (9-12). 
 HEALTH RELATED QUALITY OF LIFE AND UTILITY MEASURES 
HRQoL will be assessed in all participants (where possible) according to the schedule of assessments in the relevant 
appendix. The questionnaires are required to be completed prior to any clinical assessment and are dependent on the 
participant’s age and whether they have CF.  The age appropriate HRQoL questionnaire issued to the participant at 
the start of the study will continue to be used throughout the study even if the participant progresses to a different 
age range. HRQoL questionnaires will be made available to study sites.  All questionnaires will be made available in 
English or if available the local language version will be sourced. Questionnaires can be completed by the participant 
and/or their parent/carer via an online link to the questionnaire(s) on the trial database or if unable to access the 
electronic form these may be completed using a paper-based questionnaire.  Responses from paper-based 
questionnaires are to be entered into the trial database by trial site staff. 
 CYSTIC FIBROSIS QUESTIONNAIRE-REVISED 
The CFQ-R has been developed specifically for use in people with CF.  This questionnaire measures the impact of 
CF on overall health, daily life, perceived well-being and symptoms.  Age-appropriate questionnaires have been 
developed; CFQ-R teen/adult for adolescents and adults 14 years of age and older, the CFQ-R child for those 6-13 
years of age, and the CFQ-R parent for the parents of those aged 6-13. 
In children ≤16 years of age, the CFQ-R should be administered after the PedsQL™. 
 EQ-5D-5L 
The EQ-5D-5L questionnaire is a standardised measure of health status in adults 18 years of age and older. This 
questionnaire can be applied as a generic measure of health for clinical and economic appraisal, including the 
calculation of quality-life adjusted years (QALYs).  The EQ-5D-5L measures five dimensions: 
1. Mobility; 
2. Self-care; 
3. Usual activities; 
4. Pain/discomfort; 
5. Anxiety/depression. 
Each dimension has five possible answers; no problems, slight problems, moderate problems, severe problems and 
extreme problems.  The respondent is asked to indicate his/her health state by selecting the most appropriate 
statement. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
15 
 EQ-5D-Y 
The EQ-5D-Y is the child friendly version of the EQ-5D-5L questionnaire. The EQ-5D-Y has been developed for 
use in children 8 to 17 years of age.  The dimensions and the visual analogue scale (VAS) measured are the same as 
the EQ-5D-5L questionnaire, but with child friendly wording.  For children 4 to 7 years of age the proxy 1 version 
of the EQ-5D-Y can be utilised allowing the respondent (parent/carer) to evaluate participants QOL from 
respondents’ own view. 
 ST. GEORGE RESPIRATORY QUESTIONNAIRE (SGRQ) 
The SGRQ is to be completed by all non-CF participants 18 years of age and older. The SGRQ is a supervised self-
administered 50-item questionnaire measuring health status across three domains; symptoms, activity and impacts 
(psycho-social) in people with airway obstruction. 
 SHORT FORM- 36 HEALTH SURVEY 
The SF-36 health survey is a self-reported questionnaire applicable in all participants 16 years and older. Covering 
eight health concepts the SF-36 health survey is a generic outcome measure designed to examine a person’s perceived 
health status. 
 PEDIATRIC QUALITY OF LIFE INVENTORY  
The PedsQL™ child health questionnaire is a non-preference-based measure to assess HRQoL for children and 
adolescents from 2 years up to 16 years of age.  Children less than 16 years of age at screening will continue to use 
the PedsQLTM up until the end of the trial, rather than change to using the SF-36 if they turn 16 years of age during 
the study.   
Developmentally appropriate child self-report questionnaires are available (ages 5-7, 8-12, 13-18) together with 
parent/carer proxy-reports (ages 2-4, 5-7, 8-12 and 13-18).  If feasible, the PedsQL™ should be completed before 
the respondents complete any other health data forms and before they see their physician or healthcare provider. 
Parents/carers, children (aged 8-12) and young people (aged >12 years) may self-administer the PedsQL™ after the 
FORMaT site researcher has provided instructions.  If it is determined by the FORMaT site researcher that the child, 
young person or parent/carer is unable to self-administer the PedsQL™ the questionnaire should be administered, 
word for word by the FORMaT site researcher.  If the child has difficulty understanding the age appropriate 
PedsQL™ the preceding age questionnaire may be used.  The parent and the child must complete the questionnaires 
independently of each other and in accordance with the PedsQL™ administration guidelines (available via hyperlink 
or refer to relevant section in FORMaT Trial Site Manual of Operating Procedures (MoOP)). 
 CHILD HEALTH UTILITY 9D (CHU9D) 
The CHU9D is a generic preference-based measure of paediatric HRQoL for use in children 7 to 17 years of age.  
The use of a descriptive system and a set of preference weights allows for the calculation of QALYs for use in 
economic evaluation. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
16 
 MABS CLEARANCE FOLLOW-UP QUESTIONNAIRE 
Site investigators will be requested to complete a follow up questionnaire for eligible intervention participants to 
assess microbiological clearance of MABS at 12 months after final outcome. 
 
 
SITE REIMBURSEMENT 
For participants enrolled in Appendix A2, trial sites will be reimbursed on a per participant basis at each of the 
following time points; 
1. 
Screening; 
2. 
End of consolidation; 
3. 
Final study visit. 
Sites will be reimbursed according to their contract. Payments will be paid for each time point once the data is entered 
into the trial database and all queries finalised. Invoices should be prepared at a minimum of every 6 months. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
17 
 
 
CONSOLIDATION ONLY THERAPY DOSING REGIMENS 
Following R-Con, participants will receive consolidation treatment in accordance with the dosing tables below. Drug 
therapy, administration and duration is dependent on the treatment arm (Consolidation Arm a and Consolidation Arm 
b), age, and/or weight of the participant. The start and end points of each drug therapy, the dose of each drug therapy 
used, any changes in dosing, as well as all concomitant medications used, will be required to be entered into the 
relevant CRF. 
There are currently two proposed treatment arms that participants will be randomised to during consolidation therapy. 
Consolidation Arm a 
Consolidation Arm b 
1. Oral clofazimine, and; 
1. Inhaled amikacin 
2. Oral clofazimine, and; 
2. Oral azithromycin or oral clarithromycin, and; 
 
3. Oral azithromycin or oral clarithromycin, and; 
In combination with one to three of the following oral 
antibiotics: 
In combination with one to three of the following oral 
antibiotics: 
• 
Oral linezolid, 
• 
Oral linezolid, 
• 
Oral trimethoprim / sulfamethoxazole (co-
trimoxazole), 
• 
Oral trimethoprim / sulfamethoxazole (co-
trimoxazole), 
• 
Oral bedaquiline, 
• 
Oral bedaquiline, 
• 
Oral rifabutin, 
• 
Oral doxycycline, 
• 
Oral moxifloxacin. 
• 
Oral rifabutin, 
• 
Oral doxycycline, 
• 
Oral moxifloxacin. 
 
For participants with confirmed mixed NTM infections (slow growers + MABS), ethambutol can be added to the 
treatment arms (in accordance with the dosing tables below) if required by the treating physician. 
The consolidation therapy dosing regimen tables outlined below are separated by age (adult, paediatric) and by 
consolidation treatment arm (Arm a and Arm b). The recommended doses and frequencies are a guideline and 
participant dosing must also take into account clinical judgement and relevant prescribing information.  
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
18 
Table 1 Consolidation Only therapy dosing regimen for Consolidation Arm a in adults 
Consolidation Arm a: Adult DosingA 
Drug 
 Recommended Dose (per dose) 
Frequency  
Oral clofazimine 
100 – 300mg 
Once daily 
Oral azithromycin  
250 – 500mg 
OR 
500mg  
Once daily 
 
Thrice weekly 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Thrice weekly 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
600mg 
Once daily 
Oral trimethoprim with 
sulfamethoxazole  
160mg/800mg 
Twice daily 
Oral bedaquiline  
(Weighing at least 30kg) 
First 2 weeks 400mg 
Once daily 
For remaining 22 weeks 200mg 
Max duration 6 months 
Thrice weekly 
At least 48 hours between doses 
Oral rifabutin 
5mg/kg, max 450mg 
Once daily 
Oral doxycycline 
100mg 
Once daily 
Oral moxifloxacin 
400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg 
(round to account for tablet strength) 
OR 
Once daily 
25mg/kg 
(round to account for tablet strength) 
Thrice weekly 
 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information. 
 
 
 
 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
19 
Table 2 Consolidation Only therapy dosing regimen for Consolidation Arm b in adults 
Consolidation Arm b: Adult DosingA 
Drug 
 Recommended Dose (per dose) 
Frequency  
Inhaled amikacin (IA) 
(IV formulation) 
500mg 
Twice daily 
Oral clofazimine 
100 – 300mg 
Once daily 
Oral azithromycin 
250 – 500mg 
OR 
500mg 
Once daily 
 
Thrice weekly 
If azithromycin not tolerated, use oral 
clarithromycin. 
<40kg or poorly tolerated 
250mg 
 
Thrice weekly 
Oral clarithromycin 
Clarithromycin only for use if 
azithromycin not tolerated. 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
600mg 
Once daily 
Oral trimethoprim with 
sulfamethoxazole 
160mg/800mg  
Twice daily 
Oral bedaquiline 
(Weighing at least 30kg) 
First 2 weeks 400mg 
Once daily 
For remaining 22 weeks 200mg 
Max duration 6 months 
Thrice weekly 
At least 48 hours between doses 
Oral rifabutin 
5mg/kg, max 450mg 
Once daily 
Oral doxycycline 
100mg 
Once daily 
Oral moxifloxacin 
400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below.  
Oral ethambutol 
Ethambutol should be dosed on ideal 
body weight. 
15mg/kg  
(round to account for tablet strength) 
OR 
Once daily 
25mg/kg  
(round to account for tablet strength) 
Thrice weekly 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information. 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
20 
Table 3 Consolidation Only therapy dosing regimen for Consolidation Arm a in paediatrics 
Consolidation Arm a: Paediatric DosingA 
Drug 
Recommended Dose  
(per dose) 
Frequency 
Oral clofazimine 
Dosing may be rounded to account for capsules. 
<40kg 
3-5mg/kg, max 100mg 
Once daily 
≥40kg 
100mg 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if azithromycin 
not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
1 month – 9 years 
10mg/kg, max 450mg 
Twice daily 
10 – 12 years 
10mg/kg, max 600mg 
Daily 
>12 years 
600mg 
Daily 
Oral trimethoprim with sulfamethoxazole  
5mg/kg trimethoprim 
max 160mg trimethoprim 
Twice daily 
Oral bedaquiline 
(age ≥5 years) 
Weeks 1 and 2 
≥15kg - <20kg 
160mg 
Once daily 
≥20kg - <30kg 
200mg 
≥30kg 
400mg 
Weeks 3-24 - Max Duration 6 Months 
≥15kg - <20kg 
80mg 
Thrice weekly. 
At least 48 hours between 
doses 
≥20kg - <30kg 
100mg 
≥30kg 
200mg 
Oral rifabutin 
5mg/kg, max 300mg 
Once daily 
Oral doxycycline 
(ages ≥8 years) 
2mg/kg, max 100mg 
Once daily 
Oral moxifloxacin  
Dosing may be rounded to account for capsules. 
10-15mg/kg, max 400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg 
(round to account for tablet 
strength) 
Once daily 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information. 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
21 
Table 4 Consolidation Only therapy dosing regimen for Consolidation Arm b in paediatrics 
Consolidation Arm b: Paediatric DosingA 
Drug 
Recommended Dose  
(per dose) 
Frequency 
Inhaled amikacin (IA) 
(IV formulation) 
500mg 
Twice daily 
Oral clofazimine 
Dosing may be rounded to account for capsules. 
<40kg 
3-5mg/kg, max 100mg 
Once daily 
≥40kg 
100mg 
Oral azithromycin 
If azithromycin not tolerated, use oral clarithromycin. 
10mg/kg, max 500mg 
Once daily 
Oral clarithromycin 
Only for use if azithromycin 
not tolerated. 
Children 1 month – 11 years of age 
<8 kg 
7.5mg/kg  
Twice daily 
8-11 kg 
62.5mg 
12-19 kg 
125mg 
20-29 kg 
187.5mg 
30-40 kg 
250mg 
Children 12-18 years of age 
Dosing independent of 
weight 
500mg 
Twice daily 
In combination with one to three of the following oral antibiotics guided by participant susceptibility and tolerance. 
Oral linezolid 
1 month – 9 years 
10mg/kg, max 450mg 
Twice daily 
10 – 12 years 
10mg/kg, max 600mg 
Daily 
>12 years 
600mg 
Daily 
Oral trimethoprim with sulfamethoxazole  
5mg/kg trimethoprim 
max 160mg trimethoprim 
Twice daily 
Oral bedaquiline 
(age ≥5 years) 
Weeks 1 and 2 
≥15kg - <20kg 
160mg 
Once daily 
≥20kg - <30kg 
200mg 
≥30kg 
400mg 
Weeks 3-24 - Max Duration 6 Months 
≥15kg - <20kg 
80mg 
Thrice weekly. 
At least 48 hours between 
doses 
≥20kg - <30kg 
100mg 
≥30kg 
200mg 
Oral rifabutin 
5mg/kg, max 300mg 
Once daily 
Oral doxycycline 
(ages ≥8 years) 
2mg/kg, max 100mg 
Once daily 
Oral moxifloxacin  
Dosing may be rounded to account for capsules. 
10-15mg/kg, max 400mg 
Once daily 
For participants with confirmed mixed NTM (slow growers + MABS) infections, there is an option to add oral 
ethambutol to the treatment arm in accordance with the dosing below. 
Oral ethambutol 
Ethambutol should be dosed on ideal body weight. 
15mg/kg, max 1200mg 
(round to account for tablet 
strength) 
Once daily 
A The recommended doses and frequencies are a guideline and participant dosing must also consider clinical 
judgement and relevant prescribing information. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
22 
 
 DRUG SUPPLY, STORAGE AND DISTRIBUTION DURING 
CONSOLIDATION THERAPY 
Supply, distribution and storage of drugs will be the responsibility of the site, coming from site/institution pharmacy 
stocks as per standard of care in accordance with site-specific guidelines and requirements. 
 DRUG COMPLIANCE DURING CONSOLIDATION THERAPY 
The procedures for distribution of consolidation therapy are site dependent. Drug compliance during consolidation 
therapy will be captured from pharmacy records of drugs dispensed to the participant while enrolled in FORMaT 
Appendix A2. 
 AMIKACIN GUIDELINES 
 NEBULISER TYPE FOR IA 
Amikacin for injection preparation (not liposomal amikacin) is to be used for inhalation in participants randomised 
to inhaled amikacin. A low preservative preparation, if available, is advised to reduce the risk of bronchospasm.  The 
brand of amikacin preparation, if known, is to be recorded in the study drug CRF.  Five hundred milligrams (500mg) 
of amikacin should be administered according to local standard practices.  Prior to administration the patient should 
receive a bronchodilator, for example, salbutamol, to reduce the risk of coughing and bronchospasm.  This can be 
given nebulised or by metered dose inhaler.  Amikacin for injection may only be mixed with sodium chloride 0.9%.  
It must not be nebulised as a mixture with other nebulised drugs (e.g., salbutamol, dornase alfa or other nebulised 
antibiotics). 
High efficiency nebulisers are required to nebulise amikacin (IV formulation).  A suitable nebuliser with a filter 
attachment (e.g. SideStream Plus with filter attachment, or Pari LC Plus with filter attachment) are to be used to 
prevent environmental deposition of nebulised antibiotics and to reduce the risk of developing antibiotic resistant 
organisms.  Air flow of 6-10 L/min is required to achieve effective nebulisation of amikacin. 
 THERAPEUTIC DRUG MONITORING FOR IA 
For subjects randomised to Consolidation Only Arm b, an amikacin level should be collected at week four (4), 90 
minutes (range 60 to 120 minutes) post completion of the inhaled dose.  The time of starting and completing the 
inhaled therapy and time of blood collection should be documented.  No adjustment of the inhaled amikacin dose 
should be undertaken. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
23 
 SCHEDULE OF ASSESSMENTS 
Table 5 lists all the special considerations for the Schedule of Assessments for participants enrolled in Appendix A2: 
Consolidation Only.  Table 5, “Special considerations for Schedule of Assessments” must be used in conjunction 
with Table 6. 
Table 5 Special considerations for Schedule of Assessments 
Symbol Definition 
A 
Participant reconsent is required with IRB/ IED/HREC approved changes to the protocol that affect the 
participants rights and/or safety and/or if a child turns 18 years old during the trial and must reconsent 
as an adult participant.  
B 
Consent may be performed at any time between MABS-PD Screening and Day 0. 
C 
Visits may be conducted while an inpatient or at home if participant is receiving home-based care. 
D 
Clinic visit and some assessments at Week 4 can be completed at any time between Week 4 and Week 
6. 
E 
Refer to Section 4.0 ‘Eligibility Criteria” for detailed information on all eligibility criteria. 
F 
Refer to section 7.3 for eligibility criteria for the respiratory sampling for screening and pre-
randomisation. 
G 
Respiratory samples (three sputums (expectorated or induced) or one BAL) to be collected at least 14 
days prior to completing physician directed intensive therapy and respiratory sample culture results must 
be available for randomisation. 
H 
To determine MABS clearance, three sputum samples or one BAL sample are required to be collected 
in Week 4 (±3 days). 
I 
Participants unable to produce a sputum sample (expectorated or induced) to be marked as unproductive 
on the CRF. 
J 
Participants who have produced sputum samples during Weeks 12, 22, and 32 are requested to provide 
three additional sputum samples collected at least one week apart nearer to the end of Weeks 46. For 
participants who were unproductive (intermittent or continual) during Weeks 12, 22, 32 and 46, a BAL 
sample is to be collected during Week 50. 
K 
Adult height is to be recorded once (preferably at the screening visit). Paediatric height must be 
measured at least every six weeks. 
L 
Refer to section 7.2 for eligibility criteria for the screening visit chest CT 
M 
Week 6 chest CT scan is optional and requires participant to consent to FORMaT Sub-Study C3: 
Imaging.  The site must have approval to conduct this additional scan, be certified to perform the scan 
using the scanner specific protocol and the participant must provide additional consent.   
N 
Chest CT scan at early withdrawal visit will only be requested if clinically indicated.  
O 
Only required in female participants of childbearing potential. A serum pregnancy test is required at 
screening and final study visit. A urine or serum pregnancy test is acceptable at all other times. 
P 
Screening audiology and screening vestibular assessment can be performed if a participant has 
commenced consolidation therapy but must be performed within three (3) days of first receiving 
treatment. 
Q 
QT interval at Screening is to be corrected using the Fridericia method. Any subsequent abnormal QTc 
intervals are to be confirmed using the Fridericia method. 
R 
Six-minute walk test to be performed in participants ≥18 years of age only. 
S 
Plasma levels post inhaled amikacin are to be collected 90 minutes post dose (range 60 to 120 minutes). 
Please record inhaled amikacin start and stop times.  
T 
The EQ-5D-5L is to be administered to participants ≥18 years of age whereas the EQ-5D-5Y is to be 
administered to participants 8 to 17 years of age. The EQ-5D-Y Proxy is to be administered to 
parents/carers of participants 4 to 7 years of age. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
24 
U 
The SF-36 is to be administered to participants ≥16 years of age at time of Screening. For participants 
aged <16 years at Screening, the PedsQLTM is to be used for entire duration of trial. 
V 
The PedsQL™ is only to be assessed in participants <16 years of age at time of Screening. If both the 
PedsQL™ and the CFQ-R are administered where possible, the PedsQL™ should be administered prior 
to the CFQ-R. 
W 
The CFQ-R is only to be completed in participants with CF. The age appropriate CFQ-R assessment 
should be selected; CFQ-R adult/teen (≥14 years of age), CFQ-R child (6 to 13 years of age) and CFQ-
R parent (parent/carer of participant 6 to 13 years of age). 
X 
The Child Health Utility is only to be assessed in participants 7 to 17 years of age. 
Y 
The SGRQ is only to be assessed in non-CF participants 18 years of age and older. 
Z 
MARS-5 is only to be completed in participants in the intervention cohort on outpatient based MABS-
PD treatment. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
25 
Table 6 Schedule of Assessments for Intervention Program Participants: Consolidation Only Therapy  
 
MABS-PD 
SCREENING 
 
PRE-
RANDOMISATION 
SCREENING 
CONSOLIDATION THERAPY ONLY 
FINAL 
STUDY 
VISIT 
EARLY 
WITHDRAW
AL VISIT 
ASSESSMENT 
(-42 days from 
start of physician 
directed therapy) 
(-14 days 
from 
completion 
of physician 
directed 
therapy) 
Day 0 
 
 
Day  
1 
Week 
4 
Week 
6 
Week 
12 
Week 
22 
Week 
32 
End of 
consolidation 
(Week 46) 
+4 weeks after 
end of 
consolidation 
(Week 50) 
+30 days 
 
 
±3 days 
+24 
hours 
±3 
days 
±3 
days 
±30 
days 
±30 
days 
±30 
days 
+5 days 
+14 days 
 
Informed consent for Appendix A2 A 
✓B 
 
 
 
 
 
 
 
 
 
 
 
Clinic visit C 
 
 
✓ 
✓ 
✓D 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Review eligibility 
✓E 
 
✓E 
 
 
 
 
 
 
 
 
 
Randomisation 
 
 
 
✓ 
 
 
 
 
 
 
 
 
Adverse event monitoring 
 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Respiratory 
sample 
Sputum (expectorated or 
induced) or; 
✓F 
✓  
x3 G 
 
 
✓ 
x3H 
 
✓I 
✓I 
✓I 
✓I 
✓J 
✓ 
Broncho-alveolar 
lavage 
(BAL) 
✓F 
✓ G 
 
 
✓H 
 
 
Height K and Weight 
 
 
✓ 
 
✓D 
✓ 
 
✓ 
 
 
✓ 
✓ 
Medication Review 
✓ 
 
✓ 
✓ 
✓D 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Spirometry 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
Chest CT 
✓L 
 
 
 
 
Optional 
M 
 
 
 
 
✓ 
✓N 
Pregnancy Test and Breastfeeding Status O 
 
 
✓ 
 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Audiogram 
 
 
✓P 
 
 
✓ 
 
✓ 
 
 
✓ 
✓ 
Vestibular Monitoring 
 
 
✓P 
 
 
✓ 
 
✓ 
 
 
✓ 
✓ 
ECG Q 
 
 
✓ 
 
 
✓ 
 
✓ 
 
 
✓ 
✓ 
6-minute walk test R 
 
 
✓ 
 
 
 
 
 
 
 
✓ 
✓ 
Blood collections: 
 
 
 
 
 
 
 
 
 
 
 
 
1. Chemistry and Renal Function 
 
 
✓ 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
2. Liver Function Tests 
 
 
✓ 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
3. Full Blood Count 
 
 
✓ 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Amikacin 
Monitoring 
Post dose levels S 
 
 
 
 
✓ 
Arm B 
only 
 
 
 
 
 
 
 
Physical examination 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
26 
 
MABS-PD 
SCREENING 
 
PRE-
RANDOMISATION 
SCREENING 
CONSOLIDATION THERAPY ONLY 
FINAL 
STUDY 
VISIT 
EARLY 
WITHDRAW
AL VISIT 
ASSESSMENT 
(-42 days from 
start of physician 
directed therapy) 
(-14 days 
from 
completion 
of physician 
directed 
therapy) 
Day 0 
 
 
Day  
1 
Week 
4 
Week 
6 
Week 
12 
Week 
22 
Week 
32 
End of 
consolidation 
(Week 46) 
+4 weeks after 
end of 
consolidation 
(Week 50) 
+30 days 
 
 
±3 days 
+24 
hours 
±3 
days 
±3 
days 
±30 
days 
±30 
days 
±30 
days 
+5 days 
+14 days 
 
Health-related 
quality 
of 
life 
questionnaires: 
 
 
 
 
 
 
 
 
 
 
 
✓ 
4. EQ-5D-5L or -Y T 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
5. SF-36  U 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
6. PedsQL™ V 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
7. CFQ-R W 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
8. Child Health Utility 9D X 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
9. SGRQ Y 
 
 
✓ 
 
 
✓ 
 
 
 
 
✓ 
✓ 
Costs Questionnaire 
 
 
✓ 
 
 
✓ 
 
✓ 
 
 
✓ 
✓ 
Medication Adherence Questionnaire Z 
 
 
 
 
 
✓ 
 
✓ 
 
✓ 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
27 
 STATISTICAL ANALYSIS AND SIMULATIONS FOR APPENDIX A2 
 RANDOMISATION 
There will be one randomisation (R-Con) in the intervention program Appendix A2, dictating the treatment the 
participant will receive.  Randomisation-Short Intensive and Randomisation-Prolonged Intensive will not apply to 
Appendix A2 participants.  The R-Con randomisation will allocate participants to the consolidation therapy arms.  
Randomisation will be conducted suing the method of minimisation described in Appendix F: General Statistical 
Principles.  The consolidation phase power simulations and statistical analysis are also detailed in Appendix F: 
General Statistical Principles and the Statistical Analysis Plan (SAP). 
 
 APPLICABLE DISCOVERY STUDIES AND REGISTRY LINKAGE FOR 
APPENDIX A2 
Appendix A2 participants may be eligible to enrol in the following FORMaT Sub-Studies and Integrated Studies: 
1. Appendix C Discovery 
i. 
C1: Pharmacokinetics 
i. C1.2 Microsampling and non-blood matrix validation for amikacin therapeutic drug 
monitoring (TDM) 
ii. C1.3 Pharmacokinetics of MABS-PD therapies 
iii. C1.4 Pharmacokinetics of CFTR modulator therapy in persons with cystic fibrosis on MABS 
therapy 
ii. 
C2: Immune factors and biomarkers 
i. C2.1 Macrophage function 
ii. C2.2 Mitochondrial stress 
iii. C2.3 T-cell function  
iv. C2.4 Gene expression  
v. C2.5 Serology 
iii. 
C3: Imaging  
2. Appendix D Registry Linkage 
i. 
D1: Australian cystic fibrosis data registry 
3. Appendix E Health Economics 
i. 
E1: Cost effectiveness and Resource utilisation 
 
Please see the relevant sections of the applicable appendix for further information, including additional eligibility 
criteria. 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix A2 
Version 1.1 Date  20 February 2024 
28 
  REFERENCES 
1. 
Haworth CS, Banks J, Capstick T, Fisher AJ, Gorsuch T, Laurenson IF, et al. British Thoracic Society 
guidelines for the management of non-tuberculous mycobacterial pulmonary disease (NTM-PD). Thorax. 
2017;72(Suppl 2). 
2. 
Harrison MJ, McCarthy M, Fleming C, Hickey C, Shortt C, Eustace JA, et al. Inhaled versus nebulised 
tobramycin: A real world comparison in adult cystic fibrosis (CF). Journal of Cystic Fibrosis. 
2014;13(6):692-8. 
3. 
Nasr SZ, Chou W, Villa KF, Chang E, Broder MS. Adherence to dornase alfa treatment among commercially 
insured patients with cystic fibrosis. Journal of Medical Economics. 2013;16(6):801-8. 
4. 
Bakker EM, Volpi S, Salonini E, van Der Wiel-Kooij EC, Sintnicolaas CJJCM, Hop WCJ, et al. Improved 
treatment response to dornase alfa in cystic fibrosis patients using controlled inhalation. European 
Respiratory Journal. 2011;38(6):1328-35. 
5. 
Food US, Drug A. Guideline for the study and evaluation of gender differences in the clinical evaluation of 
drugs; notice. Fed Regist. 1993;58(139):39406-16. 
6. 
Laboratories ATSCoPSfCPF. ATS statement: guidelines for the six-minute walk test. Am J Respir Crit Care 
Med. 2002;166(1):111-7. 
7. 
Kwan YH, Weng SD, Loh DHF, Phang JK, Oo LJY, Blalock DV, et al. Measurement Properties of Existing 
Patient-Reported Outcome Measures on Medication Adherence: Systematic Review. J Med Internet Res. 
2020;22(10):e19179. 
8. 
Chan AHY, Horne R, Hankins M, Chisari C. The Medication Adherence Report Scale: A measurement tool 
for eliciting patients' reports of nonadherence. Br J Clin Pharmacol. 2020;86(7):1281-8. 
9. 
Lam WY, Fresco P. Medication Adherence Measures: An Overview. Biomed Res Int. 2015;2015:217047. 
10. 
Vrijens B, Urquhart J. Methods for measuring, enhancing, and accounting for medication adherence in 
clinical trials. Clin Pharmacol Ther. 2014;95(6):617-26. 
11. 
Farmer KC. Methods for measuring and monitoring medication regimen adherence in clinical trials and 
clinical practice. Clin Ther. 1999;21(6):1074-90; discussion 3. 
12. 
Al-Hassany L, Kloosterboer SM, Dierckx B, Koch BC. Assessing methods of measuring medication 
adherence in chronically ill children-a narrative review. Patient Prefer Adherence. 2019;13:1175-89. 
 
 
 
 
 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
i 
 
APPENDIX B - OBSERVATIONAL COHORT 
Appendix B – Observational Cohort 
Version 1.2 
 
Appendix Date 
20 February 2024 
Protocol Number  
FORMaT001 
Funding 
 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
EudraCT Number 
2020-000050-10 
EU-CT Number 
2023-506575-99-00-EU CT 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
ii 
TABLE OF CONTENTS 
3.1 
INCLUSION CRITERIA ................................................................................................................................. 1 
3.2 
EXCLUSION CRITERIA ................................................................................................................................ 1 
4.1 
INFORMED CONSENT.................................................................................................................................. 2 
4.2 
OBSERVATIONAL COHORT PROCEDURES .................................................................................................. 2 
4.2.1 Respiratory sampling ............................................................................................................................. 2 
4.2.2 MABS-PD Status .................................................................................................................................... 2 
4.2.3 Six minute walk test ............................................................................................................................... 2 
4.2.4 Health Related Quality of Life (HRQoL) and Utility Measures ............................................................ 3 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
iii 
TABLE OF TABLES 
Table 1 Special Considerations for Schedule of Assessments .................................................................................. 5 
Table 2 Schedule of Assessments for Observational Cohort ..................................................................................... 6 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
iv 
ABBREVIATIONS  
 
AE 
 
 
Adverse Event  
ATS 
 
 
American Thoracic Society 
BAL 
 
 
Bronchoalveolar Lavage 
CF 
 
 
Cystic Fibrosis 
CFQ-R  
 
Cystic Fibrosis Questionnaire-Revised 
CHU9D 
 
Child Health Utility 9D 
CRF 
 
 
Case Report Form 
CT 
 
 
Computed Tomography 
CTCAE 
 
Common Terminology Criteria for Adverse Events 
FEV1  
 
Forced Expiratory Volume in one second 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
HRQoL 
 
Health Related Quality of Life 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
PedsQL™ 
 
Pediatric Quality of Life Inventory 
QALY  
 
Quality-Life Adjusted Years 
QoL 
 
 
Quality of Life 
SAEs  
 
Serious Adverse Events 
SF-36  
 
Short form-36 
SOP 
 
 
Standard Operating Procedure 
SGRQ  
 
St George Respiratory Questionnaire 
VAS 
 
 
Visual Analogue Scale 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
1 
1 
INTRODUCTION 
Appendix B describes the schedule of assessments for participants enrolled in the Observational Cohort arm of 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment (FORMaT) study. 
 
2 
OBJECTIVES 
1. Describe the following outcomes for participants in the Observational Cohort: 
o Microbiological clearance of Mycobacterium abscessus (MABS), 
o Clinical markers including health related quality of life (HRQoL) and adverse effects on health. 
o Host immune factors and biomarkers. 
2. Describe any changes associated with the development of MABS pulmonary disease (MABS-PD) in the 
following: 
o Changes in airway microbiology, 
o Change in clinical markers including HRQoL, FEV1 z-score and CT scores, 
o Change in host immune factors and biomarkers. 
3. Characterise the genomics of human MABS strains and antibiotic resistance genes in participants enrolled in the 
Observational Cohort. 
The Common Terminology Criteria for Adverse Events (CTCAE) Version 5.0 will be applied for the coding and 
grading of all adverse events/serious adverse events (AE/SAEs) that occur during the FORMaT trial. 
 
3 
ELIGIBILITY CRITERIA 
3.1 
INCLUSION CRITERIA 
To be eligible to participate in the observational cohort the following criteria must be met: 
1. Male and female participants of any age with at least one positive respiratory culture for MABS in the 12 months 
prior to enrolment. 
2. Informed consent signed by participant or their parent/legal guardian if participant is under 18 years of age. 
3. Ability to comply with study visits and study procedures as judged by the site investigator. 
 
3.2 
EXCLUSION CRITERIA 
Potential participants will be ineligible to participate in the observational cohort if any of the following criterion are 
met: 
• 
Receiving active treatment for MABS within the previous 12 months (this includes drugs prescribed for the 
treatment of other mycobacteria and/or other indications that may have activity against MABS, as specified 
in FORMaT Prohibited Drug List SOP, except for participants taking azithromycin as part of routine 
treatment for cystic fibrosis (CF) or chronic infection-related pulmonary disease. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
2 
Participants already enrolled in the observational cohort who go on to meet MABS-PD criteria and require treatment 
for MABS-PD may transition to the Intervention Program if they meet eligibility criteria. However, if they are unable 
to be enrolled into the Intervention Program but do commence any physician led MABS-PD treatment, they are no 
longer eligible to continue participating in the observational cohort.  
4 
TRIAL CONDUCT 
4.1 
INFORMED CONSENT 
In addition to providing consent to the FORMaT Master Protocol, participants enrolling in the Observational Cohort 
are required to sign and date an additional Observational Cohort consent form.  If the participant is <18 years of age, 
then the parent/guardian will provide consent on behalf of the participant. 
4.2 
OBSERVATIONAL COHORT PROCEDURES 
In addition to the core trial procedures listed in the FORMaT Master Protocol (Master Protocol Section 5.5 Core 
Trial Procedures), the Observational Cohort participants are required to undergo further testing detailed below and 
in Table 2. 
4.2.1 
RESPIRATORY SAMPLING 
Collection of respiratory sample(s) for the identification of MABS at screening may not be required if recent 
sample(s) have been provided by the participant within the 12 months prior to screening and has been stored and is 
available as per the local laboratory guidelines (standard of care) to identify and diagnose MABS infection.  If the 
screening sample has been stored, then the sample will be analysed retrospectively once consent to participate in the 
FORMaT trial is given. 
The minimum respiratory sampling collection timepoints have been outlined in Table 2; however, monthly sputum 
sample collections are recommended for participants who continue to be productive.  For participants who become 
non-productive between screening and Week 12, one Bronchoalveolar Lavage (BAL) between Week 10 to Week 12 
can be collected in the absence of sputum samples. 
4.2.2 
MABS-PD STATUS 
Participants enrolled in the Observational Cohort are required to have their MABS-PD status reviewed in accordance 
with the American Thoracic Society (ATS) criteria for MABS-PD diagnosis (Master Protocol Section 4.2.1).  The 
MABS-PD status of Observational Cohort participants is required to be reviewed as per Table 2 and, if applicable 
the early termination visit by the treating physician.  This information is to be documented in the MABS-PD status 
question contained in the relevant Visit Case Report Forms (CRFs).  If an observation participant develops MABS-
PD they become eligible for the intervention program.  If felt appropriate by the site investigator and informed 
consent is obtained, the participant can move from the Observational Cohort into the intervention program. 
4.2.3 
SIX MINUTE WALK TEST 
A 6-minute walk test (6MWT) will be performed in adult participants only, at the time points outlined in Table 2, if 
the testing is available at the trial site.  The 6MWT will be performed according to the protocol in the ATS Statement: 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
3 
Guidelines for the Six Minute Walk Test (1) and/or local standard procedures.  Results of the 6MWT will be recorded 
in the relevant eCRF in the FORMaT database by the end of the Final Outcome visit. 
4.2.4 
HEALTH RELATED QUALITY OF LIFE (HRQOL) AND UTILITY MEASURES 
HRQoL will be assessed in all participants (where possible) according to the schedule of assessments in the relevant 
appendix.  The questionnaires are required to be completed prior to any clinical assessment and are dependent on the 
participant’s age and whether they have CF.  The age-appropriate HRQoL questionnaire issued to the participant at 
the start of the study will continue to be used throughout the study even if the participant progresses to a different 
age range. HRQoL questionnaires will be made available to study sites.  All questionnaires will be made available in 
English or if available the local language version will be sourced.  Questionnaires can be completed by the participant 
and/or their parent/carer via an online link to the questionnaire(s) on the trial database or completed using a paper-
based questionnaire.  Responses from paper-based questionnaires are to be entered into the trial database by trial site 
staff. 
 Cystic fibrosis Questionnaire-revised (CFQ-R) 
The CFQ-R has been developed specifically for use in people with CF.  This questionnaire measures the impact of 
CF on overall health, daily life, perceived well-being and symptoms.  Age-appropriate questionnaires have been 
developed; CFQ-R teen/adult for adolescents and adults 14 years of age and older, the CFQ-R child and the CFQ-R 
parent are to be completed by the child (6-13 years of age) and the parent/carer respectively of children with CF. 
In children ≤16 years of age, the CFQ-R should be administered after the PedsQL™. 
 EQ-5D-5L 
The EQ-5D-5L questionnaire is a standardised measure of health status in adults 18 years of age and older.  This 
questionnaire can be applied as a generic measure of health for clinical and economic appraisal, including the 
calculation of quality-life adjusted years (QALYs).  The EQ-5D-5L measures five dimensions: 
• 
Mobility; 
• 
Self-care; 
• 
Usual activities; 
• 
Pain/discomfort; 
• Anxiety/depression. 
Each dimension has five possible answers: no problems, slight problems, moderate problems, severe problems, and 
extreme problems.  The respondent is asked to indicate his/her health state by selecting the most appropriate 
statement. 
 EQ-5D-Y 
The EQ-5D-Y is the child friendly version of the EQ-5D-5L questionnaire.  The EQ-5D-Y has been developed for 
use in children 8 to 17 years of age.  The dimensions and the visual analogue scale (VAS) measured are the same as 
the EQ-5D-5L questionnaire, but with child friendly wording.  For children 4-7 years of age the proxy 1 version of 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
4 
the EQ-5D-Y can be utilised allowing the respondent (parent/carer) to evaluate participants quality of life (QoL) 
from respondents’ own view. 
 St George Respiratory Questionnaire (SGRQ) 
The SGRQ is to be completed by all non-CF participants 18 years of age and older.  The SGRQ is a supervised self-
administered 50-item questionnaire measuring health status across three domains: symptoms, activity and impacts 
(psycho-social) in people with airway obstruction. 
 Short Form 36 (SF-36) 
The SF-36 health survey is a self-reported questionnaire applicable in all participants 16 years and older.  Covering 
eight health concepts the SF-36 health survey is a generic outcome measure designed to examine a person’s perceived 
health status. 
 PedsQLTM 
The PedsQL™ child health questionnaire is a non-preference-based measure to assess HRQoL for children and 
adolescents from 2 years up to 16 years of age.  Children less than 16 years of age at screening will continue to use 
the PedsQLTM up until the end of the trial, rather than change to using the SF-36 if they turn 16 years of age during 
the study. 
Developmentally appropriate child self-report questionnaires are available (ages 5-7, 8-12, 13-18) together with 
parent/carer proxy-reports (ages 2-4, 5-7, 8-12 and 13-18).  If feasible, the PedsQL™ should be completed before 
the respondents complete any other health data forms and before they see their physician or healthcare provider. 
Parents/carers, children (aged 8-12) and young people (aged >12 years) may self-administer the PedsQL™ after the 
FORMaT site researcher has provided instructions.  If it is determined by the FORMaT site researcher that the child, 
young person or parent/carer is unable to self-administer the PedsQL™ the questionnaire should be administered, 
word for word by the FORMaT site researcher.  If the child has difficulty understanding the age appropriate 
PedsQL™ the preceding age questionnaire may be used.  The parent and the child must complete the questionnaires 
independently of each other and in accordance with the PedsQL™ administration guidelines (available via hyperlink 
or in relevant section of the FORMaT Trial Site Manual of Operating Procedures (MoOP)). 
 Child Health Utility 9D (CHU9D) 
The CHU9D is a generic preference-based measure of paediatric HRQoL for use in children 7 to 17 years of age.  
The use of a descriptive system and a set of preference weights allows for the calculation of quality adjusted life 
years (QALYs) for use in economic evaluation 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
5 
5 
SCHEDULE OF ASSESSMENTS 
Table 1 lists the special considerations that are applicable to Table 2 Schedule of Assessment for Observational 
Cohort. Table 1 must be used in conjunction with Table 2 Schedule of Assessments for Observational Cohort. 
Table 1 Special Considerations for Schedule of Assessments 
Symbol Definition 
A 
Participant reconsent is required with IRB/ IED/HREC approved changes to the protocol that affect the 
participants rights and/or safety and/or if a child turns 18 years old during the trial and must reconsent 
as an adult participant. 
B 
Visits may be conducted while an inpatient or at home if participant is receiving home-based care. 
C 
To be eligible to enrol in the Observational Cohort, the participant is required to have at least one (1) 
MABS-positive respiratory sample. 
D 
Observational Cohort participants are requested to provide three sputum samples at Weeks 6 and 12. If 
the participant is unable to provide sputum samples, one BAL is to be collected at Week 12 for 
microbiology assessment. 
E 
Participants unable to produce a sputum sample (expectorated or induced) to be marked as unproductive 
on the CRF. 
F 
 Participants who have produced sputum samples during Weeks 18, 28, and 38 are requested to provide 
three additional sputum samples collected at least one week apart nearer to the end of Week 56. For 
participants who were unproductive (intermittent or continual) during Weeks 18, 28, and 38 a BAL 
sample is to be collected during Week 56. 
G 
Adult height is to be recorded once (preferably at the screening visit). Paediatric height must be 
measured at least every six weeks. 
H 
Week 12 chest CT scan is optional and requires participant to consent to FORMaT Appendix C3: 
Imaging. The site must have approval to conduct this additional scan, be certified to perform the scan 
using the scanner specific protocol, and the participant must provide additional consent. Chest CT scan 
may be done as part of standard of care for clinical purposes, results of these chest CT scans will be 
collected for participants consenting to Master Protocol.  
I 
Chest CT scan at early withdrawal visit will only be requested if clinically indicated.  
J 
Six-minute walk test to be performed in participants ≥18 years of age only. 
K 
The EQ-5D-5L is to be administered to participants ≥18 years of age whereas the EQ-5D-5Y is to be 
administered to participants 8 to 17 years of age. The EQ-5D-Y Proxy is to be administered to 
parents/carers of participants 4 to 7 years of age. 
L 
The SF-36 is to be administered to participants ≥16 years of age at time of Screening. For participants 
aged <16 years at Screening, the PedsQLTM is to be used for entire duration of trial. 
M 
The PedsQL™ is only to be assessed in participants <16 years of age at time of Screening. If both the 
PedsQL™ and the CFQ-R are administered where possible, the PedsQL™ should be administered prior 
to the CFQ-R. 
N 
The CFQ-R is only to be completed in participants with CF. The age appropriate CFQ-R assessment 
should be selected; CFQ-R adult/teen (≥14 years of age), CFQ-R child (6 to 13 years of age) and CFQ-
R parent (parent/carer of participant 6 to 13 years of age). 
O 
The Child Health Utility is only to be assessed in participants 7 to 17 years of age. 
P 
The SGRQ is only to be assessed in non-CF participants 18 years of age and older. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
6 
Table 2 describes the schedule of assessments for the Observational Cohort as well as the acceptable study visit windows. 
Table 2 Schedule of Assessments for Observational Cohort 
ASSESSMENT 
SCREENING 
VISIT 
INTERIM VISITS 
FINAL 
OUTCOME 
VISIT 
EARLY 
WITHDRAWAL 
VISIT 
Day 0 
-42 days 
Week 6 
±14 days 
Week 12 
±14 days 
Week 18 
±30 days 
Week 28 
±30 days 
Week 38 
±30 days 
Week 56 
±14 days 
+30 days 
Informed Consent for Appendix B A 
✓ 
 
 
 
 
 
 
 
Clinic Visit B 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Review Eligibility 
✓ 
 
 
 
 
 
 
 
Adverse Event Monitoring 
 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Respiratory 
Sample 
Sputum (expectorated or induced) or; 
✓C 
✓x3D 
✓x3D 
✓E 
✓E 
✓E 
✓F 
✓ 
Broncho-alveolar lavage (BAL) 
✓C 
 
✓D 
 
 
 
✓F 
Height G and Weight 
✓ 
✓ 
✓ 
 
✓ 
 
✓ 
✓ 
MABS-PD Status 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
Medication Review 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
✓ 
Spirometry 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
Chest CT 
✓ 
 
OptionalH 
 
 
 
✓ 
✓I 
Physical Examination 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
6-Minute Walk Test J 
✓ 
 
✓ 
 
 
 
✓ 
✓ 
Health-related Quality of Life Questionnaires: 
 
1. EQ-5D-5L or -Y K 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
2. SF-36 L 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
3. PedsQL™ M 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
4. CFQ-R N 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
5. Child Health Utility 9D O 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
6. SGRQ P 
✓ 
✓ 
✓ 
 
 
 
✓ 
✓ 
Costs Questionnaire 
✓ 
✓ 
✓ 
 
✓ 
 
✓ 
✓ 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
7 
6 
SITE REIMBURSEMENT 
For participants enrolled in Appendix B, trial sites will be reimbursed on a per participant basis at each of the 
following time points; 
1. Screening; 
2. End of week 6; 
3. Final study visit. 
Sites will be reimbursed according to their contract.  Payments will be paid for each time point once the data is 
entered into the trial database and all queries finalised.  Invoices should be prepared at a minimum of every 6 months. 
 
7 
STATISTICIAL ANALYSIS  
The objectives will be addressed by a descriptive analysis of changes in clinical status, immune status, biomarkers, 
MABS genomics and antimicrobial resistance genes between Day 0 and final outcome.  The following data will be 
used: 
• 
Adverse events occurring between Day 0 and final outcome, 
• 
Microbiological clearance of MABS between Day 0 and final outcome, 
• 
Airway microbiology between Day 0 and final outcome 
• 
Change in HRQoL between Day 0 and final outcome, 
• 
Change in forced expiratory volume in one second (FEV1) z-score, between Day 0 and final outcome, 
• 
Change in chest computed tomography (CT) scores, between Day 0 and final outcome, 
• 
Immune factors and biomarkers (refer to the relevant substudy appendix for further detail on statistical 
analyses), 
• 
Genomics of human MABS strains and antibiotic resistance genes.  
 
8 
APPLICABLE DISCOVERY STUDIES AND REGISTRY LINKAGE 
Observational Cohort participants may be eligible to enrol in the following FORMaT Sub-Studies and Integrated 
Studies: 
1. Appendix C Discovery 
i. 
C2: Immune factors and biomarkers 
i. C2.1 Macrophage function 
ii. C2.2 Mitochondrial stress 
iii. C2.3 T-cell function  
iv. C2.4 Gene expression  
v. C2.5 Serology 
ii. 
C3: Imaging 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
8 
2. Appendix D Registry Linkage 
i. 
D1: Australian cystic fibrosis data registry 
3. Appendix E: Health Economics  
i. 
E1: Cost effectiveness and Resource utilisation 
Please see the relevant sections of the applicable appendix for further information, including additional eligibility 
criteria. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment. Appendix B  
Version 1.2 Date 20 February 2024 
9 
9 
REFERENCES 
 
1. 
Laboratories ATSCoPSfCPF. ATS statement: guidelines for the six-minute walk test. Am J Respir Crit Care 
Med. 2002;166(1):111-7. 
2. 
Zellner A. An Efficient Method of Estimating Seemingly Unrelated Regressions and Tests for Aggregation 
Bias. Journal of the American Statistical Association. 1962;57(298):348-68. 
3. 
Glick HA, Doshi JA, Sonnad SS, Polsky D. Economic Evaluation in Clinical Trials: Oxford University Press 
Catalogue; 2007. 
4. 
Hoch JS, Briggs AH, Willan AR. Something old, something new, something borrowed, something blue: a 
framework for the marriage of health econometrics and cost‐effectiveness analysis. Health Economics. 
2002;11(5):415-30. 
5. 
Fenwick E, Byford S. A guide to cost-effectiveness acceptability curves. Br J Psychiatry. 2005;187:106-8. 
6. 
Little RJ, Rubin DB. Statistical Analysis with Missing Data. 2nd edition ed: Wily-Interscience; 2002. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
i 
 
APPENDIX C1 – DISCOVERY 
Pharmacokinetics 
Appendix C1 – Discovery 
Version 1.0 
Appendix Date 
29 March 2023 
Protocol Number  
FORMaT001 
Funding 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS 
TABLE OF CONTENTS ...................................................................................................................................... 2 
ABBREVIATIONS ................................................................................................................................................ 4 
APPENDIX C: DISCOVERY .............................................................................................................................. 1 
APPENDIX C1: PHARMACOKINETICS ......................................................................................................... 2 
 
INTRODUCTION ......................................................................................................................................... 2 
 
SUB-STUDY C1.1: STEADY STATE PHARMACOKINETICS OF AMIKACIN ................................ 3 
 
PRIMARY OBJECTIVE ............................................................................................................................... 3 
 
INTRODUCTION ........................................................................................................................................ 3 
 
ELIGIBILITY CRITERIA ............................................................................................................................. 3 
 
INFORMED CONSENT................................................................................................................................ 3 
 
AMIKACIN TDM PROCEDURES ................................................................................................................ 3 
 
PHARMACOKINETIC ANALYSIS ................................................................................................................ 4 
 
MODEL DIAGNOSTICS .............................................................................................................................. 4 
 
SUB-STUDY C1.2: MICRO SAMPLING AND NON-BLOOD MATRIX VALIDATION FOR 
AMIKACIN THERAPEUTIC DRUG MONITORING .................................................................................... 6 
 
PRIMARY OBJECTIVE ............................................................................................................................... 6 
 
INTRODUCTION ........................................................................................................................................ 6 
 
ELIGIBILITY CRITERIA ............................................................................................................................. 6 
 
INFORMED CONSENT................................................................................................................................ 6 
 
MICRO SAMPLING PROCEDURES ............................................................................................................. 7 
 Choice of Micro Sampling Device ....................................................................................................... 7 
 
OPPORTUNISTIC BAL SAMPLING ............................................................................................................. 8 
 
STATISTICAL ANALYSIS PLAN ................................................................................................................. 8 
 
SUB-STUDY C1.3: PHARMACOKINETICS OF MABS-PD THERAPIES .......................................... 9 
 
PRIMARY OBJECTIVE ............................................................................................................................... 9 
 
INTRODUCTION ........................................................................................................................................ 9 
 
ELIGIBILITY CRITERIA ............................................................................................................................. 9 
 
INFORMED CONSENT................................................................................................................................ 9 
 
SUB-STUDY SPECIFIC PROCEDURES ........................................................................................................ 9 
 
STATISTICAL ANALYSIS ......................................................................................................................... 10 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
iii 
 
SUB-STUDY C1.4: PHARMACOKINETICS OF CYSTIC FIBROSIS TRANSMEMBRANE 
CONDUCTANCE REGULATOR (CFTR) MODULATORS IN PERSONS WITH CYSTIC FIBROSIS (CF) 
ON MYCOBACTERIUM ABSCESSUS THERAPY ...................................................................................... 12 
 
PRIMARY OBJECTIVE ............................................................................................................................. 12 
 
INTRODUCTION ...................................................................................................................................... 12 
 
ELIGIBILITY CRITERIA ........................................................................................................................... 12 
 
INFORMED CONSENT.............................................................................................................................. 12 
 
SUB-STUDY SPECIFIC PROCEDURES ...................................................................................................... 12 
 
STATISTICAL ANALYSIS ......................................................................................................................... 13 
REFERENCES .................................................................................................................................................... 15 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
iv 
ABBREVIATIONS  
 
AUC 
 
 
Area Under the Curve 
BAL 
 
 
Bronchoalveolar Lavage 
CART  
 
Correlation and Regression Tree 
Cmax 
 
 
Maximum serum concentration 
CRF 
 
 
Case Report Form 
DBS 
 
 
Dried Blood Spot 
FDA 
 
 
Food and Drug Administration 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
FBC 
 
 
Full blood count 
IV 
 
 
Intravenous 
LLOQ   
 
Lower Limit of Quantification 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
MDR-TB 
 
Multi Drug Resistant-Tuberculosis 
MIC 
 
 
Minimum Inhibitory Concentration 
MRL 
 
 
Mycobacterial Reference Laboratory 
NTM  
 
Non-Tuberculous Mycobacteria 
PD 
 
 
Pharmacodynamics 
PK 
 
 
Pharmacokinetics 
pwCF  
 
Persons with cystic fibrosis 
REDCap 
 
Research Electronic Data Capture 
TB 
 
 
Tuberculosis 
TDM  
 
Therapeutic Drug Monitoring 
UQCCR 
 
University of Queensland Centre for Clinical Research 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
1 
APPENDIX C: DISCOVERY 
Appendix C: Discovery, consists of research studies/programs that may be added over time and that are 
aimed at gaining understanding through collaboration with the FORMaT trial but are not specific 
components of the trial.  Participation in each discovery study may require additional consent.  Consent 
requirements are detailed within each of the discovery sub-studies.  Discovery studies may be applicable to 
all participants or only to specific sites or groups of participants.  Each study will be described in the 
following format: 
• The named Investigator leads for the sub-study; 
• The primary and secondary objectives of the sub-study; 
• An introduction to the background of the sub-study; 
• Additional eligibility and consent requirements; 
• Sub-study specific trial procedures and schedule of assessments; 
• Analysis plan. 
 
Appendix C1: Pharmacokinetics. 
Appendix C2: Immune Factors and Biomarkers. 
Appendix C3: Imaging. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
2 
APPENDIX C1: PHARMACOKINETICS  
Investigator Leads 
Dr Andrew Burke and Professor Jason Roberts 
1 
INTRODUCTION 
Appendix C1, Pharmacokinetics, addresses a key research question posed by the FORMaT trial relating to the optimal 
use of drug therapies in Mycobacterium abscessus (MABS infection).  Answering this question has been hampered 
by the lack of pharmacokinetic (PK) studies in people with mycobacterial lung disease.  Nested within Appendix C1 
are four PK sub-studies: 
SUB-STUDY C1.1: Steady State Pharmacokinetics of Amikacin; 
SUB-STUDY C1.2: Micro Sampling and Non-Blood Matrix Validation for Amikacin Therapeutic Drug 
Monitoring; 
SUB-STUDY C1.3: Pharmacokinetics of Mycobacterium abscessus Pulmonary Disease (MABS-PD) 
Therapies; 
SUB-STUDY C1.4: Pharmacokinetics of CFTR Modulators in Persons with Cystic Fibrosis (pwCF) on 
MABS Therapy. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
3 
2 
SUB-STUDY C1.1: STEADY STATE PHARMACOKINETICS OF 
AMIKACIN 
2.1 
PRIMARY OBJECTIVE 
Determine the best practice therapeutic drug monitoring recommendations for use of intravenous amikacin to 
maximise antimicrobial effect and minimise toxicity in the treatment of MABS-PD. 
2.2 
INTRODUCTION 
The optimal use of amikacin in the treatment of MABS-PD is hampered by the lack of PK studies in all people with 
mycobacterial lung disease (1).  There are no current validated maximum serum concentration (Cmax) or area under 
the curve (AUC) targets for amikacin use in the management of non-tuberculous mycobacteria (NTM) disease, with 
or without concomitant Minimum Inhibitory Concentration (MIC) data.  The development of novel anti-
mycobacterial drug assays at the University of Queensland Centre for Clinical Research (UQCCR) and Pathology 
Queensland will allow accurate measurement of drug concentrations in plasma and other body fluids including 
bronchoalveolar lavage (BAL), sputum, and oral fluids.  These data can then be analysed to inform further 
understanding of the PK of amikacin in MABS-PD patients.  It will also allow for the rational design of future studies 
on TDM for amikacin which has a narrow therapeutic window.  The increased use of TDM has been suggested in 
the treatment of multidrug resistant tuberculosis (MDR-TB) as well as for complicated NTM infections.  A better 
understanding of the PK of amikacin will therefore allow optimisation of dosing to minimise toxicity while 
maximising the likelihood of cure. 
2.3 
ELIGIBILITY CRITERIA 
In addition to meeting the eligibility criteria described in the Master Protocol, participants are required to meet the 
following inclusion criteria: 
• 
Informed consent by participant or their parent/guardian.  
• 
Receiving intravenous amikacin as part of FORMaT Intervention Program, 
• 
Availability of patient demographics including weight and height, 
• 
Accurate recording of time of drug administration and infusion time. 
2.4 
INFORMED CONSENT  
Informed consent will be obtained to use information already collected as standard of care amikacin therapeutic drug 
monitoring and in accordance with the policies described in the FORMaT Master Protocol for the purposes of this 
sub-study C1.1. 
2.5 
AMIKACIN TDM PROCEDURES 
There is currently variation in practice surrounding amikacin dosing and TDM and this is likely to be reflected in the 
recruiting centres for the FORMaT trial.  Some patients will be receiving intermittent (second or third daily dosing) 
and others once daily dosing.  The current TDM strategies that can be used in the FORMaT trial include: 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
4 
1. Trough amikacin levels (independent of MIC) using nomogram for next dose (equivalent to Cmin/ trough), 
2. Cmax/MIC target, 
3. AUC target, 
4. Cmax/MIC and minimum serum concentration (Cmin/ trough) 
5. AUC/MIC target. 
6.  Cmax (peak) 
As TDM for amikacin is already standard of care and is incorporated into the FORMaT Appendix A1, all sampling 
events will be recorded in the FORMaT trial Research Electronic Data Capture (REDCap) database.  Investigators 
will be free to use the dosing and TDM method that is their usual practice, however it will be documented what 
approach is being used to allow comparison between different strategies. 
Participants will have blood drawn through a suitable venous access device and the sample will be processed at local 
laboratory as per usual practice for that trial site.  Results to be recorded include timing and dose of amikacin, and 
frequency of dosing.  Same day serum creatinine concentrations as well as admission weight and height will also be 
recorded. 
All amikacin levels accompanied by a serum creatinine concentration within 24 hours of sampling will be included 
in analysis.  Relevant demographic data e.g., weight and height, time that study drugs have been administered and 
method of TDM utilised by treating clinicians will be recorded in the case report form (CRF). 
2.6 
PHARMACOKINETIC ANALYSIS 
To describe amikacin concentrations, one and two-compartment models will be evaluated using the Nonparametric 
Adaptive Grid (NPAG) algorithm within the Pmetrics software package for R (Los Angeles, CA).  Elimination from 
the central compartment, and intercompartmental distribution into the peripheral compartment (two compartment 
model) will be modelled as first-order processes.  Discrimination between different models will use comparison of 
the -2 log likelihood (-2LL).  A p-value of <0.05 will be considered statistically significant. 
Age, sex, body weight, renal function descriptors and other clinical descriptors will be tested as covariates.  Covariate 
selection will be performed using a stepwise linear regression from R on all covariates and Bayesian posterior 
parameters.  Potential covariates will be separately entered into the model and statistically tested by use of the -2LL 
values.  If inclusion of the covariate results in a statistically significant improvement in the -2LL values (p<0.05) 
and/or improved the goodness-of-fit plots, then it will be retained in the final model. 
2.7 
MODEL DIAGNOSTICS 
Goodness-of-fit will be assessed by linear regression, with an observed-predicted plot, coefficients of determination, 
and log-likelihood values.  Predictive performance evaluation will be based on mean prediction error (bias) and the 
mean bias-adjusted squared prediction error (imprecision) of the population and individual prediction models.  The 
internal validity of the population pharmacokinetic model will be assessed by the bootstrap resampling method 
(n=1000) and normalised prediction distribution errors (NPDEs).  Using visual predictive check (VPC) method, 
parameters obtained from the bootstrap method will be plotted with the observed concentrations. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
5 
Once the pharmacokinetic model has been developed, amikacin exposure in enrolled patients will be simulated as 
area under the concentration-time curve (AUC) from 0-24 hours and peak concentration (Cmax) during a dosing 
interval.  The association of clinical cure versus amikacin exposure will be tested using a Mann-Whitney U-test.  A 
classification and regression tree (CART) analysis will be used to propose breakpoints (e.g., Cmax, Cmax/MIC, AUC, 
AUC/MIC) which quantify the exposures associated with maximal effectiveness and can be used to guide future 
TDM processes. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
6 
3 
SUB-STUDY C1.2: MICRO SAMPLING AND NON-BLOOD MATRIX 
VALIDATION FOR AMIKACIN THERAPEUTIC DRUG MONITORING  
3.1 
PRIMARY OBJECTIVE 
Compare less intrusive micro sampling strategies to the gold standard methods for amikacin TDM. 
3.2 
INTRODUCTION 
Patients are on treatment for MABS-PD for months and repeated blood sampling for TDM and PK analysis currently 
requires venepuncture and on-site centrifuge prior to transport offsite for testing.  If same day testing cannot be done, 
then the sample requires freezing.  These factors cause discomfort to the patient and impose logistical barriers to PK 
studies in clinical trials as well as limiting the availability of TDM and its ability to influence prescribing decisions 
through real time feedback to clinicians. 
Less intrusive sampling strategies have been proposed, however, it is unknown whether these strategies can 
accurately measure amikacin levels in a diverse range of body fluids.  Dried blood spot (DBS) and Volumetric 
Absorbent Micro sampling (VAMS) performed through finger prick testing may be a practical surrogate for 
traditional methods of obtaining plasma from venepuncture.  Other sampling technologies that will be trialled 
include: hemaPEN, safeClinitube, and Drummond plasma gel separator tubes. 
As NTM infection is situated in the lower respiratory tract, the concentration of drugs in the respiratory epithelial 
fluid is the PK endpoint of most relevance.  Sampling this compartment has traditionally required bronchoscopy with 
BAL.  As well as being an invasive procedure requiring sedation, lung inflammation and mucous impaction as found 
in CF may contribute to sampling and dilutional error. Suitable alternatives to be investigated include sputum and 
oral fluid to specimens obtained from BAL. Simpler and more reliable sampling methods testing oral fluid drug 
concentrations on salivette cotton swabs are already an established and well tolerated method for obtaining cortisol 
levels in clinical practice but further investigation into the utility of these samples in MABS-PD is required. 
3.3 
ELIGIBILITY CRITERIA 
Participants at nominated Australian FORMaT trial sites will be eligible to participate in sub-study C1.2. In addition, 
participant eligibility will be based on the following inclusion criteria: 
• 
Receiving intravenous amikacin as part of the FORMaT Intervention Program, 
• 
Availability of suitable intravenous access to facilitate sample collection, 
• 
Patients may be receiving other antibiotics concurrently, 
• 
Informed consent by participant or their parent/guardian. 
3.4 
INFORMED CONSENT 
Additional blood samples are required as part of the study procedures for sub-study C1.2, therefore additional consent 
will be obtained in accordance with the policies described in the FORMaT Master Protocol. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
7 
3.5 
MICRO SAMPLING PROCEDURES 
The day of testing will be determined by the site investigator and will be after the second dose of IV amikacin. 
1. Participants receiving IV amikacin will have samples taken using two micro sampling techniques (detailed 
below) in addition to whole blood collection through phlebotomy.  
2. In addition to the amikacin trough and peak levels collected for standard of care, samples will be collected at 
three time points.  Specific time points used will be dependent on amikacin frequency of administration and 
current amikacin assay validation.  Time points are determined by the lead investigators of the PK sub-studies. 
a. For adults, this will be three (3) time points at 0 hours (pre-dose level), and 1 hour and 1.5 hours 
after the start of amikacin infusion. 
b. Paediatric patients may have collections at these time points, or alternatively samples may be 
collected at two (2) opportunistic time points that align with their standard of care blood collection 
for amikacin TDM. 
3. At each time point the following blood samples will be collected from the participant: 1 venous whole blood 
sample (4ml EDTA tube) and a sample from two micro sampling devices. 
4. Micro sampling devices to be tested include: 
• 
1 finger prick sample using 1 Guthrie card for dried blood spot (DBS) ~ 50 µl of blood, OR; 
• 
1 finger prick sample using 2 Mitra® VAMS (a fraction of a bead of blood (10µL) x2), OR; 
• 
1 finger prick sample using haemaPEN (a fraction of a bead of blood (2.5µL) x4), OR; 
• 
safeClinitube (50 µL equivalent to a drop of blood), OR; 
• 
Drummond plasma gel separator tubes (50 µL equivalent to a drop of blood). 
5. Whole blood will be drawn through a suitable venous access device kept at ambient temperature and sent via 
courier with other microsamples to UQCCR for processing. 
6. Same day full blood count (FBC) and Chem-20 tests will be performed by a local laboratory as part of the 
standard of care for the trial site to monitor haematocrit, albumin and creatinine levels. 
7. A brief patient or care giver questionnaire will be undertaken to determine level of discomfort with micro 
sampling techniques compared to venepuncture as well as degree of technique acceptability to research nurse. 
8. Amikacin assay results and other relevant pathology results will be recorded as will time, dose, and frequency of 
dosing of IV amikacin in the PK sub-study REDCap database. 
3.5.1 
CHOICE OF MICRO SAMPLING DEVICE 
The choice of which micro sampling devices to be used will be determined by the lead Investigator for the PK sub-
studies.  To maintain consistency in technique and to ensure recruitment of sufficient numbers in each testing arm, 
centres will be allocated micro sampling devices to test. 
Once participants have consented to sub-study C1.2, the micro sampling devices allocated to that participant, along 
with the TDM strategy employed, will be recorded by the trial site in the participant’s record in the Pharmacokinetic 
Study REDCap database. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
8 
Once 25 separate paired amikacin samples have been collected further testing on each device will cease pending 
results of analysis.  15-20 subjects will be required per device depending on the TDM strategy used.  Once a study 
site has completed target enrolment in the allocated microsampling device, they will be allocated another device to 
trial.  Devices will be allocated in the order of: VAMS, DBS, haemaPEN, safeClinitube and Drummond plasma gel 
separator tubes. 
3.6 
OPPORTUNISTIC BAL SAMPLING 
For those participants having bronchoscopy as part of their normal clinical care, BAL samples will be collected for 
the measurement of drug concentrations.  Before sedation or anaesthesia, a patient will be asked to provide a saliva 
sample and to perform a salivette test.  Blood will also be taken as close as possible to the time of BAL and usually 
while under sedation/anaesthesia with the time bloods were taken documented.  If not performed previously, two (2) 
samples using microsampling techniques will be collected as outlined above at the time of blood collection.  The use 
of the salivette swab is to determine whether saliva can be used as a surrogate for BAL concentrations.  Paired whole 
blood and micro samples will be transported to UQCCR, with the saliva, BAL and paired blood samples being 
transported to Pathology Queensland, Herston, Brisbane, and drug assays will be performed for study drugs including 
amikacin.  Bronchoscopy will only be performed based on clinical need and not for the primary purpose of PK 
studies. 
3.7 
STATISTICAL ANALYSIS PLAN 
The aim of the microsampling study will be to assess the utility and validate different microsampling devices.  A 
formal PK analysis will not be performed on these specimens as this will have already been conducted on plasma 
samples.  Validation of microsampling techniques will be performed with reference to the Food and Drug 
Administration (FDA) document on bioanalysis.  Intra and inter-assay precision and accuracy will be determined for 
each technique as will the lower limit of quantification (LLOQ), linearity, matrix effects, recovery, selectivity, and 
stability of dried matrix.

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
9 
4 
SUB-STUDY C1.3: PHARMACOKINETICS OF MABS-PD THERAPIES  
4.1 
PRIMARY OBJECTIVE 
Assess steady state pharmacokinetics in participants enrolled in the Intervention Program for the treatment of MABS-
PD. 
4.2 
INTRODUCTION 
Population pharmacokinetic modelling of samples across one dosing interval can give more reliable PK information 
than traditional PK analysis.  This allows for a more efficient and streamlined study on a smaller number of patients.  
Given the increasing treatment burden for MABS-PD, a more comprehensive understanding of the PK of these drugs 
is imperative in the development of safer and more effective therapies for patients with MABS-PD.  There are no 
data currently available relating to pharmacokinetics of drugs commonly used in the management of MABS-PD. 
4.3 
ELIGIBILITY CRITERIA 
In addition to meeting the eligibility criteria described in the FORMaT Master Protocol, participants are required to 
meet the inclusion criteria outlined below to enrol in sub-study C1.3: 
1. Enrolled in the Intervention Program at an Australian site, 
2. Availability of suitable intravenous access to facilitate sample collection, 
3. Patients may be receiving other antibiotics concurrently, 
4. Availability of same day (preferably pre-dose) FBC and Chem-20 test results, 
5. Informed consent by participant or their parent/guardian. 
4.4 
 INFORMED CONSENT 
Additional blood samples are required as part of the study procedures for sub-study C1.3, therefore additional consent 
will be obtained in accordance with the policies described in the FORMaT Master Protocol. 
4.5 
SUB-STUDY SPECIFIC PROCEDURES 
1. The day of study will be determined by the site investigators and will be after 5 half-lives (at least 48hrs after 
the patient is established on the planned treatment dose) of the drug with the longest half-life (excluding 
azithromycin which has a prolonged half-life) to ensure testing is done at steady state.  There should have 
been no dose adjustments in the 48hrs prior to sampling. 
2. Participants will have up to 5 ml (adults) or 3ml (paediatric participants) whole blood drawn through a 
cannula at the following times on a single day of intensive therapy treatment: 
i. 
immediately pre-dose (trough level). 
ii. 
post- dosing: at approximately 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, and 8 
hours after the administration of the first infusion or oral administration of study medications on the 
day of sampling. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
10 
iii. 
Children who cannot have a separate IV line for frequent sampling may have opportunistic testing 
of blood concentrations based on samples that are already being collected as part of routine care (i.e., 
"opportunistic" bloods).  The timing of these samples may be chosen to align with expected trough 
and peak times of infused antibiotics as determined by the lead investigator at site in collaboration 
with the PK sub-study lead.  In most cases this will include a blood draw at the end of infusion. 
3. The time of each blood draw will be recorded in the PK sub-study REDCap database and on the study-
specific clinical trial pathology form.  If the participant is on multiple IV antibiotics, the commencement of 
the infusion of each IV antibiotic will occur at different times.  The timings for commencement and 
completion of each IV drug will be recorded and entered into the PK sub-study REDCap database.  
Administration of the IV drug with the longest half-life first (e.g., tigecycline before imipenem) is 
recommended so that timing aligns. 
4. On the same day, a salivette swab will be inserted into the mouth at each time point where blood is being 
collected.  The salivette swab will be removed after being chewed for 2 minutes and will be transported to 
Pathology Queensland, Herston Brisbane with all other samples on either the same or the next day. 
5. All samples must be processed within 1 hour of collection and stored frozen at -80°C until transfer to 
Pathology Queensland, Herston Brisbane. 
6. Opportunistic BAL sampling: For participants having bronchoscopy as part of their normal clinical care, 
BAL samples will be collected for the measurement of drug concentrations.  Before sedation/anaesthesia the 
patient will be asked to perform a salivette test.  Blood will be taken as close as possible to the time of BAL 
usually under sedation/anaesthesia with the time clearly documented.  These samples will be transported to 
Pathology Queensland, Herston Brisbane and drug assays will be performed for study drugs including 
amikacin.  The use of the salivette swab is to determine whether saliva can be used as a surrogate for BAL 
concentrations.  Bronchoscopy will only be performed based on clinical need and not for the primary purpose 
of PK studies. 
7. Opportunistic clofazimine sampling: For participants that have participated in the intensive day of 
sampling as per study procedures above, regular clofazimine drug concentration testing will be conducted to 
compare drug levels between steady state during initial intensive therapy and the drug levels at the end of 
consolidation therapy.  The 5 ml sample required to perform the analysis will be taken at the same time blood 
is collected during study visits for standard of care tests.  Samples will be collected by the local phlebotomy 
service at the hospital where study visits are conducted, and samples will be processed by the local laboratory.  
These bloods will be collected at weeks 6, 12, 18, 28, 38, and the end of consolidation (week 52 or 58, 
depending on randomisation allocation of immediate consolidation or delayed consolidation). 
4.6 
STATISTICAL ANALYSIS 
Enrolment targets for sub-study C1.3 are: 50 participants ≥18 years of age and 30 participants <18 years of age. 
Participants will be on different antibiotic therapies; therefore, this allocation of participants will allow for a minimum 
of 20 participants per antibiotic. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
11 
PK indices will include volumes of distribution, Cmax, AUC and clearance.  A pharmacokinetic model will also be 
developed using a population pharmacokinetic approach.  This technique will enable the effect of patient and 
treatment characteristics on altered pharmacokinetics (e.g., patient age, weight, renal function, hepatic function, 
interacting drugs) to be quantified.  This model can then be used to assess the adequacy of current dosing regimens 
and can also be used for dosing simulations to define optimised dosing regimens for these patients. 
PK analysis will be conducted with Pmetrics software package for R (version 1.4.1., Los Angeles, CA).  Non-linear 
mixed effect modelling approach will be used.  A stepwise analysis will be performed to first determine the structural 
base model by fitting the concentration-time data to one, two and three compartment models.  Testing of additive, 
proportional or a combination of additive and proportional models will be conducted to select the best fit statistical 
error model.  Following population PK analysis, Monte Carlo simulations will be performed using MICs for target 
NTM pathogens derived from clinical specimens tested at Pathology Queensland’s Mycobacterial Reference 
laboratory (MRL).  These PK/PD parameters can be used to estimate appropriate doses in clinical practice. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
12 
5 
SUB-STUDY C1.4: PHARMACOKINETICS OF CYSTIC FIBROSIS 
TRANSMEMBRANE CONDUCTANCE REGULATOR (CFTR) 
MODULATORS IN PERSONS WITH CYSTIC FIBROSIS (CF) ON 
MYCOBACTERIUM ABSCESSUS THERAPY 
5.1 
PRIMARY OBJECTIVE 
Assess steady state pharmacokinetics of CFTR modulators in participants enrolled in the Intervention Program for 
the treatment of MABS-PD and compare the plasma concentration area under the curve (AUC) of CFTR modulators 
before MABS-PD therapy and while on MABS-PD therapy. 
5.2 
INTRODUCTION 
There is marked interpatient PK variability in CFTR modulators in people with CF which may result in variations in 
therapeutic response and toxicity.  In addition, there are significant CFTR modulator drug-drug interactions (DDIs) 
mediated through P450 enzyme pathways that complicate choice of MABS regimen (2-4).  Given the unpredictability 
of DDIs in an individual, patient therapeutic drug monitoring has been proposed as a means of optimising treatment.  
In order to determine the feasibility and utility of this, the steady state PK of CFTR modulators needs to be determined 
across multiple time points.  This may then allow the development of limited (i.e., less frequent) sampling strategies, 
in order to assist with TDM in real-world ambulatory settings.  Validated CFTR modulator drug assays are being 
developed by Pathology Queensland, Australia to assist with this study and provide a national reference laboratory 
for CFTR modulator TDM. 
5.3 
ELIGIBILITY CRITERIA 
In addition to meeting the eligibility criteria described in the FORMaT Master Protocol, participants are required to 
meet the inclusion criteria outlined below to enrol in sub-study C1.4: 
1. Enrolled in the Intervention Program at an Australian site, 
2. Have cystic fibrosis and be on CFTR modulator therapy for at least 4 weeks prior to enrolling into the 
Intervention Program, 
3. Availability of suitable intravenous access to facilitate sample collection, 
4. Patients may be receiving other antibiotics concurrently, 
5. Informed consent by participant or their parent/guardian. 
5.4 
INFORMED CONSENT 
Additional blood samples are required as part of the study procedures for sub-study C1.4, therefore additional consent 
will be obtained in accordance with the policies described in the FORMaT Master Protocol. 
5.5 
SUB-STUDY SPECIFIC PROCEDURES 
1. Patients will have CFTR modulator PK plasma samples collected on two separate days. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
13 
2. The initial pre-MABS treatment sampling day will likely be the day before MABS treatment is commenced 
in order to define baseline steady state CFTR modulator PK prior to treatment. 
3. The second sampling day of this study will be determined by the site investigator and will be after 5 half-
lives (at least 48hrs after the patient is established on the planned treatment dose) of the antibiotic with the 
longest half-life (excluding azithromycin which has a prolonged half-life) to ensure testing is done at steady 
state.  There must be no dose adjustments in the 48hrs prior to sampling.  The CFTR modulator sub study 
(C1.4) second day of sampling can occur on the same day as the antibiotic PK study (C1.3) as this will allow 
CFTR modulator samples to be taken at the same time. 
4. Adult participants will have up to 5 ml whole blood drawn through a cannula at the following times on 2 
separate days: (1) the day prior to MABS treatment starting and (2) on a single day of intensive MABS 
therapy treatment: 
i. 
immediately pre CFTR modulator dose (trough level), 
ii. 
post dosing: at approximately 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours 
after the oral administration of CFTR modulator medications on the day of sampling. 
5. Paediatric participants will have 3mL whole blood drawn through a cannula at the following times on 2 
separate days: (1) the day prior to MABS treatment starting and (2) on a single day of intensive MABS 
therapy treatment: 
i. 
Immediately pre CFTR modulator dose (trough level), 
ii. 
Post dosing: at approximately 3 hours and 6 hours after the oral administration of CFTR modulator 
medications on the day of sampling. 
6. Additional blood samples for this study may be taken at the same time as other samples taken for routine 
care or other sub-studies (C1.2 and 1.3). 
7. The time of each blood draw will be recorded in the PK sub-study REDCap database and on the study-
specific clinical trial pathology form. 
8. All samples must be processed within 1 hour of collection and stored frozen at -80°C until transfer to 
Pathology Queensland, Herston Brisbane. 
5.6 
STATISTICAL ANALYSIS 
Enrolment targets for sub-study C1.4 are: 20 participants ≥18 years of age and 10 participants <18 years of age. 
PK indices will include volumes of distribution, Cmax, AUC and clearance.  A pharmacokinetic model will also be 
developed using a population pharmacokinetic approach.  This technique will enable the effect of patient and 
treatment characteristics on altered pharmacokinetics (e.g., patient age, weight, renal function, hepatic function, 
interacting drugs) to be quantified.  This model can then be used to assess the adequacy of current dosing regimens 
and can also be used for dosing simulations to define optimised dosing regimens for these patients. 
PK analysis will be conducted with Pmetrics software package for R (version 1.4.1., Los Angeles, CA).  Non-linear 
mixed effect modelling approach will be used.  A stepwise analysis will be performed to first determine the structural 
base model by fitting the concentration-time data to one, two and three compartment models.  Testing of additive, 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
14 
proportional or a combination of additive and proportional models will be conducted to select the best fit statistical 
error model.  Following population PK analysis, Monte Carlo simulations will be performed.  The likelihood of 
reaching the effective concentration to achieve 90% of the maximal clinical effect on lung function (EC90) for CFTR 
modulators both on and off MABS therapy will be determined.  These PK/PD parameters can be used to estimate 
appropriate doses in clinical practice.

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C1 
Version 1.0 Date 29 March 2023 
15 
REFERENCES 
1. 
Sturkenboom MGG, Bolhuis MS, Simbar N, Ghimire S, Alffenaar J-WC, Akkerman OW. Amikacin Dosing 
for MDR Tuberculosis: A Systematic Review to Establish or Revise the Current Recommended Dose for 
Tuberculosis Treatment. Clinical Infectious Diseases. 2018;67(suppl_3):S303-S7. 
2. 
Hong E, Almond LM, Chung PS, Rao AP, Beringer PM. Physiologically Based Pharmacokinetic Modeling 
To Guide Management of Drug Interactions between Elexacaftor-Tezacaftor-Ivacaftor and Antibiotics for 
the Treatment of Nontuberculous Mycobacteria. Antimicrob Agents Chemother. 2022;66(11):e0110422. 
3. 
Choong E, Sauty A, Koutsokera A, Blanchon S, Andre P, Decosterd L. Therapeutic Drug Monitoring of 
Ivacaftor, Lumacaftor, Tezacaftor, and Elexacaftor in Cystic Fibrosis: Where Are We Now? Pharmaceutics. 
2022;14(8). 
4. 
Guimbellot JS, Ryan KJ, Anderson JD, Parker KL, Victoria Odom L, Rowe SM, et al. Plasma and cellular 
ivacaftor concentrations in patients with cystic fibrosis. Pediatr Pulmonol. 2022;57(11):2745-53. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
i 
 
APPENDIX C2 – DISCOVERY 
Immune Factors and Biomarkers 
Appendix C2 – Discovery 
Version 1.1 
Appendix Date 
20 February 2024 
Protocol Number  
FORMaT001 
Funding 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
EudraCT Number 
2020-000050-10 
EU-CT Number 
2023-506575-99-00-EU CT 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS ..................................................................................................................................... II 
TABLE OF TABLES ......................................................................................................................................... IV 
ABBREVIATIONS ............................................................................................................................................... V 
APPENDIX C: DISCOVERY .............................................................................................................................. 1 
APPENDIX C2: IMMUNE FACTORS AND BIOMARKERS ........................................................................ 2 
1 
INTRODUCTION ......................................................................................................................................... 2 
2 
SUB-STUDY C2.1: MACROPHAGE FUNCTION ................................................................................... 3 
2.1 
INVESTIGATOR LEADS ............................................................................................................................. 3 
2.2 
PRIMARY OBJECTIVE ............................................................................................................................... 3 
2.3 
SECONDARY OBJECTIVES ........................................................................................................................ 3 
2.4 
INTRODUCTION ........................................................................................................................................ 3 
2.5 
ADDITIONAL ELIGIBILITY CRITERIA........................................................................................................ 4 
2.6 
ADDITIONAL INFORMED CONSENT REQUIREMENTS ............................................................................... 4 
2.7 
SUB-STUDY SPECIFIC PROCEDURES ........................................................................................................ 4 
2.8 
STATISTICAL ANALYSIS ........................................................................................................................... 5 
3 
SUB-STUDY C2.2: MITOCHONDRIAL STRESS .................................................................................... 6 
3.1 
INVESTIGATOR LEADS ............................................................................................................................. 6 
3.2 
PRIMARY OBJECTIVE ............................................................................................................................... 6 
3.3 
SECONDARY OBJECTIVES ........................................................................................................................ 6 
3.4 
INTRODUCTION ........................................................................................................................................ 6 
3.5 
ADDITIONAL ELIGIBILITY CRITERIA........................................................................................................ 7 
3.6 
ADDITIONAL INFORMED CONSENT REQUIREMENTS ............................................................................... 7 
3.7 
SUB-STUDY SPECIFIC PROCEDURES ........................................................................................................ 7 
3.8 
STATISTICAL ANALYSIS ........................................................................................................................... 8 
4 
SUB-STUDY C2.3: T-CELL FUNCTION .................................................................................................. 9 
4.1 
INVESTIGATOR LEADS ............................................................................................................................. 9 
4.2 
PRIMARY OBJECTIVE ............................................................................................................................... 9 
4.3 
INTRODUCTION ........................................................................................................................................ 9 
4.4 
ADDITIONAL ELIGIBILITY CRITERIA........................................................................................................ 9 
4.5 
ADDITIONAL INFORMED CONSENT REQUIREMENTS ............................................................................. 10 
4.6 
SUB-STUDY SPECIFIC PROCEDURES ...................................................................................................... 10 
4.7 
STATISTICAL ANALYSIS ......................................................................................................................... 11 
5 
SUB-STUDY C2.4: GENE EXPRESSION SIGNATURES ..................................................................... 12 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
iii 
5.1 
INVESTIGATOR LEAD ............................................................................................................................. 12 
5.2 
PRIMARY OBJECTIVE ............................................................................................................................. 12 
5.3 
INTRODUCTION ...................................................................................................................................... 12 
5.4 
ADDITIONAL ELIGIBILITY CRITERIA...................................................................................................... 12 
5.5 
ADDITIONAL INFORMED CONSENT REQUIREMENTS ............................................................................. 12 
5.6 
SUB-STUDY SPECIFIC PROCEDURES ...................................................................................................... 12 
5.7 
STATISTICAL ANALYSIS ......................................................................................................................... 13 
5.7.1 Identifying a biomarker signature for MABS-PD microbiological cure (clearance) ........................ 13 
5.7.2 Identifying a biomarker signature of MABS-PD vs simple colonisation: .......................................... 13 
6 
SUB-STUDY C2.5: SEROLOGY FOR MABS ......................................................................................... 14 
6.1 
INVESTIGATOR LEADS ........................................................................................................................... 14 
6.2 
PRIMARY OBJECTIVE ............................................................................................................................. 14 
6.3 
INTRODUCTION ...................................................................................................................................... 14 
6.4 
ADDITIONAL ELIGIBILITY CRITERIA...................................................................................................... 14 
6.5 
ADDITIONAL INFORMED CONSENT REQUIREMENTS ............................................................................. 14 
6.6 
SUB-STUDY SPECIFIC PROCEDURES ...................................................................................................... 14 
6.7 
STATISTICAL ANALYSIS ......................................................................................................................... 15 
7 
SUMMARY OF C2 SAMPLE COLLECTION ........................................................................................ 17 
8 
REFERENCES ............................................................................................................................................ 18 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
iv 
TABLE OF TABLES 
Table 1: Sub-study C2.1 Schedule of Assessments ...................................................................................................... 4 
Table 2: Sub-study C2.2 Schedule of Assessments ...................................................................................................... 7 
Table 3: Sub-study C2.3 Schedule of Assessments .................................................................................................... 11 
Table 4: Sub-study C2.4 Schedule of Assessments .................................................................................................... 13 
Table 5: Sub-study C2.5 Schedule of Assessments .................................................................................................... 15 
Table 6: Sample collection time frames for C2 sub-studies ....................................................................................... 17 
Table 7: Sample volume requirements for C2 sub-studies ......................................................................................... 17 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
v 
ABBREVIATIONS 
BAL 
 
 
Bronchoalveolar Lavage 
CCA 
 
 
Canonical Correspondence Analysis 
CCHR  
 
Centre for Children’s Health Research 
CF 
 
 
Cystic Fibrosis 
CFTR  
 
Cystic Fibrosis Transmembrane Conductance Regulator 
CLR 
 
 
C-type Lectin Receptor 
CM 
 
 
Central memory 
CT 
 
 
Computed Tomography 
EM 
 
 
Effector Memory 
EMRA  
 
Effector Memory RA+ 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
GPLs  
 
Glycopeptidolipids 
ID 
 
 
Identification 
IQR 
 
 
Interquartile Range 
M1 
 
 
Type 1 Macrophage 
M2 
 
 
Type 2 Macrophage 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
MABS-R 
 
Rough MABS 
MABS-S 
 
Smooth MABS 
MDMs  
 
Monocyte-Derived Macrophages 
NTM  
 
Non-Tuberculous Mycobacteria 
PBMCs  
 
Peripheral Blood Mononuclear Cells 
PCA 
 
 
Principal component analysis 
PPD 
 
 
Purified Protein Derivative 
R 
 
 
Rough 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
vi 
RDA 
 
 
Redundancy Analysis 
ROS 
Reactive Oxygen Species 
RNA 
 
 
Ribonucleic Acid 
S  
 
 
Smooth 
SOP 
 
 
Standard Operating Procedure 
TLRs  
 
Toll Like Receptors 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
1 
APPENDIX C: DISCOVERY 
 
Appendix C: Discovery, consists of research studies/programs that may be added over time and that are 
aimed at gaining understanding through collaboration with the FORMaT trial but are not specific 
components of the trial.  Participation in each discovery study may require additional consent.  Consent 
requirements are detailed within each of the discovery sub-studies.  Discovery studies may be applicable to 
all participants or only to specific sites or groups of participants.  Each study will be described in the 
following format: 
• 
The named Investigator leads for the sub-study; 
• 
The primary and secondary objectives of the sub-study; 
• 
An introduction to the background of the sub-study; 
• 
Additional eligibility and consent requirements; 
• 
Sub-study specific trial procedures and schedule of assessments; 
• 
Analysis plan. 
 
Appendix C1: Pharmacokinetics. 
Appendix C2: Immune Factors and Biomarkers. 
Appendix C3: Imaging 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
2 
APPENDIX C2: IMMUNE FACTORS AND BIOMARKERS 
1 
INTRODUCTION 
Appendix C2 sub-studies will take advantage of careful clinical and microbiological phenotyping of participants 
enrolled in the FORMaT Master Protocol to examine immunological susceptibility to infection with MABS-PD 
providing an opportunity to develop new approaches to assessing risk of infection as well as approaches to 
management in the future.  A summary of sample requirements and volumes are outlined in Table 6 and 7. 
SUB-STUDY C2.1: Macrophage Function. 
SUB-STUDY C2.2: Mitochondrial Stress. 
SUB-STUDY C2.3: T-Cell Function. 
SUB-STUDY C2.4: Gene Expression Signatures. 
SUB-STUDY C2.5: Serology for MABS. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
3 
2 
SUB-STUDY C2.1: MACROPHAGE FUNCTION 
2.1 
INVESTIGATOR LEADS 
Professor Peter Sly and Dr Abdullah Tarique. 
2.2 
PRIMARY OBJECTIVE 
Determine susceptibility to Mycobacterium abscessus (MABS) infection in participants enrolled in the Observational 
Cohort compared to those with Mycobacterium abscessus pulmonary disease (MABS-PD) enrolled in the 
Intervention Program by examining impaired function of MABS infected macrophages. 
2.3 
SECONDARY OBJECTIVES 
1. Determine efficiency of macrophage phagocytosis and killing of MABS. 
2. Determine whether decreased efficiency of macrophage phagocytosis and killing of MABS contributes to the 
likelihood of chronic infection with MABS-PD. 
3. Determine whether inflammatory signalling pathways activated following MABS-PD infection are dysregulated 
in macrophages. 
4. Examine the association between aberrant phagocytosis and enhanced mitochondrial reactive oxygen species 
(ROS) production in macrophages in participants following MABS infection. 
2.4 
INTRODUCTION 
MABS exists in two morphotypes, rough (R) and smooth (S), depending on the presence of surface 
glycopeptidolipids (GPLs) (1).  Rough MABS (MABS-R), which lack surface GLP expression, and smooth MABS 
(MABS-S) are both phagocytized by human monocytes and macrophages.  MABS-R have greater ability for 
intracellular multiplication and adhere more tightly to the phagosomal membrane (2).  Macrophages play critical 
roles in the initiation and resolution of pulmonary inflammation.  Following microbial infection, macrophages 
recognise the invading bacteria via specific surface receptors including Toll-like receptors (TLRs) to engulf and 
phagocytose them into phagosomes, a compartment that restricts the mobility of the invading bacteria.  Phagosomes 
then fuse with acidic lysosomal compartments to initiate bacterial killing.  TLR signalling initiates inflammatory 
responses to the pathogen.  MABS-S are recognised via both Dectin-1, a C-type lectin molecule and TLR2 (3, 4).  A 
physical interaction between Dectin-1 and TLR2 is required to initiate phagocytosis.  FAM19A4, a recently described 
chemokine released by macrophages following bacterial infection, is involved in phagocytosis regulation in 
macrophages (5). 
Macrophages in people with Cystic Fibrosis (CF) have a reduced ability to phagocytose and kill bacteria.  Murine 
studies showed that functional Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is indispensable for 
phagolysomal killing of bacteria (6).  Lysosomes from CFTR knockout mice were less acidic than from wild-type 
mice, which led to reduced bacterial killing.  Inhibiting CFTR channel activity with specific inhibitors during 
phagocytosis significantly reduced lysosomal acidification, similar to reduced bacterial killing by human 
macrophages (7).  Furthermore, both murine and human studies showed CFTR protein as a regulator of inflammatory 
responses to bacterial infection (8, 9).  Loss of CFTR protein or function led to uncontrolled inflammation in CF.  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
4 
Macrophages from healthy individuals often display “don’t eat me” signals by surface expression of CD31 and CD47 
molecules (10, 11).  Expression of TLR2, Dectin-1, regulators of phagocytosis and “don’t eat me” molecules in 
macrophages from patients with CF have not been adequately studied. 
2.5 
ADDITIONAL ELIGIBILITY CRITERIA 
Only participants enrolled at Queensland FORMaT trial sites will be eligible to participate in sub-study C2.1. In 
addition, participants’ eligibility will be based on the following inclusion criteria: 
1. Aged six years and older. 
2. Ability to provide a minimum 5ml whole blood sample (this blood sample will be used for sub-studies C2.1, 
C2.2 and C2.3). 
3. Participant is enrolled at a FORMaT Trial site in Queensland that can comply with sampling and shipping 
requirements. 
4. Informed consent by participant or their parent/guardian. 
2.6 
ADDITIONAL INFORMED CONSENT REQUIREMENTS 
Additional blood samples are required as part of the study procedures for sub-study C2.1, therefore additional consent 
will be obtained in accordance with the policies described in the FORMaT Master Protocol. 
2.7 
SUB-STUDY SPECIFIC PROCEDURES 
5-10ml of whole blood is collected in participants 6-11 years of age.  Participants 12 years and older will be asked to 
provide up to a 20ml whole blood sample.  If participants 12 years and older are unable to provide a 20ml whole 
blood sample, a 10ml whole blood sample is acceptable.  Whole blood samples will be collected into an EDTA 
collection tube and transported to the Centre for Children’s Health Research (CCHR), South Brisbane within two 
hours of collection.  Trial identification (ID) number, date and time of collection are to be recorded on the sample 
tube. 
Samples will be collected in accordance with Table 1: Sub-study C2.1 Schedule of Assessments. 
Table 1: Sub-study C2.1 Schedule of Assessments 
ASSESSMENT 
STUDY VISITS 
Trial Start 
Week 6 
Week 12 
Final Outcome^ 
Observation Cohort Participant 
Timeframes 
Screening (Day 0; -
42 days to +3 days) 
+14 Days 
±14 Days 
±14 Days 
Combined Intensive and 
Consolidation Therapies Participant 
Timeframes 
Screening (Day 0; -
42 Days to +3 days) 
±3 Days 
±3 Days 
+14 Days 
Consolidation Only Therapy 
Participant Timeframes 
Day 1; -14 Days 
 
 
+14 Days 
^For Observation Cohort participants and Intervention Program participants randomised to short intensive, this is 
collected at Week 56. For Intervention Program participants randomised to prolonged intensive, this is collected at 
Week 62. For Intervention Program participants receiving Consolidation Only therapy, this is collected at Week 50. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
5 
2.8 
STATISTICAL ANALYSIS 
Based on previous experience, the data generated in these experiments are likely to be non-normally distributed 
(using Shapiro-Wilk test), in which case grouped data will be described by group median (27th and 75th percentile).  
Comparisons between groups will be undertaken using Mann-Whitney U-Test (Wilcoxon rank sum test), Kruskal-
Wallis test on ranks (non-parametric alternative to one-way analysis of variance), or Friedman test (non-parametric 
alternative to analysis of variance with repeated measures), as appropriate.  Regression analyses will be used to 
control for likely confounder or modifier variables, including age, sex, previous treatment, current CFTR 
corrector/potentiators therapy.  The techniques used for regression analyses will depend on the final sample size.  If 
large enough, parametric methods will be used as the key assumption is that the residuals of the regression are 
normally distributed, and the Central Limit Theorem states that as the sample size increases all distributions of 
residuals tend towards normality.  If the sample size is not sufficient a multivariable model using quantile regression, 
in which the median difference and 95% CI between groups, will be determined. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
6 
3 
SUB-STUDY C2.2: MITOCHONDRIAL STRESS 
3.1 
INVESTIGATOR LEADS 
Professor Peter Sly and Dr Abdullah Tarique 
3.2 
PRIMARY OBJECTIVE 
Determine susceptibility to MABS infection in participants enrolled in the observational program compared to those 
with MABS-PD enrolled in the Intervention Program by examining mitochondrial function. 
3.3 
SECONDARY OBJECTIVES 
Examine the association between aberrant phagocytosis and reduced mitochondrial function in macrophages in 
participants following MABS infection. 
3.4 
INTRODUCTION 
Macrophages recognise the invading bacteria via specific surface receptors to engulf and phagocytose them into 
phagosomes, a compartment that restrict the mobility of the invading bacteria.  Phagosomes then fuse with acidic 
lysosomal compartments to initiate bacterial killing.  Concurrent with this, specific bacterial products activate pattern 
recognition receptors such as the TLRs and C-type Lectin Receptors (CLRs) to induce both antimicrobial and 
inflammatory responses to the pathogen.  MABS are recognised by the CLR, Dectin-1, as well as TLR2 (3, 4).  A 
physical interaction between Dectin-1 and TLR2 is required to initiate phagocytosis. CFTR-dependent dysfunction 
in Monocyte-Derived Macrophages (MDMs) in CF that result in a decreased ability of type 1 macrophages (M1s) to 
kill phagocytosed bacteria and to polarise into the type 2 (M2) phenotype has been described (7).  These defects are 
related to a post-transcriptional defect of surface expression of the IL-13Rα, required for polarisation into M2s.  This 
defect is CFTR-dependent, as it is also seen when CFTR function is inhibited in MDMs from healthy controls.  In 
macrophages, CFTR functions as a charge shunt lowering the pH of lysosomes sufficiently to enable bacterial killing.  
However, CFTR function is also required for generation of ROS, an important component of intracellular bacterial 
killing (12).  Thus, macrophages with deficient CFTR function are likely to have limited ability to kill and clear 
MABS. 
Macrophages use a variety of methods for bacterial killing, including phagocytosis-coupled ROS generation and 
lysosome-mediated degradation.  As noted above, CFTR function is important for these rapid antimicrobial 
responses.  In addition, TLR signalling induces a suite of late-stage antimicrobial responses that facilitate clearance 
of persistent intracellular bacteria (13).  These include redistribution of intracellular zinc for metal ion poisoning of 
bacteria (14) as well as mitochondrial reprogramming to generate antimicrobial products such as itaconic acid (15) 
and mitoROS (16).  Mitochondria are dynamic organelles that, depending on the cellular environment, can exist as a 
complex network (driven by mitochondrial fusion) or as fragmented organelles (driven by mitochondrial fission, 
hereafter fission).  TLR signalling induces fission in macrophages (17), and recently fission was identified as a novel 
antimicrobial response in macrophages (unpublished).  It was also found that professional intra-macrophage 
pathogens subvert fission, and  strategies were devised to overcome this subversion to enable macrophage-mediated 
bacterial clearance (unpublished).  Specifically, deacetylation of mitochondrial fusion-promoting mitofusin-1 by 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
7 
histone deacetylase 6 (HDAC6) constrains fission (18).  Thus, inhibiting HDAC6 with a specific inhibitor (tubastatin 
A) greatly enhances fission and mitoROS generation in bacterially-infected macrophages.  However, the roles of 
antimicrobial mechanisms such as mitoROS and fission in MDM responses against MABS, and whether these 
responses are affected in CF MDMs, are unknown. 
3.5 
ADDITIONAL ELIGIBILITY CRITERIA 
Only participants enrolled at Queensland FORMaT trial sites will be eligible to participate in sub-study C2.2.  
Furthermore, samples required for sub-study C2.2 are derived from the whole blood sample obtained in sub-study 
C2.1.  Therefore, only participants enrolled in sub-study C2.1 are eligible for sub-study C2.2.  In addition, 
participants’ eligibility will be based on the following inclusion criteria: 
1. Enrolled in sub-study C2.1. 
2. Aged six years and older. 
3. Ability to provide a minimum 5ml whole blood sample (this blood sample will be used for sub-studies C2.1, 
C2.2 and C2.3). 
4. Participant is enrolled at a FORMaT Trial site in Queensland that can comply with sampling and shipping 
requirements. 
5. Informed consent by participant or their parent/guardian. 
3.6 
ADDITIONAL INFORMED CONSENT REQUIREMENTS 
Additional consent will be obtained for sub-study C2.2 in accordance with the policies describe in the FORMaT 
Master Protocol. 
3.7 
SUB-STUDY SPECIFIC PROCEDURES 
Mitochondrial samples are obtained from the 5-20 ml (age dependent) whole blood samples collected in sub-study 
C2.1.  Refer to the above section for a description of the procedures.  No additional samples are required.  Trial ID 
number, date and time of collection are to be recorded on the sample tube. 
Samples will be collected in accordance with Table 2: Sub-study C2.2 Schedule of Assessments. 
 
Table 2: Sub-study C2.2 Schedule of Assessments 
ASSESSMENT 
STUDY VISITS 
Trial Start 
Week 6 
Week 12 
Final Outcome^ 
Observation Cohort Participant 
Timeframes 
Screening (Day 0; -
42 days to +3 days) 
+14 Days 
±14 Days 
±14 Days 
Combined Intensive and 
Consolidation Therapies Participant 
Timeframes 
Screening (Day 0; -
42 Days to +3 days) 
±3 Days 
±3 Days 
+14 Days 
Consolidation Only Therapy 
Participant Timeframes 
 Day 1; -14 Days 
 
 
+14 Days 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
8 
^For Observation Cohort participants and Intervention Program participants randomised to short intensive, this is 
collected at Week 56.  For Intervention Program participants randomised to prolonged intensive, this is collected at 
Week 62.  For Intervention Program participants receiving Consolidation Only therapy, this is collected at Week 50. 
N.B. Mitochondrial samples will be obtained from the whole blood sample collected in sub-study C2.1.  No additional 
blood samples are required. 
 
3.8 
STATISTICAL ANALYSIS 
Based on previous experience, the data generated in these experiments are likely to be non-normally distributed 
(Shapiro-Wilk test), in which case grouped data will be described by group median (25th and 75th percentile).  
Comparisons between groups will be undertaken using Mann-Whitney U-Test, Kruskal-Wallis test on ranks (non-
parametric alternative to one-way analysis of variance), or Friedman test, as appropriate.  Regression analyses will 
be used to control for likely confounder or modifier variables, including age, sex, previous treatment and current 
CFTR corrector/potentiators therapy.  The techniques used for regression analyses will depend on the final sample 
size.  If large enough, parametric methods will be used as the key assumption is that the residuals of the regression 
are normally distributed, and the Central Limit Theorem tells us that as the sample size increases all distributions of 
residuals tend towards normality.  If the sample size is not sufficient a multivariable model using quantile regression, 
in which the median difference and 95% CI between groups, will be determined. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
9 
4 
SUB-STUDY C2.3: T-CELL FUNCTION 
4.1 
INVESTIGATOR LEADS 
Associate Professor David Reid and Associate Professor Severine Navarro 
4.2 
PRIMARY OBJECTIVE 
Determine susceptibility to MABS infection in in CF and non-CF patients by examining T-cell function participants 
enrolled in the Observational Cohort and Intervention Program. 
4.3 
INTRODUCTION 
T cells play a critical role in MABS sensing and MABS clearance.  It has been hypothesised that CF patients 
susceptible to MABS infection may have one or more failures in immune control.  Using high dimensional 
immunoprofiling, this hypothesis was validated and found CF patients with current or past MABS infection showed 
significant distortions in T cell subtypes and in T cell function (19).  Ex vivo differences in Treg percentages and in 
T cell activation (CD25) and exhaustion (CTLA-4 & PD-1) markers were observed, as were differences in 
polyfunctionality of CD4+ T cells (TNF-α, IFN-γ & IL-2); revealing 17 new immune biomarkers for MABS 
susceptibility.  Using these new immune biomarkers, a regression model was generated that produced an AUC of 1.  
Notably, TNF-α secretion appeared to be defective in CD4+ T cells of CF patients susceptible to MABS-PD infection.  
This is important given TNF-α directly activates macrophages to restrict mycobacterial growth and induces apoptosis 
of infected macrophages leading to bacterial killing (20).  TNF-α is also essential for granuloma formation and 
disease restriction (21) and mice deficient in TNF-α are highly susceptible to disseminated forms of mycobacteria 
(22).  These published data around immune failures in CF patients susceptible to MABS could point the way to 
immune modulating therapies to complement antibiotics and possibly predict therapeutic outcome, but this remains 
speculative. 
The FORMaT trial provides a unique opportunity to examine T cell phenotype in a much larger population of 
individuals with and without CF than has been previously possible.  The projected number of new MABS-PD 
diagnoses will allow a comprehensive study of T cell function and allow the conduct of the critical functional 
experiments that are required to pave the way for new immunomodulating therapeutics and clinical biomarkers.  To 
allow better targeting of studies of immune dysfunction in CF and non-CF individuals, further analyses will be 
undertaken with new immunoprofiling methods available through collaboration with A/Prof. Navarro, initially using 
historical stored peripheral blood mononuclear cells from CF patients with chronic MABS infection, as well as 
historical samples from patients who spontaneously cleared MABS infection and patients who underwent successful 
eradication of MABS infection and compare immunoprofiles in these disease states to that of normal, healthy 
controls. 
4.4 
ADDITIONAL ELIGIBILITY CRITERIA 
Only participants enrolled at Queensland FORMaT trial sites and in sub-studies C2.1 and C2.2 will be eligible to 
participate in sub-study C2.3.  This is because the samples required for sub-study C2.3 are derived from the samples 
obtained in sub-study C2.1 and C2.2.  These inclusion criteria are reflected below: 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
10 
1. Enrolled in sub-study C2.1 and C2.2. 
2. Aged six years and older. 
3. Ability to provide a minimum 5ml whole blood sample (this blood sample will be used for sub-studies C2.1, 
C2.2 and C2.3). 
4. Participant is enrolled at a FORMaT Trial site in Queensland that can comply with sampling and shipping 
requirements. 
5. Informed consent by participant or their parent/guardian. 
4.5 
ADDITIONAL INFORMED CONSENT REQUIREMENTS 
Additional consent will be obtained for sub-study C2.3 in accordance with the policies outlined in the FORMaT 
Master Protocol. 
4.6 
SUB-STUDY SPECIFIC PROCEDURES 
2 x 106 peripheral blood mononuclear cells (PBMCs)/ml and 5ml of plasma will be separated from the whole blood 
sample provided in sub-study C2.1.  No additional samples are required.  Trial ID number, date and time of collection 
are to be recorded on the sample tube.  All samples will be processed at the CCHR, South Brisbane.  Samples will 
be batched and sent to QIMR Berghofer Institute of Medical Research as requested. 
High-dimensional immunoprofiling will be performed by multiparametric flow cytometry followed by RNA 
sequencing of T cell populations from the same participants examined in sub-study C2.1 and C2.2.  Custom flow 
cytometry panels will be designed based on the strongest T cell biomarkers identified by RNAseq (A/Prof Coin – 
refer to sub-study C2.4 below).  To further determine susceptibility to MABS infection, we will perform T-cell 
receptor (TCR) sequencing analysis using 10x Genomics single cell V(D)J kits.  The diversity of TCR sequences 
will inform on the true biological diversity of T cells as well as the molecular genetic determinants of antigen 
specificity.  The different T cell clonotypes will be characterised and confirmed where possible, using real-time PCR 
and flow cytometry.  Two or more aliquots of PBMCs will be available from each participant.  One aliquot will be 
used for T cell analysis and one aliquot used for macrophage analysis.  Multiparametric flow cytometry will be 
conducted on major T cell subsets, including central memory (CM), effector memory (EM) and effector memory 
RA+ (EMRA).  Both CD8+ and CD4+ subsets will be profiled along antigen-specific populations using recombinant 
purified protein derivative (PPD) as a stimulus.  Multiplex assay systems (Human Immune Monitoring 65-Plex 
ProcartaPlex Panel, ThermoFisher) will be utilised to analyse up to 65 protein targets (cytokines, chemokines, growth 
factors) on tiny volumes of sample (25 - 50µL) from patients in duplicate. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
11 
Samples will be collected in accordance with Table 3: Sub-study C2.3 Schedule of Assessments. 
Table 3: Sub-study C2.3 Schedule of Assessments 
ASSESSMENT 
STUDY VISITS 
Trial Start 
Week 6 
Week 12 
Final Outcome^ 
Observation Cohort Participant 
Timeframes 
Screening (Day 0; -
42 days to +3 days) 
+14 Days 
±14 Days 
±14 Days 
Combined Intensive and 
Consolidation Therapies Participant 
Timeframes 
Screening (Day 0; -
42 Days to +3 days) 
±3 Days 
±3 Days 
+14 Days 
Consolidation Only Therapy 
Participant Timeframes 
Day 1; -14 Days 
 
 
+14 Days 
^For Observation Cohort participants and Intervention Program participants randomised to short intensive, this is 
collected at Week 56. For Intervention Program participants randomised to prolonged intensive, this is collected at 
Week 62. For Intervention Program participants receiving Consolidation Only therapy, this is collected at Week 50. 
N.B.- Tcell samples will be obtained from the whole blood sample collected in sub-study C2.1. No additional blood 
samples are required.   
 
4.7 
STATISTICAL ANALYSIS 
Flow cytometry data will be analysed using Cytobank which will include heatmap, SPADE, viSNE, dot and 
histogram overlays and CITRUS outputs.  ScRNAseq analysis of 7000 cells has >95% power to detect up to 10 
clusters with a minimum of 50 cells per cluster, assuming the smallest subset exists at 1% of the total.  Identified 
functional pathways involving the different T cell subsets will be further interrogated further using the SINCERA 
pipeline.  Cell clusters will be identified using hierarchical clustering with average linkage and Pearson’s correlation-
based distance.  Genes will be considered differentially expressed if they have an average log fold-change of at least 
0.25 and a Bonferroni-adjusted p value of 0.05 or lower.  Cell type assignment will be based on cell type-specific 
marker gene expression and validated using functional enrichment of cluster-specific differentially expressed genes.  
Cluster-specific differentially expressed genes will be identified using the two-group Welch’s t-test-based method in 
SINCERA. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
12 
5 
SUB-STUDY C2.4: GENE EXPRESSION SIGNATURES 
5.1 
INVESTIGATOR LEAD 
Associate Professor Lachlan Coin 
5.2 
PRIMARY OBJECTIVE 
Identify biomarker signatures for MABS clearance at the end of intensive therapy and at the final outcome, 
distinguishing MABS colonisation from MABS-PD between the Observational Cohort and Intervention Program 
participants. 
5.3 
INTRODUCTION 
In addition to serology biomarkers, development of gene expression signatures may provide an important adjunct for 
diagnosing and monitoring MABS infection, disease progression and response to treatment.  High quality evidence 
obtained from the FORMaT trial will guide decisions for starting treatment and measuring disease severity in patients 
with MABS-PD, influencing global practice. 
5.4 
ADDITIONAL ELIGIBILITY CRITERIA 
All Observational Cohort and Intervention Program participants are eligible to participate in sub-study C2.4 in 
accordance with the FORMaT Master Protocol eligibility and if they are able tomeet the following inclusion criteria: 
• 
Ability to provide a 2.5ml whole blood sample. 
• 
Participant is enrolled at a FORMaT Trial site that can comply with sampling and shipping requirements. 
• 
Informed consent by participant or their parent/guardian. 
5.5 
ADDITIONAL INFORMED CONSENT REQUIREMENTS 
Additional blood samples are required as part of the study procedures for sub-study C2.4, therefore additional consent 
will be obtained in accordance with the policies outlined in the FORMaT Master Protocol. 
5.6 
SUB-STUDY SPECIFIC PROCEDURES 
Whole blood samples of up to 2.5ml will be collected in 10ml PAXgene tubes optimised for ribonucleic acid (RNA).  
Whole blood samples for gene expression signature biomarkers will be collected in accordance with Table 4, Sub-
Study C2.4 Schedule of Assessments. Trial ID number, date and time of collection are to be recorded on the sample 
tube. Blood RNA tubes are to be transported to a central study laboratory at the Centre for Children’s Health 
Research, Queensland, for temporary storage at -20°C prior to batch shipping the samples to the Peter Doherty 
Institute, University of Melbourne. Alternatively, the samples can be sent directly to the Peter Doherty Institute, 
University of Melbourne, Australia for processing. The FORMaT trial management team will assist trial sites in 
coordinating transportation of samples according to FORMaT Biological Sample Management SOP.  
Samples will be collected in accordance with Table 4: Sub-study C2.4 Schedule of Assessments. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
13 
Table 4: Sub-study C2.4 Schedule of Assessments 
ASSESSMENT 
STUDY VISITS 
Trial Start 
Week 6 
Week 12 
Final Outcome^ 
Observation Cohort Participant 
Timeframes 
Screening (Day 0; -
42 days to +3 days) 
+14 Days 
±14 Days 
±14 Days 
Combined Intensive and 
Consolidation Therapies Participant 
Timeframes 
Screening (Day 0; -
42 Days to +3 days) 
±3 Days 
±3 Days 
+14 Days 
Consolidation Only Therapy 
Participant Timeframes 
Day 1; -14 Days 
 
 
+14 Days 
 
^For Observation Cohort participants and Intervention Program participants randomised to short intensive, this is 
collected at Week 56. For Intervention Program participants randomised to prolonged intensive, this is collected at 
Week 62. For Intervention Program participants receiving Consolidation Only therapy, this is collected at Week 50. 
 
5.7 
STATISTICAL ANALYSIS 
5.7.1 
Identifying a biomarker signature for MABS-PD microbiological cure (clearance) 
RNA-seq will be conducted on bloods taken at baseline and at their final outcome assessment, generating ~30m reads 
per sample. We will use Salmon (23) to calculate transcript abundance from these data, and Limma-Voom pipeline 
(24) to identify statistically significant differences in expressed transcripts between acute and convalescent time-
points. Using the ssizeRNA package in R we can estimate that this approach provides 99.5% power at a false 
discovery rate of 5% to identify genes with a 1.4 fold-change between conditions, and 50% power at a fold-change 
of 1.2. We will use the elastic net (25) to identify a biomarker signature for predicting recovery, as well as the FS-
PLS algorithm we have described previously for identifying minimal biomarker signatures of recovery (26). 
Identified biomarkers will be measured on the intermediate time-points, using the NanoString platform in order to 
investigate the variability of the biomarker signature over time. The identified biomarkers will be validated using the 
NanoString platform on blood collected from participants with MABS infection. 
5.7.2 
Identifying a biomarker signature of MABS-PD vs simple colonisation: 
RNAseq will be performed on blood collected from 100 patients recruited into the Observational Cohort. 
Approximately half of these are expected to later develop MABS-PD. As above, we will use Salmon (23) to quantify 
expression, and Limma-Voom (24) to identify significant differences in expressed transcripts between these two 
groups, as well as the elastic net (25) and FS-PLS to identify biomarkers of infection vs colonisation. These signatures 
will be validated using nanoString on a sample of a further 100 samples. As above, this approach has a 99.5% power 
to identify genes with a 1.4 fold-change. 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
14 
6 
SUB-STUDY C2.5: SEROLOGY FOR MABS 
6.1 
INVESTIGATOR LEADS 
Professor Niels Høiby and Dr Tavs Qvist 
6.2 
PRIMARY OBJECTIVE 
Identify serological markers that predict 1) the natural history of MABS colonisation and 2) progression to MABS-
PD as well as 3) treatment failure in different patient subpopulations. 
6.3 
INTRODUCTION 
Targeted therapeutic approaches to maximise clinical benefit are required in the treatment of MABS-PD. The 
development of serological assessments to help predict and identify patients who may benefit from early treatment 
and identify successful responses to treatment is required (27). In doing so, unnecessary treatment associated toxicity 
and costs are reduced, improving outcomes for MABS-PD patients. 
6.4 
ADDITIONAL ELIGIBILITY CRITERIA 
All Observational Cohort and Intervention Program participants are eligible to participate in sub-study C2.5 in 
accordance with the FORMaT Master Protocol eligibility. In addition, participants are required to meet the following 
inclusion criteria: 
• 
Ability to provide a minimum 1ml serum sample. 
• 
Enrolled at a FORMaT Trial site that can comply with sampling and shipping requirements. 
• 
Informed consent by participant or their parent/guardian. 
6.5 
ADDITIONAL INFORMED CONSENT REQUIREMENTS 
Additional blood samples are required as part of the study procedures for sub-study C2.5, therefore additional consent 
will be obtained in accordance with the policies outlined in the FORMaT Master Protocol. 
6.6 
SUB-STUDY SPECIFIC PROCEDURES 
Up to 4mL of blood is obtained by venepuncture and left to clot at ambient temperature.  Centrifuging is carried out 
to pellet the blood cells and serum is then collected by pipetting to a plastic tube (e.g., NAGLE no. 479-3222 from 
VWR) with an airtight screw cap.  Serum samples will be collected in accordance with Table 5, Sub-Study C2.5 
Schedule of Assessments. Trial ID number, date and time of collection are to be recorded on the sample tube. Once 
the sample is processed the tube containing the sample can be stored on site at -20°C.  If -20°C storage is not available 
onsite samples can be transported to a central laboratory located at the Centre for Children’s Health Research, 
Queensland, for temporary storage.  All serum samples will be batched and shipped to the Department of Clinical 
Microbiology, Copenhagen regularly (approximately every three months) by the FORMaT trial management team, 
although this may be more or less frequent depending on recruitment and site storage ability. 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
15 
Table 5: Sub-study C2.5 Schedule of Assessments 
ASSESSMENT 
STUDY VISITS 
Trial Start 
Week 6 
Week 12 
Final Outcome^ 
Observation Cohort Participant 
Timeframes 
Screening (Day 0; -
42 days to +3 days) 
+14 Days 
±14 Days 
±14 Days 
Combined Intensive and 
Consolidation Therapies Participant 
Timeframes 
Screening (Day 0; -
42 Days to +3 days) 
±3 Days 
±3 Days 
+14 Days 
Consolidation Only Therapy 
Participant Timeframes 
Day 1; -14 Days 
 
 
+14 Days 
^For Observation Cohort participants and Intervention Program participants randomised to short intensive, this is 
collected at Week 56. For Intervention Program participants randomised to prolonged intensive, this is collected at 
Week 62. For Intervention Program participants receiving Consolidation Only therapy, this is collected at Week 50. 
 
6.7 
STATISTICAL ANALYSIS 
Analysis will be descriptive and examine changes across both successful and failed treatment courses in the different 
subgroups and differences between those who develop MABS-PD and those who are colonized.  Validation studies 
will be developed in the future. 
Baseline data will be reported as median and interquartile range (IQR) for non-normally distributed continuous 
variables, and as percentages for categorical variables.  Group comparisons will be made using Kruskal-Wallis test 
on ranks (non-parametric alternative to one-way analysis of variance) and Dunn's multiple comparison test.  A p-
value of ≤0.05 will be considered statistically significant.  Longitudinal anti-MABS IgG kinetics during the 
Intervention Program will be compared to the Observational Cohort and effect of treatment will be assessed.  A 
diagnostic algorithm will be constructed based on the principle of risk stratification.  The premise of the algorithm 
will be the predictive value of one routine serum sample for anti-MABS per patient per year.  Multilevel predictive 
values, likelihood ratios and a receiver operating curve for sensitivity and specificity will be constructed.  All 
measures will be reported with confidence intervals.  Participants will be divided into phenotype groups on the basis 
of NTM culture results and clinical data captured from patient records: 
1. Participants with MABS-PD disease who are not receiving treatment (at enrolment in the Intervention Program 
or remaining in the Observation Cohort without treatment). 
2. Those that clear infection with treatment during FORMaT. 
3. Those that do not clear infection with treatment during FORMaT. 
4. Participants with positive MABS cultures but no pulmonary disease in the Observation Cohort. 
5. Control samples will also be available from patients with no known history of NTM infection and current 
negative NTM culture results.  These control samples are available through samples currently being collected as 
part of other clinical studies such as: CF control samples - Early Life Origins of CF lung disease CFFT grant 
(SLY18KO) that includes samples from adults and children (estimated 200 blood samples will be available 
matched with NTM cultures performed and full clinical history).  Non-CF control samples will also be sourced 
from other approved studies.   

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
16 
6. Recognised previous NTM infections will be documented at enrolment in the FORMaT Intervention Program 
and Observation Cohort and any new NTM infections detected during the study will also be documented.  The 
presence of past or present infection with another NTM on MABS serology will be examined. 
Coefficient of variance will be reported.  The study will be reported in accordance with the guidelines for reporting 
studies on diagnostic accuracy (STARD). 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
17 
7 
SUMMARY OF C2 SAMPLE COLLECTION 
Table 6: Sample collection time frames for C2 sub-studies 
Assessment 
Study Visit 
Screening Visit 
(Day 0) 
Week 6 
Week 12 
Final 
Outcome^ 
Review Eligibility for Sub-Studies 
✓ 
 
 
 
Observation Cohort Participant 
Timeframes 
-42 days to +3 
days 
+14 Days 
±14 Days 
±14 Days 
Combined Intensive and Consolidation 
Therapies Participant Timeframes  
-42 days to +3 
days 
±3 Days 
±3 Days 
 
+14 Days 
Consolidation Only Therapy 
Participant Timeframes 
-42 days to +3 
days 
 
 
+14 Days 
^For Observation Cohort participants and Intervention Program participants randomised to short intensive, this is 
collected at Week 56. For Intervention Program participants randomised to prolonged intensive, this is collected at 
Week 62. For Intervention Program participants receiving Consolidation Only therapy, this is collected at Week 50. 
 
 
Table 7: Sample volume requirements for C2 sub-studies 
Assessment 
Sample and Volume 
Needed 
Macrophage, Mitochondrial and T-cells Samples 
5-10ml (6-11y) whole blood 
10-20ml (12+y) whole blood 
Serology 
1ml serum (from 2-4ml whole blood) 
Gene Expression Signatures 
2.5ml whole blood  
 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
18 
8 
REFERENCES 
1. 
Whang J, Back YW, Lee KI, Fujiwara N, Paik S, Choi CH, et al. Mycobacterium abscessus 
glycopeptidolipids inhibit macrophage apoptosis and bacterial spreading by targeting mitochondrial 
cyclophilin D. Cell Death Dis. 2017;8(8):e3012. 
2. 
Byrd TF, Lyons CR. Preliminary characterization of a Mycobacterium abscessus mutant in human and 
murine models of infection. Infect Immun. 1999;67(9):4700-7. 
3. 
Shin DM, Yang CS, Yuk JM, Lee JY, Kim KH, Shin SJ, et al. Mycobacterium abscessus activates the 
macrophage innate immune response via a physical and functional interaction between TLR2 and dectin-1. 
Cell Microbiol. 2008;10(8):1608-21. 
4. 
Lee HM, Yuk JM, Kim KH, Jang J, Kang G, Park JB, et al. Mycobacterium abscessus activates the NLRP3 
inflammasome via Dectin-1-Syk and p62/SQSTM1. Immunol Cell Biol. 2012;90(6):601-10. 
5. 
Wang W, Li T, Wang X, Yuan W, Cheng Y, Zhang H, et al. FAM19A4 is a novel cytokine ligand of formyl 
peptide receptor 1 (FPR1) and is able to promote the migration and phagocytosis of macrophages. Cell Mol 
Immunol. 2015;12(5):615-24. 
6. 
Di A, Brown ME, Deriy LV, Li C, Szeto FL, Chen Y, et al. CFTR regulates phagosome acidification in 
macrophages and alters bactericidal activity. Nat Cell Biol. 2006;8(9):933-44. 
7. 
Tarique AA, Sly PD, Holt PG, Bosco A, Ware RS, Logan J, et al. CFTR-dependent defect in alternatively-
activated macrophages in cystic fibrosis. J Cyst Fibros. 2017. 
8. 
Riquelme SA, Hopkins BD, Wolfe AL, DiMango E, Kitur K, Parsons R, et al. Cystic Fibrosis 
Transmembrane Conductance Regulator Attaches Tumor Suppressor PTEN to the Membrane and Promotes 
Anti Pseudomonas aeruginosa Immunity. Immunity. 2017;47(6):1169-81 e7. 
9. 
Bruscia EM, Zhang PX, Ferreira E, Caputo C, Emerson JW, Tuck D, et al. Macrophages directly contribute 
to the exaggerated inflammatory response in cystic fibrosis transmembrane conductance regulator-/- mice. 
Am J Respir Cell Mol Biol. 2009;40(3):295-304. 
10. 
Brown S, Heinisch I, Ross E, Shaw K, Buckley CD, Savill J. Apoptosis disables CD31-mediated cell 
detachment from phagocytes promoting binding and engulfment. Nature. 2002;418(6894):200-3. 
11. 
Tsai RK, Discher DE. Inhibition of "self" engulfment through deactivation of myosin-II at the phagocytic 
synapse between human cells. J Cell Biol. 2008;180(5):989-1003. 
12. 
Bernut A, Dupont C, Ogryzko NV, Neyret A, Herrmann J-L, Floto RA, et al. CFTR Protects against 
Mycobacterium abscessus Infection by Fine-Tuning Host Oxidative Defenses. Cell Reports. 
2019;26(7):1828-40.e4. 
13. 
Stocks CJ, Schembri MA, Sweet MJ, Kapetanovic R. For when bacterial infections persist: Toll‐like 
receptor‐inducible direct antimicrobial pathways in macrophages. 2018. p. 35-51. 
14. 
Stocks CJ, Phan M-D, Achard MES, Nhu NTK, Condon ND, Gawthorne JA, et al. Uropathogenic employs 
both evasion and resistance to subvert innate immune-mediated zinc toxicity for dissemination. Proceedings 
of the National Academy of Sciences of the United States of America. 2019;116(13). 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C2  
Version 1.1 Date 20 February 2024 
19 
15. 
Alessandro M, Thekla C, Jenny G, Arnaud P, Norbert R, Oliver G, et al. Immune-responsive gene 1 protein 
links metabolism to immunity by catalyzing itaconic acid production. Proceedings of the National Academy 
of Sciences. 2013;110(19):7820. 
16. 
West AP, Igor EB, Christoph R, Dong Kyun W, Hediye E-B, Paul T, et al. TLR signalling augments 
macrophage bactericidal activity through mitochondrial ROS. Nature. 2011;472(7344):476. 
17. 
Baker B, Maitra U, Geng S, Li L. Molecular and cellular mechanisms responsible for cellular stress and low-
grade inflammation induced by a super-low dose of endotoxin. J Biol Chem. 2014;289(23):16262-9. 
18. 
Lee JY, Kapur M, Li M, Choi MC, Choi S, Kim HJ, et al. MFN1 deacetylation activates adaptive 
mitochondrial fusion and protects metabolically challenged mitochondria. J Cell Sci. 2014;127(Pt 22):4954-
63. 
19. 
Henkle E, Aksamit T, Barker A, Daley CL, Griffith D, Leitman P, et al. Patient-Centered Research Priorities 
for Pulmonary Nontuberculous Mycobacteria (NTM) Infection. An NTM Research Consortium Workshop 
Report. Ann Am Thorac Soc. 2016;13(9):S379-84. 
20. 
Bermudez LE, Young LS. Tumor necrosis factor, alone or in combination with IL-2, but not IFN-gamma, is 
associated with macrophage killing of Mycobacterium avium complex. J Immunol. 1988;140(9):3006-13. 
21. 
Roach DR, Bean AG, Demangel C, France MP, Briscoe H, Britton WJ. TNF regulates chemokine induction 
essential for cell recruitment, granuloma formation, and clearance of mycobacterial infection. J Immunol. 
2002;168(9):4620-7. 
22. 
Flynn JL, Goldstein MM, Chan J, Triebold KJ, Pfeffer K, Lowenstein CJ, et al. Tumor necrosis factor-alpha 
is required in the protective immune response against Mycobacterium tuberculosis in mice. Immunity. 
1995;2(6):561-72. 
23. 
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification 
of transcript expression. Nat Methods. 2017. 
24. 
Law CW, Chen Y, Shi W, Smyth GK. voom: Precision weights unlock linear model analysis tools for RNA-
seq read counts. Genome Biol. 2014;15(2):R29. 
25. 
Friedman J, Hastie T, Tibshirani R. Regularization Paths for Generalized Linear Models via Coordinate 
Descent. J Stat Softw. 2010;33(1):1-22. 
26. 
Herberg JA, Kaforou M, Wright VJ, Shailes H, Eleftherohorinou H, Hoggart CJ, et al. Diagnostic Test 
Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile 
Children. JAMA. 2016;316(8):835-45. 
27. 
Qvist T, Pressler T, Taylor-Robinson D, Katzenstein TL, Hoiby N. Serodiagnosis of Mycobacterium 
abscessus complex infection in cystic fibrosis. Eur Respir J. 2015;46(3):707-16. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
i 
 
 APPENDIX C3 – DISCOVERY 
 
Imaging 
 
Appendix C3 – Discovery 
Version 1.2 
Appendix Date 
20 February 2024 
Protocol Number  
FORMaT001 
Funding 
 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
EudraCT Number 
2020-000050-10 
EU-CT Number 
2023-506575-99-00-EU CT 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS ..................................................................................................................................... II 
ABBREVIATIONS ............................................................................................................................................. III 
APPENDIX C: DISCOVERY .............................................................................................................................. 1 
APPENDIX C3: IMAGING ................................................................................................................................. 2 
 
OBJECTIVES ................................................................................................................................................ 2 
 
PRIMARY OBJECTIVES ............................................................................................................................. 2 
 
SECONDARY OBJECTIVES ........................................................................................................................ 2 
 
INTRODUCTION ......................................................................................................................................... 2 
 
ELIGIBILITY CRITERIA ........................................................................................................................... 3 
 
INFORMED CONSENT ............................................................................................................................... 3 
 
CT TRIAL PROCEDURES.......................................................................................................................... 3 
 
CT SCORING ................................................................................................................................................ 4 
 
NUMBERS OF AVAILABLE SCANS ........................................................................................................ 4 
REFERENCES ...................................................................................................................................................... 6 
 
 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
iii 
ABBREVIATIONS  
 
ATS 
 
 
American Thoracic Society 
CF 
 
 
Cystic Fibrosis 
CT 
 
 
Computed Tomography 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment  
HRCT  
 
High-Resolution Computed Tomography 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
MAC  
 
Mycobacterium avium Complex 
NTM  
 
Non-tuberculous mycobacteria 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
1 
 
APPENDIX C: DISCOVERY 
 
Appendix C: Discovery consists of research studies/programs that may be added over time and that are 
aimed at gaining understanding through collaboration with the FORMaT trial but are not specific 
components of the trial.  Participation in each discovery study may require additional consent.  Consent 
requirements are detailed within each of the discovery sub-studies.  Discovery studies may be applicable to 
all participants or only to specific sites or groups of participants.  Each study will be described in the 
following format: 
• 
The named Investigator leads for the sub-study; 
• 
The primary and secondary objectives of the sub-study; 
• 
An introduction to the background of the sub-study; 
• 
Additional eligibility and consent requirements; 
• 
Sub-study specific trial procedures and schedule of assessments; 
• 
Analysis plan. 
 
Appendix C1: Pharmacokinetics. 
Appendix C2: Immune Factors and Biomarkers. 
Appendix C3: Imaging. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
2 
APPENDIX C3: IMAGING 
Investigator Leads 
Professor Harm Tiddens, Dr Daan Caudri, Dr Taryn Reddy 
 
OBJECTIVES 
 PRIMARY OBJECTIVES 
To examine the changes in structural lung disease as detected on chest computed tomography (CT) scan (PRAGMA-
CF %disease, %bronchiectasis, %mucus plugging and %trapped air) across the FORMaT Intervention Program 
associated with and without clearance of Mycobacterium abscessus (MABS) at 6 and 12 weeks and at final outcome. 
 SECONDARY OBJECTIVES 
1. Compare the progression of structural changes on chest CT scan (PRAGMA %disease, %bronchiectasis, 
%mucus plugging and %trapped air) in patients in the Intervention Program and patients in the Observational 
Cohort with and without Mycobacterium abscessus pulmonary disease (MABS-PD). 
2. Compare progression of structural changes on chest CT scan (PRAGMA % disease, %bronchiectasis, %mucus 
plugging and %trapped air) associated with the development of MABS-PD. 
3. Compare progression of structural changes on chest CT scan as assessed by the fully automatic LungQ (Thirona, 
Nijmegen the Netherlands) Bronchus-Artery (BA) analysis (Airway lumen diameter (Alumen), Airway Outer 
diameter (Aout), Airway wall thickness (Awt), Artery diameter (A), Alumen/A, Aout/A, Awt/A ) associated with the 
development of MABS-PD. 
4. Develop an automated scoring system for chest CT imaging to support diagnosis and monitoring of MABS-PD. 
5. Identify CT related biomarkers to predict treatment response. 
6. Determine variability in protocolling of CT studies in people with unknown or suspected non-tuberculous 
mycobacterium (NTM) pulmonary disease (including MABS-PD) across different institutions and develop 
optimal protocols for CT imaging of MABS-PD. 
 
INTRODUCTION 
CT scans are regarded as important components of establishing the diagnosis of MABS-PD according to the 
ATS criteria and are recommended in international guidelines as part of the assessments to be undertaken when 
starting and ending treatment in patients with MABS-PD (1).  There is also some evidence that patients who 
clear Mycobacterium avium Complex (MAC) infection have improved radiological outcomes compared with 
those who do not clear infection (2) and that early radiological improvement is a predictor of converting to 
negative sputum cultures.  In this study a relative crude image analysis was used, furthermore image acquisition 
was not standardised.  Hence, it is likely that chest CT outcomes using standardised chest CT protocols and 
more sensitive image analysis systems such as PRAGMA-CF and the BA-analysis can improve the predictive 
power for sputum conversion and radiological resolution of MABS-PD related structural changes.  This trial 
provides an opportunity to include standardised chest CT scan according to American Thoracic Society (ATS) 
criteria for MABS-PD for phenotyping of MABS-PD patients. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
3 
Using CT related phenotyping the FORMaT trial provides an opportunity to document the spectrum and changes 
in structural lung disease as detected on chest CT scan in patients with MABS who do or do not clear infection 
as well as progression in those with positive MABS cultures that do and do not develop MABS-PD.  From a 
safety and clinical perspective, MABS infection may be cleared from the sputum but this response might be 
dissociated from progression of structural lung disease as it is questionable whether sputum is reflective of 
consolidated lung areas. 
There are no specific scoring systems for MABS-PD and the FORMaT trial provides a unique opportunity for 
the development of a radiological scoring system specific for patients with MABS who do or do not have cystic 
fibrosis (CF) and this will be one of the Discovery Substudies  PRAGMA-CF is currently being automated for 
monitoring CF lung disease.  For FORMaT all CTs need to be manually annotated.  Next these annotated CTs 
can be used to adjust and train the algorithm future automated image analysis of MABS patients. 
Currently there is wide variability in the protocolling of CT studies for the investigation and follow-up of NTM 
pulmonary disease, including MABS-PD. Therefore, a CT questionnaire has been designed to ascertain the extent of 
variability in protocolling of these CT studies across different institutions, in order to formulate a more standardised 
approach in future. 
 
ELIGIBILITY CRITERIA 
No additional eligibility criteria to those outlined in the FORMaT Master Protocol apply to sub-study C3. 
 
INFORMED CONSENT 
All CT scans are performed as part of the FORMaT Master Protocol.  Additional consent is required for the Appendix 
C3 study specific chest CT scan performed at Week 6 (for Appendix A2 participants) and at Week 12 (for Appendix 
A1 participants and Appendix B participants). 
 
CT TRIAL PROCEDURES 
An inspiratory and expiratory helical chest CT scan with High-Resolution Computed Tomography (HRCT) 
reconstruction will be performed for all FORMaT trial participants in accordance with the trial procedures outlined 
in the relevant Schedule of Assessment tables. 
Each FORMaT site participating in the additional Appendix C3 study specific CT scan will have a CT scanning 
protocol developed by the Erasmus team, taking into account site specific scanning requirements, optimising the 
balance between radiation and image quality.  Site staff will undergo web-based training.  Appendix C3 study specific 
chest CT scans must be performed with the FORMaT specific CT scanning protocol using optimisation of lung 
volumes to provide standardisation longitudinally. 
Standard of care chest CT scans are strongly recommended to be performed with the FORMaT specific CT scanning 
protocol with optimisation of lung volumes where feasible. 
Images must be de-identified by the certified imaging provider and sent to the FORMaT trial management team who 
will send coded CT images electronically to Erasmus Medical Centre.  Alternatively, deidentified coded CT images 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
4 
will be sent directly from the certified imaging provider to Erasmus Medical Centre for scoring using the PRAGMA-
CF scoring system and the LungQ BA-analysis.  
To improve understanding of lung disease from infection and develop better analysis of lung images, data from de-
identified images may also be sent for further analysis and stored for research purposes by other approved 
collaborative research groups. 
A CT protocol questionnaire will be sent to the relevant radiology department at approved trial sites and contracted 
imaging providers to determine the current scanning protocols used for unknown pathology and for suspected/proven 
NTM.   
 
CT SCORING 
All scans will be manually scored initially using the PRAGMA-CF scoring system which has been extensively 
validated for quantitative analysis of CF lung disease in children and adolescents (3, 4).  Compared with other scoring 
systems, PRAGMA-CF has increased sensitivity for detecting and monitoring changes in mild as well as in advanced 
disease (including inflammatory changes, such as mucus plugging, “tree-in-bud”, consolidation and bronchiectasis 
seen in MABS-PD) and has a known expected change with time for CF, which is important for maintaining 
discriminatory ability and sensitivity to potential change from additional disease (MABS-PD).  For example, 
PRAGMA-CF has been used as outcome measure in a large Phase III clinical trial of Ataluren in 207 children and 
adults with CF.  Longitudinal analysis showed that %Disease at start of study was 9.8% and that it progressed 
significantly over the study duration (5).  No difference was detected between the ataluren and placebo group.  This 
lack of effectiveness was later confirmed in a second Ataluren phase III trial and used in a Phase III clinical trial of 
Ataluren. 
Scoring of coded CTs will be undertaken blinded to treatment allocation and clinical data by the Erasmus Medical 
Centre LungAnalysis team. 
The development of automated scoring will require an initial discovery approach using all the known clinical markers 
and manual and automated scoring analysis. The protocol developed for scoring will then require validation in two 
independent data sets with blinding as to disease progression and background disease e.g. cystic fibrosis, COPD, 
non-CF bronchiectasis, previous tuberculosis etc. One of the data sets will be from prospective FORMaT participants 
including observation and intervention participants the other will be from a separate non-FORMaT data set.   
 
NUMBERS OF AVAILABLE SCANS 
There will be 300 paired scans (N=600) from enrolment to completion of the FORMaT trial for the initial intervention 
program.  We estimate from discussions with patients and from other studies that approximately 200 participants will 
consent to a further scan at 12 weeks.  The risk related to the extra radiation of the third CT scan is low and is 
estimated to be in the order of 3-6 months background radiation (6).  New MABS notifications in Queensland 
Australia now average >100/year (≈1/3rd CF).  An audit of 51 adults with CF and MABS infection in Queensland 
found 42% did not receive treatment and so would potentially enter the observation arm, although reasons for this 
were variable.  The Royal Brompton Hospital London (pers. com. Prof Elborn and Dr. Jones) suggested 4/49 (8%) 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
5 
patients in their cohort culturing MABS had single isolates and therefore would not meet ATS criteria but would be 
eligible for the observation arm.  For the Observational Cohort we estimate that 1/3 of subjects will not meet ATS 
criteria (estimate 50 paired scans) and 1/3 would start in the observation arm but develop MABS-PD and move into 
the trial subsequently (estimate 50 paired scans) and potentially 1/3 have MABS-PD and not receive treatment 
through choice (estimate 50 paired scans).  In an observation study with 180 subjects 82% of subjects had sputum 
conversion of MAC on treatment and this was associated with a significant improvement (P<0.0001) in structural 
lung disease (2).  This suggests that the numbers of scans available in this trial will support the planned analyses. 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix C3 
Version 1.2 Date 20 February 2024 
6 
REFERENCES 
1. 
Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, Gordin F, et al. An official ATS/IDSA 
statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit 
Care Med. 2007;175(4):367-416. 
2. 
Griffith DE, Adjemian J, Brown-Elliott BA, Philley JV, Prevots DR, Gaston C, et al. Semiquantitative 
Culture Analysis during Therapy for Mycobacterium avium Complex Lung Disease. American Journal of 
Respiratory and Critical Care Medicine. 2015;192(6):754-60. 
3. 
Rosenow T, Oudraad MC, Murray CP, Turkovic L, Kuo W, de Bruijne M, et al. PRAGMA-CF. A 
Quantitative Structural Lung Disease Computed Tomography Outcome in Young Children with Cystic 
Fibrosis. Am J Respir Crit Care Med. 2015;191(10):1158-65. 
4. 
Kuo W, Andrinopoulou ER, Perez-Rovira A, Ozturk H, de Bruijne M, Tiddens HA. Objective airway artery 
dimensions compared to CT scoring methods assessing structural cystic fibrosis lung disease. J Cyst Fibros. 
2017;16(1):116-23. 
5. 
Tiddens H, Andrinopoulou ER, McIntosh J, Elborn JS, Kerem E, Bouma N, et al. Chest computed 
tomography outcomes in a randomized clinical trial in cystic fibrosis: Lessons learned from the first ataluren 
phase 3 study. PLoS One. 2020;15(11):e0240898. 
6. 
Kuo W, Ciet P, Tiddens HAWM, Zhang W, Guillerman RP, Straten Mv. Monitoring Cystic Fibrosis Lung 
Disease by Computed Tomography. Radiation Risk in Perspective. American Journal of Respiratory and 
Critical Care Medicine. 2014;189(11):1328-36. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix D1 Version 1.0 Date 29 March 
2023  
i 
 
APPENDIX D1 – REGISTRY LINKAGE 
Australian Cystic Fibrosis Data Registry 
Appendix D1 – Registry Linkage 
Version 1.0 
Appendix Date 
29 March 2023 
Protocol Number  
FORMaT001 
Funding 
 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix D1 Version 1.0 Date 29 March 
2023  
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS ..................................................................................................................................... II 
ABBREVIATIONS ............................................................................................................................................. III 
APPENDIX D: REGISTRY LINKAGE .............................................................................................................. 1 
APPENDIX D1: AUSTRALIAN CYSTIC FIBROSIS DATA REGISTRY .................................................... 2 
 
PRIMARY OBJECTIVE .............................................................................................................................. 2 
 
ELIGIBILITY CRITERIA ........................................................................................................................... 2 
 
SUB-STUDY SPECIFIC PROCEDURES .................................................................................................. 2 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix D1 Version 1.0 Date 29 March 
2023  
iii 
ABBREVIATIONS  
 
ACFDR 
 
Australian Cystic Fibrosis Data Registry 
CF 
 
 
Cystic Fibrosis 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix D1 Version 1.0 Date 29 March 
2023  
1 
 
APPENDIX D: REGISTRY LINKAGE 
 
Registries that can track important health outcomes longitudinally provide an opportunity to examine the trajectories 
of patients prior to entering a trial and following completion of a trial. Many registries are now being used for tracking 
specific diseases including cystic fibrosis and non-CF bronchiectasis. 
Where a FORMaT participant is already contributing to a disease registry aligned with the FORMaT trial, consent 
would be obtained for data from the registry to be shared with FORMaT. This data would include demographics and 
clinical information such as nutritional measures, spirometry results and respiratory microbiology results from the 
previous 5 years as well as up to 5 years post trial participation. 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix D1 Version 1.0 Date 29 March 
2023  
2 
APPENDIX D1: AUSTRALIAN CYSTIC FIBROSIS DATA REGISTRY 
Investigator Lead 
Dr Susannah Ahern 
1 
PRIMARY OBJECTIVE 
Facilitate linkage between the Australian Cystic Fibrosis Data Registry (ACFDR) and the FORMaT trial database 
for data collection and to facilitate examination of longitudinal outcomes before the onset of Mycobacterium 
abscessus pulmonary disease (MABS-PD) as well as longitudinal outcomes following completion of trial 
participation. 
2 
ELIGIBILITY CRITERIA 
Additional consent will be sought from FORMaT trial participants enrolled in the ACFDR to access longitudinal data 
for five years prior to starting the FORMaT trial and five years after completing the FORMaT trial.  All Observational 
Cohort and Intervention Program participants are eligible to participate in Appendix D1 if the following inclusion 
criteria are met: 
• 
Enrolled at an Australian FORMaT trial site. 
• 
Cystic Fibrosis diagnosis. 
• 
Enrolled in the Australian Cystic Fibrosis Data Registry. 
• 
Informed consent by participant or their parent/guardian. 
3 
SUB-STUDY SPECIFIC PROCEDURES 
Data obtained in ACFDR records five years prior to enrolling in the FORMaT Master Protocol and five years after 
participating in the FORMaT trial will be accessed to examine longitudinal data in trial participants.  Conversely, 
data obtained in the FORMaT trial in consenting participants can be provided to ACFDR to populate the database. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
i 
 
 APPENDIX E1 – HEALTH ECONOMICS 
Cost Effectiveness and Resource Utilisation 
Appendix E1 – HEALTH 
ECONOMICS 
Version 1.0 
Appendix Date 
29 March 2023 
Protocol Number  
FORMaT001 
Funding 
 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS ..................................................................................................................................... II 
ABBREVIATIONS ............................................................................................................................................. III 
APPENDIX E: HEALTH ECONOMICS ........................................................................................................... 1 
APPENDIX E1: COST-EFFECTIVENESS AND RESOURCE UTILISATION ........................................... 2 
1 
INTRODUCTION ......................................................................................................................................... 2 
2 
METHODOLOGY ........................................................................................................................................ 2 
3 
COST-EFFECTIVENESS AND RESOURCE UTILISATION FOR APPENDIX A1 ........................... 3 
3.1 
COST-EFFECTIVENESS ANALYSIS ............................................................................................................ 3 
3.2 
EFFECT MEASURE .................................................................................................................................... 4 
3.3 
COSTS ...................................................................................................................................................... 5 
3.4 
COST UTILITY ANALYSIS ......................................................................................................................... 5 
4 
COST EFFECTIVENESS AND RESOURCE UTILISATION FOR APPENDIX A2 ........................... 7 
4.1 
COST-EFFECTIVENESS ANALYSIS ............................................................................................................ 7 
4.2 
EFFECT MEASURE .................................................................................................................................... 7 
4.3 
COSTS ...................................................................................................................................................... 8 
4.4 
COST UTILITY ANALYSIS ......................................................................................................................... 9 
5 
COST-EFFECTIVENESS AND RESOURCE UTILISATION FOR APPENDIX B ........................... 10 
5.1 
COSTS .................................................................................................................................................... 10 
5.2 
COST ANALYSIS ..................................................................................................................................... 10 
6 
REFERENCES ............................................................................................................................................ 11 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
iii 
ABBREVIATIONS  
 
AE 
 
 
Adverse event 
CAHE  
 
Centre for Applied Health Economics 
CEAC  
 
Cost effectiveness acceptability curve 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment  
HRQoL 
 
Health Related Quality of Life  
ICD-10  
 
International Statistical Classification of Diseases 
ICER  
 
Incremental cost-effectiveness ratios 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
NMB  
 
Net monetary benefit 
NTM  
 
Non-tuberculous mycobacterium 
PI 
 
 
Principal Investigator  
QALY  
 
Quality adjusted life years 
UK 
 
 
United Kingdom 
WTP 
 
 
Willingness to pay 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
1 
APPENDIX E: HEALTH ECONOMICS  
 
Appendix E: Health Economics consists of components aimed at gaining understanding of the healthcare costs of 
Mycobacterium abscessus pulmonary disease (MABS-PD) through collaboration with the Finding the Optimal 
Regimen for Mycobacterium abscessus treatment (FORMaT) trial.  Additional Health Economics components may 
be added during the trial.  Participation in each Health Economics component may require additional consent and are 
detailed within each of the Health Economics appendices or supplements.  The supplements are additional documents 
that expand on the scope of the appendices and provide additional detail and information to supplement the specific 
appendix they are linked to.  Health Economics components may be applicable to specific sites or groups of 
participants. Each Health Economics appendix will be described in the following format: 
• 
The named Investigator leads; 
• 
The primary and secondary objectives; 
• 
An introduction to the background; 
• 
Additional eligibility and consent requirements; 
• 
Appendix specific trial procedures; 
• 
Analysis plan. 
 
Appendix E1: Cost Effectiveness and Resource Utilisation. 
Supplement 1: Australian Health Economics and Data Linkage  
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
2 
APPENDIX E1: COST-EFFECTIVENESS AND RESOURCE UTILISATION 
Investigator Leads 
Associate Professor Joshua Byrnes and Ms Lauren Ward, Centre for Applied Health Economics (CAHE), Griffith 
University. 
1 
INTRODUCTION 
Of the different non-tuberculous mycobacterium (NTM) infections, MABS-PD is reported to have the highest 
associated treatment costs.  To help inform health policy about the treatment of MABS-PD the healthcare costs and 
cost-effectiveness of therapies are required.  Participants who do not meet eligibility criteria for Appendix A1 or A2 
or choose not to undergo treatment may still enrol in the Observational Cohort, further informing the overall burden 
of MABS-PD.  
2 
METHODOLOGY 
To capture cost utilisation data in the treatment of MABS-PD the complete resource utilisation data set is required in 
a minimum of 20% of participants enrolled in each Intervention Program(s) and the Observational Cohort.  This 
includes country specific linked administrative healthcare utilisation data where available, treatment arm allocation, 
study medications, adverse event (AE) data, and responses to health-related quality of life (HRQoL) and costs 
questionnaires. These data will be entered in the FORMaT REDCap database by the FORMaT trial site and Health 
Economics research team members.  All other participants will require the minimum resource utilisation data set to 
be entered in the FORMaT REDCap database.  Minimum data includes country specific linked administrative 
healthcare utilisation data where available, HRQoL questionnaire responses and costs questionnaire responses. 
A health resource utilisation and cost questionnaire will be completed by all consenting FORMaT participants.  The 
survey will be administered at the time points outlined in the Schedule of Assessments tables in the relevant 
appendices.  The questionnaire is based on the ‘Annotated cost questionnaire’ originally designed for the United 
Kingdom (UK) setting but will be appropriately adapted for each country by the health economics lead investigator 
and lead Principal Investigator (PI) for each respective country.  Within the health resource utilisation and cost 
questionnaire, participants will be provided an opportunity to provide feedback.  This feedback will be used as an 
initial quality improvement measure and to confirm face and content validity.  Participants who indicate their 
willingness to be contacted to improve the questionnaire will be contacted by the health economics team and an 
unstructured interview conducted to receive feedback and suggestions for greater clarity and/or additional content to 
the questionnaire.  Interviews will be conducted via a convenient and remote mode that is available to the participant 
(e.g., phone or videoconference). 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
3 
3 
COST-EFFECTIVENESS AND RESOURCE UTILISATION FOR 
APPENDIX A1 
 
3.1 
COST-EFFECTIVENESS ANALYSIS 
The primary cost-effectiveness analysis will be conducted using a cost-utility analysis for each of the participating 
countries’ health system perspective based on trial participant data.  In addition to analyses for a) health system costs 
only, a broader perspective will also be applied to also include b) costs for both direct and indirect health care costs 
including patient/carer productivity losses. 
Comparative analysis will be completed on an intention-to-treat strategy where patients are analysed within the 
treatment group to which they were randomly allocated, regardless of, for example, whether or not they received the 
treatment medication they were allocated to.  Results will be presented as incremental cost-effectiveness ratios 
(ICERs) with their corresponding 95% confidence intervals and cost-effectiveness acceptability curves (CEACs).  
The ICER represents the additional cost for an incremental improvement in outcome when comparing between 
groups, Equation 1: 
𝐸𝐸𝐸𝐸(1)                                    𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼= ൫𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑒𝑒𝑒𝑒𝑒𝑒− 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐൯
൫𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝑒𝑒𝑒𝑒𝑒𝑒− 𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐൯
൘
 
Where: 
Cost = sum costs associated with treatment and consequences of treatment 
Effect = summary health outcome measure of interest  
exp = experimental group of interest 
comp = experimental comparator group  
 
All current treatment paths that include the intensive phase within the platform trial will be evaluated simultaneously 
prior to adjustment in the platform trial design.  Primary analysis (i) will be with respect to which therapy combination 
(including both the initial and consolidation phases) is most cost-effective.  Additional analyses will also consider 
which therapy combination is the most cost-effective with respect to initial treatment (ii); which therapy combination 
is the most cost-effective for those who are clear of Mycobacterium abscessus (MABS) at 4 weeks (iii); and which 
therapy combination is the most cost-effective for those who have remained positive for MABS at 4 weeks (iv).  Cost 
effectiveness analyses within each of the four analysis sets will be completed simultaneously with ICER results 
presented relative to the treatment group with the lowest cost.  An intervention arm will be considered cost-effective 
where the ICER is less than or equal to each countries respective cost effectiveness threshold (λ), the value of an 
incremental improvement in effect.  However, there is considerable uncertainty as to any given countries λ.  As such, 
cost effectiveness acceptability curves (CEACs) will be presented as a way to examine the probability of the 
intervention being cost effective, given various values of a countries λ. 
As the ICER is a ratio and multiple treatment strategies are being explored simultaneously, several difficulties may 
arise in its interpretation.  A positive ratio can represent both higher costs and better outcomes in the experimental 
group, and lower costs and less favourable outcomes (compared to the control group).  Moreover, a negative ratio 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
4 
can indicate higher costs coupled with worse outcomes (comparator dominates the intervention) as well as lower 
costs and better outcomes (intervention dominates the comparator).  As such, the net monetary benefit (NMB) of 
each intervention will also be estimated.  Whereby, net benefit is estimated by multiplying the outcome by λ, and 
subtracting costs, as per Equation 2: 
𝐸𝐸𝐸𝐸(2)                                    𝑁𝑁𝑁𝑁𝑁𝑁= 𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸∗ λ −Cost 
Where: 
Cost = sum costs associated with treatment and consequences of treatment 
Effect = summary health outcome measure of interest  
λ = the value of an incremental improvement in effect 
 
For each intervention the NMB will be estimated and ranked according to the largest NMB.  Again, given the 
uncertainty as to any given countries λ, the probability of an intervention being the most cost effective will be 
explored over a range of estimates of λ. 
 
3.2 
EFFECT MEASURE 
The summary health outcome measure to be included in the analysis is Quality Adjusted Life Years (QALYs). 
QALYs are estimated based on the sum of the duration of time living in respective health states.  Where health states 
are described by responses to the EQ-5D and CHU9D surveys for adults and children respectively.  The utility values 
for each health state will be informed by country specific utility valuation sets and applied respectively for each 
country specific analysis.  Generally, QALYs are estimated based on Equation 3: 
𝐸𝐸𝐸𝐸(3)                                    𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄= ෍
𝑄𝑄𝑡𝑡
(1 + 𝑟𝑟)𝑡𝑡−𝑎𝑎
𝑎𝑎+𝐿𝐿
𝑡𝑡=𝑎𝑎
 
Where:  
QALY = quality adjusted life years 
a = current age 
L = lifetime or model duration 
t = time period within that lifetime/model duration  
Q = vector of health-related quality of life weights for each time period  
r = discount rate 
 
In this analysis, individual QALYs will be estimated using an area under the curve approach (1). For each individual, 
QALYs are estimated based on the change in health-related quality of life assuming change in health state occurs 
linearly between measurements.  The unadjusted difference in QALYs between the randomisation groups is 
calculated as per Equation (2) in which the mean difference between health related quality of life utility scores are 
multiplied with the time in years between observations and divided with 4: 
𝐸𝐸𝐸𝐸(4)                                     𝐴𝐴𝐴𝐴𝐴𝐴𝑖𝑖= 1
2 ෍(𝑡𝑡𝑗𝑗+1 −𝑡𝑡𝑗𝑗)(𝑄𝑄𝑗𝑗+ 𝑄𝑄𝑗𝑗+1)
𝑛𝑛𝑖𝑖
𝑗𝑗=1
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
5 
Where:  
𝑄𝑄𝑖𝑖𝑖𝑖 = health-related quality of life weights based on quality of life survey responses  
𝑡𝑡𝑖𝑖𝑖𝑖 = represents the observation time period, 
j = 1, …ni observations  
 
i = 1, …, m participants 
 
3.3 
COSTS 
Costs will include both medication and diagnostic costs associated with treatment and monitoring as well as costs 
associated with community, hospital and emergency department presentations during treatment.  This will enable the 
inclusion of costs associated with treatment related adverse events. 
Descriptive data for treatment related and all other health care utilisation will be presented with respect to counts at 
an aggregated descriptor level.  For example, International Statistical Classification of Diseases (ICD-10) codes for 
admitted patient separations, anatomical therapeutic chemical classification for prescription medications and major 
diagnostic classification for emergency department presentations.  More formally, costs for both experimental and 
comparator groups will be estimated as Equation 5: 
𝐸𝐸𝐸𝐸 (5)                               𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶= ෍
𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑡𝑡
(1 + 𝑟𝑟)𝑡𝑡−𝑎𝑎
𝑎𝑎+𝐿𝐿
𝑡𝑡=𝑎𝑎
 
Where:  
Cost = cost incurred in period 
a = current age 
L = lifetime or model duration 
t = time period within that lifetime/model duration  
r = discount rate 
 
3.4 
COST UTILITY ANALYSIS 
Analysis of the cost-utility of the interventions will be conducted with the use of a Seemingly Unrelated Regression 
(2).  The system of Seemingly Unrelated Regression equations is being used as it has been argued that such methods 
are generally robust to skewed data and to allow for any correlation between costs and effects.  Multivariate 
regression analysis of the NMB will be undertaken with the intervention group as the primary explanatory variable 
of interest.  Linear compared to general model specification will be determined based on comparison of summary 
goodness of fit measures including Akaike’s Information Criteria and Bayesian information criterion as well as 
Pregibon and Modified Park Test.  Separate regression models will be fitted for a) the entire population b) block-
randomised sub-groups.  Within these analytical frameworks it is possible to control for baseline scores, and 
confounding variables (3, 4).  Bootstrapping will be used to obtain multiple estimates for the group difference, 
allowing a probabilistic interpretation of results: the percentage of estimates of the group difference greater than one 
– indicating better results for the experimental group – is plotted for each value of willingness to pay (WTP), resulting 
in the CEAC (5). 
All models will take into account clustering by site.  Missing data will be addressed using multiple imputation (6).  
A blinded data review will inform the imputation strategy and the selection of multivariable models.  To assess the 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
6 
effect of missing data, economic analyses will be performed on the imputed data, and on complete cases.  A complete-
case analysis will only include participants if complete cost and outcome data at all time points are available for that 
participant. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
7 
4 
COST EFFECTIVENESS AND RESOURCE UTILISATION FOR 
APPENDIX A2  
The primary analysis for this arm will be with respect to which consolidation therapy is most cost-effective. 
Specifically, cost effectiveness analyses for each of the consolidation treatment groups will be completed 
simultaneously with ICER results presented relative to the treatment group with the lowest cost.  The NMB of each 
intervention will also be estimated with intervention strategies ranked by highest NMB. 
4.1 
COST-EFFECTIVENESS ANALYSIS 
The primary cost-effectiveness analysis will be conducted using a cost-utility analysis for each of the participating 
countries’ health system perspective based on trial participant data.  In addition to analyses for a) health system costs 
only, a broader perspective will also be applied to also include b) costs for both direct and indirect health care costs 
including patient/carer productivity losses. 
Comparative analysis will be completed on an intention-to-treat strategy where patients are analysed within the 
treatment group to which they were randomly allocated, regardless of, for example, whether or not they received the 
treatment medication they were allocated to.  Results will be presented as incremental cost-effectiveness ratios 
(ICERs) with their corresponding 95% confidence intervals and cost-effectiveness acceptability curves (CEACs). 
The ICER represents the additional cost for an incremental improvement in outcome when comparing between 
groups, Equation 1: 
𝐸𝐸𝐸𝐸(1)                                    𝐼𝐼𝐼𝐼𝐼𝐼𝐼𝐼= ൫𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑒𝑒𝑒𝑒𝑒𝑒− 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐൯
൫𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝑒𝑒𝑒𝑒𝑒𝑒− 𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝐸𝑐𝑐𝑐𝑐𝑐𝑐𝑐𝑐൯
൘
 
Where: 
Cost = sum costs associated with treatment and consequences of treatment 
Effect = summary health outcome measure of interest  
exp = experimental group of interest 
comp = experimental comparator group  
 
4.2 
EFFECT MEASURE 
The summary health outcome measure to be included in the analysis is QALYs. QALYs are estimated based on the 
sum of the duration of time living in respective health states.  Where health states are described by responses to the 
EQ-5D and CHU9D surveys for adults and children respectively.  The utility values for each health state will be 
informed by country specific utility valuation sets and applied respectively for each country specific analysis.  
Generally, QALYs are estimated based on Equation 2: 
𝐸𝐸𝐸𝐸(2)                                    𝑄𝑄𝑄𝑄𝑄𝑄𝑄𝑄= ෍
𝑄𝑄𝑡𝑡
(1 + 𝑟𝑟)𝑡𝑡−𝑎𝑎
𝑎𝑎+𝐿𝐿
𝑡𝑡=𝑎𝑎
 
Where:  
QALY = quality adjusted life years 
a = current age 
L = lifetime or model duration 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
8 
t = time period within that lifetime/model duration  
Q = vector of health-related quality of life weights for each time period  
r = discount rate 
 
In this analysis individual QALYs will be estimated using an area under the curve approach (1).  For each individual, 
QALYs are estimated based on the change in health-related quality of life assuming change in health state occurs 
linearly between measurements.  The unadjusted difference in QALYs between the randomisation groups is 
calculated as per Equation 2 in which the mean difference between health-related quality of life utility scores are 
multiplied with the time in years between observations and divided with 3: 
𝐸𝐸𝐸𝐸(3)                                     𝐴𝐴𝐴𝐴𝐴𝐴𝑖𝑖= 1
2 ෍(𝑡𝑡𝑗𝑗+1 −𝑡𝑡𝑗𝑗)(𝑄𝑄𝑗𝑗+ 𝑄𝑄𝑗𝑗+1)
𝑛𝑛𝑖𝑖
𝑗𝑗=1
 
Where:  
𝑄𝑄𝑖𝑖𝑖𝑖 = health-related quality of life weights based on quality-of-life survey responses  
𝑡𝑡𝑖𝑖𝑖𝑖 = represents the observation time period, 
j = 1, …ni observations  
i = 1, …, m participants  
 
4.3 
COSTS 
Costs for the consolidation group will include both medication and diagnostic costs associated with treatment and 
monitoring as well as costs associated with community, hospital and emergency department presentations during 
treatment phase. This will enable the inclusion of costs associated with treatment related adverse events.  
Descriptive data for treatment related and all other health care utilisation will be presented with respect to counts at 
an aggregated descriptor level.  For example, ICD-10 codes for admitted patient separations, anatomical therapeutic 
chemical classification for prescription medications, major diagnostic classification for emergency department 
presentations.  More formally, costs for consolidation therapies will be estimated as, equation 4: 
 
𝐸𝐸𝐸𝐸(4)                                       𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶= ෍
𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑡𝑡
(1 + 𝑟𝑟)𝑡𝑡−𝑎𝑎
𝑎𝑎+𝐿𝐿
𝑡𝑡=𝑎𝑎
 
Where:  
Cost = cost incurred in period 
a = current age 
L = lifetime or model duration 
t = time period within that lifetime/model duration  
r = discount rate 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
9 
4.4 
COST UTILITY ANALYSIS 
Analysis of the cost-utility of the consolidation therapies will be conducted with the use of a Seemingly Unrelated 
Regression (2).  The system of Seemingly Unrelated Regression equations is being used as it has been argued that 
such methods are generally robust to skewed data and to allow for any correlation between costs and effects.  Here, 
separate regression models will be fitted for a) the entire population b) block-randomised sub-groups.  Within these 
analytical frameworks it is possible to control for baseline scores, and confounding variables (3, 4).  Bootstrapping 
will be used to obtain multiple estimates for the group difference, allowing a probabilistic interpretation of results: 
The percentage of estimates of the group difference greater than one – indicating better results for the experimental 
group – is plotted for each value of WTP, resulting in the CEAC (5). 
All models will take into account clustering by site.  Analyses will be shown for a) health system costs only and b) 
costs including direct and indirect health care costs including for example, patient/carer productivity losses.  Missing 
data will be addressed using multiple imputation (6).  A blinded data review will inform the imputation strategy and 
the selection of multivariable models.  To assess the effect of missing data, economic analyses will be performed on 
the imputed data, and on complete cases.  A complete-case analysis will only include participants if complete cost 
and outcome data at all time points are available for that participant. 
 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
10 
5 
COST-EFFECTIVENESS AND RESOURCE UTILISATION FOR 
APPENDIX B 
 
5.1 
COSTS 
Costs will include both medication and diagnostic costs associated with monitoring as well as costs associated with 
community, hospital and emergency department presentations during this time.  This will enable the inclusion of 
costs associated with adverse events. 
Descriptive data for MABS infection related and all other health care utilisation will be presented with respect to 
counts at an aggregated descriptor level.  For example, ICD-10 codes for admitted patient separations, anatomical 
therapeutic chemical classification for prescription medications, and major diagnostic classification for emergency 
department presentations.  More formally, costs will be estimated as Equation 5: 
𝐸𝐸𝐸𝐸 (5)                               𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇𝑇 𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶= ෍
𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝐶𝑡𝑡
(1 + 𝑟𝑟)𝑡𝑡−𝑎𝑎
𝑎𝑎+𝐿𝐿
𝑡𝑡=𝑎𝑎
 
Where:  
Cost = cost incurred in period 
a = current age 
L = lifetime or model duration 
t = time period within that lifetime/model duration  
r = discount rate 
 
5.2 
COST ANALYSIS 
A cost analysis will be undertaken with a descriptive analysis of the total cost per person, the total cost per month of 
follow up between Day 0 and Final outcome.  In addition, the expected cost per adverse event by adverse event type 
will be estimated. 
 

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix E1  
Version 1.0 Date 29 March 2023 
11 
6 
REFERENCES 
1. 
Walters SJ. Quality of Life Outcomes in Clinical Trials and Health-Care Evaluation: A Practical Guide to 
Analysis and Interpretation. 2009. 
2. 
Zellner A. An Efficient Method of Estimating Seemingly Unrelated Regressions and Tests for Aggregation 
Bias. Journal of the American Statistical Association. 1962;57(298):348-68. 
3. 
Glick HA, Doshi JA, Sonnad SS, Polsky D. Economic Evaluation in Clinical Trials: Oxford University Press 
Catalogue; 2007. 
4. 
Hoch JS, Briggs AH, Willan AR. Something old, something new, something borrowed, something blue: a 
framework for the marriage of health econometrics and cost‐effectiveness analysis. Health Economics. 
2002;11(5):415-30. 
5. 
Fenwick E, Byford S. A guide to cost-effectiveness acceptability curves. Br J Psychiatry. 2005;187:106-8. 
6. 
Little RJ, Rubin DB. Statistical Analysis with Missing Data. 2nd edition ed: Wily-Interscience; 2002. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
i 
 
APPENDIX F 
General Statistical Principles 
Appendix F – General Statistical 
Principles 
Version 1.0 
Appendix Date 
29 March 2023 
Protocol Number  
FORMaT001 
Funding 
1- Medical Research Future Fund, Australian Government 
Department of Health 
2- Cystic Fibrosis Foundation 
3- Anonymous Donor 
4- Thoracic Society of Australia and New Zealand 
5- The University of Queensland 
6- Children’s Hospital Foundation 
Australian and New Zealand  
Clinical Trials Registry Number 
ACTRN12618001831279 
ClinicalTrials.gov Identifier  
NCT04310930 
Sponsor 
The University of Queensland 
Contact 
FORMaTtrial@uq.edu.au 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
ii 
TABLE OF CONTENTS 
TABLE OF CONTENTS ...................................................................................................................... II 
TABLE OF TABLES .......................................................................................................................... III 
TABLE OF FIGURES ........................................................................................................................ III 
ABBREVIATIONS ............................................................................................................................... IV 
1 
INTRODUCTION ........................................................................................................................... 1 
2 
RANDOMISATION ........................................................................................................................ 1 
2.1 
BLINDING OF TREATMENT ALLOCATION ................................................................................................. 1 
2.2 
MINIMISATION ......................................................................................................................................... 1 
2.3 
BAYESIAN ADAPTIVE RANDOMISATION .................................................................................................. 2 
3 
STATISTICAL SIMULATIONS FOR POWER CALCULATIONS ........................................ 3 
3.1 
SCENARIO DEFINITIONS ........................................................................................................................... 5 
3.2 
INTENSIVE PHASE POWER SIMULATIONS .................................................................................................. 5 
3.3 
PROLONGED INTENSIVE VS SHORT INTENSIVE (IMMEDIATE CONSOLIDATION) AT 12 WEEKS POWER 
SIMULATIONS ....................................................................................................................................................... 6 
3.4 
CONSOLIDATION PHASE POWER SIMULATIONS ........................................................................................ 7 
4 
ESTIMANDS ................................................................................................................................... 7 
5 
POPULATIONS OF ANALYSIS .................................................................................................. 8 
6 
INTERIM ANALYSES, DATA MONITORING AND STOPPING GUIDELINES................ 9 
7 
FINAL ANALYSIS ......................................................................................................................... 9 
7.1 
INTERVENTION COMPARISONS WITHIN A RANDOMISATION STAGE ....................................................... 10 
7.1.1 Handling missing data ....................................................................................................................... 10 
7.1.2 Managing carry-over effects .............................................................................................................. 11 
7.1.3 Managing population time trends ...................................................................................................... 11 
7.1.4 Adjustment for multiplicity ................................................................................................................ 11 
7.2 
COMPARISON OF DYNAMIC TREATMENT REGIMENS .............................................................................. 12 
8 
REFERENCES .............................................................................................................................. 15 
 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
iii 
TABLE OF TABLES 
Table 1: Intensive phase six-week outcome probabilities ......................................................................................... 3 
Table 2: Continued intensive vs not 12-week outcome probabilities ........................................................................ 4 
Table 3: Consolidation phase long-term outcome probabilities ................................................................................ 4 
Table 4: Intensive phase outcome power for different hypotheses, 100,000 simulation replicates .......................... 5 
Table 5: 12 weeks outcome power for different hypotheses, 100,000 simulation replicates .................................... 6 
Table 6: Consolidation Power for different hypotheses, 100,000 simulation replicates ........................................... 7 
 
TABLE OF FIGURES 
Figure 1: SMART design for the FORMaT study. ..................................................................................................... 13 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
iv 
ABBREVIATIONS 
 
AE 
 
 
Adverse Event 
AI 
 
 
Adaptive intervention 
BAL 
 
 
Bronchoalveolar Lavage 
BAR 
 
 
Bayesian Adaptive Randomisation 
CI 
 
 
Confidence Interval 
CT 
 
 
Computed Tomography 
CTCAE 
 
Common Terminology Criteria for Adverse Events  
DTR 
 
 
Dynamic treatment regimen 
FEV1  
 
Forced Expiratory Volume in one second 
FORMaT 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment 
HRQoL 
 
Health Related Quality of Life 
IA 
 
 
Inhaled Amikacin 
ICE 
 
 
Intercurrent event 
iDSMB  
 
Independent Data and Safety Monitoring Board 
ITT 
 
 
Intention To Treat 
IV 
 
 
Intravenous 
IVA 
 
 
Intravenous Amikacin 
MABS  
 
Mycobacterium abscessus 
MABS-PD 
 
MABS Pulmonary Disease 
OR 
 
 
Odds ratio 
R-Con  
 
Randomisation – Consolidation  
R-PI 
 
 
Randomisation – Prolonged Intensive  
R-SI 
 
 
Randomisation – Short Intensive  
SAE 
 
 
Serious Adverse Event 
SAP 
 
 
Statistical analysis plan 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
v 
SMART 
 
Sequential Multiple Assignment Randomised Trial

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
1 
1 
INTRODUCTION 
Appendix F: General Statistical Principles, provides details of the general statistical principles of the Intervention 
Program(s) (Appendix A).  The statistical principles pertaining to the Observational Cohort, discovery sub-studies 
and integrated studies are detailed in the relevant appendices.  The Statistical Analysis Plan(s) (SAP) for Appendix 
A will provide a detailed plan of the statistical analysis of the Appendix A intervention program(s). 
 
2 
RANDOMISATION 
The initial design of the FORMaT trial detailed in Appendix A1 has 3 stages of randomisation (see Figure 1 in 
Appendix A1).  Details of the randomisation process at the 3 stages can be found in sections 6.3 and 12.1 of Appendix 
A1. 
 
2.1 
BLINDING OF TREATMENT ALLOCATION 
The initial Intervention Program detailed in Appendix A1 is randomised and open label, however the FORMaT trial 
may include placebo controlled double blind randomised interventions in the future.  If this occurs, details of the 
blinding will be provided in the relevant appendix. 
 
2.2 
MINIMISATION 
To ensure balance between arms in important patient characteristics, randomisation at each stage of the trial will use 
minimisation with a random element.  Minimisation is a dynamic randomisation approach used in clinical trials to 
balance allocation to treatment arms with respect to a number of important stratification factors.  In minimisation, 
the first participant is allocated to their treatment arm at random.  Subsequent participants are assigned to a treatment 
arm by first selecting the preferred arm that would best improve the balance of participants across the arms based on 
the stratification variables of interest in terms of the numerical difference in the sample size in each of the treatment 
arms across all of the stratification factors (1, 2).  The preferred arm is then selected with a probability of 0.7, with 
the rest of the probability split between the alternative arms. 
Where the randomisation consists of 3 or more interventions, the allocation probabilities will be updated using 
Bayesian Adaptive Randomisation (BAR, see section 2.3).  Following BAR, minimisation will be conducted using 
Biased Coin Minimisation (BCM) (3).  Under this method, the same methodology as standard minimisation will be 
used to determine the preferred intervention, but the randomisation probabilities will be altered to reflect the 
minimisation probabilities and the updated allocation ratios from the BAR as detailed in Han et al (3). 
Randomisation will be conducted electronically through the trial database following completion of all the specific 
required data entry by the study team at each site.  Participants will be randomised according to the stratification 
criteria described below using the weights specified for each factor: 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
2 
1.  Macrolide resistance*: Yes or no (weight = 50% in randomisations 1 and 2 (Randomisation-Short Intensive 
(R-SI) and Randomisation-Prolonged Intensive (R-PI), respectively), 25% in randomisation 3 
(Randomisation-Consolidation (R-Con))). 
*Any of these measurement methods are acceptable for defining macrolide resistance (in order of 
preference): Inducible at 14 days or constitutive at 3 days, and/or; Erm(41) status: Functional or 
dysfunctional, and/or; MABS subspecies: M. a. abscessus & M. a. bolletii combined or M. a. massiliense. 
2. Age: <12 years, 12-30 years and >30 years of age (weight = 20%). 
3. Sex: Male or Female (weight = 7.5%). 
4. Location: Asia Pacific as one stratum (includes Australia, New Zealand, Singapore and other Asian Pacific 
countries), United Kingdom and Republic of Ireland as one stratum, Europe as another stratum (includes 
Denmark, France, Netherlands) and Canada and the Americas as one stratum (weight = 7.5%). Parts of the 
world not listed above can be added into the regions based on closest proximity to the regions longitudinally. 
5. Cystic Fibrosis Status: Yes or no (weight = 7.5%). 
6. Mixed NTM infections at enrolment: Yes or no (weight =7.5%). 
7. MABS positive culture (at first randomisation to intensive therapy (R-SI) and for R-PI all participants will 
have a positive culture, so this factor will not be required.  However, it will be required for R-Con: Yes or no 
(weight = 25%). 
 
2.3 
BAYESIAN ADAPTIVE RANDOMISATION 
When a randomisation stage involves randomising participants between 3 or more interventions, BAR will be used 
to update the allocation ratios between the intervention arms.  When the Intervention Program (Appendix A1) initially 
begins, there will be 3 interventions in the intensive phase (R-SI), hence BAR will be used in this phase, but not the 
other randomisations.  As treatments are added into the later randomisation stages it may also be used at other 
randomisation stages (see Randomisation sections in Appendix A1 and A2).  In the intensive phase, after achieving 
the minimum number of 100 subjects to be recruited into this randomisation stage, BAR will be implemented at two 
interim updates (after 100 and 200 participants have been randomised), unless the data overwhelmingly supports 
early stopping for futility, or the maximum sample size is attained (see section 3). 
For the BAR, the following will be used to update the allocation ratios in the first randomisation.  Let 𝑝𝑝𝐴𝐴, 𝑝𝑝𝐵𝐵 and 𝑝𝑝𝐶𝐶 
represent the true probability of six-week clearance with tolerability on arms A, B and C respectively.  At each of the 
interim analyses the posterior probabilities of: 
1) Inhaled amikacin (IA) being superior to intravenous amikacin (IVA) with clofazimine, 𝑃𝑃(𝑝𝑝𝐵𝐵> 𝑝𝑝𝐴𝐴) and  
2) IVA without clofazimine being superior to IVA with clofazimine, 𝑃𝑃(𝑝𝑝𝐶𝐶> 𝑝𝑝𝐴𝐴)  
will be estimated.  To compute the posterior probabilities in 1) and 2), a prior distribution on the success probabilities 
(𝑝𝑝𝐴𝐴, 𝑝𝑝𝐵𝐵 and 𝑝𝑝𝐶𝐶) will be specified.  A beta prior distribution, 𝑏𝑏𝑏𝑏𝑏𝑏𝑏𝑏(0.2,0.8), will be used and the posterior probabilities 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
3 
𝑃𝑃(𝑝𝑝𝐵𝐵> 𝑝𝑝𝐴𝐴) and 𝑃𝑃(𝑝𝑝𝐶𝐶> 𝑝𝑝𝐴𝐴) will be computed using formula (2) in Wason and Trippa (4).  The parameters of the 
prior are chosen so that the prior distribution is centred around an initial guess 𝑝𝑝𝐴𝐴
∗. 
These will then be used to set the allocation ratio for randomising the next stage of participants respectively to arms 
A, B and C namely 𝜋𝜋𝐴𝐴, 𝜋𝜋𝐵𝐵, 𝜋𝜋𝐶𝐶.  The formula used to set the allocation is: 
𝜋𝜋𝐴𝐴= 1/3
𝜋𝜋𝐵𝐵= (2/3) ×
𝑃𝑃(𝑝𝑝𝐵𝐵> 𝑝𝑝𝐴𝐴)𝛾𝛾(𝑛𝑛/𝑁𝑁)
𝑃𝑃(𝑝𝑝𝐵𝐵> 𝑝𝑝𝐴𝐴)𝛾𝛾(𝑛𝑛/𝑁𝑁) + 𝑃𝑃(𝑝𝑝𝐶𝐶> 𝑝𝑝𝐴𝐴)𝛾𝛾(𝑛𝑛/𝑁𝑁)
𝜋𝜋𝐶𝐶= (2/3) ×
𝑃𝑃(𝑝𝑝𝐶𝐶> 𝑝𝑝𝐴𝐴)𝛾𝛾(𝑛𝑛/𝑁𝑁)
𝑃𝑃(𝑝𝑝𝐵𝐵> 𝑝𝑝𝐴𝐴)𝛾𝛾(𝑛𝑛/𝑁𝑁) + 𝑃𝑃(𝑝𝑝𝐶𝐶> 𝑝𝑝𝐴𝐴)𝛾𝛾(𝑛𝑛/𝑁𝑁) ,
 
where 𝛾𝛾(𝑛𝑛/𝑁𝑁) = 12 ∗(ቀ
𝑛𝑛
𝑁𝑁ቁ)2.5, n/N represents the proportion of planned sample size recruited so far (1/3 at first 
interim and 2/3 at second interim).  This procedure follows the one recommended by Wason and Trippa (4). 
 
3 
STATISTICAL SIMULATIONS FOR POWER CALCULATIONS 
The design of this trial, including the stopping rules and the planned sample size, will be guided by simulating data 
from realistic scenarios for the outcomes and the treatment effects obtained from discussions with content experts.  
The initial simulations will incorporate outcomes from the 3 stages of the trial simultaneously and will be used to 
explore the frequentist operating characteristics of the trial at the end of each stage.  In this section, we provide details 
of the initial simulations used to develop the trial design and sample size for Appendix A. 
We have powered the trial assuming 300 Intervention Program trial participants are recruited in total.  The sample 
size of 300 participants is based on the feasibility of recruitment and providing reasonable power for plausible effect 
sizes based on the results of the simulations.  Two interim analyses to update the allocation probabilities using BAR 
in randomisation stage 1 (R-SI) will be conducted after 100 and 200 patients have their outcome data available. 
We have considered six different scenarios for the probability of clearance with tolerability outcome at the three 
different randomisation stages.  Tables 1 to 3 show these probabilities for each scenario. 
 
Table 1: Intensive phase six-week outcome probabilities 
Arm 
Scenario 1 
Scenario 2 
Scenario 3 
Scenario 4 
Scenario 5 
Scenario 6 
Intensive A: IVA with 
clofazimine (reference 
arm) 
0.5 
0.45 
0.45 
0.5 
0.7 
0.50 
Intensive B: IA with 
clofazimine 
0.5 
0.65 
0.45 
0.7 
0.5 
0.65 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
4 
Intensive C: IVA without 
clofazimine 
0.5 
0.45 
0.65 
0.7 
0.5 
0.65 
 
Table 2: Continued intensive vs not 12-week outcome probabilities 
Pathway 
Scenario 1 
Scenario 2 
Scenario 3 
Scenario 4 
Scenario 5 
Scenario 6 
1. MABS positive, 
Prolonged intensive, 
Consolidation a (Oral only) 
0.5 
0.5 
0.7 
0.5 
0.5 
0.30 
2. MABS positive, 
Prolonged intensive, 
Consolidation b (Oral+IA) 
0.5 
0.5 
0.7 
0.5 
0.5 
0.30 
3. MABS positive, 
Immediate Consolidation a  
0.5 
0.7 
0.5 
0.6 
0.4 
0.55 
4. MABS positive, 
Immediate Consolidation b 
0.5 
0.7 
0.5 
0.6 
0.4 
0.55 
 
Table 3: Consolidation phase long-term outcome probabilities 
Pathway 
Scenario 1 
Scenario 2 
Scenario 3 
Scenario 4 
Scenario 5 
Scenario 6 
1. MABS positive, 
Prolonged intensive, 
Consolidation a 
0.5 
0.5 
0.30 
0.7 
0.60 
0.3 
2. MABS positive, 
Prolonged intensive, 
Consolidation b 
0.5 
0.7 
0.45 
0.5 
0.80 
0.5 
3. MABS positive, 
Immediate Consolidation a 
0.5 
0.5 
0.30 
0.7 
0.55 
0.5 
4. MABS positive, 
Immediate Consolidation b 
0.5 
0.7 
0.45 
0.5 
0.75 
0.7 
5. MABS negative, 
Immediate Consolidation a 
0.5 
0.5 
0.30 
0.7 
0.75 
0.7 
6. MABS negative, 
Immediate Consolidation b 
0.5 
0.7 
0.45 
0.5 
0.95 
0.9 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
5 
3.1 
SCENARIO DEFINITIONS 
• 
Scenario 1 represents the null scenario where all treatment strategies (i.e. all interventions at each stage) have 
the same effect. 
• 
Scenario 2 represents a scenario where one intensive phase treatment provides an advantage in probability 
of clearance with tolerability, prolonged intensive is worse than immediate consolidation at 12 weeks, and 
oral+IA provides an advantage over oral for consolidation for each type of patient. 
• 
Scenario 3 represents a similar scenario to Scenario 2 except prolonged intensive is better than immediate 
consolidation at 12 weeks and consolidation probabilities are lower. 
• 
In Scenario 4, both arm B and C provide advantages over arm A at 6 weeks, with oral being superior to 
oral+IA at the long-term outcome, immediate consolidation is better than prolonged intensive at 12 weeks 
with lower probabilities than in Scenario 2. 
• 
In Scenario 5, arm A is superior to B and C. Consolidation probabilities are highly variable by participant 
pathway (albeit with oral+IA having the same absolute improvement in each case), prolonged intensive is 
better than immediate consolidation at 12 weeks with a lower probability of clearance with tolerability. 
• 
Scenario 6 is similar to Scenario 5, with each pathway having generally lower probability of clearance with 
tolerability at the long-term outcome, both arm B and C provide advantages over arm A at 6 weeks with 
lower probability of clearance with tolerability and prolonged intensive is worse than immediate 
consolidation at 12 weeks with lower probabilities than in Scenarios 2 and 4. 
For each scenario, 100,000 simulation replicates were conducted. In each replicate, 300 patients have their pathways 
through the trial simulated with 6-week outcome, 12-week outcome and long-term outcome generated with a 
binomial distribution with probability according to the relevant scenario in the above tables. 
 
3.2 
INTENSIVE PHASE POWER SIMULATIONS 
The intensive phase data is analysed (in simulations) with a test of proportions assuming a normal approximation.  
Note the analysis models used in the simulations are unadjusted for covariates as it is difficult to incorporate 
covariates into a trial simulation.  For the final statistical analysis, adjustments will be made for the variables used in 
the randomisation procedure (see section 2).  It is anticipated that these adjustments will increase the statistical power.  
Table 4 shows the power of the trial for testing the two primary research questions in the intensive phase under the 
different scenarios. 
Table 4: Intensive phase outcome power for different hypotheses, 100,000 simulation replicates 
Comparison 
Scenario 1 
Scenario 2 
Scenario 3 
Scenario 4 
Scenario 5 
Scenario 6 
B vs A 
0.060 
0.870 
0.048 
0.81 
0.87 
0.56 
C vs A 
0.059 
0.052 
0.870 
0.81 
0.86 
0.56 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
6 
Generally, for cases where there is ≥20% difference between arms, the trial with 300 participants is well powered.  
The BAR procedure is advantageous when one experimental arm provides an advantage but not the other (as more 
patients are randomised to the effective arm). 
 
3.3 
PROLONGED INTENSIVE VS SHORT INTENSIVE (IMMEDIATE 
CONSOLIDATION) AT 12 WEEKS POWER SIMULATIONS 
Table 5 shows the power for the design to conclude an improvement at 12 weeks from randomising non-cleared 
patients between prolonged intensive and immediate consolidation in terms of final clearance outcome, for different 
scenarios.  When the difference between groups (prolonged intensive vs not) is greater than 25% (scenario 6) the trial 
with 300 participants has 80% power (row 1).  The adjustment for different recruitment stages (row 2, Model 1) does 
not reduce the power.  These simulations use an analysis model that is not adjusted for randomisation variables. In 
the final analysis adjusting for minimisation variables will be done which is expected to increase power (see section 
7). 
Within the simulation study different ways of analysing the data were investigated to allow adjustments for the study 
stage and treatment groups.  Row 1 shows results using a test of proportions.  The models used for analysis in the 
other rows are given below.  Rows 1 and 2 show the probability of detecting a difference between prolonged intensive 
and short intensive (immediate consolidation) at week 12, unadjusted and adjusted for stage (using Model 1) 
respectively.  Rows 3 and 4 show the probability of detecting a difference between prolonged intensive treatment 
and moving directly to consolidation arms a and b respectively (adjusted for stage using Model 2).  These simulations 
indicate that Model 1 results in similar power to the fully unadjusted analysis model, and a model testing for 
interaction between path and stage does not have enough power (results not shown here). 
Table 5: 12 weeks outcome power for different hypotheses, 100,000 simulation replicates 
Pathway 
Scenario 
1 
Scenario 
2 
Scenario 
3 
Scenario 
4 
Scenario 
5 
Scenario 
6 
Prolonged vs short intensive, 12 weeks 
(unadjusted) 
0.052 
0.67 
0.67 
0.18 
0.21 
0.80 
Prolonged vs short intensive, 12 weeks 
(adjusted for stage using Model 1) 
0.054 
0.67 
0.67 
0.19 
0.21 
0.80 
Immediate Consolidation a vs Prolonged 
intensive 
(adjusted for stage using Model 2) 
0.049 
0.48 
0.50 
0.13 
0.15 
0.62 
Immediate Consolidation b vs Prolonged 
intensive 
(adjusted for stage using Model 2) 
0.051 
0.48 
0.50 
0.13 
0.15 
0.62 
 
Where: 
Model 1: 𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙(𝑃𝑃= 1|𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡, 𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠) = 𝛼𝛼0 + 𝛼𝛼1 𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡𝑡+ 𝛼𝛼2𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑒𝑒2 + 𝛼𝛼3𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑒𝑒3  

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
7 
Treat=0 if a patient with a positive sputum (after six weeks) had an extended intensive treatment. 
Treat=1 if a patient with a positive sputum started the oral consolidation directly (either oral consolidation alone or 
plus IA).  Stage corresponds to the three recruitment periods.  𝐒𝐒𝒕𝒕𝒕𝒕𝒕𝒕𝒆𝒆𝟐𝟐= 1  if a patient was recruited during the 
second period, 𝐒𝐒𝒕𝒕𝒕𝒕𝒕𝒕𝒆𝒆𝟑𝟑= 𝟏𝟏 if a patient was recruited during the third period, and 𝐒𝐒𝒕𝒕𝒕𝒕𝒕𝒕𝒆𝒆𝟐𝟐= 𝐒𝐒𝒕𝒕𝒕𝒕𝒕𝒕𝒆𝒆𝟑𝟑= 𝟎𝟎 if a patient 
was recruited during the first period. 
Model2:𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙𝑙(𝑃𝑃= 1|𝑝𝑝𝑝𝑝𝑝𝑝ℎ, 𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠) = 𝛼𝛼0 + 𝛼𝛼1 𝑝𝑝𝑝𝑝𝑝𝑝ℎ2 + 𝛼𝛼2𝑝𝑝𝑝𝑝𝑝𝑝ℎ3 + 𝛼𝛼3𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑒𝑒2 + 𝛼𝛼4𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑠𝑒𝑒3, 
where 
path 
corresponds to one of the three pathways (immediate consolidation a, immediate consolidation b, prolonged 
intensive) followed by each patient after six weeks.  P𝐚𝐚𝐚𝐚𝐡𝐡𝟐𝟐= 1 if a patient with a positive sputum after six weeks 
started consolidation a , 𝐩𝐩𝐩𝐩𝐩𝐩𝐡𝐡𝟑𝟑= 1 if a patient with a positive sputum after six weeks started consolidation b, and 
P𝐚𝐚𝐚𝐚𝐡𝐡𝟐𝟐= P𝐚𝐚𝐚𝐚𝐡𝐡𝟑𝟑= 0 if a patient with a positive sputum after six weeks had an extended intensive treatment.  Stage 
is defined as before. 
3.4 
CONSOLIDATION PHASE POWER SIMULATIONS 
Table 6 shows the power of the design to detect differences between Consolidation a (oral consolidation) vs 
Consolidation b (oral + IA consolidation).  It appears that the planned study design has good power to detect 
differences for the scenarios considered.  The consolidation phase data is analysed using a test of proportions 
assuming a normal approximation.  Again, note that the simulations are unadjusted for randomisation covariates.  In 
the final analysis we plan on adjusting for these and this adjustment is expected to result in increased power (see 
section 7). 
Table 6: Consolidation Power for different hypotheses, 100,000 simulation replicates 
Pathway 
Scenario 1 
Scenario 2 
Scenario 3 
Scenario 4 
Scenario 5 
Scenario 6 
Consolidation b vs a 1: 
3+5 vs 4+6 
0.051 
0.86 
0.63 
0.83 
0.95 
0.90 
Consolidation b vs a 2: 
1+3+5 vs 2+4+6 
0.051 
0.95 
0.77 
0.95 
0.98 
0.95 
 
4 
ESTIMANDS 
The analytical approaches for the primary and secondary outcomes will be detailed using the estimand framework.  
An estimand is a precise description of the treatment effect reflecting the clinical question posed by a given clinical 
trial objective.  It has 5 attributes: population, treatment, variable of interest (e.g. outcome), summary measure, and 
possible intercurrent events (ICEs; an event that can occur post-randomisation and preclude or affect the 
interpretation of the variable of interest e.g. discontinuation of treatment). 
When defining an estimand, it must be made clear how possible ICEs will be handled in the analysis.  Different 
approaches can be taken towards handling ICEs and are described below: 
i) 
Hypothetical: a strategy which envisages a scenario in which the ICE would not occur, e.g. if 
participants had not switched treatment or if death had not occurred. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
8 
ii) 
Treatment policy: a strategy which seeks to understand the treatment effect on the variable regardless 
of the intercurrent event, i.e. an outcome is of interest whether or not the ICE occurred prior to the 
outcome, e.g. the final outcome is of interest irrespective of whether the participant takes additional 
medication. 
iii) 
Composite: a strategy which considers the occurrence of the ICE as informative about the participants 
outcome.  Under this strategy the ICE is included in the endpoint definition, e.g. classifying the use of 
rescue medication as failure, in addition to disease progression, in a time-to-event analysis. 
iv) 
Principal Stratification: a strategy wherein treatment effects are assessed in the stratum of participants 
who would have a specific status with respect to the ICE e.g. examining the effect of treatment in 
participants who would not require rescue medication. 
v) 
While-on-treatment: a strategy where the interest is in the response to treatment prior to the occurrence 
of the ICE.  For repeated measures, values up to the ICE are of interest but not values after the ICE.  
Generally this strategy is only useful if the duration of treatment is not relevant, either because it is not 
clinically relevant or because the rate of an event or outcome is constant over time e.g. the rate of 
adverse events, where one assumes a constant hazard. 
Within the SAP, the estimand for each objective will be described using the 5 attributes above, and will specify how 
possible ICEs will be handled in the analysis.  Possible ICEs that will be considered in this study will be;  
i) Treatment discontinuation due to an adverse event (AE) with a Common Terminology Criteria for Adverse 
Events (CTCAE) grade 3 or higher or a serious adverse event (SAE). 
ii) Treatment discontinuation due to other reasons, including AEs below CTCAE grade 3. 
iii) Treatment non-compliance (intermittent or partial treatment adherence not resulting in discontinuation). 
iv) Treatment discontinuation for any reason except death. 
v) Death. 
 
5 
POPULATIONS OF ANALYSIS 
The interim analyses and the primary analysis for all sub-studies will be conducted on the Intention-To-Treat (ITT) 
population.  This population will consist of all randomised participants, with participants analysed according to the 
intervention group to which they were randomised irrespective of the intervention received. 
It is possible that participants in the intervention trial may cease one or more of the intervention treatments for their 
allocated arm because of toxicity and may need alternate therapy introduced.  In addition, it is recognised that 
clinicians will have concerns if patients remain MABS culture positive through the duration of the trial and may 
wish to change or add treatments.  All changes in the intervention treatment allocated will be captured through 
the study database and any AEs will be reported.  Irrespective of whether treatments are ceased or altered, 
participants will remain in their assigned arm for analysis.  Participants who cease or alter their treatment during 
a study stage may continue into the next stage of the trial once they complete the previous stage.  For example, 
a participant who was unable to tolerate intravenous tigecycline in the first stage might cease tigecycline and an 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
9 
alternative treatment may be included in the intensive therapy stage.  Once the intensive stage has been 
completed, they may still be randomised at stage 2 or 3.  Change of treatment required for toxicity/AE or failure 
to clear MABS would be reflected in the primary outcome of clearance of MABS with good tolerance as they 
would fail to achieve this outcome for that stage of the trial.  Details of how the ICEs (e.g. treatment 
discontinuation due to toxicity) will be addressed in the analysis will be detailed in the SAP using the estimand 
framework described in section 4. 
 
6 
INTERIM ANALYSES, DATA MONITORING AND STOPPING 
GUIDELINES 
When a randomisation stage has 3 or more intervention arms, BAR will be used to update allocation ratios as detailed 
in section 2 using data from an interim analysis (4).  Initially this will only occur in the first randomisation stage.  
Interim analyses of the stage 1 data will be performed after every 100 participants have completed 6 weeks of 
intensive therapy.  BAR will be guided by the (posterior) probability of an intervention being found to be superior to 
the reference arm, which will be used to update the allocation probability at two interim analyses (see details in 
section 2.3). 
The results of these analyses will be presented to an independent data and safety monitoring board (iDSMB) who 
will have access to unblinded data.  Initially there are no plans to stop any arms of the study due to superiority, but 
such rules may be established as the trial continues.  These will be detailed in the relevant appendix and will also be 
based on the (posterior) probability of an intervention being found to be superior to the reference arm.  The iDSMB 
may however make a recommendation about stopping current interventions if they show poor promise or futility.  If 
stopping rules are introduced, they will be defined to guide the use of these posterior probabilities. 
 
7 
FINAL ANALYSIS 
In the FORMaT trial, there will be two analyses of interest; the comparison of interventions pertaining to each stage 
of randomisation and the comparison of dynamic treatment regimens that consider all treatment combinations in the 
trial.  The final analyses will take place after the completion of each study stage.  For instance, the analyses pertaining 
to study A1.1; the comparison of short intensive therapy arms, will take place once the required number of 
participants (initially planned for a sample size of 300 participants in the intensive program, which may potentially 
change with updates following interim analysis) complete the first 6 weeks of intensive treatment in one of the three 
therapy arms. 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
10 
7.1 
INTERVENTION COMPARISONS WITHIN A RANDOMISATION STAGE 
The analyses of interventions within a randomisation stage will be conducted using standard frequentist methodology.  
When formal statistical testing is carried out the results will be presented as group differences along with 95% 
confidence intervals (CI) and p-values.  The p-values will be interpreted as the strength of evidence against the null 
hypothesis of no group differences between treatment arms. 
For binary outcomes, the effect measure of interest will be the odds ratio (OR) of each intervention compared with 
the control, estimated via a logistic regression model fitted to the outcome with a fixed effect of treatment assignment.  
Models will be adjusted for variables used in the randomisation process (i.e. the minimisation factors).  The model 
will be as follows: 
𝒍𝒍𝒍𝒍𝒍𝒍𝒍𝒍𝒍𝒍(𝑷𝑷) = 𝜷𝜷𝟎𝟎+ 𝜷𝜷𝒕𝒕 𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕+ 𝜷𝜷𝟏𝟏𝒁𝒁𝟏𝟏+ ⋯+ 𝜷𝜷𝒌𝒌𝒁𝒁𝒌𝒌 
 
 
(1) 
Where P is the probability of success, logit(P)=log(P/(1-P)), treatment is a categorical variable representing the 
intervention arm participants are assigned to, Z1,…,Zk are the variables that will be adjusted for.  Results will be 
presented as the Adjusted ORs for each treatment compared to the control (exp (𝜷𝜷𝒕𝒕)) along with the 95% CIs and p-
values. An attempt will be made to adjust for all minimisation factors, however there may have to be variables 
dropped if there are rare categories (i.e. less than 5 events per variable).  As a sensitivity analysis, an unadjusted 
analysis will also be performed. 
For continuous outcomes multiple regression models will be used where the effect measure of interest will be a 
difference in means of each intervention compared with the control.  Denoting the continuous outcome Y, and other 
notation as above, the following model will be fitted: 
𝒀𝒀= 𝜷𝜷𝟎𝟎+ 𝜷𝜷𝒕𝒕 𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕𝒕+ 𝜷𝜷𝟏𝟏𝒁𝒁𝟏𝟏+ ⋯+ 𝜷𝜷𝒌𝒌𝒁𝒁𝒌𝒌+ 𝜺𝜺   
 
 
 
(2) 
Adjusted regression coefficients (𝜷𝜷𝒕𝒕) for the difference in mean outcomes between treatment arms, 95% CIs and p-
values will be presented. 
 
7.1.1 
HANDLING MISSING DATA 
For the final analysis of any of the intervention comparisons, missing data in the primary and secondary outcomes 
(including any data set missing due to ICEs) will be handled using multiple imputation if the proportion of missing 
outcome data is greater than 5% on average across the primary and secondary outcomes.  As missing data will be in 
outcomes measured at repeated intervals following enrolment, multiple imputation will enable exploitation of all 
information including that in partially observed cases.  Multiple imputation will be conducted using chained 
equations, also known as fully conditional specification.  Ideally this would be conducted using a single imputation 
model for all outcomes, although it may be necessary to impute outcomes using separate models for each outcome 
type including all the time points.  Ordinal variables will be imputed using ordinal regression and continuous variables 
(forced expiratory volume in one second (FEV1) Z-score, CT scores) will be imputed using linear regression, or 
predictive mean matching if non-normal.  Baseline variables will be included as auxiliary variables in the imputation 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
11 
model.  Imputation will be carried out separately by cohort, to ensure that any treatment effects are maintained, using 
50 imputed datasets.  As a sensitivity analysis, a delta-adjusted analysis will also be conducted where the incomplete 
outcomes will be allowed to be different to the observed outcomes by an amount, delta.  This analysis will be 
conducted using multiple imputation via the not at random fully conditional specification (NARFCS) procedure (5).  
Potential values for delta will be elicited from content experts.  Details of this analysis and the elicitation process will 
be provided in the SAP. 
 
7.1.2 
MANAGING CARRY-OVER EFFECTS 
It is not expected that carryover will affect the statistical properties of subsequent stages of treatment as randomising 
at each stage will be independent of the other stages, hence there is no plan to adjust for carryover effects in the 
primary analysis.  However, if it appears that treatments given at previous treatment stages may affect results of 
subsequent treatment stages, and this will taken into account  in a sensitivity analysis by including a treatment 
indicator for treatment allocation at the earlier stage(s) as a covariate in equations 1 and 2 above.  Of note, the 
simulations conducted to govern the design of this study take into account the effects of different treatment pathways 
through the trial and thus allows for the possibility of carryover effects in terms of the power of the trial. 
 
7.1.3 
MANAGING POPULATION TIME TRENDS 
BAR can be subject to time trends if the patient characteristics change during the trial.  Recent work (6) has, however, 
shown that the change in treatment outcomes must be extremely high to affect the statistical properties more than a 
negligible amount.  As a secondary analysis time will be adjusted for in order to mitigate the effect of any potential 
trial trends by including time of intensive randomisation (defined as months from randomisation of first patient) as 
an additional adjustment variable (Zt) in the models described in section 7.1 above (equations 1 and 2). 
 
7.1.4 
ADJUSTMENT FOR MULTIPLICITY 
No formal adjustments for multiplicity are planned in evaluating the primary or secondary outcomes.  The results 
will be interpreted based on the strength of evidence of the treatment effects. 
 
 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
12 
7.2 
COMPARISON OF DYNAMIC TREATMENT REGIMENS 
The FORMaT trial will use a Sequential Multiple Assignment Randomised Trial (SMART) analysis approach to 
identify a sequence of treatment options that leads to the highest MABS clearance to form the basis of treatment 
guidelines for MABS-PD. 
A SMART is a multi-stage trial design that can be used to construct effective dynamic treatment regimens (DTR) 
also known as adaptive interventions (AI) or adaptive treatment strategies.  AI provide a sequence of decision rules 
that specify whether, how, and/or when to alter the type, dosage, or delivery of the intervention at a critical decision 
point based on individual characteristics and behaviour (7). 
For the FORMaT trial, the critical decision point corresponds to the intermediate response at six weeks, when the 
patients will be tested for the clearance of the bacterium.  At this time point, a patient can have a successful clearance 
(-) or non-successful clearance (+).  An AI consists of intervention options (Intensive A, Intensive B, Intensive C, 
additional intensive therapy, consolidation phase), critical decision points at which an individual is assessed and 
treatment decisions can be made (clearance status at six weeks) and tailoring a variable (successful/non-successful 
clearance). 
The aim of the SMART analysis is to identify which AI gives the highest MABS clearance during the whole trial 
(analysed at the final outcome time point).  Figure 1 below depicts different routes that a given patient can follow. 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
13 
Figure 1: SMART design for the FORMaT study.  
The R inside a circle denotes randomisation; A denotes Intensive A (Arm A); B denotes Intensive B (Arm B); C 
denotes Intensive C (Arm C); - denotes non-successful clearance; + denotes successful clearance. 
Each AI is represented as a triplet of the form (𝑋𝑋1, 𝑋𝑋2, 𝑋𝑋3) where 𝑋𝑋1 is the first-stage intervention, 𝑋𝑋2 the second-
stage intervention for responders (successful clearance) and 𝑋𝑋3 the second-stage intervention for non-responders 
(non-successful clearance).  For instance, for the first AI below it can be stated: a patient whose initial treatment is 
Intensive IVA (first stage treatment), if they achieve MABS clearance (response) at six weeks, then the second-stage 
treatment is “Consolidation: oral + IA”, or else if they don’t achieve MABS clearance (non-response) then the second-
stage treatment is “Intensive A + Consolidation a”. 
There are 24 embedded AIs in the initial design of FORMaT (listed below).  Given this high number of AIs, any 
subgroup analysis or secondary outcomes will not be considered in the SMART analysis. 
#AI 1: (Intensive IVA, Consolidation: oral + IA, Intensive IVA + Consolidation: oral + IA”) 
#AI 2: (Intensive IVA, “Consolidation: oral + IA”, “Intensive IVA + Consolidation: oral”) 
#AI 3: (Intensive IVA, “Consolidation: oral + IA”, “Consolidation: oral + IA”) 
#AI 4: (Intensive IVA, “Consolidation: oral + IA”, “Consolidation: oral”) 
#AI 5: (Intensive IVA, “Consolidation: oral”, “Intensive IVA + Consolidation: oral + IA”) 

 
 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
14 
#AI 6: (Intensive IVA, “Consolidation: oral”, “Intensive IVA + Consolidation: oral”) 
#AI 7: (Intensive IVA, “Consolidation: oral”, “Consolidation: oral + IA”) 
#AI 8: (Intensive IVA, “Consolidation: oral”, “Consolidation: oral”) 
 
#AI 9: (Intensive IA, “Consolidation: oral + IA”, “Intensive IA + Consolidation: oral + IA”) 
#AI 10: (Intensive IA, “Consolidation: oral + IA”, “Intensive IA + Consolidation: oral”) 
#AI 11: (Intensive IA, “Consolidation: oral + IA”, “Consolidation: oral + IA”) 
#AI 12: (Intensive IA, “Consolidation: oral + IA”, “Consolidation: oral”) 
#AI 13: (Intensive IA, “Consolidation: oral”, “Intensive IA + Consolidation: oral + IA”) 
#AI 14: (Intensive IA, “Consolidation: oral”, “Intensive IA + Consolidation: oral”) 
#AI 15: (Intensive IA, “Consolidation: oral”, “Consolidation: oral + IA”) 
#AI 16: (Intensive IA, “Consolidation: oral”, “Consolidation: oral”) 
 
#AI 17: (Intensive C, “Consolidation: oral + IA”, “Intensive C + Consolidation: oral + IA”) 
#AI 18: (Intensive C, “Consolidation: oral + IA”, “Intensive C + Consolidation: oral”) 
#AI 19: (Intensive C, “Consolidation: oral + IA”, “Consolidation: oral + IA”) 
#AI 20: (Intensive C, “Consolidation: oral + IA”, “Consolidation: oral”) 
#AI 21: (Intensive C, “Consolidation: oral”, “Intensive C + Consolidation: oral + IA”) 
#AI 22: (Intensive C, “Consolidation: oral”, “Intensive C + Consolidation: oral”) 
#AI 23: (Intensive C, “Consolidation: oral”, “Consolidation: oral + IA”) 
#AI 24: (Intensive C, “Consolidation: oral”, “Consolidation: oral”) 
 
The aim of this analysis is to identify which AI gives the highest MABS clearance during the whole trial (analysed 
at the final outcome time-point).  Given the high number of pairwise comparisons, the MABS clearance rate for each 
of the 24 AIs will be estimated.  The AI with the highest clearance rate will be chosen (8).  This analysis will include 
patients, with complete data at all timepoints.  The primary outcome will be analysed in the ITT population. More 
details of the statistical methodology will be provided in the SAP.

 
Finding the Optimal Regimen for Mycobacterium abscessus Treatment Appendix F 
Version 1.0 Date 29 March 2023 
15 
8 
REFERENCES 
1. 
Taves DR. Minimization: a new method of assigning patients to treatment and control groups. Clin 
Pharmacol Ther. 1974;15(5):443-53. 
2. 
Pocock SJ, Simon R. Sequential treatment assignment with balancing for prognostic factors in the controlled 
clinical trial. Biometrics. 1975;31(1):103-15. 
3. 
Han B, Enas NH, McEntegart D. Randomization by minimization for unbalanced treatment allocation. Stat 
Med. 2009;28(27):3329-46. 
4. 
Wason JM, Trippa L. A comparison of Bayesian adaptive randomization and multi-stage designs for multi-
arm clinical trials. Stat Med. 2014;33(13):2206-21. 
5. 
Tompsett DM, Leacy F, Moreno-Betancur M, Heron J, White IR. On the use of the not-at-random fully 
conditional specification (NARFCS) procedure in practice. Stat Med. 2018;37(15):2338-53. 
6. 
Villar SS, Bowden J, Wason J. Response-adaptive designs for binary responses: How to offer patient benefit 
while being robust to time trends? Pharm Stat. 2018;17(2):182-97. 
7. 
Almirall D, Nahum-Shani I, Sherwood NE, Murphy SA. Introduction to SMART designs for the 
development of adaptive interventions: with application to weight loss research. Transl Behav Med. 
2014;4(3):260-74. 
8. 
Oetting AIaL, J.A. Statistical methodology for a SMART design in the development of adaptive treatment 
strategies.  Causality and Psychopathology: Oxford University Press 2007.