Clinical trial NCT02821832
Conditions: Pulmonary Tuberculosis
Keywords: Drug-Resistance Heteroresistance Relapse-markers Medical Imaging Treatment-shortening
Sponsor: National Institute of Allergy and Infectious Diseases (NIAID)
Start date: 2017-06-21; Completion date: 2022-02-28
Enrollment: 946 participants; Allocation: RANDOMIZED; Intervention model: SEQUENTIAL

Brief summary:
Background:

Tuberculosis (TB) is a bacterial lung infection. Typical treatment using anti-TB drugs lasts about 6 months. Some people with less severe TB might not need to take the drugs that long. Researchers think a PET/CT lung scan along with estimating how much TB is in the lungs might show who will be cured after only 4 months of treatment.

Objective:

To demonstrate that 4 months of treatment is not inferior to 6 months of treatment for people with less severe TB.

Eligibility:

People 18-75 years old who have TB treatable with standard TB drugs

Design:

Participants will be screened with:

Medical history

Physical exam

Blood and urine tests

HIV test

Sputum sample: Participants will be asked to cough sputum into a cup.

Chest x-ray

Participants will start TB drugs. They will have visits at weeks 1, 2, 4, 8, 12, and about 6 more times during the 18-month study. Visits include:

Sputum samples

Physical exam

Blood tests

PET/CT scans at 2-3 visits: Participants fast for about 6 hours before the scan. Participants get FDG, a type of sugar that gives off a small amount of radiation, through an arm vein. They lie on a table in a machine that takes pictures of the body.

Chest x-rays at 1-2 visits

Participants who we believe are likely to be cured at 4 months will be randomly assigned to get either 6 months of treatment or 4 months of treatment.

Participants may be asked to join a substudy using their sputum samples or additional blood tests.

Detailed description:
Shortening the duration of treatment for patients with drug sensitive tuberculosis from 6 to 4 months has been attempted many times in clinical trials but thus far all have failed. These failures reveal our incomplete understanding of factors driving the need for such extensive treatments. Consistently, trials have demonstrated that 80-85% of patients are successfully cured after 4 months of therapy, including the extensive set of studies from the British Medical Research Council (BMRC) in the 1970s and 1980, the Tuberculosis Research Unit (TBRU) treatment shortening study in non-cavitary patients who achieve early culture conversion, and the more recent treatment shortening trials using fluoroquinolones like REMoxTB. The current standard of care is to over-treat all patients for a total of 6-months to avoid relapse in a small subset of patients at higher risk for incompletely understood reasons.

For decades, clinical investigators have attempted to establish culture conversion as a predictor of treatment success. Despite the appealing logic, the real correlation of culture conversion as a surrogate endpoint has been consistently disappointing. In the REMoxTB trial, in particular, the intensive microbiological data collected revealed unambiguously that clearance of bacteria from the sputum did not sufficiently correlate with relapse risk to be a useful surrogate for durable cure. An important subset of patients, despite clearing their sputum of TB quickly and complying with all of their medications, still remained at high risk of relapsing with active disease after stopping treatment. Likewise there are patients who clear their sputum of bacteria slowly that nonetheless go on to achieve durable cure. Intuitively this makes sense: only those bacteria at the surface of a cavity are directly open to the airways to seed the sputum. Yet this is not the full story as there are also heterogeneous lesions within each individual patient which respond differently to treatment with chemotherapy.

This protocol builds upon the historical trials and several successful small studies that suggest that directly monitoring lung pathology using (18F)- FDG PET/CT correlates better with treatment outcome than culture status. We will prospectively identify patients at low risk based on their baseline radiographic extent of disease, and further refine this risk score by evaluating the rate of resolution of the lung pathology (CT) and inflammation (PET) at one month as well as checking an end-of-treatment GeneXpert test for the sustained presence of bacteria. Patients classified as low risk will be randomized to receive a shortened 4- month or a full 6-month course of therapy. If successful, this trial will both offer a badly needed alternative to culture status as a trial-level surrogate marker for outcome as well as provide critical information for preclinical and early clinical efforts to identify new agents and combinations with the potential to shorten therapy.

Hypothesis: A combination of radiographic characteristics at baseline, the rate of change of these features at one month, and markers of residual bacterial load at the end of treatment will identify patients with tuberculosis who are cured with 4 months (16 weeks) of standard treatment.

Arms: arm 1: Expected high risk of relapse, standard of care TB treatment arm 2: Expected low risk of relapse, standard of care TB treatment arm 3: Expected low risk of relapse, shortened TB treatment
Interventions: intervention 1: Saliva collection intervention 2: Urine collection intervention 3: Sputum collection intervention 4: Blood Collection intervention 5: PET/CT Scan intervention 6: Isoniazid, Rifampicin, Pyrazinamide and Ethambutol
Intervention descriptions: intervention 1: For biomarker assessments intervention 2: For biomarker assessments intervention 3: For primary endpoint assessments and other biomarker assessments intervention 4: For biomarker and eligibility assessments intervention 5: Imaging of the lungs to establish disease extent and severity intervention 6: Treatment-standard of care

Protocol documents:
Prot_000.pdf: 
Clifton E. Barry, III 
 
Predict Trial 
 
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National Institute of Allergy and Infectious Diseases 
 
United States National Institutes of Health 
Sponsor 
 
 
Principal Investigator (NIAID): 
 
 
 
 
 
 
 
 
 
Local Principal and Associate 
Investigators:  
National Institute of Allergy and Infectious Diseases, 
National Institutes of Health, United States of America 
 
Clifton E. Barry III, Ph.D. 
National Institute for Allergy and Infectious Diseases 
(NIAID), Laboratory of Clinical Immunology and 
Microbiology (LCIM), Tuberculosis Research Section 
(TRS), Building 33, Room 2w10, Bethesda, MD 20892 
Phone: (301) 693-4665 
         Email: cbarry@niaid.nih.gov 
 
 
See Key Study Personnel document. 
Protocol Number: 
16-I-N133 
Version Description:  
13.0 
Version Date:  
September 21, 2020 
 
Protocol Title: 
Using Biomarkers to Predict TB Treatment Duration 
Abbreviated Title: 
Predict TB Trial  
IRB/Institute Name:  
NIH/NIAID 
Proposed Dates: 
Start: June 2017 
End:  December 2022 
Accrual Ceiling/Enrollment 
Goal  
Ceiling: 1200 
Enrollment Goal: 310 into Arms B and C; randomization 
into Arm C halted on September 14, 2020, per DSMB 
recommendation 
Ionizing Radiation Use:  
Research Purposes 
Is Tissue Being Collected for 
Research Purposes? 
Yes 
Location of the Study 
Zhengzhou, China (multiple sites) 
Cape Town, South Africa (multiple sites) 
Investigational New 
Drug/Device:  
None 
Research Contact/ Lead 
Associate Investigator: 
 
 
 
Laura Via, PhD  
NIAID, LCIM, TRS Building 33, Room 2W20G 
(301) 451-9554 (p)  
(301) 480-5713 (f)  
lvia@niaid.nih.gov 
Medical Advisory Investigator:  
 
 
 
Ray Chen, MD 
NIAID, LCIM, TRS Building 33, Room 2w10  
(301) 443-5816 (office)  
(301) 451-5492 (f) 
RChen@niaid.nih.gov 


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Enrollment sites:  
 
Site Name 
Country 
City 
Henan 
Provincial Chest 
Hospital 
(HPCH)  
China 
Zhengzhou, 
Henan Province 
Kaifeng City 
Institute of 
Tuberculosis 
Prevention and 
Control 
(KCITPC) 
China 
Kaifeng, Henan 
Province 
Xinmi City 
Center for 
Disease Control 
and Prevention 
China 
Xinmi, Henan 
Province  
Zhongmu 
County Station 
for Disease 
Control and 
Prevention 
China 
Zhongmu, 
Henan Province 
Xinxiang 
Institute for the 
prevention and 
control of 
tuberculosis 
(XXCITPC) 
China 
Xinxiang, 
Henan Province 
University of 
Cape Town 
(UCT) Lung 
Institute 
South 
Africa 
Cape Town 
Stellenbosch 
University 
South 
Africa 
Tygerberg 
TASK Applied 
Science, Inc 
South 
Africa 
Bellville/Delft 
Khayelitsha Site 
B 
South 
Africa 
Khayelitsha 
South African 
Tuberculosis 
Vaccine 
Initiative 
(SATVI)  
South 
Africa 
Cape 
Town/Worcester 
 
 
 


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TABLE OF CONTENTS 
Contents 
TABLE OF CONTENTS ................................................................................................................ 3 
LIST OF TABLES AND FIGURES............................................................................................... 6 
LIST OF ABBREVIATIONS ......................................................................................................... 6 
STUDY OVERVIEW ..................................................................................................................... 9 
1 
Introduction:  Background and Rationale ............................................................................. 12 
 
Biomarkers for tuberculosis .................................................................................................. 12 
 
Surrogate markers of sputum bacterial load .......................................................................... 16 
 
Treatment Shortening ............................................................................................................ 19 
 
Goals of the Predict Trial ...................................................................................................... 20 
 
Sub-breakpoint MIC .............................................................................................................. 21 
 
Lung magnetic resonance imaging scans .............................................................................. 22 
 
COVID-19 Infection ............................................................................................................. 23 
2 
Study Hypothesis and Objectives .......................................................................................... 24 
 
Hypothesis ............................................................................................................................. 24 
 
Primary Objective ................................................................................................................. 24 
 
Secondary Objectives ............................................................................................................ 24 
3 
Study Design and Population ................................................................................................ 25 
 
Design and Arms ................................................................................................................... 25 
 
Participant Characteristics/Eligibility Criteria ...................................................................... 28 
 
Inclusion Criteria ................................................................................................................... 28 
 
Exclusion Criteria .................................................................................................................. 29 
4 
Study Schedule ...................................................................................................................... 29 
 
Participant Screening ............................................................................................................ 29 
 
Enrollment ............................................................................................................................. 30 
 
Day 0 (Baseline Visit) ........................................................................................................... 30 
 
Week 1 .................................................................................................................................. 31 
 
Week 2 .................................................................................................................................. 31 
 
Week 4 .................................................................................................................................. 31 
 
Week 8 .................................................................................................................................. 32 
 
Week 12 ................................................................................................................................ 32 
 
Randomization into Arms B and C ....................................................................................... 33 
 
Week 16 ................................................................................................................................ 33 
 
Week 20 ................................................................................................................................ 34 
 
Week 24 ................................................................................................................................ 34 
 
Week 36 ................................................................................................................................ 35 
 
Week 48 ................................................................................................................................ 35 
 
Week 60 ................................................................................................................................ 35 
 
Week 72 ................................................................................................................................ 35 
 
Recurrence ............................................................................................................................. 36 
 
Study Timeline ...................................................................................................................... 38 


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5 
Details of Research Procedures & Data Collection Methods ................................................ 40 
 
Consent Methodology ........................................................................................................... 40 
 
Treatment adherence ............................................................................................................. 40 
 
Medical History ..................................................................................................................... 41 
 
Complete Medical History .................................................................................................... 41 
 
Focused Medical History ...................................................................................................... 41 
 
Physical Examination ............................................................................................................ 41 
 
Complete Physical Examination ........................................................................................... 41 
 
Focused Physical Examination .............................................................................................. 41 
 
Sputum Collection and Mycobacterial Testing Procedures .................................................. 41 
 
Sputum Induction .................................................................................................................. 41 
 
Sputum Specimen Use .......................................................................................................... 42 
 
Isolates and Genotypic Tests ................................................................................................. 43 
 
Drug Susceptibility Testing of Isolates ................................................................................. 43 
 
Saliva Collection for Biomarkers .......................................................................................... 43 
 
Blood Collection ................................................................................................................... 43 
 
CBC, Chemistries, Liver Function Tests, HbA1c and HIV .................................................. 43 
 
Biomarkers ............................................................................................................................ 44 
 
Plasma for drug levels ........................................................................................................... 44 
 
Urine Collection and Testing ................................................................................................ 44 
 
Pregnancy Testing ................................................................................................................. 44 
 
Biomarkers in Urine .............................................................................................................. 45 
 
Imaging ................................................................................................................................. 45 
 
FDG-PET/CT scan ................................................................................................................ 45 
 
Chest Radiograph (CXR) ...................................................................................................... 45 
 
Magnetic Resonance Imaging (MRI) .................................................................................... 45 
 
COVID-19 Testing ................................................................................................................ 46 
 
Participants moved to Arm A ................................................................................................ 46 
 
Withdrawal or Termination From the Study ......................................................................... 46 
 
Study Completion .................................................................................................................. 47 
6 
Statistical Methods and Justification ..................................................................................... 47 
 
Study Hypotheses .................................................................................................................. 47 
 
Primary Hypothesis ............................................................................................................... 47 
 
Secondary Hypotheses .......................................................................................................... 47 
 
Definitions ............................................................................................................................. 48 
 
Treatment Success ................................................................................................................. 48 
 
Treatment Failure .................................................................................................................. 48 
 
Treatment Recurrence and Relapse ....................................................................................... 49 
 
Primary Endpoint .................................................................................................................. 49 
 
Secondary Endpoints ............................................................................................................. 50 
 
Statistical Methods ................................................................................................................ 50 
 
Primary Analysis ................................................................................................................... 50 
 
Secondary Analyses .............................................................................................................. 50 
 
Sample Size Considerations .................................................................................................. 50 
 
Interim analyses .................................................................................................................... 52 
 
Early stopping for inferiority of treatment shortening arm ................................................... 52 
 
Early stopping for study futility ............................................................................................ 52 
7 
PK Substudy for Sub-Breakpoint Minimum Inhibitory Concentrations (MIC) Comparison 53 
 
Substudy Procedures ............................................................................................................. 53 


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Inclusion criteria: .................................................................................................................. 54 
 
Exclusion criteria .................................................................................................................. 54 
 
Control participants ............................................................................................................... 55 
 
Substudy Remuneration ........................................................................................................ 55 
8 
Lung Magnetic Resonance Imaging Scans to Individualize Treatment Duration for 
Pulmonary Tuberculosis Patients Substudy .................................................................................. 55 
 
Substudy Procedures ............................................................................................................. 55 
 
Inclusion Criteria ................................................................................................................... 56 
 
Exclusion Criteria .................................................................................................................. 56 
 
Statistical Methods ................................................................................................................ 56 
 
Substudy Remuneration ........................................................................................................ 57 
9 
Adverse Events, Unanticipated Problems, Deviations, and Non-Compliance ...................... 57 
 
Reporting Procedures ............................................................................................................ 57 
 
Assessment of Safety ............................................................................................................ 57 
 
Reporting Procedures ............................................................................................................ 57 
 
Investigator Assessment of Adverse Events ......................................................................... 57 
 
Grading Adverse Events for Severity .................................................................................... 57 
 
Assessing Adverse Events for Relationship to Study ........................................................... 58 
 
Documenting and Recording of Events ................................................................................ 59 
 
Adverse Event Treatment ...................................................................................................... 59 
 
Expected Adverse Events ...................................................................................................... 59 
 
Investigator Reporting Responsibilities to The NIH Institutional Review Board (IRB) ...... 60 
 
Local Study Site Reporting ................................................................................................... 60 
 
To Local IRB ......................................................................................................................... 60 
 
To NIH Study Team .............................................................................................................. 61 
 
Reporting SAEs to Health Authorities and IECs / IRBs ....................................................... 61 
10 Data Management Plan - Data Collection, Sample Storage and Publication ........................ 61 
 
Data Collection ...................................................................................................................... 61 
 
Data Management ................................................................................................................. 61 
 
Data Storage .......................................................................................................................... 62 
 
Publication of Research Findings .......................................................................................... 62 
 
Sample Transfer and Storage ................................................................................................ 62 
11 Clinical Monitoring Structure ............................................................................................... 63 
 
Site Monitoring Plan ............................................................................................................. 63 
 
Data and Safety Monitoring Plan .......................................................................................... 64 
12 Human Subject Protection ..................................................................................................... 65 
 
Rationale for Participant Selection ........................................................................................ 65 
 
Participation of Children and Other Vulnerable Participants ................................................ 65 
 
Risks/Benefits Analysis including Considerations of Alternatives to Participation ............. 66 
 
Potential Benefits to Study Participants ................................................................................ 66 
 
Potential Risks to Study Participants .................................................................................... 66 
 
Privacy and Confidentiality ................................................................................................... 67 
13 References ............................................................................................................................. 67 
14 Appendix 1: Description of Changes to Early Treatment Completion Criteria (as of March 
12, 2018) ....................................................................................................................................... 71 
15 Appendix 2: Radiation Dosimetry ......................................................................................... 78 


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16 Changes to study procedures per Data Safety Monitoring Board recommendations ............ 79 
17 NIH/SOUTH AFRICA Specific Appendices ........................................................................ 79 
 
Remuneration in RSA ........................................................................................................... 79 
18 NIH/CHINA Specific Appendices ........................................................................................ 79 
 
Blood volumes in China ........................................................................................................ 79 
 
Remuneration in China.......................................................................................................... 80 
 
 
LIST OF TABLES AND FIGURES 
Table 1: Sensitivity and specificity of 2-month sputum culture conversion compared to CT and 
PET scan changes for predicting treatment outcomes in MDR-TB in humans. ......................... 133 
Table 2: Sensitivity and Specificity of Early Treatment Completion Criteria for Predicting 
Treatment Failure or Programmatic Treatment Restart .............................................................. 143 
Figure 1: Representative plots for the different patterns observed in serum cytokine levels in 
cured, failed and relapse patients during treatment. ................................................................... 155 
Table 3: TTP on week 8 MGIT stratified by per protocol treatment outcome status ................. 166 
Figure 2:  Qualitative data for noted tests at baseline and follow-up ........................................... 17 
Figure 3: Receiver-operating characteristic (ROC) curves of Xpert MTB/RIF cycle threshold 
with MGIT liquid culture negativity (3a) and patient treatment failure (3b). .............................. 18 
Table 4: Xpert MTB/RIF vs. MGIT: Sensitivity and specificity for predicting outcome ............ 18 
Table 5:  Summary of Recent Trials Aimed at Shortening TB Therapy ...................................... 19 
Figure 4: Example of pulmonary tuberculosis on MRI showing heterogenous texture (A) that 
appears homogeneous on CT (B). From Zeng J, et al. Int J Infect Dis 2019;82:138-146 ............ 22 
Figure 5: Study Flow .................................................................................................................. 265 
Table 6: Early Treatment Completion Criteria: All early treatment criteria must be met for the 
participant to be eligible for randomization ................................................................................ 276 
Table 7: Study Timeline.............................................................................................................. 387 
Table 8. Power calculations for total sample sizes of 129 and 155 per group (arms B and C) for 
different success rates across and between treatment arms. ......................................................... 51 
Table 9: Sample Sizes for 80%, 85%, and 90% power with a one-sided type I error rate of 5% for 
various non-inferiority margins, assuming equal success rates in Arms B and C. ....................... 52 
Table 10: MRI Substudy Power Calculation ................................................................................ 57 
Table 11: Expected Adverse Events ............................................................................................. 59 
Table 12:  NIAID Contact information ......................................................................................... 60 
Table 13: Early Treatment Completion Criteria: All early treatment criteria must be met for the 
participant to be eligible for randomization .................................................................................. 72 
Table 14: Proposed Revised Early Treatment Completion Criteria: All early treatment criteria 
must be met for the participant to be eligible for randomization (changes highlighted) .............. 76 
 
 
 
LIST OF ABBREVIATIONS 
Abbreviation  
Text 
AE 
adverse event 
AFB 
acid-fast bacilli  
AI 
Associate Investigator  


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Abbreviation  
Text 
ALT (SGPT) 
alanine transaminase 
AST (SGOT) 
aspartate transaminase 
ATS 
American Thoracic Society 
β-hCG 
human chorionic gonadotropin 
BCG 
Bacillus Calmette-Guérin 
BID 
Twice daily 
BMRC 
British Medical Research Council 
CDC 
Centers for Disease Control and Prevention 
CFU 
colony forming unit 
CI 
confidence interval  
CNS 
central nervous system  
CRF 
case report form  
CRP 
C-reactive protein 
CT 
Computed Tomography 
CV 
curricula vitae  
CXR 
Chest Radiograph 
DHHS 
Department of Health and Human Services  
DIR 
Division of Intramural Research  
DS-TB 
Fully Drug Susceptible Tuberculosis 
DSMB 
Data and Safety Monitoring Board  
DST 
drug susceptibility testing 
EMB 
Ethambutol 
EBA 
Early Bactericidal Activity 
ELISA 
enzyme-linked immunosorbent assay 
ESAT-6 
Early Secretory Antigenic Target 6 
FDA 
Food and Drug Administration  
FDG 
[18F]-fluoro-2-deoxy-D-glucose 
FQ 
Fluoroquinolone 
GBCA 
Gadolinium-Based Contrast Agent 
GCP 
Good Clinical Practice 
HIV 
Human Immunodeficiency Virus 
HR 
isoniazid, rifampicin 
HRCT 
high-resolution computed tomography 
HRZE 
isoniazid, rifampicin, pyrazinamide, and ethambutol 
HU 
Hounsfield Units 
IEC 
Institutional Ethics Committee 
IFN-γ 
interferon gamma  
IGRA 
interferon gamma release assay 
INH or H 
isoniazid 
IRB 
institutional review board  
IU 
International Units 
IV 
Intravenous drug administration 
LCIM 
Laboratory of Clinical Immunology and Microbiology 
LTBI 
Latent Tuberculosis Infection 
M or Mth (s) 
Month(s) 
MDR-TB 
multi-drug resistant tuberculosis  
MERM 
medication event reminder monitor 
MGIT 
Mycobacteria Growth Indicator Tube 


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Abbreviation  
Text 
MIC 
Minimum inhibitory concentration 
MOHW 
Ministry of Health and Welfare  
MRC 
Medical Research Council, UK 
MRI 
Magnetic resonance imaging 
MTA 
Material Transfer Agreement 
M.tb 
Mycobacterium tuberculosis 
MXF  
Moxifloxacin 
NHP 
Non-human primate 
NIAID 
National Institute of Allergy and Infectious Diseases 
NIH 
National Institutes of Health 
NIMR 
National Institute for Medical Research, UK 
NLME 
Non-linear mixed effects 
NMC 
National Medical Center 
NNT 
Number needed to treat 
OFLOTUB  
A multicenter, randomized, control trial of ofloxacin-containing, short-
course regimen for the treatment of pulmonary TB  
OHRP 
Office for Human Research Protections  
OHSR 
Office of Human Subjects Research  
PA 
Posterio-anterior 
PBMC 
Peripheral blood mononuclear cells  
PET 
Positron Emission Tomography 
PI 
Principal Investigator  
po 
Oral drug administration 
PPD 
Purified Protein Derivative  
PZA or Z 
Pyrazinamide 
QD 
Once daily 
QFT 
QuantiFERON 
RCA 
Research Collaboration Agreement 
RCHSPB 
Regulatory Compliance and Human Subjects Protection Branch 
RIF or R 
Rifampin  
RSA 
Republic of South Africa 
SAE 
Serious adverse event  
SAHPRA 
South African Health Products Regulatory Authority 
SMS 
Short Message Service 
SOC 
Standard of Care 
SPSS 
Statistical Package for Social Sciences  
TB 
Tuberculosis  
TGA 
Total Glycolytic Activity 
TRS 
Tuberculosis Research Section 
TTD 
Time to detection 
TTP 
Time to positivity 
TST 
Tuberculin Skin Test  
ULN 
Upper limit of normal  
US NRC 
United States Nuclear Regulatory Commission  
W or Wk (s) 
Week(s) 
WBC 
White blood cell  
WHO 
World Health Organization 


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STUDY OVERVIEW 
 
Title 
Using Biomarkers to Predict TB Treatment Duration 
Précis 
Shortening the duration of treatment for patients with drug sensitive 
tuberculosis from 6 to 4 months has been attempted many times in clinical 
trials but thus far all have failed. These failures reveal our incomplete 
understanding of factors driving the need for such extensive treatments.  
Consistently, trials have demonstrated that 80-85% of patients are 
successfully cured after 4 months of therapy, including the extensive set of 
studies from the British Medical Research Council (BMRC) in the 1970s 
and 1980 [1-3], the Tuberculosis Research Unit (TBRU) treatment 
shortening study in non-cavitary patients who achieve early culture 
conversion [4], and the more recent treatment shortening trials using 
fluoroquinolones like REMoxTB [5-7]. The current standard of care is to 
over-treat all patients for a total of 6-months to avoid relapse in a small 
subset of patients at higher risk for incompletely understood reasons. 
 
For decades, clinical investigators have attempted to establish culture 
conversion as a predictor of treatment success. Despite the appealing logic, 
the real correlation of culture conversion as a surrogate endpoint has been 
consistently disappointing. In the REMoxTB trial, in particular, the 
intensive microbiological data collected revealed unambiguously that 
clearance of bacteria from the sputum did not sufficiently correlate with 
relapse risk to be a useful surrogate for durable cure [8]. An important 
subset of patients, despite clearing their sputum of TB quickly and 
complying with all of their medications, still remained at high risk of 
relapsing with active disease after stopping treatment. Likewise there are 
patients who clear their sputum of bacteria slowly that nontheless go on to 
achieve durable cure. Intuitively this makes sense: only those bacteria at 
the surface of a cavity are directly open to the airways to seed the sputum. 
Yet this is not the full story as there are also heterogeneous lesions within 
each individual patient which respond differently to treatment with 
chemotherapy. 
 
This protocol builds upon the historical trials and several successful small 
studies that suggest that directly monitoring lung pathology using [18F]-
FDG PET/CT correlates better with treatment outcome than culture status 
[9, 10]. We will prospectively identify patients at low risk based on their 
baseline radiographic extent of disease, and further refine this risk score by 
evaluating the rate of resolution of the lung pathology (CT) and 
inflammation (PET) at one month as well as checking an end-of-treatment 
GeneXpert test for the sustained presence of bacteria. Patients classified as 


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low risk will be randomized to receive a shortened 4-month or a full 6-
month course of therapy.  
 
The NIAID Data Safety Monitoring Board conducted its 7th interim 
review of unblinded data on September 11, 2020. Following this review, 
the DSMB recommended halting randomization to Arms B and C. This 
recommendation is based on the result of the interim analysis in section 
6.7.1 of the study protocol, when 1/3 of randomized participants have been 
followed for 72 weeks from study entry. The protocol stopping guideline 
for inferiority of the treatment shortening arm was met. The DSMB was 
also presented with conditional power calculations relating to the futility 
interim analysis; although the protocol-specified time for this analysis had 
not been reached, the results of the analysis were consistent with a decision 
to terminate randomization into Arms B and C, but to continue enrollment 
into Arms A and B at the discretion of the investigators. Pre-emptive re-
treatment of participants who have completed the course of treatment in 
Arm C is not recommended and should be left to the discretion of the 
treating clinician. 
 
If successful, this trial will both offer a badly needed alternative to culture 
status as a trial-level surrogate marker for outcome as well as provide 
critical information for preclinical and early clinical efforts to identify new 
agents and combinations with the potential to shorten therapy. 
 
Hypothesis: A combination of radiographic characteristics at baseline, the 
rate of change of these features at one month, and markers of residual 
bacterial load at the end of treatment will identify patients with 
tuberculosis who are cured with 4 months (16 weeks) of standard 
treatment. 
Objectives 
Primary Objective 
To demonstrate that the 18-month treatment success rate of 
standard treatment stopped early at week 16 (Arm C) is not inferior 
to standard treatment stopped at week 24 (Arm B), in participants 
classified as low risk for disease failure and relapse by radiographic 
and bacterial load markers.  
 
Note that per the 7th NIAID DSMB review on September 11, 2020, 
the protocol stopping guideline for inferiority in treatment-
shortening arm (Arm C) was met, and randomization to Arm C was 
discontinued.  
 
Secondary Objectives 
1) To compare the treatment success rates between a representative 
6-month standard of care population vs. the strategy of shortening 
treatment in low-risk participants. 
2) To evaluate the association of demographic, radiographic, 
bacterial load, microbiologic, and immunologic markers (at 


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baseline and during treatment) for predicting treatment failure in 
the following participant cohorts: 
• 
Pooling arms A and B, participants receiving the same 
duration of therapy, to evaluate the risk criteria. 
• 
Between arms B and C, to evaluate whether there are any 
covariates which predict greater rates of failure under 
treatment shortening. 
3) To evaluate the association of demographic, radiographic, 
bacterial load, microbiologic, and immunologic markers (at 
baseline and during treatment) for predicting subsequent relapse in 
the following participant cohorts: 
• 
Pooling arms A and B, participants receiving the same 
duration of therapy, to evaluate the risk criteria. 
• 
Between arms B and C, to evaluate whether there are any 
covariates which predict greater rates of failure under 
treatment shortening. 
4) To evaluate the ability of PET scans to predict treatment outcomes 
as described in secondary objectives 2) and 3). 
5) To evaluate whether bacterial load markers (TTP and Xpert cycle 
threshold) collected at later time points are better markers of 
ultimate treatment outcomes than ones collected earlier  
6) To evaluate sub-breakpoint MICs as a significant predictor of 
treatment outcome in 16 and 24 week treatment regimens 
7) To evaluate the ratio AUC/sub-breakpoint MIC as a significant 
predictor of treatment outcome in (a subset of participants selected 
from the) 16 and 24 week treatment regimens; to compare this 
with #6 
8) To evaluate the Cmax/sub-breakpoint MIC as a significant 
predictor of treatment outcome in (a subset of participants selected 
from the) 16 and 24 week treatment regimens; to compare this 
with #6 
9) To compare MRI with PET/CT to quantitate extent of disease and 
monitor changes over time in a subset of participants. 
10) To optimize 3T lung MRI acquisition and develop quantitation 
tools for pulmonary TB patients in a subset of participants.  
11) To explore provider and participant satisfaction with the 
medication event reminder-monitor (MERM) and compare 
different adherence monitoring methods. 
12) To explore whether LAM (lipoarabinomannan) measured by an 
investigational immunoassay that quantitates LAM concentration 
in sputum can be used as a bacterial load biomarker. Correlation 
between LAM concentrations and culture results will be 
examined. 
13) To store biological samples for future analysis of potential 
biomarkers of treatment efficacy. 


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14) To investigate the effects of SARS CoV-2 and TB co-infection on 
the difference in the treatment success rates between the 16- and 
24-week treatment regimens.  
 
Design 
This is a prospective, randomized, phase 2b noninferiority trial in 
pulmonary DS-TB participants. Eligible participants will initially receive 
HRZE for 8 weeks, then switch to HR. Early treatment completion criteria 
will be evaluated for each participant up through week 16. Those who do 
not meet the early treatment completion criteria will be put into Arm A 
(2HRZE/4HR). Those who meet early treatment completion criteria will 
be randomized at week 16 either to continue therapy to week 24 (Arm B) 
or to complete therapy early at week 16 (Arm C). Per DSMB 
recommendations, randomization to Arm C was halted on September 14, 
2020. All participants will be followed until approximately 18 months 
from the start of the study, with the primary endpoint evaluated at 18 
months.  
Population 
Participants will be recruited from clinics in and around Cape Town, South 
Africa and Henan Province, China. Approximately 310 participants will be 
enrolled into Arms B&C. Per DSMB recommendations, randomization to 
Arm C was halted on September 14, 2020. 
Participant 
Duration 
Approximately 18 months 
Estimated Time 
to Complete 
Enrollment 
Approximately 3 years 
 
1 Introduction:  Background and Rationale 
 Biomarkers for tuberculosis 
Multiple potential tuberculosis biomarkers, surrogate biological markers of clinically 
meaningful outcomes, are under active study [11]. From a microbiological standpoint, 
sputum culture conversion at 2 months of treatment is the biomarker most commonly 
used to predict non-relapsing cure [12] but its true predictive ability is not great, with one 
meta-analysis showing a pooled sensitivity and specificity for predicting relapse of 40% 
(95% CI 25%-56%) and 85% (95% CI 77%-91%), respectively [13]. A review of data 
from the British Medical Research Council (BMRC) trials from the 1970s and 1980s 
found only a weak correlation (R2=0.36) for this marker as a surrogate for treatment 
failure and relapse, depending on factors such as geographic location, baseline disease 
and cavity status, and concomitantly used medications [14]. Further evidence against 
using culture conversion as a surrogate for predicting treatment outcome was recently 
demonstrated from the phase 3 TB treatment shortening trial REMoxTB [5], where 
subsequent analyses of the culture data collected demonstrated poor correlation with 
treatment outcome whether analyzed at a single time point (2 months) or over time (time 
to culture conversion or time to culture positivity) [8]. Furthermore, a small proportion of 
participants had poor outcomes despite clearing bacilli from their sputa quickly. Clearly, 
other factors independent of sputum culture conversion affect treatment outcomes and 2-


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month culture conversion is no longer an appropriate surrogate marker of treatment 
outcome for clinical trials.  
 
A number of additional factors have been associated with treatment outcome. In a study 
of 1004 pulmonary DS-TB participants from the Tuberculosis Trials Consortium 
(TBTC), a positive sputum culture at 2 months (adjusted HR 2.8, 95% CI 1.7-4.7) and a 
cavitation on initial chest x-ray (adjusted HR 3.0, 95% CI 1.5-5.8) were both independent 
predictors of treatment relapse [15]. In addition, the sterilizing efficacy of the overall 
treatment regimen is also dependent on the regimen used after 2 months, as demonstrated 
by significantly differing relapse rates in trials with arms using the same 2-month 
intensive phase regimen but differing continuation phase regimens [16] and trials using 
differing durations of continuation phase treatment [4]. 
 
The ability of early radiographic changes to predict subsequent treatment outcomes in TB 
has been recognized for over 50 years [17]. More recent analyses of radiographic 
biomarkers have moved beyond chest x-ray to using 2-deoxy-2-[18F]-fluoro-d-glucose 
(FDG) positron emission tomography/computed tomography (PET/CT) as an early 
marker of treatment response and possibly as a marker for relapse at the end of treatment. 
In macaques, changes on PET/CT correlate with TB disease activity and treatment 
response [18, 19]. Our group has analyzed human PET/CT data from a randomized 
clinical trial using metronidazole in the treatment of pulmonary multi-drug resistant 
tuberculosis (MDR-TB) participants [20]. As a substudy within the overall MDR-TB 
study, we performed PET/CT scans at 0 and 2 months and high resolution CT scans at 0, 
2, and 6 months of treatment and correlated these changes with final treatment outcomes 
30 months after treatment start (6 months after the end of therapy, Table 1).  
 
 
Table 1: Sensitivity and specificity of 2-month sputum culture conversion compared to 
CT and PET scan changes for predicting treatment outcomes in MDR-TB in humans.  
 
 
PET changes at 2 months and CT changes at 6 months appeared to be more sensitive to 
predict final treatment outcomes than sputum culture conversion at 2 months, although 
these differences were not statistically significant. These results support the potential of 
PET/CT imaging biomarkers as possible surrogate endpoints in clinical trials and larger 
cohorts are needed to confirm these results [10]. 


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In addition to the above study, which was of MDR-TB participants, 100 DS-TB 
participants from Cape Town received PET/CT scans at baseline, 1 month, and 6 months 
while receiving standard therapy through the national program. Adherence was directly 
observed for the initial 2 weeks, then monitored with monthly pill counts. The 
participants were then followed through 18 months for final treatment outcomes. In total, 
92 participants had complete PET/CT scan data, Xpert MTB/RIF cycle thresholds (see 
Section 1.2), and treatment outcomes. Table 2 describes the sensitivity and specificity of 
the early treatment completion criteria to be used in this trial (see Section 3.1, Table 6) 
for predicting treatment outcome: 
 
Table 2: Sensitivity and Specificity of Early Treatment Completion Criteria for 
Predicting Treatment Failure or Programmatic Treatment Restart  
 
Treatment Outcome  
(Numbers of Participants) 
 
Risk 
Categorization 
Cure 
Failure 
Programmatic 
Treatment 
Restart 
Total 
Low Risk 
55 
2 
8 
65 
High Risk 
18 
6 
3 
27 
Total 
73 
8 
11 
92 
 
Of these 92 participants, 73 were considered cured, 8 failed treatment, and 11 were 
restarted programmatically on TB treatment, defined by the participant restarting 
treatment during follow-up for any reason. Confirmatory culture data were only available 
for 1/11 participants and true relapse was not differentiated from re-infection. A previous 
analysis from Cape Town retrospectively analyzed TB cases from 1996-2008 and 
identified 130 recurrent cases with paired DNA fingerprinting results available. Among 
these, 64 (49%) were relapses and 66 (51%) were reinfections, with reinfection 
accounting for 9/44 (20%) cases within the first year [21]. Consequently, with the vast 
majority of the programmatic treatment restart participants in our analysis not 
microbiologically confirmed and reinfection likely playing a significant but undefined 
role, this category of participants was not weighed heavily in the development of the 
early treatment completion criteria. 
 
Given these limitations, the Predict Trial early treatment completion criteria, which 
incorporates baseline and one-month PET/CT results and a week 16 Xpert cycle 
threshold, correctly classified 75.3% (55/73) of the cured participants as low risk and 6/8 
failures (75.0%) as high risk (week 16 Xpert cycle threshold interpolated for this 
analysis). With adherence not closely monitored, the reasons for failure were not clear. In 
addition, the one failure participant classified as low risk had mixed microbiological 
results so the final determination was not clear-cut. Overall, 65/92 (70.7%) of all patients 
were classified as low risk.  
 
Host immunological biomarkers that indicate an early response to treatment and reflect 
restoration of the balance of pro-and anti-inflammatory markers would be useful for 


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Phase 2 trials and may also predict response to shortened therapy. In a separate study, we 
used the Luminex technology to evaluate the levels of 72 host inflammatory markers in 
serum samples from 83 subsequently cured patients, 15 patients where treatment failed, 
and 12 patients with bacterial strain confirmed relapse. The levels of 36 of the 72 markers 
changed significantly during treatment in successfully cured patients with different 
response patterns, with most changes observed within 2 weeks of onset of therapy. The 
marker signature obtained in the cured patients was distinctly different from that obtained 
in patients with treatment failure and relapse outcomes. 
 
 
Figure 1: Representative plots for the different patterns observed in serum cytokine 
levels in cured, failed and relapse patients during treatment.  
The differences observed in cytokine kinetics during treatment of non-responsive patients 
may reflect ongoing bacterial replication and inflammation, whereas differences in pre-
treatment levels of some markers, e.g. sIL-4R, IL-13, IL-5, MMP-2 and MMP-9, might 
reflect an underlying increased risk of treatment failure, possibly due to increased extent 
of disease or poor host response. Prediction models comprised of clinical (body mass 
index, BMI), microbiological (time to detection, TTD) and inflammatory markers 
measured at the time of diagnosis and during early treatment classified the three different 
study groups with accuracy up to 95% (95% CI 77%-97%). As these data are based on 
relatively small participant numbers, we therefore propose to collect additional host 
samples, including serum, for refinement of predictive host marker signatures and to 
evaluate them as potential surrogate markers for the PET/CT measurements. 
IFN-γ, IL-1β, sIL-4R and IL-13 levels at diagnosis, weeks 2, 4, and month 6 of treatment are shown. 
Data (pg/ml) were analysed by mixed model repeated measures ANOVA. Cured patients are indicated 
by solid lines and solid circles, failed patients by dotted lines and solid triangles and relapse patients 
by dashed lines and open squares. Values with different letters indicate that they are significantly 
different from each other (p≤0.05). Mean (log transformed) and 95% Confidence intervals are shown. 
  


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 Surrogate markers of sputum bacterial load 
There is currently no direct measure of TB sputum bacterial load available. Some 
markers, however, may serve as a surrogate. The time to positivity (TTP) or TTD of a 
positive culture on liquid mycobacterial culture systems has been correlated with various 
outcome measures, with the shorter TTP indicating a higher bacterial load. In one 
analysis among 263 smear positive pulmonary DS-TB patients, a very short TTP at 
baseline (≤3 days) was significantly correlated with delayed 2-month sputum culture 
conversion and relapse at 24 months [22]. In another analysis of 146 patients including 
only 5 failures, the mean baseline TTD among the failures was shorter than the cures 
(16.3 vs 25.4 days, p=0.003). However, 2-month culture conversion, although 100% 
sensitive for predicting cure, was only 49% specific, meaning that many cured patients 
were still positive on culture at 2 months. Changing from culture negative to TTD >21 
days at 2 months (allowing a low bacterial load) did not change the sensitivity (100%) 
but improved the specificity to 82% [23]. So although there is some correlation between 
Mycobacteria Growth Indicator Tube (MGIT) TTP and sputum bacterial load, the poor 
specificity of TTP with subsequent treatment outcomes is evident in unpublished data 
from the REMoxTB trial [5].   
 
Table 3: TTP on week 8 MGIT stratified by per protocol treatment outcome status 
 
Week 8 Time to Positivity (days) 
 
Treatment outcome  
(per protocol) 
0-4 
5-14 
15-24 
≥25 
Total 
Favorable 
7 
45 
72 
30 
154 
Unfavorable 
1 
5 
10 
2 
18 
Excluded 
2 
5 
12 
1 
20 
Total 
10 
55 
94 
33 
192 
 
As table 3 shows, there is no correlation between MGIT TTP at week 8 and treatment 
outcome (Wilcoxon rank sum test p=0.23), with most participants having favorable 
outcomes no matter their TTP. Thus, although time to culture conversion and MGIT TTP 
do correlate independently with treatment outcome, these markers do not discriminate 
well between high and low risk patients and therefore have only a limited role in 
predicting treatment outcomes of individual patients [8]. 
 
Another marker of sputum bacterial load is the Xpert assay, which is an automated rapid 
molecular diagnostic test for M. tb and resistance to rifampin with results provided 
directly from sputum within 2 hours [24]. The test is run using a polymerase chain 
reaction and the number of cycles (cycle threshold) required to obtain a positive result is 
recorded, with a lower cycle threshold suggestive of a higher bacterial load. Three studies 
have correlated Xpert MTB/RIF cycle threshold with sputum smear status, with varying 
sensitivity and specificity levels depending on the cycle threshold cut point used [25-28]. 
Another analysis by Friedrich, et al correlated Xpert MTB/RIF results with sputum smear 
and culture results, not only at baseline but also longitudinally over time as a sputum 
biomarker of treatment response [29]. The reduction in detection of quantitative Mtb 
DNA with Xpert MTB/RIF correlated with smear grades, solid culture grades, and liquid 


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culture TTP (all p<0.0001) but Xpert MTB/RIF sputum positivity rates decline more 
slowly during treatment than sputum smear and culture results.  
 
 
 
 
 
Figure 2:  Qualitative data for noted tests at baseline and follow-up 
 
Using the combined binary smear and culture results as a reference standard, sensitivity 
of Xpert MTB/RIF was excellent at 97.0% (95% CI 95.8-97.9) but specificity was poor at 
48.6% (95% CI 45.0-52.2) as the assay is unable to differentiate viable, dormant, and 
non-viable MTB bacteria. 
 
In the study mentioned previously of 100 pulmonary DS-TB participants in Cape Town, 
sputa collected during 6 months of treatment were cultured on liquid medium (MGIT) 
and tested by Xpert MTB/RIF with an Xpert MTB/RIF cycle threshold recorded. Similar 
to the Friedrich study [30], serial testing with Xpert MTB/RIF negativity (defined by 
Xpert MTB/RIF cycle threshold ≥30) correlated with MGIT culture negative status at the 
same time points (Figure 3a). All AUCs were significantly greater than 0.5, indicating the 
ability to differentiate TB from no TB, with no significant differences in AUCs between 
the different time points when adjusted for multiple comparisons. When Xpert MTB/RIF 
cycle threshold was used to predict treatment failure status at the end of treatment, week 
24 cycle threshold produced the largest AUC (Figure 3b, p=0.086, when compared to 
baseline cycle threshold). [31] A week 24 Xpert MTB/RIF cycle threshold of ≥30 
predicted failure with higher sensitivity and specificity than earlier time points. This is in 
contrast to the week 8 culture (Table 4), which has lower sensitivity (for cure) than Xpert 
MTB/RIF cycle threshold at week 24: 61% (week 8 culture) vs 89% (Xpert MTB/RIF 
cycle threshold week 24, p<0.01). Estimates of specificity (for failure) for Xpert 
MTB/RIF cycle threshold week 24 was higher than week 8 culture (88% vs 50%), but the 


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improvement was not statistically significant. Note that the 13 “unevaluable” cultures 
make direct comparison problematic. The poor performance of week 8 culture data as a 
predictor of treatment outcome is similar to what was observed in the REMoxTB trial [8]. 
 
The observation that a later test predicts outcomes better than an earlier test may be 
similar to findings in HIV infection, where baseline CD4 cell count is a strong predictor 
of mortality over time but current CD4 cell count is even stronger [32]. This has been 
seen in TB too, where culture conversion at month 6 predicts final treatment outcome 
significantly better than culture conversion at month 2 [33]. Taken together, these results 
suggest that Xpert MTB/RIF cycle thresholds collected later may be able to replace an 
earlier microbiological culture in predicting treatment outcomes, with the major 
advantage of Xpert MTB/RIF over culture being the time to test result, with Xpert 
requiring 2 hours and culture up to 6 weeks. Thus, Xpert cycle threshold may be able to 
be used as a point-of-care test whereas culture cannot. 
 
Figure 3: Receiver-operating characteristic (ROC) curves of Xpert MTB/RIF cycle 
threshold with MGIT liquid culture negativity (3a) and patient treatment failure (3b). 
 
In this data set, the sensitivity and specificity of Xpert MTB/RIF cycle threshold ≥30 at 
week 24 (sensitivity 89%, specificity 88%) is better than MGIT culture negative at week 
8 (sensitivity 61%, specificity 50%) to predict cure (Table 4).   
 
Table 4: Xpert MTB/RIF vs. MGIT: Sensitivity and specificity for predicting outcome 
 
Outcome* 
 
Cure 
Failure 
Week 24 Xpert ≥30 
89% (68/76) 
13% (1/8) 
Week 24 Xpert <30 
11% (8/76) 
88% (7/8) 
 
 
 
Week 8 MGIT TB culture negative 
61% (46/75) 
25% (2/8) 
Week 8 MGIT TB culture positive 
24% (18/75) 
50% (4/8) 


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Week 8 MGIT unevaluable** 
15% (11/75) 
25% (2/8) 
* 12 participants who programmatically restarted treatment not included due to low 
confidence in their true treatment outcome 
** One participant was missing week 8 MGIT 
 
The above data compared Xpert results with MGIT liquid culture data. The Predict TB 
study uses LJ solid culture as our primary endpoint. The TBTC-29 study collected Ct 
values and LJ culture results. In evaluating the change from Ct ≥30 used above, we 
consider the chance of missing an LJ+ result, as well as the sensitivity and specificity of 
various Ct cutpoints. In contrast to positive and negative predictive values, sensitivity and 
specificity do not depend on the underlying proportion of culture positive results, which 
varies over time and from study to study. That said, patient safety is a driving factor so 
we consider how many positive cultures might be missed for various cutpoints. This was 
defined as the probability of being LJ+ given a Xpert Ct value less than the threshold, i.e., 
P(LJ+ | Ct-). We assume what we consider are high proportions of LJ+ cultures (i.e., 10% 
and 5% at week 16 of treatment in a lower risk cohort of arm B/C) when making this 
decision. In contrast to the TBTC-29 study, which randomized all-comers and did not 
stratify participants by risk, the Predict TB study further excludes poorly adherent 
participants with too severe disease at baseline and not responding appropriately to 
treatment at one month. As a result, the expected LJ+ rates of 10% and 5% are thought to 
be on the high-side. Appendix table 2 (section 13) describes these proportions for the 
sensitivity and specificity estimates from TBTC-29. Based on these estimates, a Ct of 30 
is expected to miss 2.1% of LJ+ results, while a threshold of 28 would miss 2.5%, 
assuming a 10% LJ+ rate. This translates to an increase in less than one participant being 
missed amongst those randomized to arm C. That is, if the background LJ+ rate is 10%, 
3.3 (of 155 randomized to stop treatment at week 16) true LJ+ participants may be missed 
with Ct=30, and 3.9 may be missed with Ct=28. If the underlying LJ+ rate is 5%, this 
becomes 1.6 missed LJ+ participants with Ct=30 and 1.9 missed LJ+ participants with 
Ct=28. If the true underlying LJ+ rate is even lower, the difference between the two Ct 
values becomes even smaller. Based on this analysis, we decided to use Ct threshold ≥
28. 
 Treatment Shortening 
Shortening the treatment duration of drug sensitive (DS)-TB and multidrug-resistant 
(MDR)-TB is a major goal of TB research and several clinical trials have evaluated 
shortened treatment regimens. For DS-TB, based on promising murine data [34, 35] and 
preliminary results in human clinical trials [36-40], 3 recent trials tried to shorten 
treatment from the standard 6 months (SOC) to 4 months by substituting a 
fluoroquinolone (FQ; moxifloxacin or gatifloxacin) for either isoniazid (INH) or 
ethambutol in varying combinations [5-7]. These results are summarized in Table 5. 
 
Table 5:  Summary of Recent Trials Aimed at Shortening TB Therapy 
 
Months 1-2 
Months 3-4 
Months 5-6 
Unfavorable Outcome per protocol 
(adjusted difference from control) 
RIFAQUIN [6] 
 
Control 
HRZE 
HR 
HR 
4.9% (18 mo post randomization) 
Arm 1 
MRZE 
MP (1x/wk) 
MP (1x/wk) 
3.2% (-1.8%, 95% CI -6.9 to 3.3) 


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Arm 2 
MRZE 
MP (2x/wk) 
-- 
18.2% (13.6%, 95% CI 7.0-20.2) 
OFLOTUB [7] 
 
Control 
HRZE 
HR 
HR 
11.3% (24 mo post randomization) 
Intervention 
HRZG 
HRG 
-- 
17.7% (5.5%, 95% CI 1.6-9.4) 
REMoxTB [5] 
 
Control 
HRZE 
HR 
HR 
8% (18 mo post randomization) 
INH arm 
HRZM 
HRM 
-- 
15% (6.1%, 95% CI 1.7-10.5) 
ETH arm 
MRZE 
MR 
-- 
20% (11.4%, 95% CI 6.7-16.1) 
 
In secondary analyses, OFLOTUB patients with cavities on baseline chest x-ray had 
significantly worse outcomes in the 4-month arm compared to the 6-month arm (P=0.04). 
Patients in REMoxTB with cavities on baseline chest x-ray also did worse in the two 4-
month arms but this difference did not reach statistical significance (P=0.058 for INH 
arm, P=0.118 for ethambutol arm).  
 
These three FQ treatment-shortening trials suggest that 4 months of treatment will cure 
around 80%-85% of sputum smear positive patients. Historically, 4-month treatment 
regimens similar to the SOC used today had relapse rates ranging from 10%-16% [1, 2]. 
One review found a relapse rate for 4-month regimens of 12% (95% CI 9-16) at 2 years 
of follow-up [3]. All of these 4-month regimen outcomes, which span multiple countries 
over 30 years, have been remarkably consistent. Therefore, it is likely that when 
considering all TB patients as a whole, the current SOC regimen will cure >95% of 
patients with 6 months of treatment but only 80%-85% of patients with 4 months of 
treatment. Identifying those cured at 4 months, then, may be the key to successful 
treatment shortening. 
 
A 4th treatment shortening study in DS-TB attempted exactly this strategy. Recognizing 
that the presence of a pulmonary cavity at baseline and the lack of sputum culture 
conversion at month 2 were risk factors for relapse disease, this study shortened treatment 
to 4 months only for those who were without pulmonary cavities at baseline and were 
sputum culture negative by month 2. Although the DSMB stopped this trial early due to a 
higher relapse rate in the treatment-shortened arm compared to the 6-month SOC arm 
(7.0% vs 1.6%, P<0.01) [4], this study suggests that shortening treatment only among 
those with less severe disease resulted in a lower relapse rate compared to previous 
studies which did not employ this strategy (7% vs. about 15-20%). Refining this 
treatment-shortening algorithm beyond just lack of baseline cavity on chest x-ray and 
sputum culture conversion at month 2, such as additional baseline and follow-up 
radiological markers, may successfully identify those fully treated by month 4. 
 
Goals of the Predict Trial 
The immediate goal of this study is to determine if our criteria for patient-specific 
radiographic and bacterial load biomarkers successfully identify patients who are cured 
with 16 weeks of treatment as a proof of concept study. We understand that PET/CT 
scanners are not available in many resource-limited settings globally and thus we do not 
expect PET/CT scans to be used as a global public health tool. We expect that, if 
successful, this treatment-shortening concept can be applied to other clinical trials as a 
trial-level surrogate biomarker of treatment outcome. Our primary analysis and treatment 
shortening criteria are based on CT scans, which provide structural lung pathology data, 


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PET scans, which provide functional data about lung inflammation, and Xpert cycle 
threshold, a point-of-care measurement of remaining bacterial load. By excluding 
participants at baseline with a high disease burden (baseline PET/CT scan), participants 
at 4 weeks with an insufficient treatment response (week 4 PET/CT scan), and 
participants with residual bacterial burden at the end of treatment (week 16 Xpert cycle 
threshold), we hypothesize that we will identify a low risk cohort of participants cured 
with 16 weeks of chemotherapy. Sputum LAM concentration will be analyzed against 
sputum culture results. Additional secondary analyses will also be performed to 
determine if immunological parameters that are more readily available also correlate and 
serve as equivalent surrogate biomarkers, allowing these criteria to be applied more 
broadly in resource-limited settings. 
 
Sub-breakpoint MIC 
Minimum inhibitory concentrations (MIC) are used in standard drug susceptibility testing 
assays to determine at what drug concentrations a given “resistant” bacteria will grow in 
culture. This is typically defined as the antibiotic concentration at which 1% of bacterial 
isolates grow, compared to cultures without any antibiotics [41-43]. Conventional MIC 
testing will determine growth at one or two drug concentration “breakpoints.” The results 
of this testing are important because drug resistance is a well-known determinant of 
treatment outcome [44].  
 
Our collaborator, David Alland, has shown that just as high-level MIC resistance 
correlates with treatment outcome, low-level or sub-breakpoint MIC resistance also 
correlates with treatment outcome [45]. In the TBTC Study 22 trial [15], 1004 DS-TB 
patients were randomized after 2 months of standard isoniazid (H), rifampin (R), 
pyrazinamide (Z), and ethambutol (E) (HRZE) to 4 months of continuation phase with 
either once weekly rifapentine/isoniazid or twice weekly rifampin/isoniazid. Using data 
from this trial, sub-breakpoint MICs were tested among 57 HIV negative relapsed cases 
and 64 cured participants and found highly reproducible results with triplicate testing. 
There was in addition a significant association between baseline elevated sub-breakpoint 
MIC to INH (p=0.014) or RIF (p<0.001) and relapse. In multivariable analysis, INH 
MIC, RIF MIC, baseline cavity, bilateral disease on CXR, and low body weight were 
independent predictors of relapse. In a ROC curve of the TBTC study 22 features 
independently associated with relapse, the AUC for the ROC curve of only INH and RIF 
MICs (0.785) was comparable to the ROC of the significantly associated clinical features 
of cavitary disease, bilateral disease, low body weight, and 2-month sputum culture 
conversion (AUC 0.776). When baseline INH and RIF MICs were added to the clinical 
features, the resulting AUC was 0.888 to predict relapse.  
 
In the previously mentioned TBRU treatment-shortening study that found significantly 
higher relapse rate in the 4-month arm compared to the 6-month arm [4], sub-breakpoint 
RIF MIC testing was done on nine available M.tb isolates from 4-month arm patients 
who relapsed and nine 4-month arm patients who were cured. Similar to the TBTC study 
22 results, sub-breakpoint RIF MICs were significantly higher in the relapse cases 
compared to the cured cases.  
 


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These data, although preliminary due to small numbers, show that baseline sub-
breakpoint MIC data may be independently predictive of treatment outcome and/or 
treatment shortening and need to be further validated. As part of this study, we will batch 
sub-breakpoint MIC testing at the end of the study using saved samples.  We will also 
collect blood for PK analyses, as described further in section 7.0.   
 
Lung magnetic resonance imaging scans 
The PredictTB trial stratifies drug-sensitive pulmonary TB participants into higher risk 
and lower risk cohorts based on baseline and week 4 PET/CT scans and a GeneXpert 
MTB/RIF cycle threshold at week 16, to test whether low-risk patients can successfully 
be treated within 4 months. More recent data suggest that magnetic resonance imaging 
(MRI) scans may be more effective than PET/CT scans to measure baseline disease 
burden and treatment response. Two studies including 113 patients [46, 47] and a single 
case report [48] compared MRI with CT in pulmonary TB patients. All three studies 
consistently found that MRI characterizes TB lesion features better than CT, with MRI 
able to detect heterogeneous patterns that appear homogeneous on CT (Figure 4). 
Another study evaluated the 
histopathology of pulmonary nodules 
that were subsequently resected and 
found varying MRI intensity patterns 
on T1 vs T2-weighted images that 
correlated with caseating vs 
noncaseating granulomas, solid vs. 
liquid caseation, and fibrocalcific vs 
not fibrocalcific granulomas [49]. 
Thus, in these small studies, MRI 
image features correlate better with 
histopathologic findings of TB lesions 
than CT scan features, allowing more 
precise determination of different TB lesion types. Necrotic lesions are likely associated 
with worse outcomes, so accurately measuring the extent of caseous necrosis may guide 
treatment duration. If MRI can identify these types of higher risk lung lesions more 
accurately than CT, MRI may perform better than PET/CT in a TB treatment shortening 
stratification algorithm such as in PredictTB. MRI biomarkers could also potentially be 
applied as a precision medicine tool to guide individualized treatment, monitor treatment 
response and evaluate novel interventions. 
 
This substudy administers baseline and week 4 lung MRI scans to a subset of 60 
PredictTB participants who provide informed consent. Additional lesion information 
provided by the MRI scan will likely be most useful in those with more severe disease, 
with large, dense TB lesions that may be less well characterized by the PET/CT scan. 
Subsequently, participants with a range of disease severity will be enrolled but weighted 
towards the more heavily diseased. Only participants with a GeneXpert semiquantitative 
reading of medium and high will be included in this substudy. Quantitative analysis of 
MRI scans will be used to compare with the PET/CT scan data collected to determine if 
MRI biomarkers may provide additional baseline or treatment response information 
useful for risk stratification of participants. This would be an important advance because: 
Figure 4: Example of pulmonary tuberculosis on MRI showing heterogenous 
texture (A) that appears homogeneous on CT (B). From Zeng J, et al. Int J 
Infect Dis 2019;82:138-146 


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1) MRI scans do not involve radiation so are safer than PET/CT scans; 2) MRI scans are 
cheaper than PET/CT scans and therefore may become more widely available in resource 
limited settings than PET/CT scans. If the Predict TB trial is successful, blood, sputum, 
or urine-based biomarkers that correlate with the PET/CT signature will be sought but 
adding MRI scans provides an additional potential route to global applicability and 
scalability of the treatment shortening algorithm. For these reasons, a successful MRI-
based algorithm may have a larger global impact than a PET/CT-based algorithm. In 
addition to performing MRI scans in a subset of PredictTB trial participants, this study 
will also develop MRI scanning protocols for better visualization and conduct image 
analysis to improve quantitation of different types of TB lung lesions. This is important 
as there are many different MRI scanning and analysis techniques available so identifying 
the best one for our purposes will improve our chances of success. 
 
COVID-19 Infection 
The coronavirus disease 2019 (COVID-19) is a respiratory viral infection caused by 
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and was declared a 
global pandemic by the WHO on March 11, 2020. COVID-19 can present with influenza-
like symptoms, including fever, chills, cough, shortness of breath, myalgias, and 
headache. These symptoms may overlap with those of pulmonary tuberculosis. How co-
infection with SARS-CoV-2 affects the clinical presentation or treatment outcome of 
pulmonary TB patients is not currently known. There are no published, peer-reviewed 
reports of SARS-CoV-2 and TB co-infected patients yet, although a pre-print manuscript 
case-control study of 36 SARS-CoV-2 positive cases from China suggests that latent TB 
infection may increase COVID-19 disease severity 
(https://www.medrxiv.org/content/10.1101/2020.03.10.20033795v1).   
 
During the original SARS outbreak in 2002-2004, three case reports were published 
including 6 patients with SARS-TB coinfection, all of whom recovered [58-60]. Two 
additional cases of Middle East Respiratory Syndrome coronavirus (MERS-CoV)-TB 
coinfection have also been reported [61]. No conclusions can be drawn from such small 
numbers.  
 
To understand better the effect of SARS-CoV-2 and TB co-infection, a new exploratory 
objective will be added to the study: to explore the effect of SARS-CoV-2 infection on 
pulmonary TB treatment outcomes and recurrence. Study procedures related to this 
objective will be implemented only at the clinical sites in South Africa because there 
have been no recent cases at the clinical sites in Henan, China. Additionally, this testing 
is contingent on enough SARS-CoV-2 testing capacity and personal protective equipment 
for study staff. Not conducting the procedure pertaining to SARS-CoV-2 testing will not 
be considered a protocol deviation. This will be an exploratory objective because we do 
not know how many enrolled participants may subsequently develop SARS-CoV-2 
infection. Co-infected patients identified during screening will be excluded from the 
study due to the unpredictable course of the disease and the requirement for SARS-CoV-
2 strict isolation and the risk of nosocomial transmission to study staff, in a time when 
there are frequent and essential study contact visits. Participants who become infected 
with COVID-19 after enrollment will be maintained in the study. As far as possible, face-
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when a visit essential for randomization (W4 scan, W16 sputum collection) is scheduled, 
and strict transmission control requirements at the study site or PET Center cannot be 
maintained, the participant may be withdrawn. 
 
2 Study Hypothesis and Objectives 
 Hypothesis 
A combination of radiographic characteristics at baseline, the rate of change of these 
features at one month, and markers of residual bacterial load at the end of treatment will 
identify patients with tuberculosis who are cured with 4 months (16 weeks) of standard 
treatment. 
 Primary Objective 
To demonstrate that the 18-month treatment success rate of standard treatment stopped 
early at week 16 (Arm C) is not inferior to standard treatment stopped at week 24 (Arm 
B) in patients classified as low risk for disease failure and relapse by radiographic and 
bacterial load markers. Note that per the 7th NIAID DSMB review on September 11, 
2020, the protocol stopping guideline for inferiority in treatment-shortening arm (Arm C) 
was met, and randomization to Arm C was discontinued on September 14, 2020. 
 
 Secondary Objectives 
1) 
To compare the treatment success rates between a representative 6-month 
standard of care population vs. the strategy of shortening treatment in low-risk 
participants.  
2) 
To evaluate the association of demographic, radiographic, bacterial load, 
microbiologic, and immunologic markers (at baseline and during treatment) for 
predicting treatment failure in the following patient cohorts: 
a. Pooling arms A and B, participants receiving the same duration of therapy, 
to evaluate the risk criteria. 
b. Between arms B and C, to evaluate whether there are any covariates which 
predict greater rates of failure under treatment shortening. 
3) 
To evaluate the association of demographic, radiographic, bacterial load, 
microbiologic, and immunologic markers (at baseline and during treatment) for 
predicting subsequent relapse in the following participant cohorts: 
a. Pooling arms A and B, participants receiving the same duration of therapy, 
to evaluate the risk criteria. 
b. Between arms B and C, to evaluate whether there are any covariates which 
predict greater rates of failure under treatment shortening. 
4) 
To evaluate the ability of PET scans to predict treatment outcomes as described 
in secondary objectives 2) and 3). 
5) 
To evaluate whether bacterial load markers (TTP and Xpert cycle threshold) 
collected at later time points are better markers of ultimate treatment outcomes 
than ones collected earlier  
6) 
To evaluate sub-breakpoint MICs as a significant predictor of treatment 
outcome in 16 and 24 week treatment regimens. 


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7) 
To evaluate the ratio AUC/sub-breakpoint MIC as a significant predictor of 
treatment outcome in (a subset of participants selected from the) 16 and 24 
week treatment regimens; to compare this with #5 
8) 
To evaluate the Cmax/sub-breakpoint MIC as a significant predictor of 
treatment outcome in (a subset of participants selected from the) 16 and 24 
week treatment regimens; to compare this with #6 
9) 
To compare MRI with PET/CT to quantitate extent of disease and monitor 
changes over time in a subset of participants. 
10) To optimize 3T lung MRI acquisition and develop quantitation tools for 
pulmonary TB patients in a subset of participants.  
11) To explore provider and patient satisfaction with the medication event 
reminder-monitor (MERM) and compare different adherence monitoring 
methods. 
12) To explore whether LAM (lipoarabinomannan) measured by an investigational 
immunoassay that quantitates LAM concentration in sputum can be used as a 
bacterial load biomarker. Correlation between LAM concentrations and culture 
results will be examined. 
13) To store biological samples (sputum, saliva, blood, serum, urine) for future 
analysis of potential biomarkers of treatment efficacy. 
14) To investigate the effects of SARS CoV-2 and TB co-infection on the 
difference in the treatment success rates between the 16- and 24-week 
treatment regimens. 
 
3 Study Design and Population 
 Design and Arms 
This is a prospective, randomized, phase 2b noninferiority trial in pulmonary DS-TB 
participants.  Eligible participants who sign the informed consent will start on HRZE. At 
week 8, Z and E will be discontinued. Participants who meet randomization criteria will 
be randomized at week 16. Randomization will be stratified by site. Some participants 
will complete 16 weeks of TB therapy and others will complete 24 weeks of TB therapy, 
as determined using early treatment completion criteria (Table 6) and randomization. 
Note that per the 7th NIAID DSMB review on September 11, 2020, the protocol stopping 
guideline for inferiority in treatment-shortening arm (Arm C) was met, and 
randomization to Arm C was discontinued, and all participants will receive 24 weeks of 
TB therapy. 
 
 
 


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Figure 5: Study Flow 
 
Early treatment completion criteria (Table 6) will be evaluated at baseline (radiology), 
week 4 (radiology), and Week 16 (bacterial load and treatment adherence) of the study. 
Per DSMB recommendations, randomization to Arm C was halted on September 14, 
2020 and all participants will receive 24 weeks of TB therapy.    
 
Participants will receive a baseline PET/CT scan and those who do not meet baseline 
PET/CT early completion criteria (Table 6) will be assigned to Arm A. At week 4, 
participants still eligible for early completion will receive a 2nd PET/CT scan, and all 
others will receive a scan at this time as well if resources allow. Those who do not meet 
the radiographic early stopping criteria (Table 6) at this point will be assigned to Arm A. 
Participants still eligible for early treatment completion at week 16 will be tested by 
Xpert and, if their cycle threshold is ≥28, will be randomized either to stay on treatment 
to week 24 (Arm B) or to complete treatment early at week 16 (Arm C). Per DSMB 
recommendations, participants will no longer be randomized to complete treatment early 
at week 16 (Arm C) as of September 14, 2020. Participants who do not meet the early 
treatment completion criteria will be assigned to Arm A. Xpert testing will also be 
conducted on Arm A participants at week 16. Participants on Arms B and C will receive 
a week 16 PET/CT scan. Participants on Arm A will be randomized to receive a week 16 
or week 24 PET/CT scan, stratified by when they were placed in Arm A (baseline or 
week 4). All participants will be followed to month 18 for cure vs. failure (relapse, 
death). Participants who develop recurrent disease during follow-up will also receive a 
PET/CT scan and will be referred for retreatment per local SOC. Participant follow-up is 
to 18 months, as it has been shown that the vast majority of patients who will relapse do 


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so by one year after the end of therapy [50, 51]. Participants who develop recurrent TB 
will be referred to their local TB clinic for retreatment. These participants will be 
followed observationally until the end of retreatment to determine their retreatment 
outcome, even if this is longer than 18 months after the start of their participation in the 
trial.   
 
Table 6: Early Treatment Completion Criteria: All early treatment criteria must be met for 
the participant to be eligible for randomization 
Early 
Completion 
criteria: 
Determined at Week 16 – unless known to have failed a 
radiographic criterion at baseline or week 4.  
Radiographic 
criteria 
Baseline PET/CT: 
• No total lung collapse of a single side, AND 
• No pleural effusion, AND 
• No single cavity air volume on CT scan >30 mL, 
AND 
• CT scan hard volume (≥-100 HU density) <200 mL 
OR PET total lesion glycolysis <1500 units 
Week 4 PET/CT: 
• All individual cavities decrease by >20% (unless 
cavity <2 mL), AND 
• CT scan hard volume does not increase by >10% 
unless the increase is <5 mL OR PET total lesion 
glycoysis does not increase by >30% unless the 
increase is <50 units 
Bacterial load 
criterion 
Week 16 Xpert cycle threshold ≥28* 
Adherence 
criterion 
Minimum of 100 doses received by week 16 (Sec 5.2) 
 
 
 
*If the week 16 solid medium sputum culture is subsequently found to be positive for Mtb in a 
participant randomized to Arm B or C, this participant will be called in for evaluation and to 
provide sputum for a repeat culture. If the initial positive culture is confirmed by a second 
culture positive for Mtb, this participant will be considered to have met the study endpoint as a 
treatment failure and will be referred for continued treatment. 
 
For the research purposes of this study, all PET/CT scans will be read using the best available 
tools at the time the trial starts. As this is an evolving technology, the reading methods may 
include but are not limited to: 
• A group of 2 or more readers with consensus determination of the lesions to be read 
and standardized reading methodology.  


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• An automated reading algorithm using a custom developed software program that can 
objectively measure PET and CT characteristics of interest. 
 Participant Characteristics/Eligibility Criteria 
Participants will be recruited from clinics in and around Cape Town, South Africa (RSA) 
and Henan Province, China. Approximately 620 participants will be enrolled. Previous 
data estimated that 80-85% would be cured by 16 weeks. For this study, we estimate that 
about 50% will meet the early treatment completion criteria and undergo randomization. 
This will result in a sample size of approximately 155 per arm for Arms B and C. 
Enrollment will continue until 310 patients total are randomized into Arms B and C. Note 
that enrolled participants subsequently found to have resistance at baseline to the drugs 
used will be withdrawn from the study and replaced. If Arm A enrolls more quickly than 
expected, additional baseline factors (e.g. chest x-ray) may be used to screen high risk 
participants out from enrolling onto the study. If Arm A reaches 310 participants and the 
study is still enrolling, we will stop enrollment into Arm A.     
 
 Inclusion Criteria 
1) Age 18 to 75 years with body weight from 35 kg to 90 kg 
2) Has not been treated for active TB within the past 3 years 
3) Not yet on TB treatment  
4) Xpert positive for M.tb  
5) Rifampin-sensitive pulmonary tuberculosis as indicated by Xpert  
6) Laboratory parameters within previous 14 days before enrollment: 
a.  Serum AST and ALT <3x upper limit of normal (ULN) 
b.  Creatinine <2x ULN 
c.  Hemoglobin >7.0 g/dL 
d.  Platelet count >50 x109 cells/L 
7) Able and willing to return for follow-up visits 
8) Able and willing to provide informed consent to participate in the study 
9) Willing to undergo an HIV test  
10) At sites with sufficient SARS-CoV-2 testing capacity and personal protective 
equipment for study staff, willing to undergo COVID-19 testing: viral RNA 
PCR testing for SARS-CoV-2 to determine active infection and antibody 
testing for SARS-CoV-2 to determine prior infection 
11) Willing to have samples, including DNA, stored 
12) Willing to consistently practice a highly reliable, non-hormonal method of 
pregnancy prevention (e.g., condoms) during treatment if participant is a 
premenopausal female unless she has had a hysterectomy or bilateral tubal 
ligation or her male partner has had a vasectomy. If hormonal contraception is 
used an additional method of pregnancy prevention (as above) should also be 
used.  
 
If Arm A reaches 310 before Arms B/C are full, we will stop enrolling into Arm 
A by: 
1) Excluding on screening CXR (or CT scan if done) those with:  
a. Thickened pleura suggesting pleural (extrapulmonary) TB 
b. Complete right or left lung collapse  


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c. Large pleural effusion indicated by blunting of the costophrenic 
angle on posteroanterior (PA) or anteroposterior (AP) CXR (or either 
exceeds the first AP quartile or measures >= 3 cm of the hemithorax 
on CT) [52]  
2) Withdrawing those stratified to Arm A based on the baseline PET/CT scan 
 
 Exclusion Criteria 
1) Clinical suspicion of or confirmed extrapulmonary TB, including pleural TB 
2) Pregnant or desiring/trying to become pregnant in the next 6 months or 
breastfeeding 
3) HIV infected 
4) Currently COVID-19 infected  
5) Unable to take oral medications 
6) Diabetes as defined by point of care HbA1c ≥6.5%, random glucose ≥200 
mg/dL (or 11.1 mmol/L), fasting plasma glucose ≥126 mg/dL (or 7.0 
mmol/L), or the presence of any anti-diabetic agent (including traditional 
medicines) as a concomitant medicine 
7) Disease complications or concomitant illnesses that may compromise safety 
or interpretation of trial endpoints, such as known diagnosis of chronic 
inflammatory condition (e.g. sarcoidosis, rheumatoid arthritis, connective 
tissue disorder) 
8) Use of immunosuppressive medications, such as TNF-alpha inhibitors or 
systemic or inhaled corticosteroids, within the past 2 weeks  
9) Use of any investigational drug in the previous 3 months 
10) Substance or alcohol abuse that in the opinion of the investigator may 
interfere with the participant’s adherence to study procedures 
11) Any person for whom the physician feels this study is not appropriate   
 
4 Study Schedule  
 Participant Screening 
Interested patients who sign the main study informed consent form (ICF) (and in addition 
the Genetic Testing ICF and the Stored Samples ICF where applicable) will undergo 
screening.  The following will then be performed/obtained:  
1) Complete medical history and physical exam, including vital signs.  
2) One or more sputum samples (total sputum volume at least 3 mL) for Xpert, smear 
and culture (liquid and solid)  
3) Blood draw for  
a. Complete blood count, chemistries, liver function tests, and HbA1c 
b. Serum pregnancy testing, if applicable, before the PET/CT 
c. HIV test 
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The following will be conducted at sites with sufficient SARS-CoV-2 testing capacity 
and personal protective equipment for study staff. Not conducting the below will not be 
considered a protocol deviation: 
5) Viral RNA PCR testing for SARS-CoV-2 to determine active infection: Samples 
collected may include nasopharyngeal (NP) swabs, oropharyngeal (OP) swabs, 
sputum, and/or saliva. Patients who test positive will be excluded. 
6) Antibody testing for SARS-CoV-2 to determine prior infection: Samples collected 
may include blood and/or saliva and may be stored for batched testing at a time when 
serological testing has been established. Patients who test positive will not be 
excluded based on this test. 
7) Prior test results done by the local healthcare system within the previous 7 days may 
be accepted but may still be repeated. 
 
Screening tests may be repeated if necessary. Available labs (excluding sputa) within the 
previous 2 weeks do not need to be repeated. Phenotypic DST will be conducted from 
isolates grown using sputa samples collected during the early study visits to confirm the 
molecular DST results. If there are mixed, conflicting, or inconsistent DST results, any 
positive culture (or culture from available stored sputa) prior to conversion, may be used 
for additional DST testing.     
 Enrollment  
If eligibility is confirmed, the participant will be considered enrolled.  This can occur 
with Day 0.  
 Day 0 (Baseline Visit) 
The following will be performed/obtained at the Day 0 visit prior to medication:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) Two or more sputum samples or induced sputum (total sputum volume at least 4 mL) 
for biomarkers  
a. Storage raw 
b. Storage as 1:1 mix with Trizol for MTB mRNA  
4) One or more sputum samples (total sputum volume at least 3.5 mL) for repeat smear 
and culture, and possibly Xpert, if needed, 
5) Blood will be collected for biomarkers 
6) Urine will be collected for  
a. Biomarkers 
b. A pregnancy test, if indicated (performed prior to the scan); if within 2 days of 
the screening pregnancy test, this test may be skipped. 
7) A finger prick will be done for glucose assessment 
8) FDG-PET/CT scan, within 7 days of treatment initiation (providing pregnancy test is 
negative) 
9) Saliva sample 
 
Treatment of TB will be initiated on this day (Day 0) with standard treatment using 
HRZE at routine doses, per local dosing standards; TB drugs are not considered study 
drugs.  If an electronic adherence monitoring system is used, participants will be issued a 


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system and provided with training on how to use the system.  A questionnaire will be 
provided to some MERM users to evaluate user experience with this adherence method. 
The questionnaire will be provided at any time up to Week 2 and again at the end of the 
participant’s treatment course.  
 
If a participant’s baseline PET/CT does not meet the radiographic early completion 
criteria, that participant will be placed in Arm A after their Day 0 visit.  
 
Note that at this and all subsequent visits, if a sputum culture is found to be contaminated 
or is otherwise unevaluable, the participant may be called back to provide another sputum 
sample.  If for some reason a participant needs to come back the next day to provide 
sputum, this will not be a deviation. In addition, it will not be a protocol deviation if a 
participant is unable to provide sufficient sputa to perform all sputum-related testing at 
any study visit. 
 Week 1 
The following will be performed/obtained at the Week 1 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (total sputum volume at least 3.5 mL) for smear and 
culture (liquid and solid) 
4) Blood will be collected for biomarkers 
5) Urine will be collected for biomarkers 
6) Adherence monitoring 
 
Participants unable to provide sputa spontaneously at any point in the study may be 
induced.  
 Week 2 
The following will be performed/obtained at the Week 2 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (total sputum volume at least 2 mL) for smear and 
culture (liquid and solid) 
4) Two or more sputum samples or induced sputum (total sputum volume at least 4 mL) 
for biomarkers  
a. Storage raw 
b. Storage as 1:1 mix with Trizol for MTB mRNA 
5) Blood will be collected for biomarkers 
6) Urine will be collected for biomarkers 
7) Adherence monitoring 
 Week 4 
The following will be performed/obtained at the Week 4 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 


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3) One or more sputum samples (total sputum volume at least 3.5 mL) for Xpert testing, 
smear and culture (liquid and solid)  
4) Two or more sputum samples or induced sputum (total sputum volume at least 4 mL) 
for biomarkers  
a. Storage raw and  
b. Storage as 1:1 mix with Trizol for MTB mRNA  
5) Blood will be collected for biomarkers 
6) A finger stick will be collected for blood glucose levels (prior to PET/CT scan) 
7) Urine will be collected for  
a. Biomarkers 
b. Pregnancy test, if applicable (prior to PET/CT scan) 
8) FDG-PET/CT scan (taken 4 weeks after the date of the previous scan, with a -3/+7 
day window) for those still qualifying for randomization and also Arm A participants 
if resources allow.   
9) Saliva sample for those scanned 
10) Adherence monitoring 
 
At sites with sufficient SARS-CoV-2 testing capacity and personal protective equipment  
for study staff (not conducting the below will not be considered a protocol deviation):  
11) Viral RNA PCR testing for SARS-CoV-2 to evaluate for possible confounding effects 
on interpretation of the week 4 PET/CT scan. Patients who test positive will be 
evaluated on a case-by-case basis to determine if continuation on the study will be 
possible. Patients unable to adhere to essential study procedures (e.g. due to isolation 
requirements) may be withdrawn from the study. 
 
Participants who do not meet the early completion criteria at this point will be assigned to 
Arm A. 
 Week 8 
The following will be performed/obtained at the Week 8 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (total sputum volume at least 3.5 mL) for Xpert testing, 
smear and culture (liquid and solid)  
4) Two or more sputum samples or induced sputum (total sputum volume at least 4 mL) 
for biomarkers  
a. Storage raw and  
b. Storage as 1:1 mix with Trizol for MTB mRNA  
5) Blood will be collected for biomarkers 
6) Urine will be collected for biomarkers  
7) Adherence monitoring 
 
At week 8, PZA and ethambutol will be discontinued for all participants, per SOC.   
 Week 12 
The following will be performed/obtained at the Week 12 visit:  
1) Vital Signs 


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2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (total sputum volume at least 2 mL) for smear and 
culture (liquid and solid) 
4) Adherence monitoring 
 Randomization into Arms B and C 
Randomization assignment to determine if a participant is put into Arm B or C will occur 
at the participant’s Week 16 visit. All participants not already assigned to Arm A will be 
reviewed for early treatment completion criteria eligibility. Those who are not eligible 
will be assigned to Arm A and will complete treatment with HR through 24 weeks, 
although treatment may be extended for some as clinically indicated. Those who meet 
eligibility criteria for early treatment completion will be randomized to Arm B or C. 
Randomization will be stratified by site. Participants randomized to Arm B will continue 
on HR therapy through week 24. Those randomized to Arm C will complete treatment at 
16 weeks. Note that per DSMB recommendations, randomization of participants to Arm 
C at Week 16 visit has been halted as of September 14, 2020.  
 
Participants in Arm A will also be randomized to receive a PET/CT scan either at week 
16 or week 24, stratified by when they were placed in Arm A (baseline, week 4, or week 
16). 
 Week 16  
The following will be performed/obtained at the Week 16 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (at least 3.5 mL) for Xpert testing, smear and culture 
(liquid and solid)  
4) Two or more sputum samples or induced sputum (total sputum volume at least 6 mL) 
for biomarkers  
a. Storage raw and  
b. Storage as 1:1 mix with Trizol for MTB mRNA   
5) Blood will be collected for biomarkers 
6) A finger stick will be collected for blood glucose levels prior to PET/CT scan; Arms 
B and C only 
7) Urine will be collected for  
a. Biomarkers  
b. Pregnancy test, if applicable, prior to PET/CT scan; those eligible for Arms B 
and C and those in Arm A randomized to receive a Week 16 scan  
8) FDG-PET/CT scan for those eligible for Arms B and C and Arm A participants 
randomized to receive the scan at this time point (scan should be within +14 days, but 
ideally within +7 days of randomization)  
9) Saliva sample for those scanned 
10) Adherence monitoring 
11) MERM questionnaire, may be provided to participating users randomized to stop 
drug at Week 16 
 


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At sites with sufficient SARS-CoV-2 testing capacity and personal protective equipment 
for study staff (not conducting the below will not be considered a protocol deviation): 
12) Antibody testing for SARS-CoV-2 to determine prior infection: Samples collected 
may include blood and/or saliva and may be stored for batched testing at a time when 
serological testing has been established. 
 Week 20 
The following will be performed/obtained at the Week 20 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (total sputum volume at least 2 mL) for smear and 
culture (liquid and solid) 
4) Adherence monitoring (Arms A and B only) 
5) Blood will be collected with plasma batch tested for isoniazid and/or rifampin levels 
to confirm that Arm A and B participants are still taking drug and Arm C participants 
are no longer taking drug 
 Week 24 
The following will be performed/obtained at the Week 24 visit:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (at least 3.5 mL) for Xpert testing, smear and culture 
(liquid and solid)  
4) Two or more sputum samples or induced sputum (total sputum volume at least 6 mL) 
for biomarkers  
a. Storage raw and  
b. Storage as 1:1 mix with Trizol for MTB mRNA   
5) Blood will be collected for biomarkers 
6) A finger stick will be collected for blood glucose levels prior to scan; Arm A only  
7) Urine will be collected for  
a. Biomarkers 
b. Pregnancy test, if applicable, prior to scan; Arm A only 
8) FDG-PET/CT scan for those on Arm A randomized to receive the scan at this time 
point (scan should be within +14 days, but ideally within +7 days from stopping drug) 
9) Saliva sample for those scanned  
10) Adherence monitoring (Arms A and B only) 
11) MERM questionnaire may be provided to participating users randomized to stop drug 
at Week 24  
 
At sites with sufficient SARS-CoV-2 testing capacity and personal protective equipment 
for study staff (Not conducting the below will not be considered a protocol deviation): 
12) Antibody testing for SARS-CoV-2 to determine prior infection: Samples collected 
may include blood and/or saliva and may be stored for batched testing at a time when 
serological testing has been established. 
 
Participants in Arms A and B will complete treatment at Week 24.  An Arm A participant 
may be treated longer than 24 weeks at the discretion of the treating physician.   


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 Week 36 
The following will be performed/obtained at the Week 36 visit: 
1) 
Vital Signs 
2) 
Focused medical history/focused physical exam, if indicated 
3) 
One or more sputum samples (total sputum volume at least 2 mL) for smear and 
culture (liquid and solid) 
 Week 48 
The following will be performed/obtained at the Week 48 visit: 
1) 
Vital Signs 
2) 
Focused medical history/focused physical exam, if indicated 
3) 
One or more sputum samples (total sputum volume at least 2 mL) for smear and 
culture (liquid and solid) 
4) 
Two or more sputum samples or induced sputum (total sputum volume at least 4 
mL) for biomarkers for storage  
5) 
Blood will be collected for biomarkers 
6) 
Urine will be collected for biomarkers 
 Week 60 
Week 60 will be a phone call visit. A focus history will be discussed. If a participant 
reports TB-related symptoms, s/he will be asked to come for an in-person visit and 
sputum will be collected for smear and culture.    
 Week 72 
The following will be performed/obtained at the Week 72 visit: 
1) 
Vital Signs 
2) 
Focused medical history/focused physical exam, if indicated 
3) 
One or more sputum samples (at least 3.5 mL) for smear and culture (liquid and 
solid)  
4) 
Two or more sputum samples or induced sputum (total sputum volume at least 4 
mL) for biomarkers for storage  
5) 
Blood will be collected for biomarkers 
6) 
Urine will be collected for biomarkers 
 
At sites with sufficient SARS-CoV-2 testing capacity and personal protective equipment  
for study staff (not conducting the below will not be considered a protocol deviation): 
7) 
Antibody testing for SARS-CoV-2 to determine prior infection: Samples collected 
may include blood and/or saliva and may be stored for batched testing at a time 
when serological testing has been established. 
 
Participants with a positive culture at this visit may be asked to return for sputum culture 
confirmation. In the event that the participant is unable to return for follow-up, every 
effort will be made to contact the participant by telephone to determine his/her clinical 
status. If possible, health authorities local to where the patient is located may be asked to 
collect a sputum sample for culture. Note that the window for this visit is ±30 days. Every 
effort will be made to have the participant return during this window. However, if the 


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participant is interested but unable to return (e.g. has moved far away for work), this 
window may be extended for up to another 11 months (total up to 12 months) to allow 
the participant to return for the final study follow-up visit.  The trial itself will not be 
extended by 11 months, and therefore the last participant will still only be allotted a 30 
day window for his/her Week 72 visit.   
 
Recurrence 
The following will be performed/obtained in the event that someone on study has a 
recurrence of TB:  
1) Vital Signs 
2) Focused medical history/focused physical exam, if indicated 
3) One or more sputum samples (at least 3.5 mL) for Xpert testing, smear and culture 
(liquid and solid)  
4) Two or more sputum samples or induced sputum (total sputum volume at least 4 mL) for 
biomarkers  
a. Storage raw and  
b. Storage as 1:1 mix with Trizol for MTB mRNA  
5) Blood draw for  
a. Complete blood count, chemistries (including HbA1c), and liver function tests 
b. HIV test 
c. Biomarkers 
6) Finger stick will be collected for glucose level prior to PET/CT scanning 
7) Urine will be collected for 
a. Biomarkers 
b. Pregnancy test, if applicable, prior to scanning 
8) FDG-PET/CT scan 
9) Saliva sample 
 
At sites with sufficient SARS-CoV-2 testing capacity and personal protective equipment  
for study staff (not conducting the below will not be considered a protocol deviation): 
10) Viral RNA PCR testing for SARS-CoV-2 to determine active infection: Samples 
collected may include nasopharyngeal (NP) swabs, oropharyngeal (OP) swabs, sputum, 
and/or saliva. Patients who test positive will be evaluated on a case-by-case basis to 
determine if continuation on the study will be possible. Patients unable to adhere to 
essential study procedures (e.g. due to isolation requirements) may be withdrawn from 
the study. 
11) If appropriate, antibody testing for SARS-CoV-2 to determine prior infection: Samples 
collected may include blood and/or saliva and may be stored for batched testing at a 
time when serological testing has been established.  
 
Prior test results done by the local healthcare system within the previous 7 days may be 
accepted but may still be repeated. 
 
National/local TB records may be reviewed for unreported TB recurrence and for TB 
retreatment outcomes.   
 


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An unscheduled visit may be conducted at any time per discretion of the treating physician. 
Tests conducted at these visits will be defined by the treating physician based on the 
clinical assessment of the participant. 


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 Study Timeline  
 
Table 7: Study Timeline 


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ξ Additional sputum may be collected if contaminated or otherwise compromised 
% For participants receiving PET/CT scan at this timepoint
A  subject could be called back for this additional sputa collection, if necessary. 
D At week 8, ethambutol and pyrazinamide will be discontinued 
H Sputum at screening will also be used for screening Xpert
W PET/CT/MRI scan windows : baseline w/i 7 days after treatment initiation; W4  must be at least 4 wks after baseline
S May not be done if within 7 days of screening
scan with a -3/+7 d window; W16 and 24 scan w/i 14 d of visit; relapse ASAP, but w/i 2 wks of recurrence
h  Pregnancy testing from screening may be used for the D0 PET/CT scan if D0 is 
V  Visit windows:  Week 1-2: +/- 3 days;  Week 4-24: +/- 7 d, noting that Weeks 16 and 24  should be as close 
within 2 days of the screen
as possible to actual date; Week 36-72: +/- 30 days. 
G These will be performed at any visit if clinically significant.  
gIf sputum is not available for biomarkers, it will not be a protocol deviation. 
PT  Before any PET/CT scan, MRI or CXR is done, a pregnancy test will be done for applicable
P PK substudy visits can occur anytime after W16, the timeline above may be used as a guide 
  females. If the pregnancy test is positive, the PET/CT scan will not be performed
*Participants will receive 3rd scan at either wk16 or wk24, as determined by study
CV At sites with sufficient SARS-CoV-2 testing capacity


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5 Details of Research Procedures & Data Collection Methods  
 Consent Methodology 
Informed consent is a process where information is presented to enable persons to voluntarily 
decide whether to participate as a research participant. It is an ongoing conversation between 
the participant and the researchers, which begins before consent is given and continues until 
the end of the participant’s involvement in the research.  Discussions about the research will 
provide essential information about the study and include: purpose, duration, procedures, 
alternatives, risks, and benefits. Participants will be given the opportunity to ask questions 
and have them answered. 
 
There will be a main study informed consent (ICF) given.  Some South African sites might 
also have a Genetic Testing and Stored Sample Informed Consent (the information needed 
from these is included in the Main ICF for China).  If the person is potentially eligible and 
interested in joining the trial, the main study informed consent will be given. The informed 
consent process will be conducted by research staff, or qualified investigator. The person 
obtaining informed consent will ask questions to assess the participant’s understanding of the 
ICF and state that participation is voluntary and that participants may refuse participation or 
withdraw at any time without prejudice to their clinical care.   
 
The consent forms will be prepared in English and translated to Mandarin for China, and  
Afrikaans and Xhosa for South Africa.  The participant will sign the informed consent 
documents prior to undergoing any procedures. The researcher will also sign the ICF and 
document the consent process in the participant’s research and/or medical record. 
Participants will also be informed that study results will be made available to them in the 
future. Consent forms will be stored securely at study sites. 
 Treatment adherence  
Treatment adherence may be monitored by any of the following methods (but is not limited 
to only these), depending on local capacity: 
• Directly observed therapy either by study staff, local outreach/healthcare worker, 
participant family member, or friend 
• Pill counts at study visits 
• Electronic adherence monitoring 
• Cell phone card incentives 
• Urine drug level or color monitoring (including for those in Arm C after week 16) 
 
Total treatment duration will be determined by dose counts. Participants will receive either 
16 weeks of treatment (Arm C) or 24 weeks of treatment (Arms A and B). (Arm A 
participants may be treated longer.) Participants receiving 16 weeks of treatment will receive 
112 doses with a minimum total of 100 doses. Participants who do not meet this minimum 
dosing requirement within the 16 week visit window will not be eligible for randomization 
and will be moved to Arm A. Approximately 90% adherence is used, as missing more than 
this has been associated with an increased risk of poor outcomes [53]. Note that per DSMB 
recommendations, randomization to 16 weeks of treatment (Arm C) has been halted as of 
September 14, 2020. Participants receiving 24 weeks of treatment will receive 168 doses 
with a minimum total of 150 doses. Missed doses during the initial 8 week intensive phase 


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will be added on to the end of the intensive phase, replacing continuation phase dosing. Arm 
B participants who do not achieve the minimum 150 doses within the Week 24 visit window 
will be allowed to complete a minimum of 150 doses even if this exceeds the visit window.  
 
For sites using the Medication Event Reminder Monitor (MERM) pill box, a questionnaire 
will be given to participants at the beginning of the study and the end of their time using the 
MERM, as detailed in section 4.  In addition, study staff issuing and working with the pill 
box during the study will be provided a provider questionnaire about the pill box.  
 Medical History  
 Complete Medical History 
A complete medical history will be taken and recorded in a structured format. The 
complete medical history will cover current symptoms, past medical history, 
occupational history, family and social history, drug history, allergies, and review of 
systems.   
 Focused Medical History 
A focused medical history will be taken for cause and recorded in a structured format. 
The focused medical history will cover new medications, new symptoms, medication 
compliance (not at study entry), and review of systems, as needed.   
 Physical Examination 
 Complete Physical Examination 
A detailed complete physical exam will include examination of lymph nodes 
(cervical, axillary, inguinal), respiratory system, abdomen, skin, vital signs (temp, BP, 
pulse, respiratory rate), weight and height. Assessment will be recorded in a 
structured manner. 
 Focused Physical Examination 
A focused physical exam will be directed only at new symptoms and complaints of 
the participant to find evidence of active disease. This targeted physical exam will 
include vital signs and weight and may include examination of lymph nodes, 
respiratory system, and abdomen. The assessment will be recorded in a structured 
manner.  
 Sputum Collection and Mycobacterial Testing Procedures 
 Sputum Induction 
Sputum induction, if necessary during the study, will take place in a designated area. 
Hypertonic saline will be administered via the mouthpiece of a nebulizer to induce 
expectoration. Staff members assisting participants will wear N95 respiratory 
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 Sputum Specimen Use 
 
Xpert  
For screening, initial drug susceptibility testing (DST) and M.tb infection 
confirmation will be performed by Xpert (Cepheid, Sunnyvale, CA) and/or 
newer generation tests if available. Xpert and/or newer generation tests will be 
used to measure cycle threshold (the amplification cycle when Mtb DNA 
becomes detectable in the Xpert assay) as an indicator of changing bacterial 
load at visits indicated in the Study Timeline but are only required at screening 
and at Week 16 visit. Both Xpert MTB/RIF and Xpert Ultra may be done if 
sputum or sputum sediment is available.  
 
 
Sputum Smear and Culture  
Sputum will be cultured on solid and in liquid media at each time point to 
determine time to sputum culture conversion to negative. The time to negative 
will be determined on Lowenstein-Jensen solid agar for the primary assessment. 
The date of culture conversion will be defined as the date of the first of two 
consecutive negative cultures on solid medium over at least 4 weeks. MGIT 
liquid cultures will be used for the primary assessment of time to sputum culture 
conversion for patients with positive baseline or early MGIT cultures but 
negative baseline or early LJ cultures.   Contaminated cultures prior to the week 
60 culture will be considered “no test”, i.e. neither culture positive nor negative, 
and will be repeated to the extent possible. Cultures week 60 and after that are 
contaminated but do not grow M.tb will be considered “no test” but will not be 
repeated. To note, if a culture is contaminated or otherwise not evaluable, 
another sputum sample may be requested prior to the next study visit. 
Participants found during follow-up to have a sputum culture positive for M.tb 
that is confirmed on a subsequent culture will be referred to their physician for 
retreatment. Solid culture results that are missing will be noted as “unavailable”.   
Decontaminated and concentrated sputum sediment will be inoculated onto LJ 
medium and into the BACTEC MGIT liquid medium for measurement of time 
to positivity (TTP) as previously described [54]. The remaining sediment may 
be frozen for further examination. 
Staining for acid-fast bacilli (AFB) on collected sputum will be performed in 
the diagnostic laboratory according to standard site and/or National Health 
Laboratory Service (NHLS) SOPs. 
 
 
Biomarkers in Sputum 
Additional sputa will also be collected and saved for assessing LAM 
concentration, bacterial mRNA copies, and metabolites. Sputum may also be 
saved for detecting mixed MTB infections and/or heteroresistance (e.g. drug 
resistant mutants in the drug susceptible population) as well as attempts to 
resuscitate possible persister populations. Sediment may be tested for MTB 
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    Isolates and Genotypic Tests 
Isolates (during the study and at relapse) will be saved for further work such as strain 
typing, whole genome sequencing, minimal inhibitory concentration determination, 
and single nucleotide polymorphism (SNP) typing. 
 
Participants who develop recurrent disease will have DNA extracted from their 
recurrent TB isolate and their original TB isolate for comparison. We will use one of 
the several recognized genetic testing methods to determine the level of identity 
between two isolates. Examples include mycobacterial interspersed repetitive unit-
variable number tandem repeats patterns (MIRU-VNTR), or whole genome 
sequencing to identity single nucleotide polymorphism (SNP) patterns [55]. Other 
bacterial strain studies to characterize strains may also be performed. 
 Drug Susceptibility Testing of Isolates 
Phenotypic drug susceptibility testing for at least RIF and INH will be performed on 
one of the first-available culture isolates in real time. Saved early and later isolates 
including any relapse isolates may be tested for drug resistance by various methods 
including sub-breakpoint MICs by the research laboratories involved in the study.  
 Saliva Collection for Biomarkers 
Saliva will be collected by the use of salivettes.  Participants will chew on salivettes and the 
saliva will be collected into a tube.  Approximately 2-6 mL of saliva will be collected for 
immunological marker and metabolomics research tests.   
 
These samples will be used for discovery or validation of a biomarker set that may include 
approximately 10-15 cytokines, soluble cytokine receptors, ligands, and extracellular matrix 
proteins. The factors that we expect to measure include, but are not limited to, IL-13, IL-5, 
IFN gamma, TNF alpha, TGF beta, sIL-4R, sIL-2Ra, sIL-6R, sCD40L, MMP-2, MMP-9, 
and C-reactive protein. 
 Blood Collection  
Approximately 10-60 mL of blood will be drawn at collection time points, depending on the 
necessary testing and cultural acceptability.  
 CBC, Chemistries, Liver Function Tests, HbA1c and HIV 
Up to 10 mL of blood will be collected in a clot activator tube (with or without gel) 
for serum collection. This serum can be used for performance of HIV test, liver 
function tests (AST [SGOT], and ALT [SGPT]), creatinine and pregnancy testing.  
Up to 5 mL of blood will be collected in an EDTA tube for hematology (complete 
blood count [CBC]) and HbA1c. Samples will be processed in the hematology and 
biochemistry laboratories of participating sites or accredited lab service (e.g. National 
Health Laboratory Service in South Africa) according to local SOP.  
 
Testing may be repeated to check for or follow-up on abnormal results when needed, 
for example, at screening or after learning about an adverse event.   


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 Biomarkers 
 
Blood Immunological Markers 
Blood (approximately 10 to 42 mL) will be drawn for immunological marker 
and metabolomic research tests. The blood will be used for discovery or 
validation of a biomarker set that may include approximately 10-15 cytokines, 
soluble cytokine receptors, ligands, and extracellular matrix proteins. The 
factors that we expect to measure include, but are not limited to, IL-13, IL-5, 
IFN gamma, TNF alpha, TGF beta, sIL-4R, sIL-2Ra, sIL-6R, sCD40L, MMP-2, 
MMP-9, and C-reactive protein. In addition, serum will be used for 
metabolomics studies to identify small metabolites that are representative of 
biologic pathways that are related to differential outcomes. Blood volumes that 
may be collected include 8 mL whole blood for serum, 1 mL whole blood for 
FACS, and 30 mL whole blood for whole blood assay or PBMC isolation. 
 
 
Blood for host mRNA 
Approximately 2.5 mL blood will be collected in PAXgene tubes for 
determining host mRNA signatures. 
 
 
Blood for host DNA  
Susceptibility to MTB has not been isolated to a particular gene or immune 
pathway.  Many studies of single nucleotide polymorphisms (SNPs) have 
identified genetic variations that may contribute to disease progression. SNPs in 
genes such as NRAMP1, MCP1, TIRAP, P2X7 and TLR2 have been associated 
with either susceptibility to or protection against developing tuberculosis [56]. 
However, these and other SNPs often differ among the ethnic groups analyzed 
making it difficult to decipher the influence of environmental factors verses 
gene interactions in tuberculosis severity. Since this will be a large cohort study 
followed for treatment response rate and treatment outcome, DNA samples will 
be saved for future use in studies of genetic vulnerability.   
 
Approximately 1 mL of heparinized whole blood collected at the first blood 
biomarkers draw will have the red cells lysed and white cells pelleted for future 
DNA preparation and saved at -80C. Additional blood cell pellets from other 
assays above may also be saved for use in DNA preparation.  
 Plasma for drug levels 
Approximately 1 mL of blood will be collected in an EDTA tube and spun down for 
plasma, which will be stored frozen. Isoniazid and/or rifampin plasma levels will be 
batch tested.  
 Urine Collection and Testing 
 Pregnancy Testing 
Urine will be collected for pregnancy testing before each PET/CT scan (except for the 
initial pregnancy test which will be from blood). A commercial human chorionic 
gonadotropin (β-hCG) determination assay will be performed in accordance with 
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 Biomarkers in Urine 
Urine will also be collected and saved for future biomarker research and for research 
metabolomics studies. Approximately 1 cup will be collected mid-stream.  
 Imaging 
 FDG-PET/CT scan 
The FDG-PET/CT scan will be performed at a facility local to the study site.  The CT 
portion of the scan will be done without contrast and will be limited to the chest. 
Participants will consent to receive a maximum of 4 FDG-PET/CT scans during the 
study (baseline, Week 4, Week 16 or 24, and at recurrence); however, the vast 
majority of participants will only receive 3 scans. If resources do not allow for all 
Arm A participants to receive a week 4 scan, they may receive only 2 scans. 
Participants will be fully briefed with regard to what to expect and any precautions 
highlighted. Participants will be asked not to eat for about 6 hours prior to the scan 
but to drink plenty of water. Participants will have an assessment of blood sugar. 
Following the blood test, a venous cannula will be inserted and approximately 7 mCi 
of radiolabeled18F-FDG administered. After about 50 minutes participants will void 
urine, and at about 60 minutes after injection, the participants will undergo a FDG-
PET/CT scan of the chest. For radiation dosimetry details of the scanners used, please 
refer to the appendices.  
 Chest Radiograph (CXR) 
CXRs may be taken at participating sites if clinically indicated.  They will be 
performed according to local SOP. 
 
 Magnetic Resonance Imaging (MRI) 
Pulmonary MRIs with a macrocyclic gadolinium-based contrast will be used in a 
subset of participants who meet the substudy inclusion and exclusion criteria. 
Gadolinium highlights fibrosis, the development of which may affect treatment 
outcomes. Participants in this substudy will consent to receive a pulmonary MRI scan 
at baseline and again at Week 4 (two total scans). They will be performed according 
to local SOP. There is no ionizing radiation associated with MRI scanning.  
 
Nephrogenic systemic fibrosis (NSF) is a rare, progressive, usually fatal disease 
involving fibrosis of the skin and internal organs and occurs exclusively in patients 
with renal failure who receive gadolinium. To reduce the risk of NSF: 
• Participants with any evidence of renal insufficiency, defined as an estimated 
glomerular filtration rate (eGFR) <60 mL/min, will be excluded from the MRI 
substudy. 
• Macrocyclic chelate preparations of gadolinium are associated with lower 
levels of free gadolinium than linear chelates. Free gadolinium (Gd3+) can 
precipitate in tissues and is believed to be the toxin that causes NSF in those 
with renal failure. A macrocyclic gadolinium-based contrast agent will be 
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Gadolinium retention: There is increasing evidence that trace amounts of 
gadolinium are retained in the body for months to years, including in the bone, 
brain, and other organs. Retention seems to occur with all forms of gadolinium but 
is less with macrocyclic gadolinium contrast agents. The clinical significance of this 
retention is not clear. No adverse health effects in patients with normal kidney 
function have been directly linked to gadolinium retention and thus the FDA has 
concluded that the benefit of approved gadolinium based contrast agents outweighs 
any potential risks [57].  
 COVID-19 Testing 
Viral RNA PCR testing for SARS-CoV-2 may be conducted to determine active 
infection: Samples collected may include nasopharyngeal (NP) swabs, 
oropharyngeal (OP) swabs, sputum, and/or saliva. Antibody testing for SARS-CoV-
2 to determine prior infection may also be conducted: Samples collected may 
include blood and/or saliva and may be stored for batched testing at a time when 
serological testing has been established. Prior test results done by the local 
healthcare system within the previous 7 days may be accepted but may still be 
repeated. 
 Participants moved to Arm A 
During the trial, participants may be moved to Arm A for the following reasons: 
1) Not meeting early treatment completion criteria (including incomplete adherence) 
2) Found to be pregnant. No further PET/CT scanning will be done on these 
participants. 
3) Experiencing adverse drug effects severe enough to require permanent 
discontinuation of any individual TB drug. Drug pauses are also allowed without a 
change in arm as long as treatment adherence requirements are met (see Sec 5.2).  
 
Divided daily dosing or changing fixed-dose combination tablets to single-drug tablets is 
permitted without a change in arm as long as all standard drug components for that time 
point are maintained. 
 Withdrawal or Termination From the Study 
1) Participants with evidence of pleural TB or large pleural effusion on baseline PET/CT 
will be withdrawn and replaced.  
2) Participants with significant incidental findings on PET/CT that require immediate 
diagnostic procedures or treatment may be withdrawn from the study if in the opinion 
of the investigator, continuing on the study may not be in the participant’s best 
interests.  
3) Participants identified to have resistance on molecular or phenotypic DST will be 
withdrawn and replaced, if possible. 
4) Participants enrolled in the study based on a positive Xpert but subsequently found to 
be culture negative will be withdrawn and replaced. 
5) Participants on Arm A who are still culture positive at Week 24 will be considered to 
have treatment failure and will be discontinued from the study as having reached a 
study endpoint.  
 


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During any stage of the study, participants may be withdrawn if: 
1) Participant withdraws consent 
2) There is any reason deemed appropriate by the investigator or attending physician. 
 Study Completion 
Participants will be considered completed if they complete the final, 18-month follow-up 
visit and have not developed recurrent TB. For those who develop recurrent TB, Arm A 
participants will be considered to have completed the study at the time of recurrence 
confirmation (study endpoint) and will be referred for treatment. Arms B/C participants 
who develop recurrent TB will complete observational follow-up to the end of re-
treatment for retreatment outcome even if this exceeds 18 months. Note that participants 
who consent to participate in the PK substudy will continue in the overall study until 
completion of the PK study. 
 
6 Statistical Methods and Justification 
 Study Hypotheses 
 Primary Hypothesis 
A combination of radiographic characteristics at baseline, the rate of change of 
these features at one month, and markers of residual bacterial load at the end of 
treatment will identify patients with tuberculosis who are cured with 4 months (16 
weeks) of standard treatment. 
 Secondary Hypotheses 
 
1) The treatment success rate among low-risk participants with shortened 
treatment will be similar to that of a representative 6-month standard of care 
population.  
2) In univariate and multivariate analyses, demographic, radiographic, bacterial 
load, microbiologic, and immunologic markers are associated with treatment 
failure. 
3) In univariate and multivariate analyses, demographic, radiographic, bacterial 
load, microbiologic, and immunologic markers are associated with subsequent 
relapse. 
4) PET scans predict treatment outcomes in univariate and multivariate analyses 
that include relevant variables based on secondary hypotheses 2) and 3). 
5) Bacterial load markers (TTP and Xpert cycle threshold) collected at later time 
points are better markers of ultimate treatment outcomes than markers 
collected at earlier times. 
6) Pharmacokinetic and sub-breakpoint MIC measurements will significantly 
predict treatment outcome in 16 and 24 week treatment regimens. 
7) Baseline and week 4 MRI imaging biomarkers will stratify TB patients into 
higher risk (require longer treatment) and lower risk (cured with shorter 
treatment) cohorts in accordance with the PredictTB early treatment 
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 Definitions 
 Treatment Success 
Treatment success will be defined as a participant with at least 2 consecutive 
negative cultures on solid medium over a span of at least 4 weeks, achieved before 
the end of therapy, with no subsequent confirmed positive cultures during follow-
up. Two consecutive negative cultures on liquid medium over a span of at least 4 
weeks will be used for patients who were liquid medium positive but solid medium 
negative at the baseline or early cultures. 
 Treatment Failure 
Participants who remain culture positive on solid medium at Week 24 in Arm A 
will be considered treatment failures. Arm A participants who become culture 
negative on 2 consecutive cultures over at least 4 weeks who subsequently become 
culture positive again while still on treatment, confirmed on a subsequent culture, 
will also be considered treatment failures. This is a study endpoint. The participant 
will be discontinued from the study and will be referred to continue treatment per 
the local SOC. Participants who convert to solid culture negative who 
subsequently have a single solid culture positive for Mtb before or at week 24 need 
to have a subsequent culture positive for Mtb to be confirmed as treatment failures.  
 
Participants in Arm A only before Week 24 who develop new clinical or 
laboratory signs or symptoms of TB worsening may have their intensive phase 
treatment continued or restarted at the discretion of the treating physician. If the 
treating physician believes that additional drugs are warranted for patient safety 
before culture results are known, multiple additional sputum samples over >1 day 
should be collected before additional treatment is started. The participant will be 
considered a clinical treatment failure and discontinued from the study. 
 
Solid culture results will be used for all primary endpoint analyses with the 
exception that the liquid culture result may be used at the final week 72 study visit 
if the solid culture result is contaminated or missing and the participant cannot be 
brought back to repeat the sputum sample. In this instance, if the liquid culture 
result is negative, the sputum sample will be considered negative. For other study 
visits, only solid culture results will be used for the primary analysis. Solid culture 
results that are missing or contaminated will be classified as unavailable. Liquid 
culture results may be used for secondary analyses. 
 
Participants randomized to Arms B or C who are subsequently found to have a 
positive culture for Mtb on solid medium between and including weeks 16-24 that 
is confirmed on a subsequent culture will be considered treatment failures. These 
participants will be referred to continue treatment per local SOC and followed 
observationally until the end of their treatment to determine outcome. TB DNA 
strain typing may be done (sec 5.5.3) to confirm whether or not this is the same 
strain of DNA as the participant had at baseline.  
 


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Single positive cultures with no other corroborating clinical or laboratory evidence 
are not considered failures. Single positive cultures may arise from clerical error or 
laboratory contamination [58]. 
 
Participants determined to be treatment failures may be evaluated for COVID-19 
infection. Viral RNA PCR testing for SARS-CoV-2 may be done to determine 
active infection: samples collected may include nasopharyngeal (NP) swabs, 
oropharyngeal (OP) swabs, sputum, and/or saliva. Additionally, antibody testing 
for SARS-CoV-2 to determine prior infection may be conducted: Samples 
collected may include blood and/or saliva and may be stored for batched testing at 
a time when serological testing has been established. Prior test results done by the 
local healthcare system within the previous 7 days may be accepted but may still 
be repeated. 
 Treatment Recurrence and Relapse 
Participants who convert their sputum to culture negative (2 consecutive negatives 
over ≥4 weeks) and who subsequently become culture positive for M.tb again on 
solid medium, during follow-up after week 24, confirmed by a second (on another 
day) sputum culture positive for M.tb, will be considered recurrences. Single 
positive cultures that are negative on follow-up culture will not be considered 
recurrences. Participants with a positive, contaminated, or unevaluable culture on 
the final month 18 (week 78) follow-up visit may be asked to return for sputum 
culture confirmation. 
 
Relapses will be distinguished from re-infections by DNA strain typing (sec 5.5.3) 
and only relapses will be considered a study endpoint.  
 
Relapses on Arms B and C will have observational follow-up until the end of 
retreatment.   
 
Participants determined to be treatment recurrences or relapses may be evaluated 
for COVID-19 infection. Viral RNA PCR testing for SARS-CoV-2 may be done to 
determine active infection: samples collected may include nasopharyngeal (NP) 
swabs, oropharyngeal (OP) swabs, sputum, and/or saliva. Additionally, antibody 
testing for SARS-CoV-2 to determine prior infection may be conducted: Samples 
collected may include blood and/or saliva and may be stored for batched testing at 
a time when serological testing has been established. Prior test results done by the 
local healthcare system within the previous 7 days may be accepted but may still 
be repeated. 
 
 Primary Endpoint 
The primary endpoint will be a comparison of the rate of treatment success at 18 months 
(after treatment initiation) between Arms B and C. Final study treatment outcome data 
from participants who are unable to return at 18 months but do return during the 1 year 
following will be imputed back to the 18 month time point for the primary endpoint. 
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participants who successfully complete treatment, but are later lost to follow-up without 
evidence of Mtb. The imputation method will assume an exponential model that will 
account for the duration of missingness. Extensive sensitivity analyses will explore the 
robustness of the imputation method. The details of these analyses are provided in the 
statistical analysis plan. 
 Secondary Endpoints 
The endpoint relating to the first secondary endpoint is treatment success, as defined for 
the primary endpoint.  Other endpoints relating to secondary hypotheses are based on 
imaging, microbiology, and immunology. The endpoints from images include: PET total 
glycolytic activity in regions of interest, total volume of hard CT lesions (-100 to 100 HU), 
total volume of soft CT lesions (-500 to -100 HU), and cavity air (volume of air in 
cavities). Endpoints relating to immunologic markers will be based on serum cytokine 
levels as described in section 1. Xpert cycle threshold will be analyzed as a continuous 
variable in addition to the pre-specified thresholds. Analyses will also consider 
transformations such as delta cycle threshold. 
 Statistical Methods  
 Primary Analysis 
The primary analysis will estimate the lower bound of a one-sided 95% confidence 
interval of the difference in success rates between arms B and C. If the lower 
bound is greater than -7%, this will be evidence that the treatment-shortening arm 
is not inferior to the standard duration arm. Confidence intervals will be 
constructed using Wald intervals, with inverse weighting according to site-
estimated variances, as a stratified analysis. Additional analyses of the primary 
endpoint will consider a non-stratified-based confidence interval of the difference. 
 Secondary Analyses  
The difference (and 95% confidence interval) in treatment success rates between a 
combined A+B Arm (with Arm A participants selected to represent a true 6-month 
standard of care population) and a combined Arm A+C (with the remaining Arm A 
participants selected to represent a treatment shortening strategy arm, and no 
overlap in Arm A participants assigned to B and C). Logistic regression will be 
used to develop risk scores based on the various markers. Markers that are 
statistically significant univariately will be evaluated in multivariate models. ROC 
analyses will be conducted, when appropriate, using the non-parametric AUC 
estimator and the corresponding bootstrap variance estimators for hypothesis 
testing. Permutation methods and leave-one-out cross-validation will be 
implemented to control the family-wise error rate and adjust for over-fitting bias. 
When evaluating the relationship between time of specimen sampling with 
diagnostic ability (e.g., comparing early versus late Xpert cycle threshold as a 
predictor of relapse risk), time-dependent ROC curves will be estimated. 
 Sample Size Considerations 
For this study, the sample size is calculated for Arms B and C, which are used for the 
primary endpoint. Because these are lower risk participants, we expect a treatment success 


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rate of 97%.  Table 8 provides power calculations for sample sizes of 129 and 155 per 
group, adjusted for a 10% loss to follow-up rate.  With true success rates of 97% in both 
arms, study power is greater than 90% with only 129 participants per group. However, to 
increase power to accommodate a scenario in which the true success rate in the four-
month treatment arm is slightly lower than the six-month arm, a sample size of 155 per 
treatment arm was selected.  We expect that approximately 50% of participants will be 
classified as higher risk and be placed into Arm A, giving a total study sample size of 620 
participants. The proportion of participants considered lower risk by our treatment 
completion criteria will be monitored during the study. If it becomes expected that Arm A 
will complete enrollment (i.e., 310 participants) prior to Arms B/C, a corrective action 
plan will be developed to slow enrollment in Arm A so that Arms B/C enrollment can 
catch up. 
 
Table 8. Power calculations for total sample sizes of 129 and 155 per group (arms B and C) 
for different success rates across and between treatment arms. 
 
Success rate by study arm 
Power for concluding NI with 
7% margin, one-sided 5% type 
I error rate, and 10% loss to 
follow-up 
6-month tx 
4-month tx 
Sample size 
129 per group 
Sample size 
155 per group 
0.99 
0.99 
0.999 
1 
0.99 
0.98 
0.984 
0.994 
0.99 
0.97 
0.863 
0.912 
0.98 
0.98 
0.985 
0.994 
0.98 
0.97 
0.903 
0.942 
0.98 
0.96 
0.726 
0.792 
0.97 
0.97 
0.932 
0.963 
0.97 
0.96 
0.803 
0.862 
0.97 
0.95 
0.621 
0.689 
0.96 
0.96 
0.862 
0.911 
0.96 
0.95 
0.716 
0.782 
0.96 
0.94 
0.545 
0.609 
0.95 
0.95 
0.792 
0.851 
0.95 
0.94 
0.644 
0.711 
0.95 
0.93 
0.487 
0.547 
 
Table 9 provides sample sizes for differing non-inferiority margins. 
 
 
 


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Table 9: Sample Sizes for 80%, 85%, and 90% power with a one-sided type I error rate 
of 5% for various non-inferiority margins, assuming equal success rates in Arms B and 
C. 
 
 
Sample size (per arm) 
Treatment 
success rate 
NI margin 
80% Power 
85% Power 
90% Power 
0.90 0.04 
696 
809 
964 
0.90 0.05 
446 
518 
617 
0.90 0.06 
310 
360 
429 
0.90 0.07 
228 
265 
315 
0.95 0.04 
368 
427 
509 
0.95 0.05 
235 
274 
326 
0.95 0.06 
164 
190 
226 
0.95 0.07 
120 
140 
167 
0.97 0.04 
225 
262 
312 
0.97 0.05 
144 
168 
200 
0.97 0.06 
100 
117 
139 
0.97 0.07 
66 
85 
102 
Note that the sample size was determined based on an assumed treatment success 
rate of 95%, a non-inferiority margin of 7%, with 85% power. 
 
 Interim analyses 
 Early stopping for inferiority of treatment shortening arm 
Interim analyses will be performed for safety in Arms B and C, to evaluate whether 
the poor outcome rate is worse in the arm with earlier treatment completion. A 
Fisher’s Exact test will be performed after 1/3 and 2/3 of participants have been 
followed for 72 weeks from study entry, using a Pocock boundary. The stopping 
boundary is derived from a test of inferiority (of the treatment shortening arm) that 
corresponds to a z-score of 2.178 (i.e., a two-sided p-value of 0.029). 
 
Note that as of September 14, 2020 the Data Safety Monitoring Board recommended 
that randomization to Arm C should be discontinued following the interim analysis 
conducted after approximately 1/3 of participants were followed for 72 weeks. 
 Early stopping for study futility 
The premise of this study is that imaging and Xpert markers can identify a subset of 
participants with high success rates. If the success rate is low in this subset, this will 
call into question the basis for this study. Accordingly, monitoring for a low success 
rate is proposed. When half of the participants have completed their week 72 follow-
up, the treatment success rate will be evaluated and presented to the Data and Safety 
Monitoring Board (DSMB). If more than 16 (of 75) participants in the standard 
treatment arm (Arm B) have a relapse, a recommendation to stop the trial will be 
considered. Alternatively, a recommendation to stop randomization into Arm C will 
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will be put into Arm B. Under this scenario the highest achievable success rate in the 
standard treatment arm is 90%. Success rates lower than 90% would be concerning 
given the eligibility criteria for randomization, which represents a subset of 
participants with a low probability of relapse. Conditional power will be included in 
the DSMB reports to give guidance about the likelihood of concluding non-inferiority 
if the study continues to full enrollment. A table of conditional power computations 
will be included using a range of non-inferiority margins (e.g., ranging from 6%-
10%), since determination of an acceptable margin may depend on multiple factors. 
 
7 PK Substudy for Sub-Breakpoint Minimum Inhibitory Concentrations 
(MIC) Comparison 
 
TB patients are known to have widely variable serum PK values and these differences appear 
to affect treatment outcome [59-61]. Because a given patient’s serum drug concentration 
achieved would clearly affect the clinical interpretation of a given MIC result, a model 
incorporating both parameters may predict outcomes better than either one alone. 
 
To test the sub-breakpoint MIC concept, we would ideally identify those at highest risk of 
relapse, and those who have relapsed, to see if there were differences in sub-breakpoint MIC 
and/or PK/sub-breakpoint MIC at baseline, compared with those who did not relapse, as it is 
not practical to collect PK data on all participants. Based on preliminary data, we believe that 
participants who enter Arm A due to a residual bacterial burden at the end of treatment 
determined by a Week 16 Xpert Ct <28 are at a higher risk of relapse. We can therefore target 
this group of participants for inclusion into this PK substudy. Because not all these participants 
will ultimately relapse, we will have PK data on both participants who relapse and those who 
do not. Additionally, any participant determined to have a poor treatment outcome will be 
invited to participate in this substudy. Participants with poor treatment outcomes who agree to 
participate in the PK substudy will remain in the overall study until they complete the 
substudy. 
 Substudy Procedures 
PK data will only be collected for INH and RIF. The study timeline is as follows. (Note, PK 
visits may occur between main study visits.) 
 
• Week 16: Identification of participants who move to Arm A from Arm B/C due to Week 
16 Xpert Ct<28 and are eligible for this substudy.  
 
After these participants are identified and enrolled, they may be scheduled for PK visit 
dates at any time, even if it is not at the dates recommended below. The timeline below 
may be used as a guide. 
 
• Weeks 16-24: Site staff introduce substudy to participants who moved to Arm A from 
Arm B/C at week 16 due to Xpert Ct<28. Those willing to participate will provide 
informed consent and will be instructed to come to a subsequent substudy visit (may occur 
on or between overall study visits) without having taken their TB drug dose for the day. 
  


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• When the participant attends their first substudy visit, the time of TB medication 
intake (e.g. pill box opening times) for the two previous days are recorded. A trough 
blood (approximately 2 mL) is drawn, then the TB drug dose is taken. Blood 
(approximately 2 mL) is then drawn at approximately 1, 2, and 6 hours post-dose. 
Note that PK sampling cannot be done if the participant takes his/her TB drug dose 
before coming to the clinic and sampling will be deferred to the next study visit.  
• Windows for the blood draws are +/- 10 min for the 1 and 2 hour draws and +/- 20 min 
for the 6 hour draw.   
• Participants are instructed to come to their second substudy visit without having taken 
their TB drug dose for that day. The second substudy visit can occur on any day after 
the first substudy visit while the patient is still taking TB medicines.    
• For every participant enrolled in the substudy who moved to Arm A at week 16, a 
control participant, who did not move to arm A at week 16 and who was randomized 
to Arm B will be enrolled and PK sampling performed as described above on 2 
separate days. 
 
• Weeks 16-72: Identification of those participants who have poor treatment outcomes. 
Participants who have poor treatment outcomes be referred to the local TB clinic to 
continue or restart treatment. Concurrently, site staff will introduce the substudy to these 
participants, and those willing to participate will provide informed consent. Substudy 
participants will be instructed to come for two PK sampling visits without having taken 
their TB drug dose for the day. Substudy participants restarting treatment should schedule 
their 1st visit at least 7 days after restarting treatment to allow time for steady-state kinetics 
to develop.  
 
 
 
Participation in the substudy concludes after two days of PK sampling are completed. 
 
Two days of PK sampling per participant are necessary to differentiate inter-patient 
variability from within patient inter-occasion variability. Inter-occasion variability is 
“random” variability due to factors such as food intake, concomitant medicines, co-
morbidities, etc., that may affect absorption and that change over time. With two sets of data 
points at different times for each patient, the PK modelers will be able to differentiate signal 
from noise much more effectively.  
 Inclusion criteria: 
1) Participant moved to Arm A due to Week 16 Xpert Ct <28 OR participants determined to 
have a poor treatment outcome 
2) Willing to come for two study visits) without having taken that day’s TB drug dose, then 
stay for at least 6 hours for blood draws at 0, 1, 2, and 6 hours after taking the TB drug 
dose. 
3) Willing to have samples stored 
4) Willing to sign substudy informed consent 
 Exclusion criteria 
1) None 


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 Control participants 
Each participant transferred from Arm B/C to Arm A at week 16 due to Xpert<28  will be 
invited to participate in this substudy. Enrolled substudy participants who do not develop 
poor treatment outcomes will be treated as control participants.  
 
Participants invited to participate in the substudy following determination of a poor treatment 
outcome will not have direct controls.  
 Substudy Remuneration 
The substudy participant will be compensated $25 (350 rand; 165 yuan) for each day of PK 
sampling completed.  
 
8 Lung Magnetic Resonance Imaging Scans to Individualize Treatment 
Duration for Pulmonary Tuberculosis Patients Substudy 
 
MRI has been revolutionized in two directions over the last 40 years. Initial human MRI 
scanners used magnetic fields around 0.05-0.35 tesla (T). As hardware and software 
technology improved, higher magnetic field machines became available generating increasing 
image resolution but also higher expense due to the systems and shielding required to maintain 
high magnetic fields, with 7T systems now marketed. In contrast, more recent advances have 
emphasized a return to lower field MRI systems that are less expensive and potentially scalable 
in resource-limited settings. The software and hardware advances developed for high magnetic 
field systems are now also being applied to lower field systems to offset the decreased image 
resolution to an acceptable diagnostic level [62]. It is in this context that we hypothesize that 
baseline and week 4 MRI imaging biomarkers will stratify TB patients into higher risk (require 
longer treatment) and lower risk (cured with shorter treatment) cohorts in accordance with the 
PredictTB early treatment completion criteria.  
 
Although PET/CT scanning is unlikely to be widely available globally soon, low-field MRI 
scanning is starting to bridge the gap between developed and developing country availability 
and thus may be relevant to future global TB treatment algorithms. This substudy anticipates 
the coming wider availability of MRI systems to synergize with the ongoing PredictTB clinical 
trial, which already conducts PET/CT scans, to add a small substudy to collect additional lung 
MRI scans at baseline and week 4. If the PredictTB trial is successful, blood, sputum, or urine-
based biomarkers that correlate with the PET/CT signature will be sought but adding MRI 
scans provides an additional potential route to global applicability and scalability of the 
treatment shortening algorithm. 
 
 Substudy Procedures 
MRI image data will only be collected for participants in the PredictTB study who enroll in 
this substudy.  
• Screening visit: PredictTB main study ICF and MRI substudy ICF will be introduced and 
signed. 
• Baseline enrollment visit: Participants who meet the main study inclusion/exclusion 
criteria will be enrolled. Enrolled main study participants who also meet the MRI substudy 


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inclusion/exclusion criteria will also be enrolled, with baseline and week 4 pulmonary 
MRI scans scheduled.  
 
The following study procedures will be performed/obtained for this substudy: 
 
1) Day 0: pulmonary MRI scan, within 7 days of treatment initiation (provided pregnancy 
test is negative) 
2) Week 4: pulmonary MRI scan, taken 4 weeks after the date of the previous scan, with 
a -3/+7-day window (provided pregnancy test is negative) 
 Inclusion Criteria 
1) Enrolled onto the PredictTB study. 
2) Has a screening or baseline GeneXpert semiquantitative reading of medium or high to 
reduce the enrollment of participants with minimal disease in whom an MRI scan may be 
of less benefit. 
3) Willing to sign the MRI substudy informed consent. 
 Exclusion Criteria 
1) Unable to undergo MRI as determined by MRI safety screen (e.g., pregnancy, metal in 
body, claustrophobia) using the standard screen conducted by the MRI imaging facility. 
2) Estimated GFR <60mL/min/1.73m2 to reduce the risk of NSF. 
3) Received a MRI scan with gadolinium-based contrast agent within the last 12 months. 
4) Intolerance to macrocyclic gadolinium-based contrast agents. 
 
Note that a pregnancy test will be repeated in females before the week 4 MRI scan and, 
if positive, the participant will be withdrawn from the substudy and that scan will not be 
done. 
 Statistical Methods 
The primary statistical analysis (Aim 1) will be whether our baseline and week 4 MRI lesion 
quantitation parameters classify PredictTB patients into the PredictTB-defined high and low 
risk cohorts (final week 16 classification into Arm A (high risk) vs. Arms B or C (low risk)) 
with classification accuracy (p) greater than chance (>50%). If the true classification 
accuracy is 72%, the substudy would have a power of 90% to rule out the null hypothesis of 
p=0.5 with 60 participants (Table 10). Sensitivity (correct MRI classification amongst the 
high-risk subjects) and specificity (correct MRI classification amongst the low-risk subjects) 
will be estimated, along with 95% confidence intervals. 
 
 
Power 
Sample size 
True p 
90% 
30 
0.78 
40 
0.75 
50 
0.73 


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60 
0.72 
80% 
30 
0.75 
40 
0.72 
50 
0.70 
60 
0.69 
Table 10: MRI Substudy Power Calculation 
 
Approximately 40 participants will be enrolled in South Africa and 20 in China. The 
correlation between quantitative MRI and PET-CT variables will be tested and presented on 
Bland-Altman plots.  
 
 Substudy Remuneration 
The substudy participant will be compensated 350 rand; 100 yuan for each MRI scan 
completed.  
 
9 Adverse Events, Unanticipated Problems, Deviations, and Non-
Compliance 
  Reporting Procedures 
 Assessment of Safety 
 
AEs and other reportable events are defined in Policy 801: 
Reporting Research Events 
 Reporting Procedures 
 
Unanticipated problems, non-compliance, and other reportable 
events will be reported to the NIH IRB according to Policy 801. 
 Investigator Assessment of Adverse Events 
 Grading Adverse Events for Severity 
 
The severity of each AE will be determined using the DAIDS Table for Grading the 
Severity of Adult and Pediatric Adverse Events (Corrected Version 2.1 – July 2017).  
Any events that are not listed in this toxicity table will be graded by the local 
investigator as follows:  
 
Grade 1 -   Mild 
Transient or mild discomfort; no limitation in activity; 
no medical intervention/therapy required  
 


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Grade 2 -   Moderate 
Moderate limitation in activity – some assistance may 
be needed; no or minimal medical intervention/ 
therapy required 
 
Grade 3 -   Severe 
Marked limitation in activity; some assistance usually 
required; medical intervention/therapy required, 
hospitalizations possible 
 
Grade 4 -   Life-threatening 
Extreme limitation in activity, significant assistance 
required; significant medical intervention/therapy 
required, hospitalization or hospice care probable 
 
Grade 5 – Death 
 
 
 
 Assessing Adverse Events for Relationship to Study 
Any AE that occurs in a participant will be assessed for its relationship to the 
study. A causal relationship means an intervention caused (or is reasonably likely 
to have caused) the AE. This usually implies a relationship in time between one or 
more intervention and the AEfor example, the AE occurred shortly after the 
participant received the drugs/study agents/intervention. 
 
For all AEs, the clinician who examines and evaluates the participant will 
determine the AE’s causality based upon the temporal relationship to 
administration of the intervention, the pharmacology of any applicable study 
agents, and his/her clinical judgment.   
 
The following scale will be used to reflect the PI’s judgment as to the relationship 
between the intervention and the AE:  
 
Definitely Related: The AE is clearly related to one or more of the interventions – 
follows a reasonable temporal sequence from administration of one or more of the 
interventions, follows a known or expected response pattern to the one or more of 
the interventions that is confirmed by improvement on stopping and reappearance 
of the event in repeated exposure and that could not be reasonably explained by the 
known characteristics of the participant’s clinical state. 
 
Probably Related:  The AE and administration of the interventions are reasonably 
related in time and/or follows a known pattern of response, and the AE is more 
likely explained by one or more of the interventions than other causes. 
 
Possibly Related: AE follows a reasonable temporal sequence from administration 
of the interventions, follows a known or expected response pattern to the suspected 
intervention or interventions, but that could readily have been produced by a 
number of other factors. 
 


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Unlikely Related:  A potential relationship between one or more of the 
interventions and the AE could exist (i.e., the possibility cannot be excluded), but 
the AE is most likely explained by causes other than one or more of the 
interventions (e.g., could readily have been produced by the participant’s clinical 
state or could have been due to environmental or other interventions) 
 
Unrelated:  AE is clearly not related to one or more of the interventions– another 
cause of the event is most plausible and/or a clinically plausible, temporal 
sequence is consistent with the onset of the event and the intervention 
administration and/or event is biologically implausible. 
 Documenting and Recording of Events 
At each contact with the participant, information regarding adverse events will be elicited 
by appropriate questioning and examinations. All events, both expected/unexpected and 
related/unrelated will be recorded on a source document. Source documents will include: 
progress notes, laboratory reports, consult notes, phone call summaries, survey tools and 
data collection tools. Source documents will be reviewed in a timely manner by the 
research team. All adverse events that are identified will be recorded on the appropriate 
case report form (CRF) and in the study chart. The start date, stop date, severity of each 
reportable event, and the investigator’s judgment of the AE’s relationship and 
expectedness to the study will also be recorded on the CRF. In the event that a participant 
is withdrawn from the study due to an AE, it must be recorded on the CRF as such. 
 Adverse Event Treatment 
Once an AE is known, staff at the study site should ensure that the participant receives 
prompt and appropriate care. Should a participant call a study clinician to report an AE, it 
will be determined at that time if an extra visit(s) will be scheduled, in addition to 
providing appropriate medical advice. All actions taken by the investigator after observing 
an AE should be documented, including increased monitoring of the participant, 
suspension of any treatment, etc. Additionally, all calls will be documented in the 
participant’s study chart. 
 Expected Adverse Events 
 
Table 11: Expected Adverse Events 
Intervention or 
potential cause of 
AE 
Adverse effects 
Blood drawing 
Common: Discomfort 
Significant but rare: Hematoma, Infection, nerve damage, syncope 
FDG-PET/CT 
Significant but rare: Hematoma, thrombophlebitis, infection, nerve damage, 
syncope 
Induced Sputum 
Can have coughing, wheezing, and or bronchospasms 


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 Investigator Reporting Responsibilities to The NIH Institutional Review 
Board (IRB) 
 
All reportable events will be reported by email, telephone, or fax by the participating sites to the 
following:  
 
  
Phone 
Fax 
Email 
Address 
Clifton E. 
Barry, 3rd, 
Ph.D. 
+1-301-693-
4665 
+1-301-402-0993 
cbarry@niaid.nih.gov; 
cc:vincentjp@nih.gov  
Building 33, Room 
2w20D, Bethesda, MD 
Ray Chen, 
MD (NIAID 
Medically 
Accountable 
Investigator) 
+1-301-443-
5816 
+1-301-480-5713 
rchen@niaid.nih.gov; 
 
Building 33, Room 
2w20C, Bethesda, MD 
Table 12:  NIAID Contact information  
 Local Study Site Reporting 
 To Local IRB 
The Local PIs have the responsibility to report AEs to their local IRB. The Local 
PIs also have the responsibility to report to the NIH team. 
 
 
China Team 
In the event of an unanticipated problem (UP) 
1. The local principal investigator must initially report the UP and summary of 
the problem to the local IRB as soon as possible (usually within 24 ~ 48 
hours) after awareness.  
 
2. After the initial report, the local PI must provide a formal report to the IRB 
within 7 days of awareness including the investigator’s judgment of 
harmfulness to the participant(s) and others.  
 
 
South African Team 
In the event of an unanticipated problem (UP) 
1. The Local principal investigator must initially report the UP and summary of 
the problem to the local IRB according to the local IRB SOPs as soon as 
possible after awareness.  
 
2. After the initial report, the Local PI must provide a formal report including 
any relevant information to the IRB as necessary, including the investigator’s 
judgment of harmfulness to the subject(s) and others. 


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 To NIH Study Team 
The Local PI has the responsibility to report actual or suspected non-compliance, 
actual or suspected major deviations, actual or suspected Unanticipated Problems, 
new information that might affect the willingness of a subject to enroll or remain 
in the study, and suspension or termination of research activities within 7 days of 
awareness to allow the NIH PI time to submit to the NIH IRB. 
 
Death of a research subject that is possibly, probably, or definitely related to the 
research must be reported within 24 hours of awareness. 
 Reporting SAEs to Health Authorities and IECs / IRBs 
The site team will inform the relevant health authorities of any reportable SAEs 
according to the local regulatory requirements. The Investigators will be 
responsible for informing the IECs or IRBs that reviewed the trial protocol as per 
the relevant IEC/IRB’s SOPs. 
 
10 Data Management Plan - Data Collection, Sample Storage and 
Publication 
 Data Collection 
Study data will be collected on standardized paper CRFs. The local study team will use 
only NIAID study team-approved CRFs. These forms are to be completed on an ongoing 
basis during the study. Any type of corrections to paper CRFs must be initialed and dated 
by the person making the correction. The PI is responsible for assuring that the data 
collected are complete, accurate, and recorded in a timely manner. The CRFs will be 
collected and placed into a participant-specific binder. Source documentation (the point of 
initial recording of a piece of data) should support the data collected on the CRF, and be 
signed and dated by the person recording and/or reviewing the data. Some CRFs may also 
be source documents. Source documents include all recordings of observations or 
notations of clinical activities and all reports and records necessary for the evaluation and 
reconstruction of the clinical trial. Source documents include, but are not limited to, the 
participant medical records, electronic chart records, laboratory reports, electrocardiogram 
(EKG) tracings, x-rays, radiologist reports, biopsy reports, ultrasound photographs, 
participant progress notes, pharmacy records and any other similar reports or records of 
procedures performed during the participant’s participation in the protocol. Data for CRFs 
will be collected during participant visits by health care providers and abstracted from the 
medical record. Once the data are collected, it will be reviewed by the local site 
monitoring team or their contractors. Any data compiled for statistic or other manipulation 
will be handled in a database. The scientific results from this study will require various 
formats, depending on the data type. Locked copies of these files containing the results 
will be compiled by the research supervisor and made available to monitoring and 
regulatory agencies as necessary.  
 Data Management 
Data entered onto the CRF will be transferred into the study database, which will be 
managed and monitored by the study team. Access to the database is password controlled 


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and will be limited to those with data entry and management responsibilities, as well as 
monitors. Records are protected by ownership control and a complete log of all activities 
within the system is recorded. All study related data will be maintained on servers located 
at the sites and NIH and image files will be stored and indexed in the system. 
 Data Storage 
All essential documentation for all study participants including history and physical 
findings, laboratory data, and results of consultations are to be maintained by the 
investigators in a secure storage facility for a minimum of three years per NIH policies. 
These records are to be maintained in compliance with IRB/EC (Institutional Review 
Board/Ethics Committee), local and government requirements, whichever is longest. All 
records are to be kept confidential to the extent provided by federal, state, and local law. 
 
It is the investigator’s responsibility to retain copies of source documents until receipt of 
written notification to the contrary from NIH. No study document should be destroyed 
without prior written agreement between NIH and the Principal Investigator. 
 
Should the investigator wish to assign the study records to another party and/or move 
them to another location, the investigator must provide written notification of such intent 
to NIH with the name of the person who will accept responsibility for the transferred 
records and/or their new location. NIH must be notified in writing and written NIH 
permission must be received by the site prior to destruction or relocation of research 
records. 
 Publication of Research Findings 
Collaborating protocol team members will own the data generated by or resulting from 
this project, and they may arrange for publication of this original research (with consent of 
all study investigators) in a primary scientific journal, and for copyright by the journal 
unless the journal's copyright policy would preclude individuals from making or having 
made a single copy of any such article for their own use.    
 Sample Transfer and Storage 
Sputum, blood, plasma, urine, and other tissue specimens will be collected at the sites and 
processed in the respective research labs.  
Should sharing of specimens with institutions not on the protocol be desired, an 
amendment will be submitted to the NIH IRB and the sites’ relevant IECs for review. 
Clinical information shared about the samples would similarly require prior IRB/IEC 
approval. The research use of stored, unlinked or unidentified samples may be exempt 
from the need for prospective IRB review and approval. Exemption requests will be 
submitted in writing to the NIH Office of Human Subjects Research, which is authorized 
to determine whether a research activity is exempt. Cultured bacterial isolates may be 
transferred, with the agreement of the PI, without additional IRB review only as 
anonymous strains with limited data including no personal identifiers. 
A 20% loss of or destruction of samples will constitute a compromise of the scientific 
integrity of the data collected and will be reported to all IRBs. At the termination of the 


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NIAID study, any remaining samples will be retained or disposed of as determined by the 
study sites and their respective IRBs, according to relevant South African or Chinese laws. 
11 Clinical Monitoring Structure 
 Site Monitoring Plan 
The Office of Clinical Research Policy and Regulatory Operations (OCRPRO) of the 
Division of Clinical Research (DCR) of NIAID/NIH will contract monitors for this trial 
for source document verification and regulatory compliance. The OCRPRO monitoring 
team will discuss a detailed monitoring plan with the PI. 
The study will be conducted in compliance with this protocol, International Conference on 
Harmonization of Good Clinical Practices (ICH GCP) and all applicable regulatory 
requirements. This study monitoring will be conducted according to the “NIAID 
Intramural Clinical Monitoring Guidelines.” Monitors under contract to the 
NIAID/OCRPRO will visit designated clinical research sites to monitor all aspects of the 
study in accordance with the appropriate regulations and the approved protocol. The 
objectives of a monitoring visit will be as follows:  
1) To verify the existence of signed informed consent documents and 
documentation of the ICF process for each monitored participant 
2) To verify the prompt and accurate recording of all monitored data points, and 
prompt reporting of all SAEs 
3) To compare abstracted information (CRFs, data pulls) with individual 
participant’s records and source documents (participant’s charts, laboratory 
analyses and test results, physicians’ progress notes, nurses’ notes, and any 
other relevant original participant information) 
4) To help ensure investigators are in compliance with the protocol 
 
The monitors will also inspect the clinical site’s regulatory files to ensure that applicable 
regulatory requirements are being followed. During the monitoring visits the investigator, 
and/or designee, and other study personnel will be available to discuss the study. The 
investigator (and/or designee) will make study documents (e.g., consent forms, CRFs) and 
pertinent hospital or clinical records readily available for inspection by the local IRB/IEC, 
the FDA, the China FDA, the Ministry of Food and Drug Safety (MFDS), the South 
African Health Products Regulatory Authority (SAHPRA), the site monitors, any other 
relevant local health authorities, and the NIAID staff for confirmation of the study data. 
 
A specific protocol monitoring plan will be discussed with the Principal Investigator and 
study staff prior to enrollment. The plan will outline the frequency of monitoring visits 
based on such factors as study enrollment, data collection status and regulatory 
obligations. 
 
Any changes or additions to the protocol will be submitted to all necessary IRBs/IECs and 
relevant regulatory agencies for review. The written IRB approvals will be filed in the 
investigator’s study binder, and a copy of the approvals will be forwarded to the 
monitoring team. Furthermore, essential documents will be collected in the study binders 
and will include the following: 


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1) IRB/EC approvals for the study protocol and all amendments 
2) All source documents and laboratory records 
3) CRF copies 
4) Informed consent forms 
 Data and Safety Monitoring Plan 
A Data and Safety Monitoring Board (DSMB) comprised of global TB experts will 
provide oversight on the study. The NIAID Intramural DSMB includes independent 
experts that do not have direct involvement in the conduct of the study and have no 
significant conflicts of interests as defined by NIAID policy. The board will review the 
study data to evaluate the safety, study progress, and conduct of the study.  The DSMB 
will meet at least twice per year to evaluate safety, study conduct, and scientific validity 
and integrity of the trial. As part of this responsibility, DSMB 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 DSMB 
will also assess the performance of overall study operations and any other relevant issues, 
as necessary. The first DSMB review will occur after IRB approval and before the 
initiation of the study. Additional DSMB reviews will occur with the interim analyses. 
The DSMB may also convene additional reviews as necessary. All treatment-related 
adverse events grade 3 or higher and serious adverse event reports will be sent by the PI 
electronically to the DSMB members and the DSMB Executive Secretary before each 
meeting and within 7 days after knowledge of a relapse, or per DSMB guidelines. Serious 
adverse events determined to be possibly, probably, or definitely related to study 
medication or procedures will be reported to the DSMB at the same time they are reported 
to the IRB. Enrollment will continue unless the DSMB requests stopping enrollment to 
perform a more in-depth review. The PI will notify the board at the time pausing or halting 
criteria are met and obtain a recommendation concerning continuation, modification, or 
termination of the study. The PI will submit the written DSMB summary reports with 
recommendations to the IRB. The DSMB will also be available for other clinical advice as 
requested.  
 
Items reviewed by the DSMB include but are not limited to: 
 
1) SAE and AE line listings and SAE narratives 
2) Demographic information on study participants 
3) TB disease recurrences 
4) Interim analysis of treatment success rates  
5) Factors that might affect the study outcome or compromise the confidentiality 
of the trial data (protocol violations, unmasking, etc.) 
6) Factors external to the study, such as scientific or therapeutic developments, 
that may adversely affect participant safety or the ethics of the study 
 
Interim analyses will be conducted according to section 6.7.  During this time, the DSMB 
will continue to review the safety data as scheduled.   
During annual Continuing Reviews, the study team will report the number of DSMB 
meetings that occurred since the last continuing review and forward any reports based 


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upon these meetings to the NIH IRB.  Reports/recommendations issued by the DSMB that 
necessitate any changes in the conduct of the study will be reported to the NIH IRB within 
3 weeks of the PI’s notification. 
 
12 Human Subject Protection  
This protocol must receive the approval of all sites’ Review Boards prior to implementation.  
Each site may start implementing the protocol separately if that respective site and NIAID have 
approval, as long as local regulations are also met. The study will be conducted in accordance 
with the design and specific provisions of this IRB approved protocol, in accordance with the 
ethical principles that have their origin in the Declaration of Helsinki, and that are consistent with 
Good Clinical Practice (GCP) and any applicable regulatory requirement(s), as well as in 
accordance with the NIH policies.  The PI will assure that no deviation from, or changes to the 
protocol will take place without prior agreement and documented approval from the IRB, except 
where necessary to eliminate an immediate hazard(s) to the trial participants. The PI will 
promptly report to the IRBs and to NIH IRB any changes in research activity and will promptly 
report to the IRBs all unanticipated problems involving risk to human participants, or others. 
 
Rationale for Participant Selection 
According to a World Health Organization 2015 global TB report, South Africa has the sixth 
highest rate of new tuberculosis (TB) cases in the world, the highest incidence of TB/HIV in 
the world, and the 10th highest number of drug-resistant TB.  According to a WHO 2015 
report, the prevalence of tuberculosis in South Africa is approximately 375,840 (696/100,000 
population), but with an annual incidence of 450,000 persons per year. HIV/TB co-infected 
patients constitute about 2/3 of the annual TB incidence in South Africa and is typically 
associated with a higher burden of disease. As previously mentioned, HIV participants will 
be excluded in this study. Although this excludes a significant TB-infected population, our 
rationale in this initial study is twofold: 
1) The PET noise from HIV even in absence of IRIS may substantially confound the 
ability to tease out drug effects on TB alone. 
2) Immunologic markers may respond differently in HIV+ participants compared to HIV- 
participants. 
 
The population treated by the HPCH was selected for study for several reasons: (1) China has 
one of the highest rates of TB infection in the world with an estimated number of 89 cases of 
active tuberculosis per 100,000 (as reported by the World Health Organization for 2015). 
Henan province has a population of ~100 million people, and therefore a large concentration 
of TB; (2) Existence of a well-managed, specialized hospital with highly-trained staff and 
experienced in conducting clinical trials. 
 
Participation of Children and Other Vulnerable Participants 
Only persons 18 years of age and older will be enrolled as this is the age of consent in both 
South Africa and China. It is rare for patients less than 18 years old to be hospitalized at 
HPCH so very few participants will be functionally excluded on this basis. In addition, it 
remains culturally unacceptable to expose the under-age or elderly to risk without benefit in 
China. Pregnant woman will be excluded because of the risks for PET/CT scanning.   


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Risks/Benefits Analysis including Considerations of Alternatives to 
Participation 
 Potential Benefits to Study Participants 
Participants who stop drug early and are cured of their TB will not be exposed 
unnecessarily to 8 additional weeks of potentially toxic drugs. Those who receive 24 
weeks of treatment receive an indirect benefit of having their TB managed closely 
and they therefore may have a better outcome than others who are not on the study. 
   
 Potential Risks to Study Participants 
For those who stop drug early, there is a risk that they will not yet be cured of the TB 
bacteria and will relapse. We expect this risk to be small because those with the most 
severe disease will not stop treatment early. Only those who meet the early 
completion criteria will discontinue treatment early. However, if our hypothesis is 
incorrect and the early completion criteria do not correctly identify people who are 
cured after 16 weeks of treatment, their chance of relapse will be higher than if they 
had received a full 24 weeks of treatment. To note, risk of relapse is also related to 
medication adherence. Even those who would otherwise have been cured with 16 
weeks of treatment may relapse if their medication adherence is poor. If relapse does 
occur, we will refer the participants to the local TB clinic to restart treatment.  The 
study team will provide the TB clinic with any available drug resistance data for this 
participant.  
 
There are minor risks related to blood drawing, including discomfort, hematoma, and 
rarely an infection. Sputum collection may also be uncomfortable and sputum 
induction can cause wheezing or a tightness in the airways. It is generally thought to 
be a safe procedure. There is a risk, although rare, that placing an IV for the FDG-
PET may result in a hematoma, thrombophlebitis, infection, or nerve damage.  
 
Rifampin is a strong inducer of the hepatic cytochrome P450 enzyme system, which 
is the system that metabolizes many other drugs and therefore may cause a decrease 
in these other drug levels. Use of these other drugs are not prohibited, however they 
should only be used together with caution as dose adjustments of the concomitant 
drug may be necessary. Drugs include but are not limited to: warfarin, saquinavir and 
other HIV protease inhibitors, birth control pills or other hormonal contraception, 
phenytoin, digoxin, clarithromycin, caspofungin, voriconazole, ketoconazole, 
itraconazole, diltiazem, verapamil, lorazepam, atorvastatin, rosiglitazone, and 
celecoxib.  
 
There is also risk associated with radiation exposure from imaging. Radiation from 
CXR is negligible. CXR will not be done during the study unless Arm A fills up 
faster than expected. In this case, a screening CXR may be used to screen out 
participants who have CXR features consistent with not meeting inclusion/exclusion 
criteria or early treatment completion criteria. These participants will not be 
considered further for the study. Both PET and CT components of the scan will 
expose participants to ionizing radiation. We have considered ways to limit the 
amount of radiation exposure participants will receive. By restricting the CT scan to 
the chest as the area of interest rather than performing a whole body scan (which is 


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customary for PET/CT) we will reduce radiation exposure. We have also reduced the 
radiation dose for the 3rd and possible 4th scans, by decreasing the energy current.  
This will result in a lower resolution CT scan, but should be adequate for the more 
marked changes expected over a longer period. The vast majority of participants will 
undergo 3 PET/CT scans in a calendar year during the course of the study. A small 
group of participants who relapse will receive an extra scan, and therefore it is 
possible that this small group would receive four scans within one calendar year. The 
expected maximum effective dose a participant will receive from scans scheduled as 
part of the study over one calendar year is in the appendix for each country.  
 
Participants involved in the MRI imaging substudy may experience nervousness 
and/or claustrophobia during the MRI. While generally safe, it is not known whether 
an MRI would harm a fetus. Pregnant women are excluded from scanning. 
Gadolinium-based contrast agents (GBCAs) are used with MRI to improve 
visualization of internal organs, blood vessels, and tissues. The use of GBCAs also 
carries some risk, including side effects such as allergic reactions to the contrast 
agent. To date, the only known adverse health effect related to gadolinium retention is 
a rare condition called nephrogenic systemic fibrosis (NSF) that occurs in a small 
subgroup of patients with pre-existing kidney failure. Therefore, participants with any 
evidence of renal insufficiency will be excluded from the MRI substudy. There is 
evidence that small amounts of gadolinium can stay in the body. It is not known how 
gadolinium deposition may affect the body, but so far, studies have not found harmful 
effects in patients who have healthy renal function. Only macrocyclic GBCAs, which 
cause less retention than linear GBCAs, will be administered for MRI scans.  
 
Privacy and Confidentiality 
All laboratory specimens, evaluation forms, reports, and other records that leave the site will 
be identified by coded number only to maintain participant confidentiality. All records will 
be kept locked. All computer entry and networking programs will be done with coded 
numbers only. Clinical information will not be released without written permission of the 
participant, except as necessary for monitoring by the contract monitors, IRBs, NIAID, 
Office for Human Research Protections (OHRP), or other regulatory agencies. 
 
 
13  References 
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Rizzi, E.B., et al., Detection of Pulmonary tuberculosis: comparing MR imaging with 
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Zeng, J., et al., MRI evaluation of pulmonary lesions and lung tissue changes induced by 
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Buzan, M.T.A., et al., MRI as indicator of pulmonary tuberculosis activity: from 
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14 Appendix 1: Description of Changes to Early Treatment Completion 
Criteria (as of March 12, 2018) 
 
Based on prior data as summarized in the background of the protocol (sec 1.3), an estimated 80-
85% of all pulmonary drug-sensitive TB subjects are cured with 4 months of standard treatment. 
For the Predict TB study, we conservatively reduced this estimate to 50% of participants enrolled. 
The sample size calculated for the Predict TB trial is 310 participants to Arms B and C (155/arm). 
Based on the estimate that 50% of all participants would be cured at 4 months of treatment and 
therefore eligible to be randomized to Arms B and C, a total sample size of 620 was selected for 
the study with the understanding that the actual total would depend on the true proportion of 
participants randomized to Arms B and C (protocol section 3.2). If the proportion stratified to 
Arm A is <50%, the total sample size needed will be less than 620. If the proportion stratified to 
Arm A is >50%, more than 620 total participants will be needed. In addition to implications for 
resources and funding, an increase in total sample size raises questions about the relevance of 
study results. For example, if only 25% of participants are eligible for randomization, a successful 
study result will be much less generalizable and globally applicable because most TB patients 
would likely not meet such stringent requirements. Thus, we monitor carefully the proportion of 
participants to each arm. 
 
Figure 1. describes the current arm distribution plot. At baseline imaging criteria evaluation, 
61.4% (27/44) remain eligible for early treatment completion. At week 4, this proportion drops to 
43.6% (17/39), with another 5 pending their week 4 PET/CT results. At week 16, the proportion 
eligible for early treatment completion falls to 23.5% (8/34), with another 10 still pending week 
16 evaluation. Even if all 10 went to arms B and C, this would still only be 40.9% (18/44). We 
believe these data demonstrate that a significant arm imbalance exists in the study that threatens 
the overall scientific validity and that changes to the early treatment completion criteria are 
therefore justified. Changes to the criteria are needed early so that results remain valid. 
 
Figure 1: Predict TB arm distribution plot based on current criteria (data as of March 7, 2018) 


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The current early treatment completion criteria are described below (taken from table 6 in the 
protocol): 
 
Table 13: Early Treatment Completion Criteria: All early treatment criteria must be met for the 
participant to be eligible for randomization 
Early 
Completion 
criteria: 
Determined at Week 16 – unless known to have failed a 
radiographic criterion at baseline or week 4.  
Radiographic 
criteria 
Baseline PET/CT: 
• No total lung collapse of a single side, AND 
• No pleural effusion, AND 
• No single cavity air volume on CT scan >30 mL, AND 
• CT scan hard volume (-100 to +100 HU density) <200 
mL, AND 
• PET total activity <1500 units 
Week 4 PET/CT: 
• All individual cavities decrease by >20% (unless cavity 
<2 mL), AND 
• CT scan hard volume does not increase by >10% unless 
the increase is <5 mL, AND 
• PET total activity does not increase by >30% unless the 
increase is <50 units 


Clifton E. Barry, III 
Predict Trial 
 
Version 13.0, September 21, 2020 
 
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Bacterial load 
criterion 
Week 16 Xpert cycle threshold ≥30 
Adherence 
criterion 
Minimum of 100 doses received by week 16 
 
We propose making two changes to these criteria. The first is to change the week 16 Xpert 
MTB/RIF (Xpert) cycle threshold (Ct) cutpoint. The second is to change the baseline and week 
4 radiographic criteria. 
 
 
GeneXpert cycle threshold 
 
We propose to change the Xpert Ct cutoff from Ct ≥30 to Ct ≥28. The initial criterion for Ct at 
week 16 was based on a cohort study in South Africa with MGIT culture, the only data available 
to us at the time. We adopted a stringent Ct value of 30 based upon analysis of these data for 
subjects to be randomized to Arms B and C. Xpert detects only DNA and does not determine the 
viability of detected bacilli. Note that LJ culture is the basis for outcome determination in Predict 
TB.  
 
We recently received results from study TBTC-29, which collected Ct values and LJ culture. In 
evaluating the change, we consider the chance of missing an LJ+ result, as well as the sensitivity 
and specificity of various Ct cutpoints. In contrast to positive and negative predictive values, 
sensitivity and specificity do not depend on the underlying proportion of culture positive results, 
which varies over time and from study to study. That said, patient safety is a driving factor so we 
consider how many positive cultures might be missed for various cutpoints. This was defined as 
the probability of being LJ+ given a Xpert Ct value less than the threshold, i.e., P(LJ+ | Ct-). We 
assume what we consider are high proportions of LJ+ cultures (i.e., 10% and 5% at week 16 of 
treatment in a lower risk cohort of arm B/C) when making this decision. In contrast to the TBTC-
29 study, which randomized all-comers and did not stratify participants by risk, the Predict TB 
study further excludes poorly adherent participants with too severe disease at baseline and not 
responding appropriately to treatment at one month. As a result, the expected LJ+ rates of 10% 
and 5% are thought to be on the high-side. Table 1 describes these proportions for the sensitivity 
and specificity estimates from TBTC-29. Based on these estimates, a Ct of 30 is expected to miss 
2.1% of LJ+ results, while a threshold of 28 would miss 2.5%, assuming a 10% LJ+ rate. This 
translates to an increase in less than one participant being missed amongst those randomized to 
arm C. That is, if the background LJ+ rate is 10%, 3.3 (of 155 randomized to stop treatment at 
week 16) true LJ+ participants may be missed with Ct=30, and 3.9 may be missed with Ct=28. If 
the underlying LJ+ rate is 5%, this becomes 1.6 missed LJ+ participants with Ct=30 and 1.9 
missed LJ+ participants with Ct=28. If the true underlying LJ+ rate is even lower, the difference 
between the two Ct values becomes even smaller. 
 
 


Clifton E. Barry, III 
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Version 13.0, September 21, 2020 
 
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Table 2: Sensitivity and specificity estimates from TBTC-29 for various Xpert Ct cutpoints, 
along with estimates of missed LJ+ and missed LJ- results for assumed (16 week) culture-
positivity rates of 10% and 5%. 
Xpert Ct 
Cutpoint 
Sensitivity: 
P(Ct<c|LJ+) 
Specificity: 
P(Ct>c|LJ-) 
Chance of 
missed LJ+ 
P(LJ+|Ct-) 
with 10% 
LJ+ rate 
Chance of 
missed LJ+ 
P(LJ+|Ct-) 
with 5% LJ+ 
rate 
Chance of 
missed LJ+ 
P(LJ+|Ct-) 
with 2.5% 
LJ+ rate 
Ct=31 
0.93 
0.43 
0.018 
0.008 
0.004 
Ct=30 
0.91 
0.46 
0.021 
0.010 
0.005 
Ct=29 
0.89 
0.49 
0.024 
0.012 
0.006 
Ct=28 
0.88 
0.52 
0.025 
0.012 
0.006 
Ct=27 
0.86 
0.55 
0.028 
0.013 
0.006 
Ct=26 
0.84 
0.60 
0.029 
0.014 
0.007 
Ct=25 
0.79 
0.66 
0.034 
0.016 
0.008 
 
 
Within Predict TB, 12 active participants have been eligible for Xpert Ct testing. (Note, the 
current protocol only allows for Xpert testing at week 16 amongst those not already allocated to 
arm A).  Of the 12 participants with Xpert Ct results, 8 (67%) were negative on Xpert. All 8 
participants with week 16 Xpert negative results were also LJ- on their most recent cultures. The 
remaining 4 had Ct values as described in Table 3. 
 
Table 3: LJ culture results for participants with non-negative Xpert values at week 16. 
Xpert 
LJ results 
18.2 
TB+ up to week 2; other results NA 
25.2 
TB- at weeks 8 and 12; week 16 NA 
28.4 
TB- at weeks 4 and 8, other results 
NA 
28.5 
TB- at weeks 8, 12 & 16 
 
Thus changing the Xpert Ct cutpoint to 28 would have only retained an additional 2 participants 
in arms B and C. This change by itself would not be sufficient to correct the arm imbalance. 
 
 
Radiographic criteria 
 
To further correct the arm imbalance, we also propose to change the baseline and week 4 
radiographic criteria. Our current early treatment completion criteria involve quantitating cavity 
air volume, CT hard volume, and PET total activity (also referred to as “total lesion glycolysis,” 
or TLG). Prior studies (protocol sec 1.1) have validated that cavity on baseline CXR is a risk 
factor for treatment relapse. In our analyses of prior data, cavity size was also the strongest factor 
in predicting poor treatment outcome so we decided not to adjust this criterion. The data for CT 
hard volume and PET total activity as a risk factor for poor treatment outcomes, however, are 
weak. We selected these criteria based on our retrospective analysis of 92 pulmonary TB patients 
with baseline and week 4 PET/CT scans, as summarized in protocol sec 1.1. Figure 2 shows the 


Clifton E. Barry, III 
Predict Trial 
 
Version 13.0, September 21, 2020 
 
Page 75 of 80 
 
 
distribution of participants stratified to Arm A at baseline by the original radiology criteria. The 
numbers in the circles represent the number of participants that fall into arm A according to the 
defined criteria. 
 
Figure 2 Venn diagram of the original baseline PET/CT criteria by which participants are 
stratified to Arm A.  
 
 
The hard volume and total activity criteria are relatively well correlated in capturing participants, 
with only 5 participants moved to Arm A based on a single criterion, hard volume or PET total 
lesion glycolysis. Thus, instead of arbitrarily increasing the hard volume and PET total activity 
cutpoints, we decided to change the criteria from requiring both hard volume AND total activity 
to be below the thresholds to be considered low risk, to only requiring 1 criterion. That is, 
participants that have either hard volume OR total activity below the threshold at both baseline 
and week 4 will be considered low risk. The thresholds themselves will not change. Applying this 
change to the PET/CT criteria results in the following revised Venn diagram, which is the same as 
Figure 2 except for the 5 participants moved to Arm A based on hard volume or PET activity 
alone are no longer considered high risk. 
 
 
 


Clifton E. Barry, III 
Predict Trial 
 
Version 13.0, September 21, 2020 
 
Page 76 of 80 
 
 
Figure 3: Venn diagram of the revised baseline PET/CT criteria by which participants are 
stratified to Arm A 
 
Proposed new early treatment completion criteria 
The proposed revised early treatment completion criteria incorporating both Xpert Ct and 
radiographic criteria changes are: 
 
Table 14: Proposed Revised Early Treatment Completion Criteria: All early treatment criteria must be 
met for the participant to be eligible for randomization (changes highlighted) 
Early 
Completion 
criteria: 
Determined at Week 16 – unless known to have failed a 
radiographic criterion at baseline or week 4.  
Radiographic 
criteria 
Baseline PET/CT: 
• No total lung collapse of a single side, AND 
• No pleural effusion, AND 
• No single cavity air volume on CT scan >30 mL, AND 
• CT scan hard volume (-100 to +100 HU density) <200 
mL OR PET total activity <1500 units 
Week 4 PET/CT: 
• All individual cavities decrease by >20% (unless cavity 
<2 mL), AND 
• CT scan hard volume does not increase by >10% unless 
the increase is <5 mL OR PET total activity does not 
increase by >30% unless the increase is <50 units 
Bacterial load 
criterion 
Week 16 Xpert cycle threshold ≥28 
Adherence 
criterion 
Minimum of 100 doses received by week 16 
 


Clifton E. Barry, III 
Predict Trial 
 
Version 13.0, September 21, 2020 
 
Page 77 of 80 
 
 
The original early treatment completion criteria, when applied to the data from an earlier study of 
92 pulmonary TB patients from Cape Town, yielded the following stratification: 
 
Table 5: Treatment outcome by original Predict TB early treatment completion risk 
stratification 
 
Treatment Outcome  
(Numbers of Participants) 
 
Risk 
Categorization 
Cure 
Failure 
Programmatic 
Treatment 
Restart 
Total 
Low Risk 
40 
1 
6 
47 
High Risk 
33 
7 
5 
45 
Total 
73 
8 
11 
92 
 
However, we know that our current Predict TB population is different from these earlier 
participants as more than half of these earlier participants were stratified as low risk (Arms B or 
C), in contrast with our current Predict TB participants. Applying the revised criteria to this 
earlier dataset results in the following new stratification: 
 
Table 6: Treatment outcome by revised Predict TB early treatment outcome risk stratification 
  
Treatment Outcome  
(Numbers of Participants) 
  
Baseline Risk 
Categorization 
Cure 
Failure 
Programmatic 
Treatment 
Restart 
Total 
Low Risk 
55 
2 
8 
65 
High Risk 
18 
6 
3 
27 
Total 
73 
8 
11 
92 
 
Applying the revised criteria to the current active Predict TB participants results in the following 
arm distribution: 
 
 


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Predict Trial 
 
Version 13.0, September 21, 2020 
 
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Figure 4: Predict TB arm distribution plot based on revised criteria (data as of March 7, 2018) 
 
 
Using the revised baseline imaging criteria evaluation, 72.7% (32/44) remain eligible for early 
treatment completion. At week 4, this proportion drops to 61.5% (24/39) with another 5 
pending their week 4 PET/CT results. At week 16, the proportion eligible for early treatment 
completion falls to 41.4% (12/29), with another 15 pending week 16 evaluation. Note that the 
additional 5 “pending” participants compared to the original criteria arm distribution plot at 
week 16 (Figure 1) are original Arm A participants who now moved to Arm B/C but did not 
get a week 16 Xpert Ct, which was not done in Arm A. The Xpert Ct evaluation of the 15 
pending participants will determine the final arm stratification outcome, as there are currently 
no adherence issues. If 2/3 (10/15) achieve Ct ≥28, that will result in a 50/50 split. Currently, 
12/14 (85.7%) participants had a Ct ≥28 at week 16. If this proportion holds, this proposed 
change will be sufficient to re-balance the arm distribution over time.  
 
Finally, note that the currently randomized participants will not be affected by this change. 
Only participants before their week 16 randomization visit will be eligible to be stratified by 
these revised criteria, once all regulatory approvals have been obtained. 
 
 
15 Appendix 2: Radiation Dosimetry 
 
The FDG-PET/CT scans in South Africa and China will be performed on approved scanners 
using settings approved by the NIH Radiation Safety Committee to allow for a maximum of 4.5 
rem per participant for 4 PET/CT scans and 1 CXR in a 12-month period. This radiation dose is 


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Predict Trial 
 
Version 13.0, September 21, 2020 
 
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less than the maximal permissible annual research exposure of 5 rem/yr [63], however most 
participants will only receive 3 PET/CT scans. The NIH Radiation Safety Committee has 
reviewed the use of radiation in this research study and has approved this use as involving slightly 
greater than minimal risk and necessary to obtain the research information desired. 
 
16 Changes to study procedures per Data Safety Monitoring Board 
recommendations 
 
The NIAID Data Safety Monitoring Board conducted its 7th interim review of unblinded data on 
September 11, 2020. Following this review, the DSMB recommended halting randomization to 
Arms B and C. This recommendation is based on the result of the interim analysis in section 6.7.1 
of the study protocol, when 1/3 of randomized participants have been followed for 72 weeks from 
study entry. The protocol stopping guideline for inferiority of the treatment shortening arm was 
met. The DSMB was also presented with conditional power calculations relating to the futility 
interim analysis; although the protocol-specified time for this analysis had not been reached, the 
results of the analysis were consistent with a decision to terminate randomization into Arms B and 
C, but to continue enrollment into Arms A and B at the discretion of the investigators. Pre-
emptive re-treatment of participants who have completed the course of treatment in Arm C is not 
recommended and should be left to the discretion of the treating clinician. 
 
 
17 NIH/SOUTH AFRICA Specific Appendices 
 
In South Africa a saliva sample will be collected at both week 16 and week 24 visits for 
biomarkers irrespective of the PET/CT scan visit.   
 
Remuneration in RSA 
Study participants will receive the following compensation for each type of visit.  If possible, 
the participants will be paid by SMS.     
Screening:   
 
150 Rand (approximately $12) 
Each Study Visit:  
150 Rand (approximately $12) 
Each PET/CT:    
350 Rand (approximately $25) 
Extra sputum visit:  
50 Rand (approximately $4);  SATVI site: 150 Rand 
(approximately $12) 
Each MRI scan: 
350 Rand (approximately $25) 
 
Travel expenses incurred will be paid according to the site’s guidelines. Participants may 
receive further incentives, such as a phone card, as mentioned in section 5.2. 
 
18 NIH/CHINA Specific Appendices   
 Blood volumes in China 
Due to concerns about total blood volumes collected in China, the Chinese sites will not 
participate in all blood immunological marker analyses. Per section 5.7.2, China sites will 
NOT collect whole blood for FACS (1 mL) nor whole blood for PBMC isolation (30 mL). 
They will collect whole blood for serum (8 mL), blood for host mRNA (2.5 mL), and blood 
for host DNA (2 mL) for a total of approximately 12.5 mL whole blood at any one visit. Note 


Clifton E. Barry, III 
Predict Trial 
 
Version 13.0, September 21, 2020 
 
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that the 2 mL blood for plasma drug levels (sec 5.7.3) occurs only at week 20, when blood 
biomarkers are not collected.  
 
 
 
 
 
 
 Remuneration in China 
Study participants will receive the following compensation for each type of visit:   
Screening:    
50 Yuan (approximately $8) 
Each Study Visit:     80 Yuan for visits D0-W12, 100 Yuan for W16 (plus 100 if they 
have completed every visit up to this time point), 20, 36, and 
48, 300 Yuan for week 24, and 350 Yuan for week 72 (plus 
350 Yuan if they have completed every visit up to this time 
point).  At recurrence, participants will receive 100 Yuan.  
Each PET/CT: 
100 Yuan (approximately $15) 
Each MRI scan: 
100 Yuan (approximately $15) 
 
Travel expenses incurred will be paid according to the site’s guidelines. Participants may 
receive further incentives, such as a phone card, as mentioned in section 5.2. 
 

SAP_001.pdf: 
Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 1 of 18 
 
 
PredictTB Trial 
NIAID # 16-I-N133 
Using Biomarkers to Predict TB Treatment Duration 
Statistical Analysis Plan 
Trial Statistician 
Principal Investigator 
 
Lori E Dodd, PhD 
Biostatistics Research Branch 
Division of Clinical Research, NIAID 
5601 Fishers Lane, Room 4C31  
Mail Stop Code: 9820 
Bethesda, MD 20892  
Phone: 240-669-5247 
Email: doddl@mail.nih.gov 
 
 
Clifton E. Barry III, Ph.D. 
National Institute for Allergy and 
Infectious Diseases (NIAID), 
Laboratory of Clinical Infectious 
Diseases (LCID), Tuberculosis 
Research Section (TRS), Building 33, 
Room 2w10 
Bethesda, MD 20892 
Phone: (301) 693-4665 
         Email: cbarry@niaid.nih.gov 
 
 
Enrollment sites:   
Site Name 
Country 
City 
Henan Provincial Chest Hospital 
(HPCH)  
China 
Zhengzhou, Henan Province 
Kaifeng City Institute of 
Tuberculosis Prevention and Control 
China 
Kaifeng, Henan Province 
Xinmi City Center for Disease 
Control and Prevention 
China 
Xinmi, Henan Province  
Xinxiang City Institute of 
Tuberculosis Prevention and Control 
China 
Xinxiang, Henan Province 
Zhongmu County Station for Disease 
Control and Prevention 
China 
Zhongmu, Henan Province 
University of Cape Town (UCT) 
Lung Institute 
South Africa 
Cape Town 
Stellenbosch University 
South Africa 
Tygerberg 
TASK Applied Science, Inc 
South Africa 
Bellville/Delft 
Khayelitsha Site B 
South Africa 
Khayelitsha 
South African Tuberculosis Vaccine 
Initiative (SATVI)  
South Africa 
Cape Town/Worcester 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 2 of 18 
 
 
 
 
1 
Introduction 
 
PredictTB is a randomized controlled trial evaluating the PredictTB treatment-shortening criteria (a 
combination of imaging, GeneXpert and treatment adherence results). The study will prospectively 
identify patients at low risk based on their baseline radiographic extent of disease, and further refine 
this risk score by evaluating the rate of resolution of the lung pathology (CT) and inflammation (PET) 
at one month as well as checking an end-of-treatment GeneXpert MTB/RIF test for the sustained 
presence of bacteria. Patients classified as low risk will be randomized to receive a shortened 4-month 
or a full 6-month course of therapy. If successful, this trial will both offer a badly needed alternative to 
culture status as a trial-level surrogate marker for outcome as well as provide critical information for 
preclinical and early clinical efforts to identify new agents and combinations with the potential to 
shorten therapy. 
 
2 
Design and objectives 
This is a prospective, randomized, phase 2b noninferiority trial in pulmonary drug suscpetible-
TB participants.  Eligible and consented participants will start on standard treatment (“HRZE”) 
and undergo evaluations to determine eligibility for treatment shortening according to the 
PredictTB criteria (Table 1). Participants who meet the PredictTB criteria will be randomized 
at week 16 to arm B (standard-duration treatment) or arm C (shortened treatment).  All 
participants will be followed for 72 weeks (18 months) following treatment initiation. 
 
 
 
 
Screening
4        8
12      16
weeks
Not 
Eligible 
to 
Complete 
Early 
Complete 
HR
Follow up 
completed
Follow-up
20     24
A
Start HRZE
HR only
4        8      12      16
weeks
Start HRZE
HR only
No Early 
Completion: 
24 Week
ARM
Randomization 
for those eligible 
for early 
completion only
Complete 
HR
18 months
Early 
Completion: 
16 Week 
ARM
16      20     24
Complete 
HR
B
C
Fail Early Completion 
Criteria—Join Arm A
Legend
PET/CT
If Person 
Passes Early 
Completion 
Criteria
Enrollment
18  months          
Primary 
Endpoint 
and 
Follow up 
completed
Primary 
Endpoint 
and 
Follow up 
completed
Primary 
Endpoint 
and 
18  months         
16     20 
24
W4 PET/CT will be done in Arm A if resources allow
PET/CT for Arm A at either Week 16 OR Week 24


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 3 of 18 
 
 
Figure 1: Study Flow 
 
 
Table 1: Early Treatment Completion Criteria: All early treatment criteria must be met for the 
participant to be eligible for randomization 
Early 
Completion 
criteria: 
Determined at Week 16 – unless known to have failed a 
radiographic criterion at baseline or week 4.  
Radiographic 
criteria 
Baseline PET/CT: 
• No total lung collapse of a single side, AND 
• No single cavity air volume on CT scan >30 mL, 
AND 
• CT scan hard volume (-100 to +100 HU density) 
<200 mL, OR 
• PET total activity <1500 units 
Week 4 PET/CT: 
• All individual cavities decrease by >20% (unless 
cavity <2 mL), AND 
• CT scan hard volume does not increase by >10% 
unless the increase is <5 mL, OR 
• PET total activity does not increase by >30% unless 
the increase is <50 units 
Bacterial load 
criterion 
Week 16 Xpert MTB/RIF cycle threshold ≥28* 
Adherence 
criterion 
Minimum of 100 out of 112 doses received by week 16 
(Sec 5.2) 
 
 
 
Study objectives and hypotheses 
Primary Objective 
To demonstrate that the 72 week poor outcome proportion under shortened treatment at week 16 (Arm 
C) is not inferior (NI margin=0.07) to that from  standard-duration treatment (stopped at week 24; Arm 
B), in participants classified as low risk for disease failure and relapse the PredictTB criteria. 
Primary hypothesis: Amongst participants who satisfy the PredictTB criteria, the proportion of poor 
outcomes will be similar between participants undergoing 16 and 24 weeks of standard treatment. 
 
Secondary Objectives 
1) The compare the proportion of poor outcomes from low-risk participants with shortened treatment 
to that of a representative 6-month standard-of-care population.  
Hypothesis: The poor outcome rate among low-risk participants with shortened treatment will be 
like that of a representative 6-month standard of care population.  


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 4 of 18 
 
 
 
2) To evaluate the association of demographic, radiographic, bacterial load, microbiologic, and 
immunologic markers (at baseline and during treatment) for predicting treatment failure in the 
following participant cohorts: 
• 
Pooling arms A and B, participants receiving the same duration of therapy, to evaluate 
the risk criteria. 
• 
Between arms B and C, to evaluate whether there are any covariates which predict 
greater rates of failure under treatment shortening. 
 
Hypothesis: In univariate and multivariate analyses, demographic, radiographic, bacterial load, 
microbiologic, and immunologic markers are associated with treatment failure. 
 
3) To evaluate the association of demographic, radiographic, bacterial load, microbiologic, 
and immunologic markers (at baseline and during treatment) for predicting subsequent relapse in 
the following participant cohorts: 
• 
Pooled arms A and B (i.e., participants receiving the same duration of therapy) to 
evaluate the risk criteria. 
• 
Between arms B and C, to evaluate whether there are any covariates which predict 
greater rates of relapse under treatment shortening. 
Hypothesis: In univariate and multivariate analyses, demographic, radiographic, bacterial 
load, microbiologic, and immunologic markers are associated with subsequent relapse. 
 
4) To compare the ability of bacterial load (TTP and Xpert MTB/RIF cycle threshold) at different 
time points to distinguish between poor and good outcomes. 
Hypothesis: Bacterial load markers (TTP and Xpert MTB/RIF cycle threshold) collected at 
later time points are better markers of poor outcomes than markers collected at earlier times. 
  
5) To evaluate sub-breakpoint MICs as a significant predictor of poor outcomes in 16 and 24 week 
treatment regimens in a subset of participants. 
 Hypothesis: Pharmacokinetic and sub-breakpoint MIC measurements are associated with   
poor outcomes in 16 and 24 week treatment regimens.  
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 5 of 18 
 
 
 
 
Study visit schedule 
 
Screening
D0
W1V 
(D7)
W2 
(D14) W4 (D28) 
W8D 
(D56) 
W12 
(D84) 
At Week 
16
W16 
(D112) 
W20 
(D140) W24 (D168) 
W36 
(D252) 
W48 
(D336) 
W60 
(D420) 
W72 
(D504) 
TB 
Recurrence
Main Study Informed Consent (Plus 
Genetic and HIV in RSA) 
X
Medical History/Focused History
X
X
X
X
X
X
X
X
X
X
X
X
phone 
call
X
X
Physical Exam/Focused Physical 
Exam
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Sputum Collectionξ
Smear/Culture
XXH
(X)S
X
X
X
X
X
X
X
X
X
X
X
X
GeneXpert
X
(X)S
X
XE
X
X
X
Biomarkers
X
X
Xg
Xg
Xg
Xg
X
X
Xg
Saliva
X
X
X
X
X
Blood collection
CBC/Chems/LFTG
X
X
Biomarkers
X
X
X
X
X
X
X
X
X
X
Pregnancy TestP (serum at screening, 
urine for others)
xh(serum)
HIV Testing
X
X
Plasma drug levels
X
Finger Stick
X
X% 
Arms B/C  
and 
randomized 
A
Randomized  
for scan in 
Arm A only
X
Urine collection
Biomarkers
X
X
X
X
X
X
X
X
X
X
Pregnancy TestP (serum at screening, 
urine for others)
X
X% 
Arms B and 
C only 
Arms A and B 
only
X
CXR
X
Arm C only
Arms A and B 
only
X
FDG-PET/CTW
X
X% 
Arms B/C  
and 
randomized 
A
Randomized  
for scan in 
Arm A only
X
Adherence monitoring
X
X
X
X
X
X
Arms A 
and B 
only
Arms A and B 
only
ξAdditional sputum may be collected if contaminated or otherwise compromised 
performed. The CXR may still be performed with appropriate shielding.
A subject could be called back for this additional sputa collection, if necessary. 
E for those eligible for randomization
H Sputum at screening will also be used for screening Xpert
D At week 8, ethambutol and pyrazinamide will be discontinued 
S Day 0 culture/smear/Xpert only done if NOT within 7 days of screening, or per site's procedures.   W PET/CT scan windows : baseline w/i 7 days after treatment initiation; W4  must be at least 4 wks after baseline
h  Pregnancy testing from screening may be used for the D0 PET/CT scan if D0 is 
scan with a -3/+7 d window; W16 and 24 scan w/i 14 d of visit; relapse ASAP, but w/i 2 wks of recurrence
within 2 days of the screen
V  Visit windows:  Week 1-2: +/- 3 days;  Week 4-24: +/- 7 d, noting that Weeks 16 and 24  should be as close 
G These will be performed at any visit if clinically significant.  
as possible to actual date; Week 36-72: +/- 30 days. 
P  Before any PET/CT scan or CXR is done, a pregnancy test will be done for applicable
gIf sputum is not available for biomarkers, it will not be a protocol deviation. 
  females. If the pregnancy test is positive, the PET/CT scan will not be 
% Arms B and C will have PET/CT (with prior finger stick and pregnancy test ).  Arm A will have if logistically possible. 
RANDOMIZE to Arm 
B or C
then
and if not assigned to Arm 
A, 
Review treatment completion criter


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 6 of 18 
 
 
 
 
 
Randomization. 
Participants who satisfy the PredictTB criteria at week 16 will be randomized to stop treatment 
immediately or continue for the standard duration. Randomization is stratified by site, using 
random block sizes of four and six, resulting in nine separate randomization files.  Participant 
randomization will occur through the DataFax system, as documented in the Data Management 
Plan. 
Participants who are considered high-risk for relapse (i.e., Arm A) will be randomized to obtain a 
third image at either week 16 or week 24.  This randomization is stratified according to when the 
subjects move to arm A (i.e., baseline, week 4 or week 16).  Participant randomization will occur 
through the DataFax system. 
 
Sample Size Considerations 
For this study, the sample size is calculated for Arms B and C, which are used for the primary 
endpoint. Because these are lower risk participants, we expect a treatment success rate of 97%, 
corresponding to a poor outcome rate of 3%.  Table 2 provides power calculations for 
demonstrating noninferiority (with NI margin 0.07) using a 90% confidence interval with 
sample sizes of 129 and 155 per group, adjusted for a 10% loss to follow-up rate.  With true 
success rates of 97% in both arms, study power is greater than 90% with only 129 participants 
per group. However, to increase power to accommodate a scenario in which the true success 
rate in the four-month treatment arm is slightly lower than the six-month arm, a sample size of 
155 per treatment arm was selected.  We expect that approximately 50% of participants will be 
classified as higher risk and be placed into Arm A, giving a total study sample size of 620 
participants. In the event that the proportion of participants considered lower risk by our 
treatment completion criteria is less than 50%, participant enrollment will continue until 155 
participants per arm are enrolled into Arms B and C and at least 200 participants are enrolled 
into Arm A. Note that the power calculations were based on an exact binomial CI of the 
difference in poor outcomes, as an approximation to the primary analysis, which will be based 
on the Kaplan-Meier based estimates of poor outcomes at week 72. 
 
Table 2. Power calculations for total sample sizes of 129 and 155 per group (arms B and C) for 
different poor outcome rates across and between treatment arms. 
 
 Poor outcome rate by 
study arm 
Power for concluding NI 
with 7% margin, 5% type I 
error rate, and 10% loss to 
follow-up 
6-month tx 
4-month 
tx 
Sample size 
129 per 
group 
Sample size 
155 per 
group 
0.01 
0.01 
0.999 
1 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
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0.01 
0.02 
0.984 
0.994 
0.01 
0.03 
0.863 
0.912 
0.02 
0.02 
0.985 
0.994 
0.02 
0.03 
0.903 
0.942 
0.02 
0.04 
0.726 
0.792 
0.03 
0.03 
0.932 
0.963 
0.03 
0.04 
0.803 
0.862 
0.03 
0.05 
0.621 
0.689 
0.04 
0.04 
0.862 
0.911 
0.04 
0.05 
0.716 
0.782 
0.04 
0.06 
0.545 
0.609 
0.05 
0.05 
0.792 
0.851 
0.05 
0.06 
0.644 
0.711 
0.05 
0.07 
0.487 
0.547 
 
 
 
Interim Analyses 
 Early stopping for inferiority of treatment shortening arm 
Interim analyses will be performed for safety in Arms B and C, to evaluate whether the 
poor outcome rate is worse in the arm with earlier treatment completion. The Kaplan-
Meier based estimator of poor outcomes at week 72 will evaluated after 1/3 and 2/3 of 
participants have been followed for 72 weeks from study entry, using a spending function 
that mimics the Pocock boundary. The stopping boundary is derived from a test of 
inferiority (of the treatment shortening arm) that corresponds approximately to a z-score 
of 2.178 (i.e., a two-sided p-value of 0.029), although the precise boundary depends on the 
exact amount of information at the interim analyses. 
 Early stopping for study futility 
The premise of this study is that imaging and Xpert markers can identify a subset of 
participants with high success rates. If the relapse rate is high in this subset, then the basis 
for this study must be called into question. Therefore, when about half of the participants 
have completed their week 72 follow-up, the poor outcome proportions will be evaluated 
and presented to the Data and Safety Monitoring Board (DSMB). If more than 16 (of 75) 
participants in the standard treatment arm (Arm B) have a poor outcome, a 
recommendation to stop the trial will be considered. Alternatively, a recommendation to 
stop randomization into Arm C will also be considered.  In this scenario, participants who 
would be eligible for shortening would be put into Arm B. Under this scenario the lowest 
achievable poor outcome in the standard treatment arm (by the end of the trial) would be 
11% (16/150).  Poor outcome rates higher than 11% would be concerning given the 
eligibility criteria for randomization, which represents a subset of participants with a low 
probability of relapse. Conditional power will be included in the DSMB reports to give 
guidance about the likelihood of concluding non-inferiority if the study continues to full 
enrollment. A table of conditional power computations will be included using a range of 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
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non-inferiority margins (e.g., ranging from 6%-10%), since determination of an acceptable 
margin may depend on multiple factors. 
 
 
 
3 
Analysis Populations 
 
Modified intention-to-treat (mITT) 
This study is different from many others in that participants must have adequate adherence for the 16 
weeks of treatment prior to randomization. All randomized participants will be included in the mITT 
cohort, unless it is later determined that a participant is considered a protocol violation prior to 
randomization (e.g., documentated error in the PredictTB criteria). The following four scenarios will 
result in censoring at the times specified below. 
1) Participant infected with a new strain (i.e., a TB strain that differs from that identified at 
baseline) after converting to culture negative. Participant will be censored at time of re-
infection. 
2) Participant died from a violent cause or trauma (e.g., traffic accident). Participant will be 
censored at time of violent death. 
3) Participants who are lost to follow-up after completion of 6-month treatment phase with a 
negative last available LJ culture (for both arms B & C).  Participants will be censored at the 
time of the last observed culture. 
4) Participants who are able to produce sputum at week 72, but whose week 72 sputum samples 
are both contaminated or missing, who cannot be brought back for repeat cultures, provided 
they have not already been classified as unfavorable and provided that their last positive 
culture was followed by at least two negative cultures. 
 
Note that participants lost to follow-up after week 16 and before week 24 will be considered as a poor 
outcome. 
 
Per protocol 
Additional participants will be excluded from the mITT subset for a per-protocol analysis. These 
include:  
1) Participants who did not complete the treatment course to which they were randomized (e.g., a 
participant randomized to continue treatment until week 24, who stops treatment at week 20). 
2) Participants whose treatment was modified or extended for reasons other than an unfavorable 
response to treatment. 
 
 
 Pharmacokinetic sub-studies 
The Pharmacokinetic (PK) sub-study aims to identify those patients at highest risk of relapse to see if 
differences in sub-breakpoint MIC and/or PK/sub-breakpoint MIC were present at baseline. This will 
be compared to those who did not relapse. Based on preliminary data, we believe that participants who 
enter Arm A due to a poor response on the Week 4 PET/CT scan are at the highest risk of relapse. 
Hence, we will target this group of participants for inclusion into this PK sub-study. At week 4 the 
PET/CT scan from the main study will be collected. A matching participant (i.e., a “control”) from the 
low risk arm will be similarly invited to participate. If consented and enrolled, participants will 
undergo PK sampling at week 12 and 16. The sub-study concludes after two days of PK sampling are 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
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completed but no later than the week 24 study visit. Control participants who are later randomized to 
Arm C must complete PK sampling no later than the week 16 study visit as they will conclude 
treatment at that time. 
 
4 
Outcome Measures 
 Please refer to Figure 2 and Table 4 for the flow of outcomes.  The primary efficacy endpoint will be 
the proportion of poor outcomes in arms B and C 72 weeks following treatment initiation. Poor 
outcomes include those that experienced a treatment failure (section 4.1), confirmed relapse (section 
4.2), or died (non-violent death). 
 
Solid culture results will be used for all primary endpoint analyses, with one exception.  If the week 72 
solid culture result is contaminated or missing and the participant cannot be brought back for an 
additional sputum sample, the liquid culture result may be used at the final week 72 study visit. For 
other study visits, only solid culture results will be used for the primary analysis. Solid culture results 
that are missing or contaminated will be classified as unavailable. Liquid culture results may be used 
for secondary analyses. 
 
Participants randomized to Arms B or C who are subsequently found to have a positive culture for Mtb 
on solid medium between and including weeks 16-24 that is confirmed on a subsequent culture will be 
considered treatment failures. These participants will be referred to continue treatment per local SOC 
and followed observationally until the end of their treatment to determine outcome. TB DNA strain 
typing may be done (sec 5.5.3) to confirm whether this is the same strain of DNA as the participant 
had at baseline.   Single positive cultures that are not confirmed on a subsequent sputum sample are 
not considered failures as these may have arisen from clerical error or laboratory contamination [1] 
 
 
Treatment Failure 
Participants who remain culture positive on solid medium at Week 24 in Arm A will be 
considered treatment failures and will be withdrawn from the study and referred to continue 
treatment per the local SOC. Participants who convert to solid culture negative and subsequently 
have a single solid culture positive for Mtb before or at week 24 need to have a subsequent 
culture positive for Mtb to be confirmed as treatment failures.  
 
 
Treatment Recurrence and Relapse 
Participants who convert their sputum to culture negative (2 consecutive negatives over ≥4 
weeks) and who subsequently become culture positive for M.tb again on solid medium, during 
follow-up after week 24, confirmed by a second (on another day) sputum culture positive for 
M.tb, will be considered recurrences. Single positive cultures that are negative on follow-up 
culture will not be considered recurrences. Participants with a positive, contaminated, or 
unevaluable culture on the final month 18 (week 78) follow-up visit may be asked to return for 
sputum culture confirmation.  


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
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Relapses will be distinguished from re-infections by DNA strain typing and only relapses will be 
considered a study endpoint.  
 
Treatment Success 
Treatment success will be defined as a participant with at least 2 consecutive negative cultures 
on solid medium over a span of at least 4 weeks, achieved before the end of therapy, with no 
subsequent confirmed positive cultures during follow-up.  
 
 
Losses to follow-up 
Participants who are lost to follow-up prior to week 72, will be included in the analysis up to 
and including the last time culture results were received. From that point forward, they will be 
considered censored for the purposes of analyses.    
 
5 
Data analysis details 
 
 
Baseline tables 
Table 3. Summary of baseline characteristics will be reported overall and by country as below. 
Site-level summaries can be included in appendices for the primary manuscript 
 
Arm A 
(n=) 
 
Arm B 
(n=) 
 
Arm C 
(n=) 
Sex 
Males N (%) 
 
 
 
Age 
Mean (Range) 
 
 
 
Weight (kg) 
Mean (SD) 
 
 
 
BMI 
Mean (SD) 
 
 
 
# of participants with at least one previous TB 
episodes not within the past 3 years 
N (%) 
 
 
 
Current smoker 
N (%) 
 
 
 
Previous smoker—those who are not current 
smokers but report a history of smoking 
N (%) 
 
 
 
Duration of smoking (years) 
Mean (Range) 
 
 
 
Number of cavities (>2 mL) 
None 
N (%) 
 
 
 
1 
N (%) 
 
 
 
2 
N (%) 
 
 
 
3 
N (%) 
 
 
 
>=4 
N (%) 
 
 
 
Total cavity volume (>2 mL) 
Mean (SD) 
 
 
 
Xpert CT – Week 0 
Mean (SD) 
 
 
 
Time to positivity on MGIT (days) – Week 0 
Mean (SD) 
 
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
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Race (tabulate by reported categories) 
 
 
 
 
 
 
CONSORT diagram 
A flow diagram describing the reasons for exclusion will be included following the CONSORT 
criteria [2]. 
 
Statistical analysis of primary outcome 
The primary analysis will be based on the proportion of poor outcomes (as defined in section 
4) at 72 weeks between Arms B and C based on the MITT population.  A two-sided 90% 
confidence interval for the difference of the proportions (pC-pB, where p represents the 
proportion of poor outcomes and the subscripts indicate the treatment arm) will be based on 
proportion of poor outcomes from the Kaplan-Meier curve at week 72 and the Greenwood 
variance formula [3]. The advantage of using the Kaplan-Meier estimator at week 72 is the 
inclusion of participants who contribute outcome data after randomization but are lost to 
follow-up before week 72.  Differences below zero indicate worse outcomes for arm C. 
Therefore, if the lower bound of the confidence interval is greater than or equal to -0.07, the 
null hypothesis will be rejected, and non-inferiority of arm C will be concluded. 
Table 4. Primary outcome breakdown. 
Variable 
Arm B  
(N=) 
Arm C 
(N=) 
Arm A 
(N=) 
 
Favorable outcome – no. (%) 
Patients with outcome  
 
 
 
Unable to produce sputum  
 
 
 
Unable to produce sputum at 72 weeks but 
culture negative status earlier 
 
 
 
 
Missing data on LJ culture at 72 weeks and 
MGIT negative 
 
 
 
 
 
Poor outcome – no. (%) 
Through week24 (or through treatment if extended in Arm A) 
Death presumable related to TB   
 
 
 
Treatment failure – Culture-confirmed  
 
 
 
Treatment failure – Not culture-confirmed  
 
 
 
Withdrawal of consent  
 
 
 
Lost to follow-up  
 
 
 
No completion of treatment  
 
 
 
Adverse event severe enough to stop the 
treatment 
 
 
 
 
PET/CT findings that required immediate 
procedures or treatment 
 
 
 
 
Possible unfavorable outcome  
 
 
 
After Week 24 (or after treatment if extended 
in Arm A) 
 
 
 
 
Death presumable related to TB   
 
 
 
Treatment failure – Culture-confirmed  
 
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 12 of 18 
 
 
Treatment failure – Not culture-confirmed  
 
 
 
Treatment relapse  
 
 
 
Lost to follow-up  
 
 
 
Possible unfavorable outcome  
 
 
 
 
 
Secondary Analyses 
 
1) As a sensitivity analysis, the primary analysis will be repeated but using the per-protocol 
cohort. 
2) As another sensitivity analysis, the primary analysis will be repeated using MGIT results to 
define final outcomes. 
3) The difference (and 90% confidence interval) in treatment success rates between a 
combined A+B Arm and a combined Arm A+C, with weighting to represent the 
population. Let pA and pBC denote the proportion of A and B/C participants, respectively.  
Let FA, FB and FC be the Kaplan-Meier estimates of success rates at week 72.  The overall 
success rates for each arm can be computed as pA FA + pBC FB  and pA FA + pBC FC  . 
4) Univariate and multivariate logistic regression models will be fitted to demographic, 
radiographic, microbiologic and immunologic variables with outcomes of treatment failure 
vs cures.   Markers from images include: PET total glycolytic activity in regions of interest, 
total volume of hard CT lesions (-100 to 100 HU), total volume of soft CT lesions (-500 to 
-100 HU), and cavity air (volume of air in cavities). Endpoints relating to immunologic 
markers will be based on serum cytokine levels as described in section 1. Xpert MTB/RIF 
cycle threshold will be analyzed as a continuous variable in addition to the pre-specified 
thresholds. Analyses will also consider transformations such as delta cycle threshold.  A 
training and test split-sample approach will be employed as a validation step. 
5) Univariate and multivariate logistic regression models will be fitted to demographic, 
radiographic, microbiologic and immunologic variables with outcomes of relapses vs cures, 
excluding treatment failures.   Markers from images include: PET total glycolytic activity 
in regions of interest, total volume of hard CT lesions (-100 to 100 HU), total volume of 
soft CT lesions (-500 to -100 HU), and cavity air (volume of air in cavities). Endpoints 
relating to immunologic markers will be based on serum cytokine levels as described in 
section 1. Xpert MTB/RIF cycle threshold will be analyzed as a continuous variable in 
addition to the pre-specified thresholds. Analyses will also consider transformations such as 
delta cycle threshold.  A training and test split-sample approach will be employed  as a 
validation step. 
4) Based on the limited number of models selected under 2) and 3) above, area under the ROC 
curves (AUCROC) will be estimated to summarize diagnostic accuracy.  Time-dependent 
ROC curves will be estimated. [4,5] 
5) To compare the diagnostic accuracy of TTP and GeneXpert cycle threshold as a marker of 
outcomes, analyses of these variables at different time points will be conducted.  
Specifically, AUCROC’s will be compared across time points. 
6) ROC curve analysis will evaluate the accuracy of PK parameters of sub-breakpoint MIC, 
AUC/sub-breakpoint MIC, Cmax/sub-breakpoint MIC comparing treatment failures vs 
cures (and relapses vs cures), along with 95% confidence intervals. 
 
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
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Figure 2 TB outcome flow  
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 14 of 18 
 
 
Table 5: TB Positive/Negative Flow for South Africa  
 
LJ Culture: 
CRF 
Scenarios with LJ culture in SA (based on China) 
Test 
Line 
Item 
SPUTUM 
6 
Produced by 
Induced or 
Spontaneous and 
SPUTUM 
7 
Approx 
Volume 
< 2 ml and 
>= 2 ml and 
SPUTUM 
8 
Usage 
Microbiology = 
Yes 
Microbiology = Yes 
LJ 
2 
LJ Growth 
  
NO 
YES/Contaminated 
LJ 
3 
AFB SMEAR 
  
  
ND/NA 
AFB - 
AFB + or Mixed 
LJ 
4 
Date 
  
NA 
NA 
Date 
MGIT 
8 
TB antigen 
  
  
  
  
Positive 
Neg/Not done 
MGIT 
9 
Speciation 
result/HAIN 
  
  
  
  
  
MTB complex 
or MTB/NTM 
Any thing else 
LJ 
5 
TB antigen 
  
Missing or Not done/Not available  
LJ 
6 
Speciation 
result/HAIN 
  
  
  
Missing or Not 
required 
Missing or 
Not required 
  
MTB 
NTM 
MTB & 
NTM 
Missing, Not re
No res
RESULT 
  
  
Alarm 
TB - 
Contaminated 
Contaminated 
TB + 
TB + 
TB + 
TB - 
TB + 
Alarm
Outcome 
 
TB- 
Contaminated Contaminated 
TB + 
TB+ 
TB+ 
TB- 
TB+ 
Alarm
 
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 15 of 18 
 
 
MGIT Culture: 
CRF line 
Scenarios with MGIT culture in RSA 
Test 
Line 
Item 
SPUTUM 
6 
Produced by 
alarm 
Spontaneous and 
SPUTUM 
7 
Approx Volume 
< 2 ml and 
>= 2 ml and 
SPUTUM 
8 
Usage 
Microbiology = Yes* 
Microbiology = Yes* 
MGIT 
3 
MGIT result 
  
Error / No result 
Negative 
Contaminated 
Positive 
MGIT 
4 
TTD 
  
  
  
  
DD:HH 
MGIT 
5 
AFB Smear 
  
  
  
  
AFB + / Mixed 
MGIT 
6 
Date 
  
  
  
  
Date 
MGIT 
7 
BAP 
  
  
  
  
Pos / Neg / ND-NA 
MGIT 
8 
TB antigen 
  
  
  
  
Positive 
Negative 
ND/NA/Missing 
MGIT 
9 
Speciation 
result/HAIN 
  
  
  
  
  
MTB 
complex or 
MTB/NTM 
Any 
thing 
else 
  
RESULT 
Alarm 
Undetermined 
TB - 
Contaminated 
TB +  
TB +  
TB - 
Alarm 
outcome 
 
Undetermined 
TB - 
Contaminated 
TB +  
TB +  
TB - 
Alarm 
 
Table 6: TB Positive/Negative Flow for China 
 
LJ Culture: 
CRF 
Scenarios with LJ culture in China 
Test 
Line 
Item 
SPUTUM 
6 
Produced by 
Induced or 
Spontaneous and 
SPUTUM 
7 
Approx Volume 
< 2 ml and 
>= 2 ml and 
SPUTUM 
8 
Usage 
Microbiology = 
Yes 
Microbiology = Yes 
LJ 
2 
LJ Growth 
  
NO 
YES/Contaminated 
LJ 
3 
AFB SMEAR 
  
Blank or NA 
AFB - 
AFB + / Mixed 
ND/NA 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 16 of 18 
 
 
LJ 
4 
Date 
  
Blank or NA 
Date 
Date 
Any 
value or 
missing 
MGIT 
8 
TB antigen 
  
do not 
reference 
Any value or 
missing 
Positive 
Neg or Not done-NA or blank 
Any 
value or 
missing 
LJ 
5 
TB antigen 
  
Blank or NA 
Any value or 
missing 
Any 
value or 
missing 
Positive 
Negative or ND/NA 
Any 
value or 
missing 
LJ 
6 
Speciation 
result/HAIN 
  
Blank, Not 
required or No 
result 
Any value or 
missing 
Any 
value or 
missing 
Any 
value or 
missing 
Test not 
required, 
but if 
“MTB 
Complex” 
or “both 
MTB and 
NTM” 
Test not 
required, 
but if 
“NTM” 
or “No 
Result” 
Missing 
or Not 
required 
Any 
value or 
missing 
RESULT 
  
  
Alarm 
TB - 
Contaminated 
TB + 
TB + 
TB + 
TB - 
TB - 
Alarm 
Outcome 
  
  
edit check* 
TB-  
Contaminated 
TB + 
TB + 
TB + 
TB - 
TB - 
Alarm 
* was able to get all these results with SPUTUM6= Induced or SPUTUM7 < 2ml 
MGIT Culture: 
CRF line 
Scenarios with MGIT culture in China 
Test 
Line 
Item 
SPUTUM 
6 
Produced by 
Induced or 
Spontaneous and 
SPUTUM 
7 
Approx 
Volume 
< 2 ml and 
>= 2 ml and 
SPUTUM 
8 
Usage 
Microbiology = Yes* 
Microbiology = Yes* 
MGIT 
3 
MGIT result 
  
Error / No result 
Negative 
Contaminated 
Positive 
MGIT 
4 
TTD 
  
Blank or NA 
Blank or 
NA 
any 
DD:HH 
MGIT 
5 
AFB Smear 
  
Blank or NA 
Blank or 
NA 
Blank or NA 
AFB + / Mixed 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 17 of 18 
 
 
MGIT 
6 
Date 
  
Blank or NA 
Blank or 
NA 
Any value or 
missing 
Date 
MGIT 
7 
BAP 
  
Blank or NA 
Blank or 
NA 
Blank or NA 
Pos / Neg / ND-NA 
Blank or ND/NA 
Pos/N
MGIT 
8 
TB antigen 
  
ND/NA 
ND/NA 
ND/NA 
Positive 
Negative 
ND/NA/Missing 
Blank or ND/NA 
Pos
RESULT 
Alarm 
Undetermined 
TB - 
Alarm 
TB +  
TB - 
Alarm 
Alarm 
TB+
Outcome 
edit check*  
Undetermined 
TB - 
Contaminated 
TB+ 
TB- 
Alarm 
Alarm 
TB+
* was able to get all these results with SPUTUM6= Induced or SPUTUM7 < 2ml 
 
 


Predict TB Trial SAP v1.0; 31 Jan 2020 
 
Page 18 of 18 
 
 
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positive cultures from the sputum of patients in four studies of short course chemotherapy in 
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2. Schulz KF, Altman DG, Moher D. CONSORT 2010 statement: updated guidelines for reporting 
parallel group randomised trials. BMC medicine. 2010 Dec;8(1):18. 
3. Greenwood M. The natural duration of cancer (report on public health and medical subjects no 
33). London: Stationery Office. 1926. 
4. Heagerty PJ, Zheng Y. Survival model predictive accuracy and ROC curves. Biometrics. 2005 
Mar;61(1):92-105 
5. Saha P, Heagerty PJ. Time‐dependent predictive accuracy in the presence of competing risks. 
Biometrics. 2010 Dec;66(4):999-1011.