Increasing Notifications of Tuberculosis From Private Practitioners: A Randomised Controlled Trial
Phase: NA
Conditions: Tuberculosis
Sponsor: Universitas Padjadjaran

 
‘INSTEP2’  
INCREASING NOTIFICATIONS OF TUBERCULOSIS FROM 
PRIVATE PRACTIONERS: A RANDOMISED CONTROLLED 
TRIAL 
 
 
 
Protocol Number: 1 
Principal Investigator: Philip C Hill 
Sponsor: University of Otago 
Funded by: e-Asia 
Version Number:  v. 1.0 
18 April 2019 
 
 
Summary of Changes from Previous Version: 
Affected 
Section(s) 
Summary of Revisions Made 
Rationale 
 
 
 
 
 
 

  
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Table of Contents 
STATEMENT OF COMPLIANCE ................................................................................................................. 1 
1 
PROTOCOL SUMMARY ................................................................................................................... 2 
1.1 
Synopsis................................................................................................................................... 2 
1.2 
Schema .................................................................................................................................... 3 
1.3 
Schedule of Activities (SoA) .................................................................................................... 4 
2 
INTRODUCTION ............................................................................................................................... 4 
2.1 
Study Rationale ........................................................................................................................ 4 
2.2 
Background .............................................................................................................................. 5 
2.3 
Risk/Benefit Assessment ......................................................................................................... 6 
3 
OBJECTIVES AND ENDPOINTS ...................................................................................................... 6 
4 
STUDY DESIGN ................................................................................................................................ 6 
4.1 
Overall Design ......................................................................................................................... 6 
4.2 
Scientific Rationale for Study Design ....................................................................................... 7 
4.3 
End of Study Definition ............................................................................................................ 7 
5 
STUDY POPULATION ...................................................................................................................... 7 
5.1 
Inclusion and Exclusion Criteria ............................................................................................... 7 
5.2 
Strategies for Recruitment and Retention ................................................................................ 8 
6 
STUDY INTERVENTION ................................................................................................................... 8 
6.1 
Study Intervention(s) Administration ........................................................................................ 8 
6.1.1 
Recruitment and Eligibility of pps ........................................................................... 8 
6.1.2 
Intervention ............................................................................................................ 9 
6.2 
Preparation/Finalisation of Intervention package .................................................................... 9 
6.3 
Measures to Minimize Bias: Randomization and Blinding ..................................................... 10 
6.4 
Study Intervention Compliance .............................................................................................. 11 
7 
STUDY INTERVENTION DISCONTINUATION AND PARTICIPANT 
DISCONTINUATION/WITHDRAWAL ......................................................................................................... 11 
7.1 
Participant Discontinuation/Withdrawal from the Study ......................................................... 11 
7.2 
Lost to Follow-Up ................................................................................................................... 11 
8 
STUDY ASSESSMENTS AND PROCEDURES ............................................................................. 12 
8.1 
Efficacy Assessments ............................................................................................................ 12 
8.2 
Safety and Other Assessments ............................................................................................. 12 
8.2.1 
Safety 
 ............................................................................................................... 12 
8.2.2 
Private Practitioners ............................................................................................. 12 
8.2.3 
TB patients ........................................................................................................... 12 
8.3 
Adverse Events and Serious Adverse Events ....................................................................... 13 
8.3.1 
Events of Special Interest .................................................................................... 13 
8.4 
Unanticipated Problems ......................................................................................................... 13 
8.4.1 
Definition of Unanticipated Problems (UP) .......................................................... 13 
8.4.2 
Unanticipated Problem Reporting ........................................................................ 13 
9 
STATISTICAL CONSIDERATIONS ................................................................................................ 14 
9.1 
Statistical Hypotheses ............................................................................................................ 14 
9.2 
Sample Size Determination – key considerations ................................................................. 14 
9.3 
Statistical Analyses ................................................................................................................ 15 
9.3.1 
General Approach ................................................................................................ 15 
9.3.2 
Baseline Descriptive Statistics ............................................................................. 15 
9.3.3 
Analysis of the Primary Efficacy Endpoint(s) ....................................................... 15 
9.3.4 
ANALYSIS OF THE SCONDARY EFFICACY ENDPOINT(S) ................ 15 
9.3.5 
PLANNED SAFETY ANALYSES ................................................................... 15 
9.3.6 
PLANNED INTERIM ANALYSES .................................................................. 15 

  
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SUPPORTING DOCUMENTATION AND OPERATIONAL CONSIDERATIONS ........................... 16 
10.1 
Regulatory, Ethical, and Study Oversight Considerations ..................................................... 16 
10.1.1 
Informed Consent Process .................................................................................. 16 
10.1.2 
Study Discontinuation and Closure ...................................................................... 16 
10.1.3 
Confidentiality and Privacy ................................................................................... 17 
10.1.4 
Future Use of Stored Specimens and Data ......................................................... 17 
10.1.5 
Key Roles and Study Governance ....................................................................... 17 
10.1.6 
Safety Oversight................................................................................................... 19 
10.1.7 
Quality Assurance and Quality Control ................................................................ 19 
10.1.8 
Data Handling and Record Keeping .................................................................... 19 
10.1.9 
Protocol Deviations .............................................................................................. 20 
10.1.10 
Publication and Data Sharing Policy .................................................................... 20 
10.1.11 
Conflict of Interest Policy ..................................................................................... 20 
11 
Sub-Study ........................................................................................................................................ 20 
11.1 
Objectives and endpoints....................................................................................................... 20 
11.2 
Background/rationale ............................................................................................................. 21 
11.3 
Overall design ........................................................................................................................ 21 
11.4 
Inclusion and exclusion criteria .............................................................................................. 21 
11.5 
consent, Assesssments and procedures ............................................................................... 22 
11.6 
Safety ..................................................................................................................................... 23 
11.7 
Analysis .................................................................................................................................. 23 
12 
Abbreviations ................................................................................................................................... 25 
13 
Protocol amendment history ............................................................................................................ 26 
14 
REFERENCES ................................................................................................................................ 27 
 

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STATEMENT OF COMPLIANCE 
 
 
The Principal Investigator will assure that no deviation from, or changes to the protocol will take place 
without prior agreement from the Institutional Review Board (IRB). The protocol, informed consent 
form(s), recruitment materials, and all participant materials will be submitted to the IRB for review and 
approval.  Approval of both the protocol and the consent form will be obtained before any participant is 
enrolled.  Any amendment to the protocol will require review and approval by the IRB before the changes 
are implemented to the study.  All changes to the consent form will be IRB approved.  
 
The sponsor will have no role or authority in: study design; in collection, management, analysis and 
interpretation of the data; in writing of reports; in the decision to submit reports for publication. 
 
This study is conducted as a collaboration between researchers at Universitas Padjadjaran and the 
University of Otago, which operates under a signed Memorandum of Understanding.  
 
 

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1 
 
PROTOCOL SUMMARY 
1.1 
SYNOPSIS  
Title: 
Increasing notifications of TB cases from private practitioners (PP): a 
randomised controlled trial 
Study Description: 
This is a cluster randomised controlled intervention trial. The multi-
component public health intervention will be administered to private 
practitioners in Community Health Centre (CHC) clusters. The change in the 
number of tuberculosis (TB) notifications over 12 months before, and 12 
months after, the intervention will be compared between study arms.  
Hypothesis related to the Primary Efficacy Endpoint: A tailored intervention 
in PPs will increase TB notifications.  
Objectives: 
 
Primary objective: To evaluate whether a tailored intervention package 
increases notifications of TB from PPs in Bandung, Indonesia.  
Secondary objectives: (1) To calculate the proportion of referrals from PPs 
in the intervention arm that are actually diagnosed with TB; (2) To conduct 
a restricted analysis of the primary endpoint, limited to notifications of 
patients who live in the CHC area where they are notified. 
Primary Endpoint: 
The primary endpoint is the change in the number of notifications of TB 
from the 12 months before to the 12 months after the intervention is fully 
implemented. This change in the number of notifications will be compared 
between intervention clusters (n=15) and control clusters (n=15). 
Study Population: 
All those living in the 30 CHC clusters 
Phase: 
Pragmatic public health intervention efficacy trial. 
Description of Sites/Facilities 
Enrolling PPs: 
The intervention will be administered to PPs in areas around 15 CHCs 
(clusters), at their place of practice. PPs in the control areas will receive no 
intervention.  
Description of Study Intervention: 
(1) An electronic referral and notification system; (2) Education about signs 
and symptoms of TB and TB management; (3) An individualised practitioner 
plan for diagnostic and management pathways.  
Study Duration: 
3 years 
PP involvement Duration: 
2 years 
Sub-study 
Sub-study objectives: On notified TB cases, to use social network analyses, 
whole genome sequencing and phenotypic drug susceptibility testing to 
inform clinical algorithms for drug resistant-TB and the design of a 
transmission study.  
Study population: Pulmonary TB cases in selected study intervention 
clusters (sub-study) 
Description of study: M. tuberculosis isolates from 150 notified TB cases will 
be sequenced and genomic and phenotypic drug susceptibility test results 
compared. Social network data from interviews and genomic data will be 
combined to explore transmission of M. tuberculosis to inform design of a 
future study.  
 
 

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1.2 
SCHEMA 
 
Prior to  
Enrollment 
 
 
 
 
 
 
 
 
 
 
Enroll private 
practitioners 
 
 
 
Refreshers 
 
 
 
 
 
 
Record 
notifications 
 
 
 
 
 
 
Completion of  
12 months follow- 
up after intervention 
established 
 
 
Total 30 CHC areas:  pilot intervention in non- study areas. Finalise intervention. Establish 
link to notifications files in sub-districts of the study and abstract 12 months of pre-
intervention notification data 
Enroll private 
practitioners and 
administer 
intervention  
Real-time recording of notifications from routine data from CHCs in both arms 
Final abstraction of notification 
data from CHCs in both arms 
Arm 2 
15 CHC areas 
Arm 1 
15 CHC areas 
1-month visit to 
private practitioners 
to reinforce 
intervention plus 2-
monthly electronic 
refreshers 
Randomise sub-districts 
No intervention: 
No private 
practitioners 
enrolled 
 

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1.3 
SCHEDULE OF ACTIVITIES (SOA) 
 
 
 
Overall timeline summary: 
Year 1:  
Months 1-6:   Finalise protocol, complete design and piloting of intervention, including app. Pre-
intervention data abstraction. 
Months 7-12: Implement intervention 
Year 2: 
Months 1-5: Complete intervention 
Months 6-12: Commence follow-up period 
Year 3 
Months 1-6: Complete follow-up and data abstraction 
Months 7-12: Analysis and write-up 
 
2 
 
INTRODUCTION 
 
2.1 
STUDY RATIONALE  
 
Tuberculosis (TB) is the third leading cause of death in Indonesia. The 2014/15 TB prevalence survey 
estimated that there were 1 million cases of TB, second only to India globally for burden of TB.(1) 
Disturbingly, the prevalence survey showed that over half of TB cases in Indonesia are not notified. The 
huge private sector in Indonesia, comprising an estimated 70,000 practitioners, provides over 50% of 
health care but notifies less than 10% of all diagnosed TB cases.(2) TB patients managed in the private 
sector are often treated sub optimally and have poorer outcomes.(3, 4) The majority of people with 
symptoms of TB initially engage private practitioners (PPs), but 80% of the facilities they attend cannot 
diagnose TB.(5) As part of advancing Public-Private Mix (PPM) the government made TB notification 
Procedures 
Pre-enrollment 
Enrollment/Baseline 
Visit 1, Day 1 
Study Visit 2  
Month 1 
Electronic refresher 
Month 2 
Electronic refresher 
Month 4 
End of follow-up 
(12 months after 
intervention rolled 
out) 
Post-completion of 
data collection 
Informed consent 
 
X 
 
 
 
 
 
Demographic data collection 
 
X 
 
 
 
 
 
Administer study intervention 
 
X 
 
 
 
 
 
Complete initial visit form  
 
X 
 
 
 
 
 
Complete follow-up visit form 
 
 
X 
 
 
 
 
Extract notification data 
X 
 
 
 
 
X 
 
Analysis and report writing 
 
 
 
 
 
 
x 

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mandatory in 2016, but intervention is likely to be needed for notifications to increase substantially. Such 
intervention needs to be based on a sound understanding of contextual factors around PPs and how they 
relate to the public sector with respect to the diagnosis, treatment and reporting of TB cases. 
2.2 
BACKGROUND  
 
PPM can impact all aspects of TB suspect management pathways (see figure below). Indonesia is 
committed to enhancing PPM to improve TB control.(6) An initial focus was on private-public hospital 
partnerships.(7) The benefits of PPM initiatives have yet to be fully realized across the country.(8)  
We have been conducting research to inform the design of interventions to increase notifications of TB 
from PPs in Indonesia. PPs are medically trained general practitioners or specialists. They work outside 
government Community Health Centres (CHC), either in solo practice or private clinics. When they 
diagnose TB patients, they are supposed to refer and notify them to the CHC or other DOTs treatment 
facility. Some have an agreement with the CHC to continue to treat their patients using free TB drugs 
supplied by the government. In a feasibility study of a mobile ‘app’ for notification,(9) we showed that 
40% of participating PPs have inadequate knowledge of TB symptoms and/or signs. The app was well 
received, utilized, and showed potential to increase TB notifications, although not all PPs had phones that 
supported it. We are currently conducting a USAID funded project, ‘INSTEP’, to describe and understand 
the health care pathways of patients seeking treatment for TB, and of PP practice. We have discovered 
that only 65% of officially registered PPs can be found. We have identified 245 of 1200 PPs in the 30 study 
areas that had diagnosed at least 1 TB case in the previous 3 months (total n=870 TB cases) - less than 
20% had been notified. In 2018, we are exploring patient diagnostic pathways and PP diagnostic and 
treatment practices. 
With our recent studies, a strong relationship with the National TB Control Programme, and our proven 
track record in intervention trials, our collaborative team is in a strong position to refine and evaluate an 
intervention in PPs. The primary goal of this randomised controlled trial is to increase notifications of TB 
by PPs through a tailored intervention.  
 
Figure. Schematic diagram of a generic PPM. Reproduced from Lei et al.(10)  
 
 

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2.3 
RISK/BENEFIT ASSESSMENT   
 
The risk of any referral for TB treatment is over treatment i.e. treatment of individuals for TB who do not 
actually have TB. These individuals are placed at risk from side effects of TB medications. However, part 
of the intervention is to work with the practitioners to identify an appropriate diagnostic approach to their 
patients and the risk is further outweighed by the risk of TB cases being managed with the wrong 
medications in the wrong way, if not referred for treatment to the National TB Programme (NTP). 
Furthermore, we plan for the paperwork for notifications to be done by the NTP, after confirmation of the 
patients’ diagnoses following referral. There are no obvious risks to PP’s health or safety of receiving this 
public health intervention. 
 
3 
OBJECTIVES AND ENDPOINTS 
 
OBJECTIVES 
ENDPOINTS/KEY MEASURES 
Primary 
 
To evaluate whether a tailored 
intervention 
package 
increases 
notifications of tuberculosis (TB) by 
private practitioners in Bandung, 
Indonesia.  
The primary endpoint is the change in 
the number of notifications of TB from 
the 12 months before to the 12 
months after the intervention is fully 
implemented.  
Secondary objectives of trial 
 
To compare the proportion of 
referrals 
from 
PPs 
in 
the 
intervention and control arms that 
are actually diagnosed with TB 
 
To conduct a restricted analysis of 
the primary endpoint, limited to 
notifications of patients who live in 
the CHC area where they are 
notified. 
The change in proportion of referrals 
from PPs in the intervention arm that 
are actually diagnosed with TB from 
the 12 months before to the 12 
months after the intervention is fully 
implemented. 
 
The same as primary endpoint, 
restricted to notifications of patients 
who live in the CHC area where they 
are notified. 
 
 
4 
STUDY DESIGN  
 
4.1 
OVERALL DESIGN 
 
Hypothesis related to the Primary Efficacy Endpoint: A tailored intervention in PPs will increase TB 
notifications. 
 
This is a cluster randomised controlled trial of a multi-component public health intervention to increase 
notifications of TB from PPs in one city, Bandung, in Indonesia. Clusters are CHC areas and the intervention 

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will be administered directly to PPs in sub-districts randomised to the intervention arm. The CHCs in both 
arms will be informed about the study and asked, through the National TB Control Programme, to make 
their notification data available and their willingness will be recorded. No intervention will be given to PPs 
in the control arm. Notifications will be obtained directly from routine records, with accompanying 
information gathered about the address of the patient and referring doctor. Notified TB cases are, by 
definition, TB cases who have been commenced on TB treatment, noting that some referred ‘TB cases’ will 
be diagnosed as not having TB by CHC staff. Data on address of the patient will identify the extent of the 
‘contamination’ between arms.  
  
4.2 
SCIENTIFIC RATIONALE FOR STUDY DESIGN 
 
Cluster randomisation of sub-districts is required because individual PPs within the cluster are likely to 
relate to the same CHC and thereby potentially be influenced by that CHC. Individual randomisation, 
therefore, would be subject to greater contamination. There will still be some contamination between 
arms due to peculiarities of PP practice and individual patient health seeking behaviour (as described in 
the statistical considerations section). The control arm will simply continue standard practice; a placebo 
is not indicated.  
 
4.3 
END OF STUDY DEFINITION 
 
The end of the follow-up is defined as the last day of the 12-month period of observation post-
intervention. The end of the study is the end of the following 6 month period of analysis and write up. 
 
5 
STUDY POPULATION 
 
5.1 
INCLUSION AND EXCLUSION CRITERIA 
 
Of 73 Community Health Centre (CHC) areas in Bandung, 30 were randomly selected for the INSTEP study, 
proportional to their catchment population’s size, and will be included in the RCT. Bandung is divided into 
sub-districts (see map below). Some sub-districts have more than one CHC, while CHC each still have 
defined catchment populations. The map therefore shows 22 sub-districts where the 30 CHC areas are 
found.   
The study population consists of all the people who may visit a PP in any of the study areas during the 
during the year before and the year after the intervention – outcome is measured on  all people who 
visit a PP in a study area, are diagnosed with suspected TB and reported to the CHC. 
 
 
 
 
 
 

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Figure. Selected (blue shaded) areas for the INSTEP study and intervention trial. 
  
5.2 
STRATEGIES FOR RECRUITMENT AND RETENTION 
 
Outcome data are all obtained from routinely collected data, so processes for retention of individuals 
are not required. Recruitment is at the cluster level, and only PPs in intervention clusters are contacted 
to receive the intervention. The details for that process are given in section 6. 
 
6 
STUDY INTERVENTION 
 
6.1 
STUDY INTERVENTION(S) ADMINISTRATION 
 
6.1.1 RECRUITMENT AND ELIGIBILITY OF PPS 
 
All medically qualified PPs in the CHC in the intervention arm who reported having diagnosed at least one 
TB case in the past 3 months when visited in the INSTEP study will be eligible for the intervention. They 
will intend to work in the current location for the duration of the study as their primary place of private 
practice. 
They will be excluded from the intervention if:  
 
they are unable to use an electronic device for referral;  

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 
more than 3 months of non-practice during the study period is anticipated; 
 
they are not a qualified medical practitioner, with the appropriate medical authority in 
Indonesia 
Through the INSTEP study, we identified that 245 of 1200 PPs in the 30 CHC areas had diagnosed at least 
1 TB case in the previous 3 months (total n=870 TB cases from 245 PPs) and less than 20% had been 
notified. The study will be conducted starting mid-2019, flowing directly on from the INSTEP study to 
minimize the effect of PPs exiting the areas. We will personally approach, at their place of work, each of 
the 245 PPs identified above who are in the intervention arm (approximately half). They will be fully 
informed about the study, invited to participate and provide written informed consent. A schedule will be 
generated for their education and their follow-up (every 2nd month). We expect around 80% of 
approached PPs will be willing to participate in the study. 
 
PPs participating in the intervention will have the non-financial incentive of a certificate of proficiency 
issued by the Indonesian Medical Association that provides them with credits that can be used as proof 
of continuing medical education for renewing their license to practice. 
 
6.1.2 INTERVENTION 
 
The Intervention will comprise:  
 
1. An electronic referral and notification system, based on evolution of the mobile ‘app’ designed for the 
feasibility study; 
2.  A standardized education about the signs and symptoms of TB and TB management;  
3.  An individualised plan for each PP with respect to their approach to the diagnosis and management 
of TB suspects, considering the type of PP and their context. 
4.  1 month follow-up visit from the study team.  
5.  2-monthly electronic reminder/refresher.  
 
6.2 
PREPARATION/FINALISATION OF INTERVENTION PACKAGE 
 
1. Electronic system. This system is a refinement of the electronic referral and report-back system using a 
mobile phone ‘app’ that was developed in collaboration with information technology (IT) at Telkom 
University, Bandung.(9) The system will enable essential data to be uploaded, consistent with National 
TB Control Programme forms, including: patient identity, symptoms, diagnostic examinations, TB type, 
treatment, and follow-up care. Inputted information will be sent to a secure centralised server and will 
be able to be monitored through log-in by the authorized individuals in a web-based application that 
is compatible with both android and apple operating systems. Any PPs without a compatible cell phone 
will be provided with one, and internet connection issues will be addressed. The system includes a 
reminder system so the PPs can complete patient management steps and it will provide an electronic 
education refresher every second month. Piloting will include final consultation with the National TB 
Control Programme, who have an interest in electronic notification. 

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2. Education. This is a refinement of the education package that we developed for the feasibility study. It 
is focused on TB suspect identification, provisional diagnosis and referral, including how to use the 
mobile phone ‘app’.  Since we found in the feasibility study that not all PPs have time to attend a 1-day 
training, the education will be two 2-hour sessions (one to each individual at their place of work and 
the other in groups) and electronic follow-up (see above). A certificate of proficiency will be available 
from the Indonesian Medical Association, which can be used towards meeting continuing medical 
education requirements. 
 
3. Patient management pathways. Data from the INSTEP study will inform individualised agreed patient 
management pathways for each PP. The INSTEP study is conducting patient pathway analyses through 
a survey of TB cases (n=400), quality assessment through standardized patients attending PPs (n=20) 
and key informant interviews and focus groups of PPs, stakeholders and patients (n=50). These data  
will inform, for each PP, a simple individualised approach for the management of TB suspects, which 
takes into account the context around each PP’s practice, identifying the most efficient and feasible 
approach to obtaining a diagnosis and notifying TB patients.(11) 
 
4. Piloting. The intervention package will be piloted with 10 PPs who practice outside of the 30 selected 
CHC areas, over one month. Following feedback from the PPs and study staff, it will be refined further 
and finalised for the start of the implementation period in the second half of year 1.  
 
6.3 
MEASURES TO MINIMIZE BIAS: RANDOMIZATION AND BLINDING 
 
Randomisation: Using the randomly selected areas from the previous INSTEP study, we will randomly 
select 15 areas as intervention areas, repeating the randomisation 100 times. From this we will select the 
10 allocations that meet the criteria of i) including having the least number of adjacent CHC areas between 
intervention and control arms, to minimize contamination between the arms, and ii) balancing by CHC 
numbers of TB cases diagnosed per annum. Then we will randomly select the final allocation from those 
10. 
 
Trial randomisation codes will not be broken until the study is closed and analysis is commenced. Since 
there are no anticipated serious adverse events, no criteria for breaking the codes have been set.  
 
Investigators and CHC staff will not be blinded to study arm as this is not practical in this type of trial. 
Because of the electronic referral from PPs in the intervention arm, the clinics receiving and recording 
notifications will be aware of which study arm they are in. Staff conducting diagnostic investigations 
(laboratory personnel and radiologists) will not be part of the study team and will be blinded to study arm. 
Notification data will be abstracted from routine records so they will not be influenced by study staff.  
 
Diagnosis of TB cases: It is expected that the notifications from referrals by PPs will be a mixture of TB 
cases diagnosed by sputum test, x-ray, and clinical presentation only. This will be captured through the 
app. We will record the basis of diagnosis for each notified case,  classifying each as ‘definite’, ‘probable’, 

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‘possible’ or ‘not TB’, using a standard operating procedure (SOP). This will enable a secondary analysis, 
showing the proportion of referrals by PPs that probably don’t have TB and whether the mix of notified 
TB cases changes with respect to the basis of their diagnosis.  
 
6.4 
STUDY INTERVENTION COMPLIANCE 
 
Once the PPs have received the intervention, real-time monitoring of referral practice of patients for 
diagnosis and notification will be undertaken through the web-link to the app. At the 1-month visit, 
adherence to the intervention will be assessed according to pre-determined indicators, and a standard 
form filled with the results. At the end of the visit, any issues will be rectified through re-education. The 
intervention period will then be complete, while electronic refreshers will continue. 
 
7 
STUDY INTERVENTION DISCONTINUATION AND PARTICIPANT 
DISCONTINUATION/WITHDRAWAL 
 
7.1 
PARTICIPANT DISCONTINUATION/WITHDRAWAL FROM THE STUDY 
 
Participating PPs are free to withdraw from the intervention at any time upon request.  
An investigator may discontinue or withdraw a PP from the intervention for the following reasons: 
 
 
PP unable to receive the study intervention within 1 month. 
 
If the PP meets an exclusion criterion (either newly developed or not previously recognized) that 
precludes further study participation 
The reason for PP discontinuation or withdrawal from the study will be recorded on a specific form.  
7.2 
LOST TO FOLLOW-UP 
 
No PPs will be lost to follow-up, but will be considered lost to intervention if he or she is not able to be 
found on the scheduled visit, no activity related to the app is occurring, and is unable to be contacted by 
the study site staff. The following actions will be taken under such a circumstance: 
 
The study staff will attempt to contact the PP, schedule a visit and counsel the PP on the 
importance of activity in the study and ascertain if the PP wishes to and/or should continue in the 
study. 
 
Before a PP is deemed lost to intervention, the investigator or designee will make every effort to 
regain contact with the PP (where possible, 3 telephone calls and, if necessary, a certified letter 
to the PP’s last known mailing address or local equivalent methods). These contact attempts will 
be documented in the PP’s record or study file.  
 
Should the PP continue to be unreachable, he or she will be considered to have withdrawn from 
the study with a primary reason of “lost to intervention”. 
 
 

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8 
STUDY ASSESSMENTS AND PROCEDURES 
 
8.1 
EFFICACY ASSESSMENTS  
To support the determination of efficacy, as per the primary objectives, data abstraction from routine 
notification data will be done by trained researchers. The 12-month period before intervention 
commences will be defined clearly and data abstraction will take place as soon as possible at the end of 
this period. The 12-month follow up period will be defined clearly. The start date will be immediately after 
the last PP to receive the intervention has had their 1-month follow up visit. Data abstraction will be done 
as soon as possible after this 12-month period is completed.  
 
8.2 
SAFETY AND OTHER ASSESSMENTS 
 
8.2.1 SAFETY 
 
The following procedures and evaluations will be done as part of the study to monitor safety.  
 
 
Interviews:  all interviews of PPs will be conducted in private and in confidence, under a standard 
operating procedure (SOP).  
 
8.2.2 PRIVATE PRACTITIONERS 
 
The following information will be collected, onto a form, from PPs in the intervention arm who undergo 
intervention: name, gender, age, and self-reported number of TB cases diagnosed in the last 3 months. 
This will enable comparison of basic characteristics between those who participate in the intervention 
and those who don’t.  
 
8.2.3 TB PATIENTS 
 
The following data will be abstracted from routine records of TB cases at the CHCs: Referring 
facility/practitioner, date, gender, patient identification, patient address (to the level of CHC area),  sputum 
status, basis of TB diagnosis.  
 
PPs who refer patients for confirmation of diagnosis and notification will enter the following data about 
the patient into the app: name, gender, age, basis of presumptive/definitive diagnosis, other practice 
addresses.  
 
Inputted information from PPs will be sent to a secure centralised server and will be able to be monitored 
through log-in by the authorized individuals in a web-based application that is compatible with both 
android and apple operating systems. 
 
 
 
 
 

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8.3 
ADVERSE EVENTS AND SERIOUS ADVERSE EVENTS 
 
It is not expected that this public health intervention will be associated directly with any adverse events 
or serious adverse events in TB patients.  
 
Staff involved in administering the intervention to PPs are at risk of accidents related to travel to and from 
the place of work of PPs.  
 
Patients diagnosed with TB by PPs are at risk of over-treatment from mis-diagnosis. However, this should 
be reduced, rather than increased as in this study they are referred for confirmation of diagnosis and 
subsequent notification by the National TB program.  
 
8.3.1 EVENTS OF SPECIAL INTEREST  
 
Events that merit reporting to the study leadership include failures such as malfunction of the app and 
loss of network connection for periods of time. These will be reported using a specific form.  
 
8.4 
UNANTICIPATED PROBLEMS 
 
8.4.1 DEFINITION OF UNANTICIPATED PROBLEMS (UP) 
 
The Office for Human Research Protections (OHRP) considers unanticipated problems involving risks to 
participants or others to include, in general, any incident, experience, or outcome that meets all of the 
following criteria: 
 
• 
Unexpected in terms of nature, severity, or frequency given (a) the research procedures that are 
described in the protocol-related documents, such as the Institutional Review Board (IRB)-
approved research protocol and informed consent document; and (b) the characteristics of the 
participant population being studied; 
• 
Related or possibly related to participation in the research (“possibly related” means there is a 
reasonable possibility that the incident, experience, or outcome may have been caused by the 
procedures involved in the research); and 
• 
Suggests that the research places participants or others at a greater risk of harm (including 
physical, psychological, economic, or social harm) than was previously known or recognized. 
 
8.4.2  UNANTICIPATED PROBLEM REPORTING  
 
The investigator will report unanticipated problems (UPs) to the reviewing Institutional Review Board 
(IRB) and to the Data Coordinating Center (DCC)/lead principal investigator (PI). The UP report will include 
the following information: 
 
• 
Protocol identifying information: protocol title and number, PI’s name, and the IRB project 
number; 
• 
A detailed description of the event, incident, experience, or outcome;  

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• 
An explanation of the basis for determining that the event, incident, experience, or outcome 
represents an UP;  
• 
A description of any changes to the protocol or other corrective actions that have been taken or 
are proposed in response to the UP. 
 
To satisfy the requirement for prompt reporting, UPs will be reported using the following timeline:   
 
• 
UPs will be reported to the IRB and to the DCC/study sponsor within 1 month of the investigator 
becoming aware of the problem.  
 
9 
STATISTICAL CONSIDERATIONS  
 
9.1 
STATISTICAL HYPOTHESES 
 
Primary outcome: A tailored intervention package for private practitioners increases notifications of 
tuberculosis (TB) in Bandung, Indonesia.  
9.2 
SAMPLE SIZE DETERMINATION – KEY CONSIDERATIONS 
 
Less than 10% of PPs work privately in more than one CHC area. Those who also practice within the public 
system should not affect notifications from that public system, as it has a high notification rate (>95%) 
already.  
 
While the majority of notified TB patients are diagnosed and treated in their own CHC area, a number 
are diagnosed outside of their ‘home’ CHC area (up to 35%; INSTEP study). Those from a different CHC 
area will have an approximately 1 in 5 chance of being from another intervention area, 1 in 5 chance of 
being from a control area, and 3 in 5 chance of being from a non-study CHC area (n=43 non-study CHC 
areas within Bandung). Therefore ‘contamination’ of the intervention into control areas is estimated to 
be <10% (35% x 1/5 = 7%).   
 
We will have data on the number of individuals from CHC areas outside the intervention areas who are 
notified by PPs in the intervention arm. Any change in notifications in the control arm will also provide 
insight into contamination. The primary analysis will compare the change in total number of notifications 
of patients between intervention and control areas.  
 
Assuming (1) PPs in each arm diagnose at least 500 TB patients in 12 months (INSTEP data); (2) 65% of 
PP TB diagnoses are patients from their CHC area and 35% are from outside their area; and (3) a 15% 
baseline notification rate changing to 50% post-intervention in the intervention arm: PP notifications in 
the control arm areas will change from 75 to 87 notified cases while the change will be from 75 to 201 
cases in the intervention arm. Total notifications (adding 475/arm from non-PP) will change from 550 to 
562 and 550 to 676 respectively.  

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Taking the above into account, we will have approximately 90% power to detect a rate ratio of 1.2 
(676/562) at the p=0.025 level (one sided).   
 
9.3 
STATISTICAL ANALYSES 
 
9.3.1 GENERAL APPROACH 
 
The primary analysis will be intention-to-treat, where all patients notified by intervention and control PPs 
to a CHC will be included. Analysis will be carried out at the cluster level, taking into account correlations 
within a cluster. 95% confidence intervals will be calculated and a significance level of 0.025 (one-sided) 
will be used. 
 
9.3.2 BASELINE DESCRIPTIVE STATISTICS 
 
Study arms will be compared on baseline characteristics, including demographics of the PPs and the 
diagnosed TB cases, using descriptive statistics. No inferential statistics will be used. 
 
9.3.3 ANALYSIS OF THE PRIMARY EFFICACY ENDPOINT(S) 
 
For the primary trial analysis we will estimate the rate ratio comparing TB notifications in the intervention 
and control groups. A generalised mixed model will be used with repeated measures of TB notification 
(pre- and post- intervention) and treatment* time interaction, a log link, Poisson errors and a random 
effect for PKM to account for over-dispersion. 
 
 
9.3.4 ANALYSIS OF THE SCONDARY EFFICACY ENDPOINT(S) 
 
1. The proportions of true TB cases among the reported TB cases will be compared in intervention 
and control arms using a generalised estimation equation. The model will be fit to repeated 
measures of the proportions of true positive TB notifications for each CHC (pre- and post- 
intervention) with a treatment by time interaction, a log link, and Poisson errors, with robust 
standard errors to allow for both the binary data and over-dispersion. 
 
2. The primary trial analysis will be repeated excluding patients who were notified by a PP from a 
different CHC to their area of residence.  
 
9.3.5 PLANNED SAFETY ANALYSES  
 
There are no planned safety analyses 
 
9.3.6 PLANNED INTERIM ANALYSES  
 
There is no plan to conduct an interim analysis. 
 

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10 SUPPORTING DOCUMENTATION AND OPERATIONAL CONSIDERATIONS 
 
10.1 REGULATORY, ETHICAL, AND STUDY OVERSIGHT CONSIDERATIONS 
 
10.1.1 INFORMED CONSENT PROCESS 
 
10.1.1.1 CONSENT/ASSENT AND OTHER INFORMATIONAL DOCUMENTS PROVIDED TO 
PARTICIPANTS 
 
Consent forms describing the study are given to the head of each CHC institution. For PPs undergoing 
intervention, consent forms describing in detail the study intervention, study procedures, and risks are 
given to the PP and written documentation of informed consent is required prior to starting 
intervention/administering study intervention.  The consent forms are provided as an attachment. 
 
10.1.1.2 CONSENT PROCEDURES AND DOCUMENTATION 
 
Consent forms will be Institutional Review Board (IRB)-approved and the PP will be asked to read and 
review the document. The investigator will explain the research study to the participant PP and answer 
any questions that may arise. A verbal explanation will be provided in terms suited to the PP’s 
comprehension of the purposes, procedures, and potential risks of the study and of their rights as research 
PPs.  PPs will have the opportunity to carefully review the written consent form and ask questions prior 
to signing. The PPs will have the opportunity to discuss the study with their family or surrogates or think 
about it prior to agreeing to participate. The PP will sign the informed consent document prior to any 
intervention. PPs will be informed that participation is voluntary and that they may withdraw from the 
study at any time, without prejudice. A copy of the informed consent document will be given to the PPs 
for their records. The informed consent process will be conducted and documented in the source 
document (including the date), and the form signed, before any intervention. The rights and welfare of 
the PPs will be protected by emphasizing to them that there will be no negative repercussions if they 
decline to participate in this study, including no reporting of discontinuation to government authorities. 
 
10.1.2 STUDY DISCONTINUATION AND CLOSURE 
 
This study may be temporarily suspended or prematurely terminated if there is sufficient reasonable 
cause.  Written notification, documenting the reason for study suspension or termination, will be provided 
by the suspending or terminating party to participating CHC, PPs, investigator, funding agency, and 
regulatory authorities.  If the study is prematurely terminated or suspended, the Principal Investigator (PI) 
will promptly inform participating CHCs, PPs, the Institutional Review Board (IRB), and sponsor and will 
provide the reason(s) for the termination or suspension.  Participating PPs will be contacted, as applicable, 
and be informed of changes to study visit schedule. 
  
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Demonstration of efficacy that would warrant stopping    
 
Insufficient compliance to protocol requirements 
 
Data that are not sufficiently complete and/or evaluable 
 
Determination that the primary endpoint has been met 
 
Determination of futility 
 
 The study may resume once any concerns are addressed, and satisfy the sponsor, and IRB. 
 
10.1.3 CONFIDENTIALITY AND PRIVACY  
 
Participating PPs confidentiality and privacy is extended to cover any information relating to them. 
Therefore, the study protocol, documentation, data, and all other information generated will be held in 
strict confidence. No information concerning the study or the data will be released to any unauthorized 
third party without prior written approval of the sponsor.  
 
All research activities will be conducted in as private a setting as possible. 
 
The study monitor, other authorized representatives of the sponsor, representatives of the Institutional 
Review Board (IRB), may inspect all documents and records required to be maintained by the investigator. 
PPs’ contact information will be securely stored for internal use during the study. At the end of the study, 
all records will continue to be kept in a secure location for as long a period as dictated by the reviewing 
IRB, Institutional policies, or sponsor requirements. 
 
PP research data, which is for purposes of statistical analysis and scientific reporting, will be stored. This 
will not include the PP’s contact or identifying information. Rather, individual PPs and their research data 
will be identified by a unique study identification number. The study data entry and study management 
systems will be secured and password protected. At the end of the study, all study databases will be de-
identified and archived. 
 
10.1.4 FUTURE USE OF STORED SPECIMENS AND DATA  
 
Data collected for this study will be analyzed and stored. After the study is completed, the de-identified, 
archived data will be transmitted to and stored, for use by other researchers including those outside of 
the study. Permission to transmit data will be included in the informed consent.  
 
10.1.5 KEY ROLES AND STUDY GOVERNANCE 
 
Principal Investigator 
Philip Hill, MBChB MPH, MD, FRACP, 
FNZCPHM, Professor 
University of Otago, New Zealand  

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Address 
University of Otago  
 
 
Medical School,  
 
 
PO Box  56, Dunedin 9054, 
 
 
New Zealand 
Phone Number  +64 21 279 7214 
Email   
philip.hill@otago.ac.nz 
 
Other Investigators 
Institution 
Role 
Dr Sue McAllister 
University of Otago 
Epidemiologist, trial 
documentation and site visit 
monitoring 
Assoc Prof Katrina Sharples 
University of Otago 
Trial Statistician 
Prof Reinout van Crevel 
Radboud University 
Physician 
 
 
 
Dr Bachti Alisjahbana 
University of Padjadjaran 
Site- PI, Indonesia 
Dr Lidya Chaidir 
University of Padjadjaran 
Molecular Biologist, lead for 
microbiology and key co-
investigator for pathogen 
genomics 
Dr Bony Lestari 
University of Padjadjaran 
Clinical epidemiologist 
Dr Panji Hadisoemarto 
University of Padjadjaran 
Clinical epidemiologist, trial 
‘manager’ responsible for the 
running of the project overall in 
Indonesia. 
TBA 
University of Padjadjaran 
Data manager 
 
 
 
Prof Megan Murray 
Harvard University 
Epidemiologist, member of 
overall project steering group 
and lead for Social networking 
and genomic epidemiology 
study 
Chuan-Chin Huang 
Harvard University 
Bio-informatics specialist 
The project will have an Executive committee comprising the PI, and one representative from each 
major partner – Dr Alisjahbana and Prof Megan Murray. The group will meet electronically every three 
months to discuss strategic aspects of the project and may invite specific co-investigators to join certain 
meetings.  
The trial will have a Data Monitoring Committee (DMC) comprising the PI, lead statistician (Co-I 
Sharples) and …. The DMC will operate under a charter and will review data on study conduct.  
The project will have a Project Management Group (PMG) comprising Co-I Hadisoemarto, the data 
manager, Co-I Chaidir, and…..The PMG will operate under a charter.  

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10.1.6 SAFETY OVERSIGHT 
 
Safety oversight by a Data and Safety Monitoring Board (DSMB) will not be required for this public health 
intervention trial.  However, an internal Data Monitoring Committee (DMC) will be established to oversee 
the study, focused on data quality.  
 
10.1.7 QUALITY ASSURANCE AND QUALITY CONTROL 
 
A quality management plan will be developed to describe a site’s quality management. Quality control 
(QC) procedures will be implemented beginning with the data entry system and data QC checks that will 
be run on the database will be automatically generated on a weekly basis and any  quality issues identified 
will be reviewed by the DMC and a plan put in place for resolution. 
 
Following written Standard Operating Procedures (SOPs), visiting investigators (Dr Sue McAllister or 
substitute) will verify that the trial is conducted and data are generated, documented (recorded), and 
reported in compliance with the protocol.  
 
The investigational site will provide direct access to all source data/documents, and reports for the 
purpose of the verification visits. 
 
10.1.8 DATA HANDLING AND RECORD KEEPING  
 
10.1.8.1 DATA COLLECTION AND MANAGEMENT RESPONSIBILITIES  
 
Data collection is the responsibility of the trial staff at the site under the supervision of the site 
investigator. The investigator is responsible for ensuring the accuracy, completeness, legibility, and 
timeliness of the data reported. 
 
All source documents will be completed in a neat, legible manner to ensure accurate interpretation of 
data.   
 
Hardcopies of the study visit worksheets will be provided for use as source document worksheets for 
recording data for each PP enrolled in the study.  Data recorded in the electronic case report form (eCRF) 
derived from source documents will be consistent with the data recorded on the source documents.  
 
Clinical data, and clinical laboratory data, will be entered into REDCAP(12) electronic database. The data 
system includes password protection and will be checked automatically for data that appear inconsistent, 
incomplete, or inaccurate. Clinical data will be entered directly from the source documents. 
 
10.1.8.2 STUDY RECORDS RETENTION  
 
Study documents will be retained for a minimum of 10 years after completion of the trial. These 
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will be destroyed without the written consent of the sponsor, if applicable. It is the responsibility of the 
sponsor to inform the investigator when these documents no longer need to be retained. 
 
10.1.9 PROTOCOL DEVIATIONS  
 
A protocol deviation is any noncompliance with the clinical trial protocol. The noncompliance may be 
either on the part of the PPs, the investigator, or the study site staff. As a result of deviations, corrective 
actions are to be developed by the site and implemented promptly.  
 
It is the responsibility of the site investigator to use continuous vigilance to identify and report deviations 
within 5 working days of identification of the protocol deviation, or within 5 working days of the scheduled 
protocol-required activity.  All deviations must be addressed in study source documents, and reported 
according to the reviewing IRB requirements.  
 
10.1.10 
PUBLICATION AND DATA SHARING POLICY 
 
This study is not subject to any particular publication and data sharing policies and regulations. 
 
10.1.11 
CONFLICT OF INTEREST POLICY 
 
Any actual conflict of interest of persons who have a role in the design, conduct, analysis, publication, or 
any aspect of this trial will be disclosed and managed. Furthermore, persons who have a perceived conflict 
of interest will be required to have such conflicts managed in a way that is appropriate to their 
participation in the design and conduct of this trial.  The study leadership has established policies and 
procedures for all study group members to disclose all conflicts of interest and will establish a mechanism 
for the management of all reported dualities of interest. 
 
11 SUB-STUDY 
 
11.1 OBJECTIVES AND ENDPOINTS 
 
Objectives  
Endpoints 
On notified TB cases, to use social 
network analyses, whole genome 
sequencing and phenotypic drug 
susceptibility testing to inform 
clinical algorithms for drug 
resistant-TB and the design of a 
transmission study. 
 
 
Concordance between phenotypic 
and genotypic DST results.  
 
Single nucleotide polymorphism 
(SNP) differences between M. 
tuberculosis strains. 
 
Concordance between SNP 
differences and social/spatial 
network analyses 
 
 

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11.2 BACKGROUND/RATIONALE 
 
We will use whole genome sequencing (WGS) of M. tuberculosis isolates from notified TB cases to identify 
drug resistant mutations (to inform clinical algorithms with respect to drug resistance), and to combine 
with social network analyses to provide preliminary data for designing a larger study of M. tuberculosis 
transmission. WGS has great potential as a tool in the fight against TB drug-resistance, especially in 
combination with routine surveillance.(13) WGS directly from the first positive culture of TB cases could 
be used to complement and ultimately replace phenotypic drug susceptibility testing (DST). It could detect 
resistance to most if not all antibiotics within 24 hours, as demonstrated already.(14) We are conducting 
a series of studies to explore the introduction of WGS in this way into practice in Indonesia. As part of this, 
contextual studies that document circulating resistance mutations in the local population are of great 
benefit. WGS could provide the ultimate molecular resolution for epidemiological typing at the population 
level, which has previously been an unrealistic aspiration in many lower and middle- income countries. 
WGS technology is likely to bypass more traditional impractical and less precise typing methods.(15, 16) 
Emerging strains (17) can be identified and changes in strain diversity can be monitored, reflecting relative 
prominence of recent or past transmission. A high sampling fraction (the proportion of all TB cases in a 
population that have an isolate typed), more possible when cases from both private and public health 
facilities are captured, reduces the misclassification of clusters and of recent versus remote 
transmission.(18) The combination of high precision genotyping, expanded social network questionnaires 
and network analyses provides opportunity to explore M. tuberculosis transmission.(16, 19, 20) 
 
11.3 OVERALL DESIGN 
In real-time, we will culture M. tuberculosis isolates from 150 consecutively notified TB cases in 
purposively (contiguous) selected CHCs in the intervention arm, which is expected to have the highest 
sampling fraction because of a successful public health intervention. They will have whole genome and 
phenotypic drug susceptibility testing, enabling comparison between the two tests, to inform clinical 
algorithms for suspected drug resistant TB. Notified cases will be interviewed and undergo a social 
network questionnaire. Relatedness according to sequencing data will be linked to social network and 
spatial analyses to explore possible transmission events and inform design of a large M. tuberculosis 
transmission study. 
Identification of drug resistance, phenotypically and/or genotypically, will be reported to the patient’s 
attending doctor, regardless of the time since the sputum specimen was taken.  
 
11.4 INCLUSION AND EXCLUSION CRITERIA 
 
Inclusion criteria: Diagnosed as a case of pulmonary TB in one of the purposively selected CHC 
intervention areas within the designated follow-up period. Lived the majority of the time in the selected 
CHC area during the study period.  

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Exclusion criteria: TB cases unable to produce sputum for culture; sputum smear negative; <14 years of 
age 
11.5 CONSENT, ASSESSSMENTS AND PROCEDURES 
 
Each notified TB case, at each CHC selected for the sub-study will be asked by the CHC staff if they are 
willing to be part of a research study and consent for their name and contact details to be passed on to 
the researchers. If they consent to this, they will be contacted by research staff, fully informed about the 
study, invited to participate and provide written informed consent. Consent forms for the sub-study TB 
patients are attached to this protocol. Consent forms will be Institutional Review Board (IRB)-approved 
and the participant will be asked to read and review the document. The investigator will explain the 
research study to the participant and answer any questions that may arise. A verbal explanation will be 
provided in terms suited to the participant’s comprehension of the purposes, procedures, and potential 
risks of the study and of their rights as research participants.  Participants will have the opportunity to 
carefully review the written consent form and ask questions prior to signing. The participants should have 
the opportunity to discuss the study with their family or surrogates or think about it prior to agreeing to 
participate. The participant will sign the informed consent document prior to any data gathering or 
investigations. Participants will be informed that participation is voluntary and that they may withdraw 
from the study at any time, without prejudice. A copy of the informed consent document will be given to 
the participants for their records. The informed consent process will be conducted and documented in 
the source document (including the date), and the form signed, before any intervention. The rights and 
welfare of the participants will be protected by emphasizing to them that there will be no negative 
repercussions if they decline to participate in this study, including no reporting of discontinuation to 
government authorities. 
 
The following data will be collected, onto a form, from newly diagnosed pulmonary TB cases enrolled in 
the sub-study: name, gender, age, street address and geo-coordinates, symptoms, diagnostic examination 
results, TB type, treatment, and follow-up care. A specific social network questionnaire will collect the 
following information: socio-economic information; tobacco, alcohol, and drug use; whether the patient 
knows other people diagnosed with TB  within the previous year  and if so, when that contact took place; 
place of residence; and areas to which patient travelled within the past year, places where the patient has 
spent time at work or socially within the past year, who the patient has spent time with over the past year 
and the duration of that contact.   
M. tuberculosis culture will be done from sputum using Microscopic Observation Drug Susceptibility 
(MODS) Assay which is a rapid culture-based for primary culture in pararallel with RIF- and INH-resistance. 
Phenotypic DST using MGIT960 to seven TB drugs (RIF, INH, STR, EMB, OFL, KAN, CAP) will be done to all 
isolates. Additionally, MIC of 12 TB drugs will be measured for respective isolates, with respect to: RIF, INH, 
OFL, MXF, AMI, STR, RFB, PAS, ETH, CYC, KAN, EMB)  
DNA from positive culture will then be extracted using a commercial kit and sent for Whole Genome 
Sequencing  on an Illumina HiSeq2000 instrument (Illumina.Inc, SanDiego, CA) using 2x100 bp paired-end 
reads. After sequencing, the raw FASTQ sequence reads will be filtered, including removal of adapter 

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sequences, contamination, and low-quality reads that had more than 10% N base calls or had a quality 
score 4 in more than 40% of the bases. Raw FASTQ sequencing files will be uploaded for analysis.  
 
With the participant’s approval and as approved by local Institutional Review Boards (IRBs), de-identified 
M. tuberculosis isolates from the sub-study will be stored with the same goal as the sharing of data. These 
samples could be used to understand phylogeny and drug resistance at local and international levels. A 
code-link will allow linking the biological specimens with data from each participant, maintaining the 
blinding of the identity of the participant. 
 
During the conduct of the study, an individual participant can choose to withdraw consent to have 
biological specimens stored for future research. However, withdrawal of consent with regard to 
biosample storage may not be possible after the study is completed.  
 
Participants will be informed about any results if, in the opinion of the principle investigator, they are 
considered to be relevant to them. With respect to evidence of drug resistance, the attending doctor for 
such patients will be expected to make a judgement call about the relevance of the finding to the patient’s 
care at the time the result is received, and to act accordingly. 
 
Patient confidentiality is extended beyond their basic clinical and demographic data to cover testing of 
biological samples and genetic tests. Therefore, the study protocol, documentation, data, and all other 
information generated will be held in strict confidence. No information concerning the study or the data 
will be released to any unauthorized third party without prior written approval of the sponsor.  
 
 
11.6 SAFETY 
 
The following procedures and evaluations will be done as part of the study to monitor safety.  
 
Interviews:  all interviews of TB patients will be conducted in private and in confidence, under an 
SOP, and will include Personal Protection Equipment (PPE) for interviewer and interviewee.  
 
Sputum sampling and culture: Sputum must be taken in a sputum collection room (if available) 
or outside of the building. The study nurse must coach study participant on how to cough 
sputum. Sputum processing and culture will be done in the TB research laboratory equipped 
with Biosafety Cabinet Level 2A for sputum processing and culturing. 
 
DNA extraction will be done in an accredited laboratory, following standard safety precautions 
under an SOP. In our previous study, we re-inoculated 75 DNA samples after extraction on 
Middlrbrook 7H10 (media selective for M. tuberculosis) and we did not see any growth of the 
mycobacterium after 60 days of incubation. 
 
11.7 ANALYSIS 
 
The sub-study is a pilot study to inform the design of a large transmission study. Therefore, the sample 
size has been calculated based on practical considerations such as the minimum size the researchers 

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believe is required to provide input data to that design and what can be achieved with the available 
budget. 
 
We will use whole genome sequencing to: assess the sensitivity and specificity of Whole genome 
sequencing as a predictor of drug resistance phenotypes as determined by routine drug susceptibility 
testing; and to will evaluate social and spatial connectivity as a function of genomic differences.  
 
Comparison of genotypic and phenotypic resistance 
Genotypic predictions of resistance will be based on mutations in, or upstream of, genes associated with 
resistance to isoniazid (ahpC, inhA, fabG1, katG), rifampicin (rpoB), ethambutol (embA, embB, embC), and 
pyrazinamide (pncA).  Isolates containing resistance-mutations will be classified as genotypically resistant 
whereas those containing only wild-type sequence, or mutations considered consistent with 
susceptibility, will be considered susceptible. Using phenotypic results as a gold-standard, we will estimate 
sensitivity, specificity, negative and positive predictive value for the correct assignment of susceptibility 
or resistance. The χ2 test will be used to statistically test the association between M. tuberculosis lineage 
and drug susceptibility. Cohen’s k will be used to determine the level of agreement between WGS and 
phenotypic DST for first-line drugs. In addition, enrichment values will be calculated for drug resistance 
per lineage based on the ratio of lineage-specific observed and expected occurrence of drug resistance. 
The ratios will be visualised in a heat map as a measure of association between M. tuberculosis lineage 
and drug susceptibility. 
 
Genomic and social network analyses 
Genomic data can also be used to infer spatial and social distances within a transmission network. Here, 
we will determine pairwise distances between each of the 150 TB patients in the sub-study, after removing 
snps in highly repetitive genes such as the PE/PPE genes and in loci under strong selection (drug resistance 
mutations).  Using snp distances as the gold standard for “epidemic proximity,” we will determine whether 
snp distances are a function of spatial distance, age assortativeness, and other shared social activities 
(attendance at a specific school or religious institution, shared work-place). These data will help inform 
the future design of a transmission study based on whole genome sequencing. 
  
For all possible pairs of samples, we will estimate measures of geographic distance using the Open Source 
Routing Machine, which is a publicly available tool that analyzes OpenStreetMap road network data, to 
obtain the shortest motor vehicle travel time between points in minutes. We will also calculate great-
circle distances between points using the geosphere package in R, which takes into account the Earth’s 
ellipsoid shape. 
 
In previous work, we have determined that close genetic relatedness is best represented by a difference 
of <=1 snp. We will therefore estimate odds ratios comparing the odds of having <=1 snp pairwise distance 
for a range of spatial and social distances (age differences, socioeconomic distances, attends same 
school/religious institution/workplace, and travel time to the odds of close genetic relatedness for some 
specified reference value for each measure. For example, for spatial distance, we will compare the odds 
of any pair having <= snp difference for a range of travel time distances compared to the odds of a 30 
minute or more travel time distance.  For these measures of association, we will obtain 95% Wald 
confidence intervals from jackknife standard errors. Jackknifing will be performed by sequentially 
excluding each study participant from the analysis. 
 
 
 
 

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12 ABBREVIATIONS 
 
AE 
Adverse Event 
COC 
Certificate of Confidentiality 
CRF 
Case Report Form 
DCC 
Data Coordinating Center 
DSMB 
Data Safety Monitoring Board 
EC 
Ethics Committee 
eCRF 
Electronic Case Report Forms 
GCP 
Good Clinical Practice 
WGS 
Whole Genome Sequencing 
IB 
Investigator’s Brochure 
ICH 
International Conference on Harmonisation  
IRB 
Institutional Review Board 
ISM 
Independent Safety Monitor 
ISO 
International Organization for Standardization 
MOP 
Manual of Procedures 
PI 
Principal Investigator 
CHC 
Community Health Centre 
PP 
Private practitioner 
QA 
Quality Assurance 
QC 
Quality Control 
SAE 
Serious Adverse Event 
SAP 
Statistical Analysis Plan 
SMC 
Safety Monitoring Committee 
SOA 
Schedule of Activities 
SOP 
Standard Operating Procedure 
UP 
Unanticipated Problem 
 
 
 

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13 PROTOCOL AMENDMENT HISTORY 
The table below is intended to capture changes of IRB-approved versions of the protocol, including a 
description of the change and rationale. A Summary of Changes table for the current amendment is 
located in the Protocol Title Page.  
 
Version 
Date 
Description of Change  
Brief Rationale 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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14 REFERENCES  
 
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