Expanding Xpert Ultra Testing for TB Diagnosis Among HIV-positive Patients Admitted to Hospital in Africa
Phase: NA
Conditions: Tuberculosis, HIV Coinfection, Diagnoses Disease
Sponsor: Foundation for Innovative New Diagnostics, Switzerland

 
Protocol short title: EXULTANT 
 
 
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Protocol number: TB043 -3/1 -MOZ 
Protocol Version: 4.0 
 
  
 
 
Clinical Trial Protocol 
 
 
Protocol Title: Expanding Xpert Ultra testing for TB diagnosis among 
HIV-positive patients admitted to hospital in Tanzania 
and Mozambique. 
Short Title: EXULTANT 
Protocol number: TB043-3/1-MOZ 
Registration number: NCT04568967 (ClinicalTrials.gov) 
Trial Sponsor: Foundation for Innovative Diagnostics (FIND) 
Trial Coordinator: Barcelona Institute for Global Health (ISGlobal) 
 
 
 
 
 
Protocol Version: 5.0 
Date: 13 September 2023 
 
 
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Protocol number: TB043 -3/1 -MOZ 
Protocol Version: 4.0 
 
 
 
Confidentiality Statement: 
 
 
The information contained in this document, especially unpublished data, is the 
property of FIND (or under its control) and may not be reproduced, published or 
disclosed to others without prior written authorization from FIND. 
 
 
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Table of contents 
1. Clinical Trial Partners ...................................................................................................................................... 5 
2. Signatures page .............................................................................................................................................. 7 
SPONSOR: .............................................................................................................................................................................................. 7 
CLINICAL TRIAL COORDINATOR .................................................................................................................................................. 7 
OTHER CLINICAL TRIAL PARTNERS ............................................................................................................................................. 8 
Statement of Principal Investigator..................................................................................................................... 9 
3. Protocol History/Amendment Summary* ..................................................................................................... 11 
3. List of Abbreviations and Acronyms .............................................................................................................. 12 
4. Protocol Synopsis .......................................................................................................................................... 13 
5. Introduction ................................................................................................................................................... 18 
5.1 Background and statement of the problem ...................................................................................... 18 
5.2 Promising specimens for TB diagnosis using Xpert Ultra .................................................................. 19 
5.3 Other promising tests and specimens ............................................................................................... 20 
6. Aim and hypothesis ....................................................................................................................................... 22 
6.1 Benefit/Risk Assessment ................................................................................................................... 22 
7.  Objectives ..................................................................................................................................................... 23 
8. Endpoints ....................................................................................................................................................... 24 
8.1 Primary Endpoint(s) ........................................................................................................................... 24 
8.2 Secondary endpoints ......................................................................................................................... 24 
8.3 Exploratory endpoints ....................................................................................................................... 26 
9. Trial Design and study arms........................................................................................................................... 27 
9.1 Study population and trial setting ..................................................................................................... 27 
9.2 Participant eligibility criteria .............................................................................................................. 30 
9.3 Sample size ........................................................................................................................................ 31 
10. Study procedures......................................................................................................................................... 31 
10.1 Pre-eligibility screening ..................................................................................................................... 31 
10.2 Informed consent .............................................................................................................................. 32 
10.3 Assessment for eligibility ................................................................................................................... 32 
10.4 Recruitment ....................................................................................................................................... 32 
10.5 Randomization .................................................................................................................................. 33 
10.6 Blinding .............................................................................................................................................. 33 
10.7 Minimisation of Error and Bias .......................................................................................................... 33 
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10.8 Allocation to study arm ..................................................................................................................... 34 
10.9 Arm-specific procedures (See table 2)............................................................................................... 34 
10.10 Follow up procedures (table 2) ........................................................................................................ 36 
10.11 Participant study completion (week 8) ........................................................................................... 37 
10.12 Retention ......................................................................................................................................... 37 
10.13 Participant termination and withdrawal criteria ............................................................................. 37 
10.14 Trial discontinuation ........................................................................................................................ 37 
10.15 End of trial ....................................................................................................................................... 37 
10.16 Safety Assessments ......................................................................................................................... 37 
10.17 Safety and Incident Reporting ......................................................................................................... 38 
10.18 Retrospective data collection .......................................................................................................... 40 
11. Schedule of visits (table 2) ........................................................................................................................... 41 
12. Laboratory procedures and storage of samples .......................................................................................... 42 
12.5 Sample Storage details: ....................................................................................................................................................... 44 
13. Statistical considerations and data analysis ................................................................................................ 45 
13.1 Sample Size calculations .................................................................................................................... 45 
13.2 Data analysis ...................................................................................................................................... 46 
14. Data management ....................................................................................................................................... 49 
14.1 Type of data that will be collected .................................................................................................... 49 
14.2 CRFs ................................................................................................................................................... 49 
14.3 Data entry .......................................................................................................................................... 50 
14.4 Data monitoring and quality assurance ............................................................................................. 50 
14.5 Record retention ............................................................................................................................... 51 
15. Ethical considerations .................................................................................................................................. 52 
15.1 Confidentiality ................................................................................................................................... 52 
16. Timeline ....................................................................................................................................................... 53 
18. 
Appendices ............................................................................................................................................ 57 
Appendix 1: Incident Definition and Reporting .................................................................................................................. 57 
Appendix 2: FujiLAM testing ....................................................................................................................................................... 59 
 
 
 
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1. Clinical Trial Partners 
SPONSOR REPRESENTATIVE: 
Foundation for Innovative Diagnostics (FIND) 
Dr Vinzeigh Nicholas Leukes  
Email: Adam.Penn-Nicholson@finddx.org 
Address: Chemin des Mines 9, Campus Biotech, 1202 Geneva, Switzerland 
 
CLINICAL TRIAL COORDINATOR: 
Barcelona Institute for Global Health (ISGlobal) 
Dr Alberto L. García-Basteiro 
Email: alberto.garcia-basteiro@isglobal.org 
Address: Rosselló 132 4/2 08036 Barcelona, Spain 
 
CLINICAL TRIAL SITES: 
 
Mozambique 
Instituto Nacional de Saude (INS) 
Address: Vila De Marracuene. Estrada Nacional 1, Parcela 3934, Provincia 
de Maputo,  Mozambique 
Centro de Investigação em Saúde de Manhiça (CISM) 
Address: Rua 12, Bairro Cambeve, Vila da Manhiça, Provincia de Maputo, Mozambique 
 
Tanzania 
National Institute for Medical Research (NIMR) – Mbeya Medical Research Centre (MMRC) 
Address: P.O. Box 2410 Mbeya, Tanzania 
Ifakara Health Institute Trust (IHI) 
Address: Plot 463, Kiko Avenue, Mikocheni, Dar es Salaam, Tanzania, 
 
 
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OTHER CLINICAL TRIAL PARTNERS 
Ospedale San Raffaele SRL (OSR) 
Address: Via Olgettina 60, 20132 Milano, Italy, 
 
Ludwig – Maximilians – Universitaet Muenchen 
(LMU) 
Address: Geschwister Scholl Platz 1, 80539 
Munich, Germany, 
 
Swiss Tropical and Public Health Institute (Swiss 
TPH) 
 Address: Socinstrasse 57, 4051 Basel, Switzerland 
 
African Society for Laboratory Medicine (ASLM) 
Address: Nega City Mall, 8th Floor, Joseph Tito Street, Kirkos Subcity, Kebele 08, 
Addis Ababa, Ethiopia 
 
University of Heidelberg (UoH) 
Address: Im Neuenheimer Feld 324, 69120 Heidelberg, Germany 
 
 
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2. Signatures page 
Protocol Title: Expanding Xpert Ultra testing for TB diagnosis among HIV-positive 
patients admitted to hospital in Tanzania and Mozambique. 
Protocol number: TB043-3/1-MOZ 
The signatures below confirm that the signatories have reviewed and approved this 
document which shall govern the conduct of the specified research study. 
 
 
SPONSOR: 
Foundation for Innovative New Diagnostics (FIND) 
 
 
 
Name 
Signature 
Date 
 
 
CLINICAL TRIAL COORDINATOR 
Barcelona Institute for Global Health (ISGlobal) 
 
 
 
Name 
Signature 
Date 
 
 
DocuSign Envelope ID: 321646C8-ADAB-4D7A-B633-6CC2C8D9A8B0
19-Mar-2024
Alberto Garcia-Basteiro
25-Nov-2023
Vinzeigh Leukes

 
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OTHER CLINICAL TRIAL PARTNERS 
 
 
Ludwig-Maximilians-Universitaet Muenchen (LMU) (optional) 
 
 
 
Name 
Signature 
Date 
 
 
Ospedale San Raffaele SRL (OSR) (optional) 
 
 
 
Name 
Signature 
Date 
 
 
Swiss Tropical and Public Health Institute (Swiss TPH) (optional) 
 
 
 
Name 
Signature 
Date 
 
 
African Society for Laboratory Medicine (ASLM) (optional) 
 
 
 
Name 
Signature 
Date 
 
 
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Statement of Principal Investigator 
Protocol Title: Expanding Xpert Ultra testing for TB diagnosis among HIV-positive 
patients admitted to hospital in Africa. 
Trial Number: TB043 -3/1 - MOZ 
 
In signing this page, I, the undersigned, agree to conduct the trial according to the protocol and 
ICH-GCP E6 (R2) guidelines and in compliance with applicable regulations. 
 
I will ensure that the requirements relating to obtaining Institutional Review Board (IRB)/ 
Independent Ethics Committee (IEC) review and approval are met. I will promptly report to the 
IRB/IEC any and all changes in the research activities covered by this protocol. 
 
I have sufficient time to properly conduct and complete the trial within the agreed trial period and I 
have adequate resources (staff and facilities) for the foreseen duration of the trial.   
 
I am responsible for supervising any individual or party to whom I delegate trial related duties and 
functions conducted at the trial site. Further, I will ensure this individual or party is qualified to 
perform those trial-related duties and functions. 
 
I certify that key individuals involved with the conduct of this trial, including myself, have completed 
GCP training and, if applicable, Human Subjects Protection Training. 
 
I understand that all information obtained during the conduct of the trial with regard to the subjects’ 
state of health will be regarded as confidential. No participant’s names or personal identifying 
information may be disclosed.  All participant data will be anonymized and identified by assigned 
numbers on all Case Report Forms, laboratory samples and other trial related information (such as 
essential documents) forwarded to FIND. Monitoring and auditing by FIND, and inspection by the 
appropriate regulatory authority(ies), will be permitted. 
 
I will maintain confidentiality of this protocol and all other related investigational materials. 
Information taken from the trial protocol may not be disseminated or discussed with a third party 
without the express consent of FIND. 
 
Clinical Trial Site:  
Centro de Investigação em Saúde de Manhiça (CISM) 
 
 
 
 
 
 
 
 
Name of Principal Investigator:  
Dinis Nguenha 
 
Signature:  
 
Date:  
  
 
 
 
       
 DD/MMM/YYYY 
 
 
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27-Nov-2023

 
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Statement of Principal Investigator 
Protocol Title: Expanding Xpert Ultra testing for TB diagnosis among HIV-positive 
patients admitted to hospital in Africa. 
Trial Number: TB043 -3/1 - MOZ 
 
In signing this page, I, the undersigned, agree to conduct the trial according to the protocol and 
ICH-GCP E6 (R2) guidelines and in compliance with applicable regulations. 
 
I will ensure that the requirements relating to obtaining Institutional Review Board (IRB)/ 
Independent Ethics Committee (IEC) review and approval are met. I will promptly report to the 
IRB/IEC any and all changes in the research activities covered by this protocol. 
 
I have sufficient time to properly conduct and complete the trial within the agreed trial period and I 
have adequate resources (staff and facilities) for the foreseen duration of the trial.   
 
I am responsible for supervising any individual or party to whom I delegate trial related duties and 
functions conducted at the trial site. Further, I will ensure this individual or party is qualified to 
perform those trial-related duties and functions. 
 
I certify that key individuals involved with the conduct of this trial, including myself, have completed 
GCP training and, if applicable, Human Subjects Protection Training. 
 
I understand that all information obtained during the conduct of the trial with regard to the subjects’ 
state of health will be regarded as confidential. No participant’s names or personal identifying 
information may be disclosed.  All participant data will be anonymized and identified by assigned 
numbers on all Case Report Forms, laboratory samples and other trial related information (such as 
essential documents) forwarded to FIND. Monitoring and auditing by FIND, and inspection by the 
appropriate regulatory authority(ies), will be permitted. 
 
I will maintain confidentiality of this protocol and all other related investigational materials. 
Information taken from the trial protocol may not be disseminated or discussed with a third party 
without the express consent of FIND. 
 
 
 
Clinical Trial Site:  
Instituto Nacional de Saúde (INS)  
 
 
 
 
 
 
 
 
Name of Principal Investigator:  
Bindiya Meggi 
 
Signature:  
 
Date:  
  
 
 
 
       
 DD/MMM/YYYY 
 
 
 
 
 
 
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25-Nov-2023

 
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3. Protocol History/Amendment Summary* 
 
Version number 
Release date 
Comments 
3.0 
28 NOV 2021 
Initial version (subsequent to TB-CAPT EXUBERANT 
revised study for new protocol) 
3.1 
01 APR 2022 
Revisions after IRB/IEC review 
4.0 
16 JAN 2023 
Minor changes and clarifications included 
5.0 
13 SEP 2023 
Minor changes 
 
*Refer to Appendix Document for Protocol Amendment History 
 
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3. List of Abbreviations and Acronyms 
 
AHD:  
Advanced HIV disease 
ASLM:  
African Society for Laboratory Medicine 
ARV:   
Antiretroviral Therapy 
AlereLAM:  Alere Determine TB LAM Ag 
CFU:   
Colony Forming Units 
CISM:  
Centro de Investigação em Saude de Manhiça (Mozambique) 
CNBS:  
Centro Nacional Bioética para a Saude (National Bioethics Committee) 
CRF:   
Case Report Form 
DST:   
Drug susceptibility testing 
FIND:  
Foundation for Innovative New Diagnostics 
FujiLAM:  
Fujifilm SILVAMP TB LAM 
HDSS:  
Health and Demographic Surveillance System 
HIV:   
Human immunodeficiency virus 
INS:   
Instituto Nacional de Saúde (Mozambique) 
IHI:   
Ifakara Health Institute Trust (Tanzania) 
LF-LAM:  
Lateral flow urine lipoarabinomannan assay 
ISGlobal:  
Barcelona Institute for Global Health  
LJ:  
 
Lowenstein Jensen (solid culture) 
LMU:  
Ludwig-Maximilians-Universitaet Muenchen 
LPA:   
Line probe assays 
Mtb:   
Mycobacterium tuberculosis 
MDR-TB:  
Multi drug resistant tuberculosis 
MHC             Macia Health Centre 
MHC             Magude Health Centre 
MDH  
Manhiça District Hospital 
MHC              Maracuene Health Centre 
NIMR:  
National Institute for Medical Research (Tanzania) 
NTP:   
National Tuberculosis Programme 
OSR:   
Ospedale San Raffaele SRL 
PLHIV:  
People living with HIV  
RIF:   
Rifampicin 
RR:   
Rifampicin resistance 
RS:   
Rifampicin susceptible. 
Swiss TPH:  Swiss Tropical and Public Health Institute 
TB:   
Tuberculosis 
Ultra:  
Xpert® MTB/RIF Ultra 
XDR-TB:  
Extensive drug resistant tuberculosis 
Xpert:  
Xpert® MTB/RIF 
XRH  
Xinavane Rural Hospital 
 
 
 
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4. Protocol Synopsis 
Protocol Title 
Expanding Xpert Ultra testing for TB diagnosis among HIV-positive patients 
admitted to hospital in Africa. 
Protocol number 
TB043-3/1-MOZ 
Short Title 
EXULTANT 
Sponsor 
Foundation for Innovative New Diagnostics (FIND) 
Study Centres 
This will be a multi-centre study involving 4 sites in 2 African  countries (Mozambique 
and Tanzania) 
Name of 
investigational 
products 
Xpert MTB/RIF Ultra (Ultra), AlereLAM, Fujifilm SILVAMP TB LAM (FujiLAM), LumiraDx  
Indication 
TB diagnosis in hospitalized adults living with HIV (PLHIV) 
Background 
Among people living with HIV, microbiological confirmation of TB is suboptimal due 
to sputum collection challenges and paucibacillary sputum resulting in poor 
diagnostic yield. The limitations of existing sputum-based tests for M. tuberculosis 
(Mtb) diagnosis among PLHIV  admitted to hospital create imperatives to explore the 
usefulness of easy to collect, non-respiratory specimens which could improve TB 
diagnosis, while supporting and accelerating treatment guidance. 
Objectives 
Primary Objective(s): 
 
To investigate the effect of an expanded TB screening strategy    among 
HIV-positive patients admitted to hospital (including Ultra on sputum, stool 
and urine, and AlereLAM on urine, performed regardless of presence of TB 
symptoms) on the proportion of bacteriologically confirmed TB cases 
starting treatment within 72 hours of enrolment, compared to Ultra testing 
(on sputum/any tissue) and AlereLAM (on urine) in only those patients who 
are symptomatic for TB or fulfill WHO testing recommendations. 
Secondary Objectives: 
 
to assess the impact of this screening strategy on 2-month all- cause 
mortality. 
 
to assess the feasibility of multiple specimen collection for TB diagnosis 
within 72 hours of enrolment. 
Exploratory objectives 
 
To assess the diagnostic accuracy of CRP on blood compared to TB 
symptoms screening in those with microbiologically confirmed TB. 
 
To compare the bacteriological TB confirmation rate in the control arm (Ultra 
on sputum/any tissue) and urine AlereLAM in only those patients who are 
symptomatic for TB or fulfill WHO testing recommendations, to local 
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standard of care (current testing algorithms implemented at the 
participating sites before study initiation). 
Study Design 
This is a multicentre, parallel, individually randomized, controlled diagnostic trial in 
consecutively enrolled HIV positive adults admitted to hospital in selected sites in 
Mozambique and Tanzania. 
Intervention arm 
The intervention arm for this trial consists of HIV patients with TB testing performed 
regardless of presence of TB symptoms. Testing will be done on expectorated 
sputum, stool and concentrated urine with Ultra, and urine with AlereLAM. 
To fulfil exploratory objectives, we will also collect and store 2x tongue swabs for 
molecular TB diagnostic assay (Xpert Ultra and/or LumiraDx) testing, blood for 
testing with CRP, and urine samples which will be stored for retrospective FujiLAM 
testing and analysis. 
Control arm 
The control arm for this trial will consist of patients managed according to the current 
WHO recommended TB testing practices for HIV positive inpatients (as of Q1 2020). 
TB testing will be done as follows: 
Sputum Ultra performed whenever the patient has cough, fever, weight loss over 
night sweats 
and/or 
Ultra performed on any tissue (including lymph nodes) from patients with clinical 
suspicion of extrapulmonary TB. 
and/or: 
Urine Alere TB-LAM performed if patients have signs and symptoms of TB 
(pulmonary and/or extrapulmonary), or with advanced HIV disease, or who are 
seriously ill, or else irrespective of signs and symptoms of TB, but combined with a 
CD4 cell count of less than 200 cells/mm3. 
Study Population and 
Sample Size 
Our study population will be adult HIV-positive patients admitted to  hospital and 
living in the catchment areas within the 4 participating district hospitals in Tanzania 
and Mozambique, regardless of presence of TB attributable symptoms. 
Sample size was chosen to be sufficient to detect a 36.8% relative increase in the 
primary endpoint in the intervention arm (as compared to the control arm). 
Calculations were based on following assumptions: 
- Alpha: 0.05 
- Beta: 0.2 (power=80%) 
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- Estimated proportion of participants with microbiologically confirmed TB in the 
control arm: 19% 
- Estimated proportion of participants with microbiologically confirmed TB in the 
intervention arm: 26% 
- Lost to follow up rate for primary endpoint: 5% of recruited participants. 
Based on these estimates, the study will require a total of 586 HIV participants to be 
enrolled per trial arm. For both arms together, this amounts to 1172 patients in total 
(293 per site). 
Inclusion/Exclusion 
Criteria 
Inclusion Criteria: 
1. Adults (18 years old and above) 
2. Confirmed HIV infection (including both antiretroviral (ART)- naïve and 
experienced) 
3. Being admitted to the hospital 
Exclusion criteria: 
1. Unable to provide informed consent (if no authorized relatives are in the 
position to provide the consent) 
2. Living outside the catchment area of the participating hospital(s) 
3. With plans to migrate outside the catchment area within 2 months after 
recruitment. 
4. Currently receiving anti-TB therapy or having received anti-TB therapy (or a 
TB diagnosis) in the last 6 months prior to enrolment 
5. Currently receiving or having received preventive TB treatment in the 
preceding 6 months 
6. Patients admitted for traumatic reasons, acute abdomen, delivery or 
pregnancy (maternal conditions) or for planned/scheduled surgery. 
7. Referred from other reference hospital 
8. Positive result to a SARS-CoV-2 test (RT-PCR, antigen test, or other similar test 
that might define COVID-19 case in the study site)* 
*AND patients under investigation for COVID-19 if this situation 
hinders the execution of study activities (as judged by the site PI) 
Evaluation Criteria 
Primary Endpoint(s): 
The proportion of participants diagnosed with microbiologically confirmed TB and 
started on TB treatment within 72 hours of enrolment* in whom TB is 
microbiologically confirmed*/**, separately  for control and intervention arms. 
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*The numerator of the primary endpoint includes participants per study arm who are 
diagnosed with microbiologically confirmed TB and initiated TB treatment within 72 hrs of 
enrolment. The denominator is the number of enrolled  patients in each study arm. 
**Patients are defined to have microbiologically confirmed TB if at least one confirmatory TB 
test (Ultra, AlereLAM) gives a positive result. 
Secondary endpoints: 
 
Eight-week all-cause mortality (main secondary endpoint) among all 
participants enrolled. The numerator will be number  of deaths during eight 
weeks after enrolment, the denominator is the number of participants 
enrolled. 
 
Time to TB treatment initiation among microbiologically confirmed cases 
and among all TB cases since enrolment. We  will estimate Kaplan Meier 
curves and hazard ratios at day 7, 14, 28 and 56. Additionally we will 
compare the time to related estimates (mean and standard deviation) of 
intervention and control group. 
 
Proportion of cases re-admitted to hospital. The numerator will be the 
number of admissions after initial discharge and within 8 weeks from 
enrolment. The denominator will be the  number of participants enrolled. 
 
Proportion of participants who are diagnosed with TB (irrespective of 
bacteriological confirmation) and are started   on TB treatment within 72 
hours of enrolment. 
 
Proportion of participants who are diagnosed with microbiologically 
confirmed TB and are started on treatment  at 7 days, 14 days, 4 and 8 weeks 
of enrolment. 
 
Proportion of study participants who are able to provide the different 
specimens (sputum, stool and urine samples) within 24, 48 and 72 hours of 
enrolment. 
 
Time to laboratory confirmed TB diagnosis and any TB diagnosis since 
enrolment. We will estimate Kaplan Meier curves and hazard ratios at days 
7, 14, 28 and 56. Additionally we will compare the time related estimates 
(mean and standard deviation) of intervention and control group. 
 
In-hospital and 4-week all-cause mortality among all participants enrolled 
(assessed as the eight-week all-cause mortality). 
 
Proportion of participants started on treatment without Rif resistance 
information (only AlereLAM or FujiLAM positive) 
 
Exploratory endpoints 
 
Diagnostic performance of a molecular TB diagnostic assay (Xpert Ultra 
and/or LumiraDx) on tongue swabs and FujiLAM on urine stool against a 
microbiological reference standard (defined as any test positive in the 
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intervention arm) or against a composite reference standard that includes 
bacteriologically confirmation or/and clinical evidence resulting in therapy 
initiation. 
 
Diagnostic accuracy of CRP in blood compared to TB symptom’s screening 
in those with microbiologically confirmed TB.   
Comparison of primary and secondary endpoints of the intervention arm with the 
local standard of care at the sites before the study initiation (a retrospective data 
collection from  consecutive PLHIV admitted at participating hospitals). 
 
Sub-analysis 
 
Primary endpoint will be calculated at different intermediate timepoints (48 
hours, 7 days and 14 days from enrolment). 
 
Primary and selected secondary endpoints will be calculated 
for participants’ subgroups including CD4 cells/mm3 ≥200, <200 and 
<100, among participants with any TB symptoms, severely ill participants or with AHD, 
and among participants providing at least one sputum and (or) one urine sample for 
testing. 
Study Timeline 
Estimated period for ethics clearance                May / 2022 
Import permits and importation 
               Jan-May / 2022 
Kick off / training meeting                                  Nov / 2021  
Estimated date of first participant enrolled:        Sep/ 2022  
Estimated date of last participant enrolled:         Jan/ 2024  
 Estimated date of last participant completed:     Mar/ 2024 
Estimated date for end of data cleaning:             May / 2024 
Estimated date for end of data analysis:               July / 2024 
Estimated date for first manuscript draft:             Sep / 2024 
 Total duration of study: 
                47 months 
 
 
 
 
 
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5. Introduction 
5.1 Background and statement of the problem 
Tuberculosis (TB) is a leading cause of death worldwide and ranks above HIV/AIDS as the leading 
cause of mortality from a single infectious agent1,2. The World Health Organization (WHO) estimated 
that there were around 10 million new cases and 1.5 million deaths in 2018.2 Nine and 17% of the 
total number of TB cases and deaths respectively occurred in people living with HIV (PLHIV), with 
70% of these occurring in the African region.2 PLHIV are at increased risk of acquiring Mycobacterium 
tuberculosis (Mtb) infection and have a >20-fold increased risk of TB disease progression compared 
to HIV-uninfected peers.3–5 In addition, mortality during TB treatment remains as high as 11% 
globally, although fatal outcomes of PLHIV under TB treatment are even higher in Sub-Saharan 
African countries.2 
 
One of the main barriers for ensuring timely TB treatment in PLHIV is the lack of an optimal 
diagnostic work up.6 In fact, TB case detection among people with HIV remains disappointingly low 
and almost half (45%) of all HIV associated TB cases are estimated to be undiagnosed or 
unreported.2 Mortality associated with undiagnosed TB among people with HIV is assumed to be 
higher than 70%.7 Although the lack of a proper diagnosis is a multifactorial problem associated 
with quality of health care, social, economic and anthropological factors, the unavailability of rapid, 
sensitive and cheap diagnostic tools has been deemed as an important factor contributing to under- 
and misdiagnosis. In addition, poor awareness of TB by health care workers and lack of established 
diagnostic algorithms further hinder adequate TB diagnosis in many high burden settings.8,9 
Autopsy studies conducted in sub-Saharan Africa show high rates of clinico-pathological 
discrepancies and missed TB which lead to high mortality 8,10–12 
 
Among PLHIV, microbiological confirmation of TB is suboptimal due to sputum collection 
challenges and paucibacillary sputum resulting in poor diagnostic yield.13–15 Despite increasing 
availability, sputum Xpert® MTB/RIF (Cepheid Inc., Sunnyvale, CA, USA, hereinafter Xpert) confirms 
TB in only 77% of adult cases with HIV-infection16 and only 66%  of culture-positive pediatric cases.17 
Sensitivity of the next-generation Xpert MTB/RIF Ultra (hereinafter Ultra) is estimated to increase 
among adult TB patients with documented  HIV-infection (90%)16. Yet, performance in 
immunosuppressed HIV positive patients (in whom sample collection is often unavailable) is 
probably suboptimal. Thus, estimates of Xpert diagnostic performance in general HIV positive 
patients may not reflect test performance within the majority of TB cases in hospitalized PLHIV. In 
addition, although Xpert results could, in theory, be available within a few hours, results are often 
available within several days after sample collection,18,19 delaying TB treatment if not empirically 
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provided. The most sensitive test for TB diagnosis, liquid culture, is further handicapped as  it is slow, 
expensive and contaminated 5-8% of the times.20 
 
Options that have been recommended by WHO to ensure earlier diagnosis and reduce mortality 
include strategic placement of rapid molecular TB diagnostics such as Xpert21 or Ultra22 within HIV 
care settings (which could enable availability of results within 24 hours), and uptake of the lateral 
flow urine lipoarabinomannan assay (LF-LAM)23 strip-test – the Alere Determine™ TB LAM Ag 
(AlereLAM) for seriously ill PLHIV. However, despite AlereLAM being a cheap and fast test, only 9 of 
the 30 high TB and HIV burden countries have a national policy and algorithm indicating the routine 
use of urine LF-LAM (with various levels of implementation). 2 A recent study showed that urine-
based TB screening of  PLHIV admitted to hospital might reduce 56-day mortality in those with low 
CD4 counts, severe anaemia or clinically suspected tuberculosis.24 A recently published meta-
analysis showed that, as an screening test among PLHIV, AlereLAM has limited sensitivity of 45% 
(95% CI: 29-63) and specificity of 92% (80-97) against a composite microbiological reference 
standard.25 However, screening with AlereLAM improves the likelihood of being diagnosed with TB 
during admission. The WHO recently expanded the recommendations for the use of AlereLAM to 
include adults, adolescents and children living with HIV with signs and symptoms of TB (inpatient 
and outpatient setting) or irrespective of signs and symptoms of TB with CD4 cell count under 200 
cells/mm3 in inpatient settings irrespective of the CD4 cell count in outpatient settings.26 The 
unavailability of CD4 counts upon admission or the assessment of the criteria for severely-ill or 
advanced HIV disease might delay quick testing of PLHIV in whom AlereLAM is recommended. In 
addition, LAM tests do not provide any information on potential resistance to anti TB drugs, which 
might hinder its implementation in high TB drug resistance settings. 
 
The limitations of existing sputum-based tests for M. tuberculosis (Mtb) diagnosis create imperatives 
to explore the usefulness of easy to collect, non-respiratory specimens which could improve 
performance of all tests, while supporting treatment guidance and monitoring. In fact, the WHO has 
specified the need for rapid non-sputum based TB diagnostics among their high priority target 
product profiles for new TB diagnostics.27 
 
5.2 Promising specimens for TB diagnosis using Xpert Ultra 
 
Urine 
Although there is no recommendation on the use of urine as a sample for Xpert TB testing, several 
diagnostic accuracy studies have shown an important added yield when used in hospitalized patients. 
Studies by Lawn in South Africa28,29, showed that Xpert testing in urine among newly admitted 
unselected HIV-positive adults improved bacteriological confirmation relative to sputum Ultra, 
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sputum culture or urine LF-LAM. Xpert in urine provided the highest incremental diagnostic yield, 
with high specificity when used combined with sputum testing.28,29 A recent clinical trial by Gupta-
Wright and colleagues showed a lower diagnostic yield of urine-Xpert compared to TB LAM30, 
although it was the only test positive in 6% of microbiologically confirmed patients in the intervention 
arm. 
 
Another analysis in a South African cohort of unselected HIV-positive hospitalized patients, showed 
a sensitivity of Urine Xpert of 41.8% (59/141) against a microbiological reference standard, very 
similar to that of AlereLAM (43.3% 61/141).31 Interestingly, 15 cases detected with Urine Xpert were 
not detected with Alere LAM and 17 cases were detected with AlereLAM, but not with Urine Xpert. 
 
Stool 
Similarly to urine, no recommendation has been made about the use of Xpert or Ultra in stool so far. 
However, recent studies on stool Xpert in pediatric pulmonary TB suggest that it could be helpful in 
paucibacillary TB patients. A metanalysis showed the sensitivity and specificity of stool Xpert in 67% 
and 99%, respectively, being higher in HIV positive children32, and other groups have reported a 
greater sensitivity (73%) compared to traditional tools33. Moreover, Xpert Ultra showed higher 
sensitivity in stool compared to Xpert34. While results of stool Xpert in adults are promising, showing 
a sensitivity of 90.2%-100% and specificity of 100% 35 and 81% in smear-negative patients35, data is 
limited. Results of alternative in-house PCR show promising value in stool support of this specimen 
for PTB diagnosis (sensitivity 95-97% in smear positive and 77% in smear negative33,36 and 69% for 
EPTB33). Although there are no published reports on HIV positive admitted patients, the 
abovementioned data suggest that the use of stool as a specimen for TB diagnosis could provide 
additional diagnostic yield in this vulnerable population.  
 
5.3 Other promising tests and specimens 
 
The Fujifilm SILVAMP TB LAM (FujiLAM) 
A urine-based test which also detects LAM in urine, has shown promising results in frozen samples 
and is currently undergoing prospective evaluations in several settings. Recently published results 
using biobanked samples from studies conducted in South Africa showed higher sensitivity of 
FujiLAM compared to AlereLAM (70.4% vs 42.3%, using a microbiological reference standard), while 
maintaining high specificity.31 FujiLAM performance includes a 5-step procedure according to 
manufacturer’s instructions and takes around 50-60 minutes from sample collection to results 
availability. Thus, it is also considered a true point of care test, since results could easily be handed 
out the same day the patient provides the sample. 
 
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Given the substantially improved sensitivity of FujiLAM compared to AlereLAM, it could easily be the 
best test for immunosuppressed HIV positive patients, and has the potential for being an important 
tool for TB diagnosis in this population subgroup. In addition, it might have a potential to impact 
on mortality. A recent study in South Africa showed that FujiLAM conducted retrospectively 
predicted TB mortality among hospitalized patients.37 However further studies in different 
populations and settings, with endpoints including patient important outcomes are needed to 
further assess its impact where it is most needed. The FujiLAM assay is undergoing a version change 
for large scale manufacturing. The new version will not be available until the end of the planned 
trial, so analysis for FujiLAM will be done retrospectively on banked urine samples collected as part 
of this study. 
 
Oral swabs 
As sputum can be difficult to collect in some patient groups, alternative specimens for TB diagnosis 
have been evaluated in recent years. In 2015, a study conducted in South Africa38 demonstrated the 
presence of M.tb in oral swabs. The diagnostic performance of this sample collected in tongue 
dorsum that two samples per subject showed a combined sensitivity of 92.8% and specificity of 
91.5%.39 A recent study40 showed lower sensitivity and specificity when collecting tongue swabs on 
different days (88%-94.4% and 79.2%, compared to sputum Xpert). However, despite these 
promising results, further validation studies are needed to assess the potential utility of these 
innovative specimens. 
 
CRP  
C-reactive protein (CRP) indicates inflammation and can be detected on capillary blood. WHO has 
recently recommended CRP as a method for TB screening among ambulant people living with HIV 
who are newly in care and not yet on antiretroviral treatment, based on similar sensitivity and 
specificity to symptom screening in HIV-positive populations41. 
 
LumiraDx  
LumiraDx is a recently developed point-of-care instrument that is currently available for SARS-CoV-
2 testing in anterior nasal specimen, Dimer-D and CRP quantification in venous blood 
(https://www.lumiradx.com/us-en/what-we-do/diagnostics/test-technology/). While its use has not 
yet been tested for TB, the company is developing a Mtb kit to be tested in tongue swabs. LumiraDx 
is a fast (10min) and easy-to-use device, with potential for adding innovative POC solutions to TB 
diagnosis.  
 
 
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6. Aim and hypothesis 
The overall aim of this study is to assess the potential of an expanded TB testing strategy to increase 
the number of HIV-positive patients with microbiologically diagnosed TB who are started on 
treatment in adult wards of sub-Saharan Africa. 
 
Previous studies have shown that Xpert testing of urine and stool are capable of confirming Mtb in 
patients who would otherwise test negative with traditional sputum-based methods. Evidence 
shows that these diagnostics may detect additional cases that are not detected by AlereLAM. Thus, 
an algorithm using the different tests (sputum Ultra, urine Ultra and stool Ultra) offered as a 
screening intervention to admitted HIV positive patients should increase the Mtb bacteriological 
yield (compared to current WHO recommended screening and testing strategies**) and contribute 
to earlier initiation of TB treatment. Given that some detected cases may not present with classical 
TB symptoms at the time of hospitalization, we believe that this strategy will increase the overall 
number of patients with diagnosed TB and started on treatment and ultimately reducing mortality. 
 
** Current WHO recommended strategies include sputum Xpert Ultra MTB/RIF whenever the patient has TB attributable 
symptoms, and urine Alere TB-LAM, if patients have signs and symptoms of TB, or with advanced HIV disease (1) or who are 
seriously ill (2) or else irrespective of signs and symptoms of TB and with a CD4 cell count of less than 200 cells/mm3. These 
interventions will constitute the “control arm” across all study sites. Note that the current WHO recommended strategies 
might not be currently applied in a standardized manner as part of the local standard of care. 
 
6.1 Benefit/Risk Assessment 
The study poses participants with minimal or no risk, given that no experimental intervention is 
provided to participants, but rather to samples from participants. The potential risks are associated 
to those associated to blood drawn, or discomfort produced while providing the sputum, urine or 
stool samples. The benefits of the study include probability of earlier confirmatory diagnosis of 
tuberculosis, which would allow immediate treatment initiation. This might have an impact on 
mortality in the first two months after enrolment. These benefits need to be confirmed as they are 
endpoints of the study. The study would surely allow a close clinical follow-up by study staff during 
the participants’ involvement in the clinical trial. 
 
 
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7.  Objectives 
Primary Objective(s) 
 
To investigate the effect of an expanded TB screening strategy among HIV-positive patients 
admitted to hospital (including sputum Ultra, urine AlereLAM and urine and stool Ultra  
assay) on the proportion of microbiologically-confirmed TB cases starting treatment within 
72 hours of enrolment, compared to Ultra testing (on sputum/any tissue) and AlereLAM (on 
urine) in only those patients who are symptomatic for TB or fulfill WHO testing 
recommendations 
 
Secondary Objectives 
 
to assess the impact of this screening strategy on 2-month all-cause mortality. 
 
to assess the feasibility of multiple specimens' collection for TB diagnosis within 72 hours of 
enrolment. 
 
Exploratory Objectives 
 
To assess the added yield of a molecular TB assays (Xpert Ultra and/or LumiraDx) tongue 
swabs, and urine FujiLAM testing in microbiological TB confirmation 
 
To assess the diagnostic accuracy of CRP in blood compared to TB symptoms screening in 
those with microbiologically confirmed TB. 
 
To compare the bacteriological confirmation rate of our control arm (Ultra on sputum/any 
tissue and AlereLAM in only those patients who are symptomatic for TB or fulfill WHO testing 
recommendations) to local standard of care (current testing algorithms implemented at the 
participating sites before study initiation). 
 
 
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8. Endpoints 
8.1 Primary Endpoint(s) 
The primary endpoint is: 
 
The proportion of participants diagnosed with microbiologically confirmed TB and started 
on TB treatment within 72 hours of enrolment, separately for intervention and control arm. 
The numerator is the number of participants per study arm who are diagnosed with 
microbiologically confirmed TB and start on treatment within 72 hours of enrolment. The 
denominator is the number of participants enrolled per study arm. We will compare this 
indicator between both study arms. 
Patients are defined to have microbiologically confirmed TB if at least one confirmatory TB 
test (Ultra, AlereLAM) gives a positive result. 
 
Hospitalized PLHIV experience high mortality and TB underdiagnosis and misdiagnoses are frequent. 
TB diagnosis is important when you can quickly start appropriate therapy. This endpoint will capture 
both diagnostic dimensions of the intervention (higher rates of Mtb laboratory confirmation) as well 
as the relevant patient outcome (TB treatment initiated). 
 
Diagnosic procedures and treatment initiation (if appropriate) should be completed within 72 hours 
of enrolment given the intervention is aimed at rapid collection of samples for all patients upon 
admission and that Ultra testing can provide results within a few hours from specimen collection at 
all participating sites. 
 
The numerator of the primary endpoint also includes patients whose bacteriological confirmation 
might arrive after 72 hours of enrolment. There might be cases where liquid or solid culture might 
be requested and results arrive after 72 hours. If the patient had been put on treatment empirically 
(before a positive culture results has arrived), that case will contribute to the numerator, given that 
treatment would have been started in a “true” TB case. 
 
8.2 Secondary endpoints 
 
Eight-week all-cause mortality (main secondary endpoint) among all participants enrolled. 
The numerator will be number of deaths during eight weeks after enrolment, the 
denominator is the number of participants enrolled. We will compare this indicator between 
both study arms. In addition, this endpoint will also be calculated considering right censored 
observation when a participant is lost to follow up during the observation period or a 
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participant experiences a different event that makes further follow up impossible. 
 
Time to TB treatment initiation among microbiologically confirmed cases and among all TB 
cases since enrolment. We will estimate Kaplan Meier curves (event= TB treatment initiation 
among laboratory confirmed TB patients and among all TB cases) and hazard ratios at day 
7, 14, 28 and 56. Additionally we will compare the time to related estimates (mean and 
standard deviation) of intervention and control group. 
 
Proportion of cases re-admitted to hospital. The numerator will be the number of admissions 
after initial discharge and within 8 weeks from enrolment. The denominator will be the 
number of participants enrolled. 
 
The proportion of participants who are diagnosed with TB (irrespective of bacteriological 
confirmation) and started TB treatment within 72 hours of enrolment. The numerator is the 
number of participants diagnosed with TB (with or without bacteriological confirmation) who 
started treatment within 72 hours of enrolment; the denominator is the number of 
participants enrolled. 
 
The proportion of participants who are diagnosed with microbiologically confirmed TB and 
are started on treatment at 7 days, 14 days, 4 weeks and 8 weeks of enrolment. In addition, 
this endpoint will also be calculated considering right censored observation when a 
participant is lost to follow up or dead during the observation period or a participant 
experiences a different event that makes further follow up impossible. 
 
Proportion of participants who are able to provide sputum, stool and urine samples for 
Ultra/AlereLAM testing within 24, 48 and 72 hours of enrolment (the numerator is the 
number of urine samples or (and) sputum samples provided within 72 hours of admission 
and the denominator is the number of patients enrolled). 
 
Time to laboratory confirmed TB diagnosis and any TB diagnosis since enrolment. We will 
estimate Kaplan Meier curves (events = laboratory confirmed diagnosis and any TB 
diagnosis) and hazard ratios at day 7, 14, 28 and 56. Additionally we will compare the time 
related estimates (mean and standard deviation) of intervention and control group. 
 
In-hospital and 4-week all-cause mortality as assessed by estimating a proportion 
(numerator: number of deaths occurring at the hospital over the number of enrolled 
participants and number of deaths by week 4 (irrespective of where it occurs) over the 
number of enrolled participants) 
 
Proportion of participants started on treatment without RIF resistance information (only 
AlereLAM positive) 
 
 
The study has been powered to detect a statistically significant difference in the primary endpoint. 
Nonetheless, given that some patients might not present typical TB symptoms and TB misdiagnosis 
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is frequent among admitted HIV-positive patients, we believe the intervention  could be associated 
with a higher proportion of patients diagnosed with TB (irrespective of bacteriological confirmation) 
and thus, overall survival. In consequence, several secondary endpoints are related to survival at 
different time points. 
 
8.3 Exploratory endpoints 
 
 
Diagnostic performance of a molecular TB diagnostic assay (Xpert Ultra and/or LumiraDx) 
on tongue swabs, and FujiLAM on urine against a microbiological reference standard (as 
defined in intervention arm) or against a composite reference standard that includes 
bacteriologically confirmation or/and clinical evidence resulting in therapy initiation. This 
endpoint will only be studied in participants of the  intervention arm 
 
Diagnostic accuracy of CRP in blood in order to evaluate compared to TB symptom’s 
screening in those with microbiologically confirmed TB.   
 
Comparison of primary and secondary endpoints of the intervention arm with the local 
standard of care at the sites before the study initiation (a retrospective data collection from 
consecutive HIV-positive patients admitted at participating hospitals). 
 
 
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9. Trial Design and study arms 
This is a multicentre, parallel, individually randomized controlled diagnostic trial in consecutively 
enrolled HIV positive adults to evaluate the impact of the extended use of Xpert Ultra (3 specimens) 
for TB diagnosis, using sputum, stool and urine, AlereLAM among consecutive PLHIV admitted to 
hospitals in 4 sites of 2 high burden African countries (Tanzania and Mozambique). Thus, the 
intervention arm for this trial will include TB testing performed irrespective of the presence of TB 
symptoms. Testing will be done on expectorated sputum, stool and urine with Ultra and urine with 
AlereLAM. 
To fulfil exploratory objectives, we will also collect 2x tongue swabs for molecular TB diagnostic 
assay (Xpert Ultra and/or LumiraDx) testing, blood for CRP, and urine samples which will be stored 
for retrospective FujiLAM testing and analysis. 
 
The control arm for this trial consist of patients managed according current WHO testing 
recommendations (as of Q1 2020) for HIV-positive inpatients. TB testing will be done as follows: 
a) Sputum Ultra whenever the patient has cough, fever, weight loss or night sweats and/or 
Ultra performed on any tissue (including lymph nodes) in patients with clinical suspicion 
of extrapulmonary TB. 
and/or 
b) Urine Alere TB-LAM, if patients have signs and symptoms of TB (pulmonary and/or 
extrapulmonary), or with advanced HIV disease or who are seriously ill or else irrespective 
of signs and symptoms of TB and with a CD4 cell count of less than 200 cells/mm3. 
 
As part of a secondary objective, we will retrospectively collect data of a cohort of consecutively 
hospitalized HIV-positive patients that were admitted prior to the trial initiation (third arm), that 
will be used to compare the difference between the intervention arm or control arm with the real 
standard of care practiced at the sites. 
 
9.1 Study population and trial setting 
Our study population will be adult (≥18 years) PLHIV admitted to hospital and living in the catchment 
areas of 4 district hospitals in Mozambique and Tanzania. 
 
 
 
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These two countries are included in the World Health Organization’s high TB and HIV burden 
country list. In 2020 Mozambique and Tanzania had estimated TB incidence rates of 368 and 222 
per 100 000 population respectively. The prevalence of HIV among new TB patients was 27 and 21% 
in 2020, respectively. The following table shows basic epidemiological indicators from the World 
Tuberculosis Report 2021 released by the World Health Organization. 
 
Mozambique 
Tanzania 
TB incidence Rate (per 100 000 population) 
368 
222 
HIV-positive TB incidence (per 100 000 population) 
101 
47 
HIV-positive TB mortality (per 100 000 population) 
20 
16 
Proportion of pulmonary TB who are bac confirmed (%) 
35% 
44% 
TB treatment coverage (%) 
84% 
64% 
TB case fatality ratio (%) 
11% 
22% 
TB patients with known HIV status who are HIV-positive (%) 
27% 
21% 
TB treatment success in HIV positive patients (2019)(%) 
88% 
90% 
Table 1. Basic World Health Organization TB burden of disease indicators (year 2020)42 
 
Four research institutions from 2 different countries will be recruiting participants for the trial at 
associated district hospitals (non-referral hospitals). All the research sites have: 
 
 
Capacity to enroll at least 270 eligible patients in a year. 
 
Continuous power supply 
 
Access to laboratory testing which can provide Ultra results and other relevant TB tests 
(AlereLAM) within 24 hours. 
 
Access to CD4 cells count testing and blood chemistry services. 
 
Adequate space for the research team to work in or to erect a temporary structure if the 
existing facility is not adequate to accommodate the research team. 
 
At least one physician on the research team with experience in management of patients with 
TB and HIV in order to make the relevant clinical decisions. 
 
Storage capacity for samples that will be analyzed at a later stage. 
 
 
 
 
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9.1.1 Mozambique 
9.1.1.1 Manhiça District Hospital (MDH) and Xinavane Rural Hopsital (XRH) are two health 
facilities located in the district of Manhica,  80 and 120 km north from Maputo (respectively). MDH 
is a 110-bed rural hospital (60 beds in the adult ward), receiving referrals from 11 health care centers 
of the district. It is adjacent to Centro de Investigação em Saude de Manhiça (CISM), which provides 
support with clinical staff and performing some of the laboratory procedures for the hospital. It 
offers obstetric services including obstetric emergency care, operation room and, in collaboration 
with CISM, a morbidity surveillance 24h 7 days per week, hospital-based morbidity surveillance 
system for children under 15 years of age attending the MDH. XRH is a 50-bed rural hospital, 50km 
from MDH with 40 beds in the adult ward, receiving referrals from 3 health care centers of the 
northern part of Manhiça district. Both hospitals have acess to smear microscopy, GeneXpert, X-Ray 
facilities. 
XRH is a 50-bed rural hospital (40 beds in the adult ward), receiving referrals from 3 health care 
centers of the northern part of Manhiça district. XPH is a provincial 40 – bed provincial hospital in 
the adult ward and MHC a relatively small health centre with a hospitalization capacity of 10 beds 
in the adult ward. 
 
Additional sites such as the Maracuene, Magude and Macia Health Centres could be considered 
during the study if the recruitment rate in the MDH and XRH is inadequate. These 3 Health Centres 
are relatively small health centres surrounding the Manhiça District Hospital, located at 50, 150 and 
160 km from Maputo (respectively), with a hospitalization capacity of 10, 54 and 31 beds 
(respectively) in the adult wards. 
 
 
9.1.1.2 Mavalane General Hospital (MGH) and José Macamo General Hospital (JMGH) are 
hospitals located in Maputo city, with 72 and 70 adult beds respectively. Both hospitals collaborate 
with the Instituto Nacional de Saúde (INS), the national state funded health research institution in 
Mozambique. Both hospitals have access to smear microscopy, GeneXpert®, X-ray and CD4 cell 
count and HIV testing. Both hospitals serve some of the poorest regions of the city, have integrated 
Emergency Department (for children and adults), with those requiring intensive care transferred to 
Maputo Central Hospital.  
 
9.1.2 Tanzania 
9,1,2,1 NIMR Mbeya Medical Research Center is located on the same ground of the Mbeya Zonal 
Referral Hospital (MZRH), a public tertiary healthcare facility serving a population of about 8 million 
people in Southwestern regions of Tanzania. MZRH has the average number of hospital admissions 
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of 30,000 per year and total of 400 bed capacity. MZRH admit over 200 HIV positive patients per 
month. NIMR work very closely with MZRH which provide a pool for recruitment of participants into 
various research studies carried out by NIMR. For this study recruitment of study participants will 
be conducted within the inpatient ward of MZRH and Mbeya Regional Referral hospital (MRRH). 
MRRH is a 150-bed regional hospital located in Mbeya city, Tanzania. It receives around 100 to 150 
admissions of HIV infected patients per month. It works closely with NIMR Mbeya Center. It has 
microscopy, GeneXpert and X-ray facilities. Sputum, urine and other samples will be processed and 
tested at the NIMR laboratory. 
 
 
 
9.1.2.2 St Francis referral hospital (SFRH) is located in the south-east of Morogoro region in 
Kilombero district. SFRH is a non-profit making organization belonging to the Roman Catholic 
Dioceses of Ifakara. It is a 371 beds Hospital and was declared a District (Council) Designated 
Hospital for Kilombero and Ulanga Districts in 1976 with catchment population of about 600,000 
habitants and in 2010, the hospital was upgraded to the level of Referral Hospital. SFRH offers 
preventive, curative, rehabilitative and teaching services. SFRH is divided into departments for 
Surgery, Internal Medicine, Gynecology and Obstetrics, Pediatrics, Chronic Diseases and Intensive 
Care. Additionally, there are outpatients’ departments and wards for Tuberculosis, Dental Medicine, 
Physiotherapy, Occupational Therapy, Psychiatry, Leprosy, Rehabilitation, an X-ray department, 
laboratory and a special laboratory for the production of infusions. SFRH in collaboration with the 
Ifakara Health Institute runs a HIV cohort with over 11,000 HIV positive patients ever enrolled. The 
cohort has been running since 2005. The average number of inpatients treated per year is 16,480. 
 
9.2 Participant eligibility criteria 
9.2.1 Pre-eligibility screening criteria 
Adult HIV-positive patients admitted in the hospitalization wards of the participating hospitals. 
9.2.2 Inclusion Criteria: 
1. Adults (18 years old and above) 
2. Confirmed HIV infection (including both antiretroviral (ART)- naïve and experienced) 
3. Admitted to the hospital (adult medical wards) at the time of enrolment. 
 
9.2.3 
Exclusion criteria: 
 
1. Unable to provide informed consent (if no authorized relatives are in the position to 
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provide the consent) 
2. Living outside the catchment area of the participating hospital(s) 
3. With plans to migrate outside the catchment area within 2 months after recruitment. 
4. Currently receiving anti-TB therapy or having received anti-TB therapy (or a TB diagnosis) in 
the last 6 months prior to enrolment 
5. Currently receiving or having received preventive TB treatment in the preceding 6 months 
6. Patients admitted for traumatic reasons, acute abdomen, delivery or pregnancy (maternal 
conditions), or for planned/scheduled surgery. 
7. Referred from other reference hospital. 
8. Positive result to a SARS-CoV-2 test (RT-PCR, antigen test, or other similar test that might 
define COVID-19 case in the study site)* 
*AND patients under investigation for COVID-19 if this situation hinders the execution of study 
activities (as judged by the site PI) 
 
9.3 Sample size 
In order to detect a 36.8% relative difference (26% vs. 19%) in the proportion of admitted PLHIV 
who are bacteriologically confirmed TB positive between the intervention and control arm, the study 
will require a total of 586 participants to be enrolled per trial arm, whereby drop-out rates are 
considered (details see below). For both arms together, this yields 1172 patients in total. Given that 
4 sites will be recruiting patients, this represents a mean of 293 participants per site (147 per arm at 
each site). Further details on sample size estimation can be found in (statistical considerations). 
 
10. Study procedures 
10.1 Pre-eligibility screening 
Initial pre-eligibility based on HIV status will be assessed by study staff, who will visit the adult medical 
wards every morning to identify any newly admitted patients. HIV documentation can be written 
proof of a positive HIV test, CD4 count records or ART prescription. From the information available 
in-patient registers and/or patient files, only those with unknown or documented HIV-positive status 
will be approached to participate in the study. Routine health personnel need to be aware of the 
study and contact study personnel whenever a new  admission occurs. 
 
For those with unknown HIV status, a rapid antibody-based test will be performed (further  details 
under laboratory procedures) by authorized personnel (after ICF is obtained). 
 
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Basic anonymized information on participants who are admitted in the adult ward but not enrolled 
in the study will be recorded in a pre-screening log which should include: age, gender and the reason 
not eligible for trial participation, or if they are eligible but declined. 
 
10.2 Informed consent 
Informed consent will be sought from potential participants using information sheets and consent 
forms available in relevant languages. Written informed consent will be sought, with the assistance 
of a translator or a witness where necessary, using standard consent forms. In occasions where the 
participant is not able to undergo the informed consent process (mental retardation, altered level 
of consciousness, somnolence, obtundation, stupor or certain psychiatric conditions) an authorized 
relative might provide the written consent as a witness. In the case these conditions are temporal, 
patients would be reconsented when they are in full capacity. Participants unable to read or write 
will be asked to make a mark or thumbprint in the presence of a witness. Details on standard 
informed consent procedures will be specified in site standard operating guidelines. The ICF will 
include a section to access to medical records and collection of relevant data from them. 
 
10.3 Assessment for eligibility 
All inclusion/exclusion criteria must be assessed among those HIV-positive patients admitted in the 
ward and who have signed the informed consent. 
 
For those patients who are not eligible, study staff will inform them that they will not be able to 
participate in the study and will receive the local standard of care. 
 
10.4 Recruitment 
A participant is considered recruited for the study when the participant has signed the informed 
consent, meets all the inclusion criteria and does not fulfill any of the exclusion criteria.  
For those patients enrolled in the study, all the screening procedures will be documented in the 
screening logs and appropriate case report forms (CRFs) will be completed before starting the 
procedures specific to the control or intervention arm, including: 
a) Basic socio-demographic information 
b) Relevant medical history 
c) Physical exam 
Basic sociodemographic information and relevant medical history will be collected from the 
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participant/caregiver or, if available, from existing medical records. A locator form (as a source 
document) will include contact information of the participant and/or caregiver or relative (with  at 
least one mobile phone number to reach out the participant after discharge). 
Time from admission (as recorded in medical history) to study enrolment will be recorded. However, 
this time should be as short as possible, preferably less than 12-24 hours. 
10.5 Randomization 
This is an individually randomized clinical trial. Eligible participants will be randomized to either the 
intervention or control arm, with an expected 50% of participants allocated to each of the arms. 
Randomization will be conducted using a web-based application (Enketo software) that can be used 
in any smartphone device or computer with internet connection. The day of randomization for each 
participant will be the enrolment day (study Day 0). At the time a participant is randomized, the 
study staff enters in the application several key data (patient study number and date of birth) and 
in reply, the randomization arm is provided a few seconds later in the same application interface. 
Thus, internet connection is needed for randomizing participants. Pre-registered users of the study 
team will be allowed to use the randomization application. 
Developing a reliable training plan by which study teams (at the clinic and at the lab) are fully aware 
of the diagnostic allocation is critical so that arm-specific testing can be implemented without 
mistakes in a timely manner. This includes careful strategic measures (posters, signs, weekly 
meetings, etc) as part of the site internal planning, which also need to consider staff shifts, holidays 
(both in the hospital and at the laboratory). A screening and randomization log  need to be daily 
updated. Day 0 CRF needs to be data entered in a timely manner to allow the central monitoring of 
number of recruited subjects per arm, site and week and overall mapping  of participants included 
in the study. 
 
10.6 Blinding 
This is an unblinded trial. Neither participants, nor study staff will be blinded to tests practiced or 
test results. 
Enrolment and testing will be done by study staff. AlereLAM will be done at the hospital or at a 
short distance from hospital (for example, same building hospital laboratory). Results of all tests will 
be provided to routine clinical staff who will make decisions on treatment initiation. 
10.7 Minimisation of Error and Bias 
Selection bias will be minimized by a) the randomization process and b) consecutive enrolment of 
participants meeting inclusion criteria (and not meeting exclusion criteria). Study staff from all sites 
will be trained prior to study initiation in order to guarantee that inclusion and exclusion criteria and 
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well understood and applied homogenously across sites. 
Other potential sources of bias (ascertainment, information, interpretation), will be also addressed. 
Laboratory procedures will be standardized across sites, using the same laboratory SOPs and 
specific lab training, in order to minimize differences by site. Given that most tests are different by 
arm, and that AlereLAM will be preferably done at the health facility (by the bed side), no blinding 
of attending physician or lab technologist will be possible. In order to explore the differences 
between WHO recommended procedures and real standard of care at the sites, there is an 
exploratory objective aiming at assessing the current yield of TB investigations under routine 
conditions prior to the study initiation at all sites. This will be consecutive collection of retrospective 
data from PLHIV admitted at participating hospitals prior the start of the study. The quality and 
completeness of this data might differ from  participating sites. 
Decision to start TB treatment will be based on any test results  and the criteria of the physician 
responsible for the patient’s care.  
 
10.8 Allocation to study arm 
 
Enrolled patients will be randomly assigned to receive the diagnostic procedures specified for the 
intervention or control arm. Date and time of patient admission and recruitment need to be clearly 
recorded in the patient file (hour and when possible, minutes). Once the patient has provided the 
relevant baseline information specified above (recruitment section), the researcher will proceed to 
randomization and then, will open a patient file where the patient trial identification number will be 
clearly visible. A specific study card with study team contact information and patient study number 
will be handed to the participant. 
 
The allocation of the study arm will be recorded in the participant study file under the appropriate 
CRF. Different coloured study files (to identify allocation) should be used. Patients could be recruited 
any day of the week although teams are encouraged to plan the relevant shifts over the weekend 
periods. 
 
10.9 Arm-specific procedures (See table 2) 
 
10.9.1 Intervention arm 
The intervention arm for this trial will consist of testing sputum, stool and urine with Ultra and urine 
with AlereLAM in all recruited patients regardless of symptoms. Thus, all patients allocated to this 
arm will be asked to provide urine, stool and/or sputum. 
 
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If urine or sputum cannot be provided spontaneously at the time of recruitment, participants will 
be asked to do so within 72 hours (aim: within 24 hours from enrolment). Patients will be 
encouraged to drink water to stimulate diuresis (unless contraindicated). Urine will be collected in 
specific containers and stored for future testing. Ultra on Stool will be performed in fresh specimen 
according to the KNCV SOS method33. 
Additionally, we will ask for stool and oral swabs specimen for Xpert Ultra/ LumiraDx testing. 
 
We aim to collect all samples specified for each intervention (including those for exploratory studies) 
within 72 hours from enrolment. Efforts will be made to collect all samples within the first 24 hours. 
Time of sample collection will be specified in the sample collection log and CRF. 
 
10.9.2 Control Arm 
The control arm screening and testing strategy will consist of: 
 
Sputum Ultra whenever the patient has cough, fever, weight loss or night sweats and/or Ultra on 
any tissue (including lymph nodes) from patients with suspected extrapulmonary TB. 
Urine Alere TB-LAM, if patients 1) have signs and symptoms of TB (pulmonary and/or 
extrapulmonary), or 2) have advanced HIV disease* or 3) are seriously ill**. The latter two are all 
irrespective of signs and symptoms of TB. 
 
*Adult patients with advanced HIV disease are those with CD4 cell count <200 cells/mm3 or a WHO 
clinical stage 3 or 4 event at presentation to the clinic. 
 
**A seriously ill patient is any individual with HIV or of unknown HIV status presenting with one or 
more of the following danger signs: 
 
Unable to walk unaided 
 
A respiratory rate over 30/min 
 
A fever of more than 39ºC, and/or 
 
A pulse rate of over 120/min 
Thus, sputum and urine collection will only be conducted for Ultra and AlereLAM testing if the 
above-mentioned symptoms/criteria are present. Otherwise, urine alone will be collected in specific 
containers and stored for future testing. Patients will be encouraged to drink water to stimulate 
diuresis (unless contraindicated). 
The control arm for this trial follows WHO recommendations (as of January 2020) for bacteriological 
testing among hospitalized HIV-positive individuals. 
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Study staff will collect the samples for both arms. 
In case any sample cannot be obtained within the first 72 hours from enrolment, reasons should be 
recorded in the appropriate CRF. In case the participant can provide the required sample(s) after 72 
hours from enrolment, samples should still be collected and processed with clear indication of date 
and time. Special measures need to be implemented locally so the laboratory is aware of the tests 
to be performed despite some potential delay in specimen testing. After 72 hours from enrolment 
have passed, patient will be managed as per national guidelines. 
Other than TB, patient clinical management will follow established national guidelines and protocols 
for hospitalized HIV-positive patients. 
10.10 Follow up procedures (table 2) 
Hospitalization stay (daily) 
During hospitalization (daily) and at discharge, study team will verify and record whether a TB 
diagnosis has been made and/or anti TB treatment started. The study team will be working jointly 
with the routine health care staff so clinical decisions are made jointly. Study team will also record 
any ad-hoc TB investigation (additional Ultra, LAM testing, X-ray, etc)  and their result. HIV care will 
follow national guidelines. . 
Scheduled visits 
After enrolment, there are two scheduled visits that need to take place unless the patient remains 
hospitalized (week 4 and week 8). These visits can occur either in the outpatient clinic, as home visits 
or by call or video-call depending on the patient and team preferences and COVID-19 
epidemiologic situation. However, outpatient visits are recommended. A member of the study team 
will verify whether a TB diagnosis has been made on the relevant medical records (hospital or NTP 
office) and/or anti TB treatment started after discharge. Study staff will also record any ad-hoc TB 
investigation that was initiated by the care provider for clinical reasons (additional Ultra, LAM 
testing, X ray, etcetera) and their result (both by checking patient records and by asking the patient). 
HIV care will follow national guidelines. Vital status will also be recorded at these two visits. These 
visits will have a window period of -/+ 3 days (at week 4) and -3/+7 days at week 8. 
In case a discharged participant does not attend the week 4 or week 8 visit, three phone call 
attempts will be made and, if unsuccessful, at least one home visit will be performed in order to 
collect relevant data to that visit. These attempts should be recorded in a patient tracking log. Week 
4 visit should be sought until week 8 window visit opens, although will be considered a protocol 
deviation if done outside the week 4 window visit. 
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10.11 Participant study completion (week 8) 
Patients might terminate their participation in the study at any point. Reason, if available, should be 
recorded in the patient file. Once participants have completed their week 8 visit (at the 
hospital/outpatient clinic or as home visit), they will be considered having completed their 
participation in the study. For those not attending week 8 visit, they will be considered lost to follow 
up after the three phone call attempts and home visit have occurred. Deaths occurring during the 
study at patient’s household will be documented and relatives will be asked about signs and 
symptoms before death. In settings where verbal autopsies are routinely conducted (CISM), this 
data will be considered a study source document and information captured in the off-study-form. 
10.12 Retention 
Based on previous studies conducted at the sites, we expect a 5% lost to follow up rate at month 2. 
Sites will implement several strategies to maximize the retention rate, such as recording of several 
phone numbers in the locator form at recruitment, careful recording of physical address, additional 
contact information from relatives and friends, travel reimbursement to compensate them for the 
cost of transport to the clinic for study visits, etcetera, always according to local practice. 
10.13 Participant termination and criteria 
The study physician responsible and the PI may withdraw a patient from the trial (or certain 
procedures of the trial) for appropriate medical reasons, because of individual adverse events or 
new information gained about a diagnostic or a treatment. The physician should contact the Trial 
Management Team to inform of this decision. Likewise, any patient can withdraw from the study 
any time without explaining the reasons. 
 
10.14 Trial discontinuation 
The study may be discontinued at any time by the funder, sponsor, investigators, or by any of the 
relevant regulatory bodies and reasons for this decision will be appropriately communicated to the 
sites and enrolled patients. 
10.15 End of trial 
The sponsor will notify the authorities of the end of the clinical trial field activities within 90  days of 
its completion (the date of the last visit of the last patient undergoing the trial). 
 
10.16 Safety Assessments 
Refer to Section 10.17 
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Laboratory safety assessments will be done during study site assessment and/or study initiation 
visits to ensure that potentially infectious specimens are processed according to national and/or 
international guidelines. 
Medical device incidents will be recorded and reported according to the MEDDEV 2.12/1 Rev 8 (see 
summary in 10.17.1 Medical Device Incidents (including Malfunctions)). 
10.17 Safety and Incident Reporting 
The probability of an AE or SAE occurring to a trial participant to be associated with the 
investigational products, or with the additional procedures used (such as sputum and urine 
collection, venipuncture for those HIV patients and fingerstick), is extremely low. 
 
10.17.1 Serious adverse events (SAE) reporting 
An SAE is any unfavourable and unintended sign (including abnormal laboratory finding), symptom 
or disease temporally associated with the use of an investigational product, whether or not related 
to the investigational product with a) results in death b) is life-threatening; c) requires inpatient 
hospitalization or prolongation of existing hospitalization; d; results in persistent disability/incapacity; 
e) is a congenital anomaly/birth defect or f: requires intervetnion to prevent permanent impairment 
or damage to the human subject. 
 
Given the nature of this study (in which no investigational product is administered to the participant), 
SAE reporting is limited in scope to: 
 
a) SAEs that may be associated with sputum, urine and blood collection 
b) SAEs which results in death. 
 
SAE reports must be sent to the FIND on a six monthly basis (line listing format). Contacts for SAE 
reporting can be found on the front of the protocol. SAE reports should be sent to national IRB and 
regulatory authorities with a similar frequency or as per national regulations for diagnostic clinical 
trials.  
 
10.17.2 Medical Device Incidents (including Malfunctions) 
 
Medical devices are being provided for use in this Trial for TB diagnosis in PLHIV. In order to fulfil 
regulatory reporting obligations worldwide, the investigator is responsible for the detection and 
documentation of events meeting the definitions of incident or malfunction that occur during the 
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trial with such devices. The definition of a Medical Device Incident can be found in Appendix 1. 
 
NOTE: Incidents fulfilling the definition of an SAE related to a medical device will also follow the 
processes outlined above and in Appendix 1 of the protocol. 
 
10.17.3 Time Period for Detecting Medical Device Incidents 
 
Medical device incidents or malfunctions of the device that result in an incident will be detected, 
documented, and reported during all periods of the trial in which the medical device is used. 
If the investigator learns of any incident at any time after a participant has been discharged from the 
trial, and such incident is considered reasonably related to a medical device provided for the trial, the 
investigator will promptly notify FIND. 
The method of documenting Medical Device Incidents is provided in Appendix 1. 
10.17.4 Follow-up of Medical Device Incidents 
 
The investigator is responsible for ensuring that follow-up includes any supplemental investigations 
as indicated to elucidate the nature and/or causality of the incident. New or updated information 
will be recorded on the originally completed form with all changes signed and dated by the 
investigator. 
 
10.17.5 Reporting of Medical Device Incidents to FIND 
 
Medical device incidents will be reported to FIND within 24 hours after the investigator  determines 
that the event meets the protocol definition of a medical device incident. 
The Medical Device Incident Report Form will be sent to the sponsor scanned by e-mail. If e-mail is 
unavailable, then the investigator should phone the sponsor and send an e-mail as soon as possible. 
Contact details will be provided in the Trial Manual. 
The same individual will be the contact for the receipt of medical device reports. Medical device 
incidents will then be communicated by the sponsor to the manufacturer within 24 hours after the 
sponsor has received the Medical Device Incident Report Form. 
 
10.17.6 Regulatory Reporting Requirements for Medical Device Incidents 
 
The investigator will promptly report all incidents occurring with any medical device provided for 
use in the Trial for FIND to fulfil the legal responsibility to notify appropriate regulatory 
authorities and other entities about certain safety information relating to medical devices being 
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used in clinical studies. 
The investigator, or responsible person according to local requirements (e.g., the head of the medical 
institution), will comply with the applicable local regulatory requirements relating to the reporting 
of incidents to the IRB/IEC. 
 
10.18 Retrospective data collection 
Given that our control arm may not represent the local standard of care across sites, we will compare 
the main study endpoints of both study arms with a third cohort of patients, which follows the real 
standard of care at the different sites. We will retrospectively collect data of a cohort of consecutively 
hospitalized HIV-positive patients that were admitted prior to the trial initiation. Data to allow the 
evaluation of primary objectives will be collected from medical records (source documents) in an 
anonymized fashion.  We aim to collect data from patients who were admitted to the site two 
months or more before the day of the trial first study patient recruitment. Patient records will be 
selected from consecutive admissions from that day backwards until completing the sample size 
(around 147 cases per site). Data collection will be obtained retrospectively in order to capture the 
real practice at the different sites, including potential phone calls to confirm the life status of the 
patients after two months of hospitalization, minimizing the effect of a potential Hawthorne effect. 
Given the complexity and often impossibility of obtaining informed consent from patients that have 
been discharged, no informed consent will be sought for these patients. This IC exemption is an 
exception contemplated in the International Ethical Guidelines for Health-related Research Involving 
Humans of the Council for International Organizations of Medical Sciences (CIOMS) (Geneva, 2016). 
The study has not been powered to detect differences in the primary endpoint between intervention 
or control arm and the retrospective cohort (which may vary between sites). This is a secondary 
objective that will be analyzed at site level.  
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11. Schedule of visits (table 2) 
Day 0 
(recruitment) 
Day 0 
(recruitment) 
Day 0-3 
Daily 
At discharge 
If discharged before 
day 28/56 
Week 4                 Week 8 
+/- 3 days 
                                                                                       Control arm 
   Intervention arm 
(<72h) 
Baseline Evaluation 
 
 
Informed consent 
X 
X 
Eligibility criteria verified 
X 
X 
CD4 count / Viral Load& 
X 
X 
Locator information 
X 
X 
Brief medical history 
X 
X 
Proof of HIV status stored 
X 
X 
WHO Symptom screening 
X 
X 
X 
TB Investigations 
Samples collected and tests 
 
 
Results issued 
Urine 
AlereLAM# 
Sputum Ultra* 
 
Blood CD4 
Sputum Ultra 
Stool  
Ultra  
Urine Ultra  
Urine AlereLAM  
2x Oral Swabs 
Urine FujiLAM  
Blood CD4 
Blood for CRP 
X 
Further contacts 
Verification TB diagnosis / ad hoc TB 
investigations 
 
 
 
X 
 
 
X 
 
 
X 
 
 
X 
Verification TB treatment initiation 
 
X 
X 
X 
X 
Verification vital status 
 
X 
X 
X 
X 
HIV care / ART 
 
X 
X 
X 
X 
*Sputum Ultra whenever the patient has cough, fever, weight loss or night sweats and/or Ultra on any tissue (including lymph nodes) from patients with suspected extrapulmonary TB  
#Urine LAM if patients have currently signs and symptoms of TB (pulmonary and/or extrapulmonary), or with advanced HIV disease (1) or who are seriously ill (2) or else irrespective of signs and symptoms 
of TB and with a CD4 cell count of less than 200 cells/mm3. 
&CD4 count testing will be done if not available within the last 3 months. Most recent viral load will be captured (if available) 
**urine should be collected in all participants in the control arm, irrespective of whether LAM test is done. 
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12. Laboratory procedures and storage of samples 
Samples will be processed and results issued back to attending physicians as soon as possible. 
AlereLAM results should be available within two hours from specimen collection. Ultra results 
should be provided within 24 hours from being collected at the participating hospital laboratory 
associated facilities. 
 
12.1 Xpert Ultra for TB 
This WHO recommended assay, which is currently substituting the previous version (Xpert), uses 
a cartridge-based polymerase chain reaction platform.   
 
12.1.1 Sputum: Ultra testing will be performed in a sample of raw sputum (without any prior 
decontamination) and it requires mixing sputum with a buffer (proportion 2:1) for 15 minutes. 
Following incubation, 2ml of the sputum-buffer mix are transferred into the Ultra cartridge, 
which is placed in the Xpert instrument. Results are ready within 100 minutes. It detects Mtb 
DNA in a sputum sample and is able to detect a mutation in the resistance-determining 
region (RRDR) of the rpoB gene which is the responsible of 95% of drug resistance to 
rifampicin (Rif).33 Rifampicin resistance is generally considered to be predictive of MDR since 
most Rif resistant strains are also resistant to isoniazid. 
12.1.2 Stool: Ultra testing on stool will be done in a sterile loop from bulk stool following 
the KNCV SOS method (https://www.kncvtbc.org/en/sos-stoolbox/).  
12.1.3 Urine: Following the removal of 200 µL of urine for AlereLAM testing (see below) and 
12 ml for storage for future testing the remaining urine (around  40-50mls) will be cooled 
centrifuged at 3000g for 15mins in a bucket centrifuge. The supernatant will be discarded, 
and the urine pellet resuspended in approximately 2ml of PBS. 0.75ml of the resuspended 
pellet will be added to 1.25ml of Ultra sample reagent and incubated for 15 minutes, then 
added to the cartridge and processed as per the manufacturer’s instructions.  
12.1.4 Tongue swab:  After the sample is collected (from brushing the swab along the 
length/breadth of the anterior 2/3 of the tongue dorsum for about 10 seconds) the head of 
the swab will be broken off and the shaft of the swab discarded. The tubes will be stored dry 
and later Ultra and/or LumiraDx (see 12.3) testing will be performed following instructions in 
SOPs developed. 
 
 
 
 
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12.2 Other urine-based tests procedures:  
12.2.1 AlereLAM testing: 
Recommended by WHO for TB diagnosis in severely immunocompromised HIV-positive 
patients, will be performed under the specified criteria in the control arm and in all 
participants in the intervention arm. A urine sample (at least 1-3 ml) will be taken at the 
hospital facilities (see below). The test is performed by applying 60 μL of unconcentrated 
urine to the Alere Determine™ TB LAM Ag assay strip and  incubating at room temperature 
for 25 minutes (time-set). The strip is then inspected by eye. 
The intensity of any visible band on the test strip is graded by comparing it with the 
intensities of the bands on a manufacturer-supplied card (LAM positive will be deemed 
using the grade 1 cut-off on the manufacturer’s post 2014 reference card). AlereLAM tests 
will be interpreted by two independent readers at the clinic, and results will be recorded. In 
case of discrepancy, a third reader will be used as a tie-breaker. Invalid tests will be repeated 
using the same urine. Indeterminate results will be repeated with a different urine sample. 
Alere-LAM test strips will be stored until the end of the study for data monitoring purposes. 
Alere-LAM tests will be read prior to the results of the sputum Ultra (if performed) and 
without knowing any clinical details of the patient to reduce bias. 
 
12.2.2 FujiLAM testing (Appendix 2): Briefly, urine is added to the reagent tube up to the 
indicator line (approximately 200 μL), mixed, and incubated for 40 min (set timer) at ambient 
temperature. After mixing again, two drops of urine are added to the test strip. Following 
this, button two is immediately pressed to release a reducing agent for silver amplification. 
After the Go Next colour  indicator mark turns orange (within 3–10 min), button 3 is pressed 
to release a silver-ion solution to activate the silver amplification reaction. The result has to 
be read within 10 min (set timer). The FujiLAM assay does not use a reference scale card and 
any line identified on the test line is deemed positive. This test will be done retrospectively in 
banked samples. 
 
12.3 LumiraDx: The test strip is introduced into the LumiraDx device through opening the 
instrument’s door. A drop of the prepared oral tongue swab / blood specimen is applied to the test 
strip and a confirmation of the sample detection appears in the instrument’s screen. After this, the 
door is closed immediately. The results are provided with in 10 minutes.  
 
12.4 HIV testing: Rapid point-of-care antibody-based HIV testing will be performed in those 
patients with unknown or undocumented HIV status using fingerprick blood. Testing will be done by 
trained health care workers. If the result of the first “rapid” test (Determine®, Abbott Laboratories, 
USA) is positive, a second confirmatory test will be performed. CD4 counts will be obtained from al TB 
cases coinfected with HIV (if no recent documented CD4 counts are available-within last 3 months) 
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as well as all newly identified HIV-positive cases. CD4 testing will be done at each site using point of 
care PIMA equipment or FACSCalibur flow cytometers. Newly diagnosed HIV- positive patients will 
be referred to appropriate counselling services at each of the sites. 
 
12.5 Sample Storage details: 
Storage of all specimens will follow detailed SOP which will be similar at all participating sites. 
Specimen storage is not a mandatory component of the protocol, but will be encouraged to 
accomplish exploratory objectives and retrospective testing. Storage should be done the same day 
of sample collection. 
12.5.1 Urine samples. After removing necessary volumes for Ultra and AlereLAM testing, transfer 
raw urine (12 ml) to a sterile 50ml tube. Aliquot the supernatant in two 3.5 ml aliquots. Aliquots 
should be stored at -80 or -70ºC. In case no criteria for AlereLAM testing is in place in the control 
arm, urine would still be collected for storage. 
12.5.3 Tongue swabs samples: Two tongue swabs will be collected. After sample collection, the head 
of both swabs will be broken off and stored dry in a 5ml tube at -80°C for later testing with Ultra 
and the LumiraDx platform. 
 
 
 
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13. Statistical considerations and data analysis 
13.1 Sample Size calculations 
Recent studies using Alere LAM and sputum Xpert to screen unselected admitted HIV positive 
patients in Southern Africa24,29,31 show that around 17% of these patients are laboratory confirmed 
for tuberculosis. The added yield of using Xpert Ultra instead of Xpert would involve an 11-17%43–
45 relative increase in bacteriological confirmation. Thus, universal AlereLAM testing and sputum 
Ultra would likely confirm around 20% of unselected admitted HIV participants in our study. We 
estimate that the bacteriological confirmation in our control arm would be slightly lower than 
20%, around 19%, given that we will not use a universal screening strategy but the WHO 
recommendations (sputum Ultra if TB compatible symptoms and AlereLAM testing if TB 
compatible symptoms or in those with advanced HIV disease, or seriously ill, or with a CD4 cell 
count of less than 200 cells/mm3). Based on existing literature, we estimated that up to 10% of 
participants in our control arm would not receive either Xpert Ultra or LAM testing.  
We estimated that the intervention arm would yield around 26% of bacteriologically confirmed 
cases by universal testing (irrespective of symptoms) with AlereLAM and Xpert Ultra on 
sputum, urine, and stool. As mentioned before, universal AlereLAM and sputum Xpert Ultra would 
yield around 20% of bacteriological confirmation. Studies show that Xpert urine could increase 
bacteriological confirmation by 4%. Although there is limited evidence on the potential benefits 
of stool Xpert Ultra in adults, there are promising results observed in children (who, as HIV positive 
patients, often have extrapulmonary TB). Thus, we assume that adding stool Xpert could increase 
our bacteriological confirmation about 1%. If we apply a similar gain (observed in sputum) in urine 
and stool by substituting Xpert by Ultra, the combined added yield would be of around 6%. Thus, 
we expect to have a 26% bacteriological confirmation in our intervention arm by using universal 
LAM testing and Xpert Ultra on sputum, stool and urine. This would translate into a 7% difference 
(19-26%) between our control and intervention arm. 
The estimation of the bacteriologically confirmed cases in both the control and intervention arm 
could have the following limitations: 
 We estimate the increased yield of Ultra in urine and stool as if this additionality were 
independent, considering that this yield would come from potentially different phenotypes 
of TB patients. Otherwise, some of the gain observed by Urine Xpert Ultra or Stool Xpert 
Ultra might overlap and thus we could be overestimating the expected additionality in 
bacteriological confirmation in these samples.  
 We obtained the Xpert Ultra added yield from studies performed in TB presumptive HIV 
positive inpatients and outpatients. Estimates of added yield vary widely in the literature. 
However, given that major gain of Xpert Ultra has been observed in HIV positive patients 
and smear negative patients, we think that the added yield of Ultra in our population 
(strictly admitted PLHIV) could be higher, and potentially greater in extrapulmonary 
samples such as stool or urine (as a recent study -Kabir et al, 2021 -of Stool Ultra in children 
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has shown). In this regard, we have taken a conservative approach by using the reference 
of Dorman et al, 2018.  
 The added yield of Ultra over Xpert does not consider that some of that additional yield 
might be picked up by Urine AlereLAM (optimistic approach). 
 Some of these limitations may impact both the control and the intervention arm and thus 
would probably have a limited effect on our expected difference in bacteriologically 
confirmed cases that we aim to detect through this study.  
 
Assuming that we will find 19% of bacteriologically confirmed cases in the control arm following 
the WHO indications for sputum Xpert® Ultra and AlereLAM in HIV hospitalized patients (based 
on previously mentioned data), and a two-sided type I error of 5%, the inclusion of patients per 
arm would provide an 80% power to detect a 7% increase in the percentage of bacteriologically 
confirmed TB diagnosis allowing for a loss to follow-up of 5%. 
 
Based on these estimates, the study will require a total of 586 PLHIV participants to be enrolled 
per trial arm. For both arms together, this yields 1172 patients in total. 
 
Given that 4 sites will be recruiting patients, this means approximately 293 participants per site 
(around 147 per arm at each site). 
 
13.2 Data analysis 
A separate statistical analysis plan will be developed containing all details of the analysis strategy. 
13.2.1 Analysis set 
 
We will analyze the data using primarily an intention to treat analysis approach. This dataset is 
composed for all randomized patients by their assigned intervention. It also includes patients who 
might not complete week-4 and week-8 visit or who died or who did not receive the full assigned 
intervention. Lost to follow up patients and deaths will be considered for specific secondary 
endpoints. 
 
13.2.2 Statistical methods 
Variables will be summarized using descriptive statistical methods. Continuous data will be 
described using the mean and standard deviation statistics when these values follow the normal 
distribution. Otherwise we will use the median and interquartile range when we will not assume 
this distribution. Categorical values will be summarized using frequency and/or percentages. 
 
For categorical comparisons we will use a Chi-square test or Fisher exact test according to the 
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data characteristics. Likewise, the continuous comparisons will be tested by Student t-test, Anova 
test or Kruskal Wallis test. 
 
When necessary, we will transform the continuous data, especially laboratory data, in non-linear 
scale. For these cases we will describe these data with geometric mean. Heterogeneity between 
sites will be analyzed. 
 
Assessment of loss to follow-up as random across arms 
We will analyze the baseline characteristics between lost and non-lost follow up patients and 
across arms to ensure that loss to follow up occurs randomly. If we find any significant attribute 
we will adjust the analysis by this/these factors. 
 
Time-to-event data 
Time-to-event data (such as time to mortality, time to TB diagnosis or time to treatment initiation 
(among lab confirmed or all TB)) will be presented using Kaplan-Meier curves with a log rank test 
(two-sided 0.05 significance level). The analysis of covariates on time-to-event data will be 
performed using a Hazard Ratios estimated through Cox regression models. 
Comparisons between control and intervention arm will be established at prespecified time 
points (day 7, day 14, day 28 and day 56). Mean time (and SD) to event per study arm will also 
be estimated. 
 
Significance levels 
The significance level for most comparisons is p=0.05. For selected secondary endpoints measured 
at several timepoints and subgroup analysis, the significance level will be p=0.01 
 
Study discontinuations & patient disposition 
Patient disposition and reasons for premature discontinuations and their frequencies will be 
tabulated. 
 
Datasets analyzed 
Number of patients in each analysis set will be tabulated and listings of any patients excluded 
from any analysis set will be provided. 
 
Efficacy analysis 
The primary efficacy endpoint has a composite numerator ‘microbiologically confirmed TB and 
therapy initiated within 72 hours from admission’ (success), ‘non lab-confirmed TB or therapy 
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not initiated within 72 hours’ (failure). 
Microbiological confirmation may arrive later than 72 hours after enrolment (to account for 
scenarios in which culture is requested or there is any delay on sample processing). 
The primary efficacy analysis will be compared between the proportion of microbiologically 
confirmed TB and therapy initiated within 72 hours of enrolment in each study arm. 
Adjustment for other variables (country, hospital, seasonality or other possible confounders) 
may be considered and will be described in detail in the analysis plan. 
Missing values will be examined in detail. We may consider a multiple imputation procedure if 
necessary (variables with more than 10% of missing values). 
We will accept as significant difference the p-values less than 0.05. 
13.2.3 Pre-specified sub-analysis 
 
Primary and selected secondary endpoints among PLHIV with ≥200 CD4, <200 CD4 and 
<100 CD4 cells/mm3 and 
 
Primary and selected secondary endpoints among admitted HIV positive patients 
providing at least one sputum, stool and (or) one urine sample for testing. 
 
The primary and selected secondary endpoints will also be calculated among those who 
had their test result available and were started on treatment within 72h of enrolment in 
both arms (as in a classical per-protocol (PP) analysis). 
 
Both the main clinical trial analyses (related to primary and secondary objectives) and that related 
to the exploratory objectives (oral swab Ultra and LumiraDx and urine FujiLAM sub-studies) will 
be expanded in separate statistical analysis plans. 
 
13.2.4 Interim analysis 
For this study no formal interim analysis is planned. 
 
13.2.5 Software documentation 
 The statistical analysis will be performed with the Stata software. We will use the Stata 17 version 
or the last most up to date available version when analysis takes place. Scripts used in the analysis 
can be published as supplementary material of the main publication or uploaded into a public 
repository 
 
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14. Data management 
14.1 Type of data that will be collected 
a) Participants’ personal data 
This trial will collect pseudonymized demographic and clinical data. This includes variables such 
as TB symptoms, weight, height, medical history (history of diabetes, renal failure, others), current 
and past medication, HIV status, ART use, tobacco and alcohol use, previous TB episodes, 
existence of TB contact at home, among others. 
b) Laboratory parameters (biological data) derived from laboratory analyses of participants’ 
specimens 
Results from all TB microbiological assays performed to patients including CD4 counts (if not 
available within the last 3 months) and HIV test (if not documented status available), will be 
linked to study participant’s information through a unique study identifier number. All samples 
and databases will not contain patient’s name but only laboratory barcodes and anonymized 
patient study numbers. 
 
14.2 CRFs 
We have developed 10 main CRFs for all participants: 
 
Consent & Eligibility CRF 
 
Baseline Characteristics CRF 
 
Specimen Collection CRF 
 
AlereLAM & CRP CRF 
 
FujiLAM Results CRF 
 
Xpert Ultra Tongue Swab Results CRF 
 
Lumira Dx Test Results CRF 
 
Hospitalization assessment CRF 
 
4 Week visit CRF 
 
8 Week visit CRF 
 
Lab results CRF (including TB specific and other lab results (CD4 counts, viral load) 
 
Study Completion CRF(whenever a patient stops being part of the study (completed all 
procedures -at week 8), death before week 8, or LTFU at any point within the first 8 weeks). 
 
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In addition, a retrospective local standard of care CRF will be used (Retrospective CRF). 
 
 The Lab result CRF might be used at 
any point within the study period if additional TB tests are performed on the patient. 
 
14.3 Data entry 
Data will be collected on paper based CRFs and entered to a secured encrypted and password 
protected electronic CRF system using OpenClinica® Software (Enterprise version 4), a secure web 
application for building and managing online surveys and databases. While OpenClinica can be 
used to collect virtually any type of data, it is specifically geared to support online data capture 
for research studies and operations. 
Data collection and entry will be performed by study specific personnel trained in data collection 
and human subjects data protection. Data managers will design the electronic CRF, ensure all data 
quality and provide support whenever a problem occurs. Each completed CRF should be data 
entered within a week from its completion. 
Although main data capture will be based on paper CRFs replicating electronic CRFs, there will be 
handwritten data source documentation (additional patient medical history, HIV proofs, X ray 
data, printouts of Ultra results, clinical follow up information and other), which will be kept with 
patient study files locally and that might be used for data quality checks. All personnel with direct 
access to data will be trained on human subjects’ data protection and maintain training records. 
Different data access privileges to OpenClinica will be set for different user types (local data clerks, 
local data managers, local study coordinators, site PIs, and project overall data manager from LMU). 
The Site PI and site project manager/study coordinator are responsible for assuring that the data 
entered into OpenClinica is complete, accurate, and recorded in a timely manner. 
In addition to data capture, sites will maintain logbooks to record the dates of completed and 
upcoming study visits, specimen collection, transport and receipt at the respective laboratories, 
and time of receipt of test results. Laboratory tests will be requested on study laboratory test 
requisition forms. All logbooks and laboratory requisition forms will be kept in locked filing 
cabinets when not in use and will be accessible only by designated clinic personnel. 
 
14.4 Data monitoring and quality assurance 
Electronic CRFs will be designed in order to minimize data capture errors. Drop-down menus, 
data range limits/edit checks and data type protection will be included in open data collection 
fields. Data will be curated by local data clerks and routine data checks performed by local data 
managers. The project main data manager at LMU will periodically generate a list of data queries 
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derived from the reconciliation of different clinical and lab project data. Automated syntaxes will 
be designed in order to improve the efficiency of the quality assurance process. 
No official onsite data monitoring visits will be done in this study. Central/remote monitoring will 
happen remotely through LMU/FIND. 
14.5 Record retention 
Study records (source documents, signed informed consent forms, IRB/IEC correspondence and 
approval letters, and screening logs) will be kept in a secure location accessible only to authorized 
study staff, investigators, and monitors. Secure archives are available at the sites for preliminary 
storage after study closure, before moving them to an off-site, secure storage facility. All records 
will be archived in a secure storage facility for at least ten years after the completion of the study. 
 
 
 
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15. Ethical considerations 
This study will be conducted according to the ethical principles set forth in the Declaration of 
Helsinki, ICH-GCP, and local regulatory requirements as applicable. 
 
Written informed consent will be obtained from each participant prior to any protocol-specified 
procedures being conducted. An added IC for specimen storage (and future use) might be 
required at some sites. The protocol and informed consent form(s) will be reviewed and approved 
by the IRB or IEC of each participating clinical site prior to patient enrollment. Site investigators 
are responsible for ensuring that the protocol is reviewed by an IRB/IEC with the appropriate 
composition (per site guidelines). The investigator will inform the IRB/IEC as to the progress of the 
study at applicable intervals as defined by IRB/IEC policy. Depending on national policies, the 
protocol might be reviewed by national regulatory authorities. 
 
FIND will act as the main sponsor for this study. Delegated responsibilities will be assigned locally 
and documented. FIND holds Public Liability ("negligent harm") and Clinical Trial ("non-negligent 
harm") insurance policies which apply to this trial. 
 
15.1 Confidentiality 
 
Adequate measures to ensure personal data protection and confidentiality will be taken, 
according to the European General Data Protection Regulation (EU) 2016/679 (GDPR) on the 
protection of natural persons with regard to the processing of personal data and on the free 
movement of such data. National regulations on personal data protection will be implemented 
to safeguard patients’ confidentiality throughout the duration of the clinical trial. 
 
 
All study related data (study CRFs and clinical specimens) will be pseudonymized linked to an 
individual patient study number, and samples will be numbered/barcoded in accordance. Names 
or other obvious identifiers will not be used on study CRFs, they only will appear at each site on 
source documents. Any hardcopy links between patient names and patient study numbers or 
data will be kept in a locked cabinet at each study site, under the responsibility of the PI/site 
coordinator. All informed consent forms will also be maintained in a locked cabinet at each of 
the sites. All study personnel and investigators will be trained prior to study initiation on all 
aspects related to patient’s confidentiality. Study results will be reported and published in 
summary form without any patient-identifying information. 
 
 
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16. Timeline 
 
 
 
 
 
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17. References 
1. 
GBD Tuberculosis Collaborators. The global burden of tuberculosis : results from the 
Global Burden of Disease Study 2015. 3099, 1–24 (2017). 
2. 
World Health Organization. Global Tuberculosis Report 2019. (2019). 
3. 
Getahun, H., Gunneberg, C., Granich, R. & Nunn, P. HIV infection-associated tuberculosis: 
the epidemiology and the response. Clin. Infect. Dis. 50 Suppl 3, S201-7 (2010). 
4. 
Harries, A. D. et al. Deaths from tuberculosis in sub-Saharan African countries with a high 
prevalence of HIV-1. Lancet (London, England) 357, 1519–23 (2001). 
5. 
Palme, I. B., Gudetta, B., Bruchfeld, J., Muhe, L. & Giesecke, J. Impact of human 
immunodeficiency virus 1 infection on clinical presentation, treatment outcome and survival 
in a cohort of Ethiopian children with tuberculosis. Pediatr. Infect. Dis. J. 21, 1053– 61 (2002). 
6. 
Naidoo, K., Gengiah, S., Singh, S., Stillo, J. & Padayatchi, N. Quality of TB care among people 
living with HIV: Gaps and solutions. Journal of Clinical Tuberculosis and Other Mycobacterial 
Diseases vol. 17 (2019). 
7. 
Tiemersma, E. W., van der Werf, M. J., Borgdorff, M. W., Williams, B. G. & Nagelkerke, N. J. 
D. Natural history of tuberculosis: duration and fatality of untreated pulmonary tuberculosis 
in HIV negative patients: a systematic review. PLoS One 6, e17601 (2011). 
8. 
Ordi, J. et al. Clinico-pathological discrepancies in the diagnosis of causes of death in adults 
in Mozambique: A retrospective observational study. PLoS One 14, e0220657 (2019). 
9. 
Noé, A. et al. Knowledge, attitudes and practices regarding tuberculosis care among health 
workers in Southern Mozambique. BMC Pulm. Med. 17, 2 (2017). 
10. 
Karat, A. S. et al. Measuring mortality due to HIV-associated tuberculosis among adults in 
South Africa: Comparing verbal autopsy, minimally-invasive autopsy, and research data. 
PLoS One 12, e0174097 (2017). 
11. 
Karat, A. S. et al. Autopsy prevalence of tuberculosis and other potentially treatable 
infections among adults with advanced HIV enrolled in out-patient care in South Africa. 
PLoS One 11, 1–16 (2016). 
12. 
Bates, M. et al. Burden of tuberculosis at post mortem in inpatients at a tertiary referral 
centre in sub-Saharan Africa: a prospective descriptive autopsy study. Lancet Infect. Dis. 15, 
544–51 (2015). 
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13. 
Cavanaugh, J. S., Shah, N. S., Cain, K. P. & Winston, C. A. Survival among Patients with HIV 
Infection and Smear-Negative Pulmonary Tuberculosis - United States, 1993–2006. PLoS 
One 7, e47855 (2012). 
14. 
Colebunders, R. & Bastian, I. A review of the diagnosis and treatment of smear-negative 
pulmonary tuberculosis. Int. J. Tuberc. Lung Dis. 4, 97–107 (2000). 
15. 
Dorman, S. E. Diagnosis of HIV-associated tuberculosis. Curr. Opin. HIV AIDS 13, 462–468 
(2018). 
16. 
Dorman, S. E. et al. Xpert MTB/RIF Ultra for detection of Mycobacterium tuberculosis and 
rifampicin resistance: a prospective multicentre diagnostic accuracy study. Lancet Infect. Dis. 
18, 76–84 (2018). 
17. 
Detjen, A. K. et al. Xpert MTB/RIF assay for the diagnosis of pulmonary tuberculosis in 
children: a systematic review and meta-analysis. Lancet. Respir. Med. 3, 451–61 (2015). 
18. 
Htwe, K. K. et al. Pre-treatment loss to follow-up and treatment delay among 
bacteriologically-confirmed tuberculosis patients diagnosed in Mandalay Region, Myanmar. 
Trop. Med. Health 47, (2019). 
19. 
Soeroto, A. Y. et al. Evaluation of Xpert MTB-RIF guided diagnosis and treatment of 
rifampicin-resistant tuberculosis in Indonesia: A retrospective cohort study. PLoS One 14, 
e0213017 (2019). 
20. 
Siddiqi, S. & Rüsch-Gerdes, S. MGIT Procedure Manual. (Foundation for Innovative 
Diagnostics (FIND), 2006). 
21. 
World Health Organization. Xpert MTB/RIF assay for the diagnosis of pulmonary and 
extrapulmonary TB in adults and children. Policy update. (2013). 
22. 
World Health Organization. WHO Meeting Report of a Technical Expert Consultation: Non- 
inferiority analysis of Xpert MTB/RIF Ultra compared to Xpert MTB/RIF. (2017). 
23. 
World Health Organization (WHO). The use of lateral flow urine lipoarabinomannan assay 
(LF-LAM) for the diagnosis and screening of active tuberculosis in people living with HIV. 
Policy guidance. (2015). 
24. 
Gupta-Wright, A. et al. Rapid urine-based screening for tuberculosis in HIV-positive patients 
admitted to hospital in Africa (STAMP): a pragmatic, multicentre, parallel-group, double-
blind, randomised controlled trial. Lancet 392, 292–301 (2018). 
25. 
Shah, M. et al. Lateral flow urine lipoarabinomannan assay for detecting active tuberculosis 
in 
HIV-positive 
adults. 
Cochrane 
database 
Syst. 
Rev. 
CD011420 
(2016) 
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doi:10.1002/14651858.CD011420.pub2. 
26. 
World Health Organization. Lateral flow urine lipoarabinomannan assay (LF-LAM) for the 
diagnosis of active tuberculosis in people living with HIV Policy update (2019). (2019). 
27. 
World Health Organization. High-priority target product profiles for new tuberculosis 
diagnostics : report of a consensus meeting. (WHO/HTM7TB/2014.18, 2014). 
28. 
Lawn, S. D. et al. Rapid microbiological screening for tuberculosis in HIV-positive patients 
on the first day of acute hospital admission by systematic testing of urine samples using 
Xpert MTB/RIF: A prospective cohort in South Africa. BMC Med. 13, 1–13 (2015). 
29. 
Lawn, S. D. et al. Diagnostic accuracy, incremental yield and prognostic value of Determine 
TB-LAM for routine diagnostic testing for tuberculosis in HIV-infected patients requiring 
acute hospital admission in South Africa: a prospective cohort. BMC Med. 15, 67 (2017). 
30. 
Gupta-Wright, A Corbett, E. et al. Urine-Based Screening for Tuberculosis: A Randomized 
Trial in HIV-Positive Inpatients. CROI. March 4–7, 2018 Boston, Massachusetts 
http://www.croiconference.org/sessions/urine-based-screening-tuberculosis-randomized- 
trial-hiv-positive-inpatients (2018). 
31. 
Broger, T. et al. Novel lipoarabinomannan point-of-care tuberculosis test for people with 
HIV: a diagnostic accuracy study. Lancet Infect. Dis. 19, 852–861 (2019). 
32. 
Sossen, B. et al. ‘SILVAMP TB LAM’ rapid urine tuberculosis test predicts mortality in 
hospitalized HIV patients in South Africa. Clin. Infect. Dis. (2020) doi:10.1093/cid/ciaa024. 
33. 
Ramaswamy, S. & Musser, J. M. Molecular genetic basis of antimicrobial agent resistance in 
Mycobacterium tuberculosis: 1998 update. Tuber. Lung Dis. 79, 3–29 (1998). 
34. 
SOS Stoolbox - KNCV - Tuberculosefonds. https://www.kncvtbc.org/en/sos-stoolbox/ 
(accessed April 23, 2021). 
 
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18. 
Appendices 
 
Appendix 1: Incident Definition and Reporting 
 
Incident: Any malfunction or deterioration in the characteristics and/or performance of a device, 
as well as any inadequacy in the labeling or the instructions for use which, directly or indirectly, 
might lead to or might have led to the death of a patient, or USER or of other persons or to a 
serious deterioration in their state of health. 
The following criteria as defined in sections 1.1, 1.2 and 1.3 are to be considered to determine 
whether an adverse incident has occurred. Please note that all three criteria must be met to be 
deemed as reportable. Please also refer to MEDDEV 2.12-1, Guidelines on a Medical Devices 
Vigilance System for further guidance. 
 
1.1 
An Event has Occurred 
 
This also includes situations where testing performed on the device, examination of the 
information supplied with the device or any scientific information indicates some factor 
that could lead or has led to an event. 
Typical events include, but are not limited to: 
1.1.1 
A malfunction or deterioration in the characteristics or performance (should be for 
intended purpose and follow manufacturer’s instructions). 
1.1.2 
For IVDs where there is a risk that an erroneous result would either (1) lead to a 
patient management decision resulting in an imminent life-threatening situation to 
the individual being tested, or to the individual’s offspring, or (2) cause death or 
severe disability to the individual or foetus being tested, or to the individual’s 
offspring, all false positive or false negative test results shall be considered as 
events. 
For all other IVDs, false positive or false negative test result falling outside the 
declared performance of the test shall be considered as events. 
1.1.3 
Unanticipated adverse reaction or side effect. 
1.1.4 
Interactions with other substances or products. 
1.1.5 
Degradation / destruction of the device. 
1.1.6 
Inappropriate therapy. 
1.1.7 
Inaccurate labelling, Instructions for Use (IFU) and / or promotional materials 
(includes omissions and deficiencies but not those generally known by user). 
 
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1.2 
The Manufacturer’s Device is Suspected to be a Contributory Cause of the Incident 
 
1.2.1 
In assessing the link between the device and the Incident, the Manufacturer should 
take account of: 
1.2.1.1 
Results of the manufacturer’s own preliminary assessment of the 
incident. 
1.2.1.2 
Evidence of previous, similar incidents. 
1.2.1.3 
Any other relevant evidence held by the manufacturer. 
1.2.2 
Where there are a number of devices involved, the manufacturer should always 
assume their device contributed to the incident until proven otherwise. 
 
1.3 
The Event Led, or Might Have Led, to One of the Following: 
 
1.3.1 
The death of a patient, user or other person. 
1.3.2 
Serious deterioration in the health of a patient, user or other person that can 
include: 
1.3.3 
Life-threatening illness. 
1.3.4 
Permanent impairment of a body function or permanent damage to a body 
structure. 
1.3.5 
A condition necessitating medical or surgical intervention to prevent the two 
points above; for example clinically relevant increase in surgical procedure, a 
condition requiring hospitalisation or prolongation of existing hospitalisation. 
1.3.6 
Any indirect harm as a consequence of incorrect diagnostic or IVD test result 
when used within the manufacturer’s IFU (use errors reportable under section 
5.1.5.1 of MEDDEV 2.12/1 must also be considered) 
1.3.7 
Foetal distress, foetal death or any congenital abnormality or birth defect. 
 
 
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Protocol short title: EXULTANT 
 
 
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Page 59 of 59 
Protocol number: TB043 -3/1 -TAN 
Protocol Version: 3.1 
 
 
Appendix 2: FujiLAM testing 
 
 
 
 
Figure 1: FujiLAM TB test device, test procedure and test principle. (MTX-Man refers to mannose caps further 
modified with a 5-methylthio-D-xylofuranose residue). Au=gold. C=control line. MTX-LAM=5-methylthio- 
D-xylofuranose-lipoarabinomannan. T=test line. Image obtained from Broger et al, 2019.31 
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