DIAgnostics for Multidrug Resistant Tuberculosis in Africa

Study Overview
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Brief Summary
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Recent advances in molecular diagnostics of tuberculosis, especially the GeneXpert Mycobacterium tuberculosis/Rifampicin test have reduced the time to diagnose Rifampicin Resistant Tuberculosis (RR-TB) but only rifampicin resistance is diagnosed, leading to presumptive diagnosis of resistance to isoniazid and maybe other drugs. Thus in low and middle income countries, most drug sensitivity testing relies on phenotypic drug resistance testing, which takes up to 4 months. In addition, currently, culture on monthly sputum samples is recommended by the World Health Organization for follow-up of Rifampicin Resistant Tuberculosis patients under treatment. Unfortunately, culture is often not locally available and samples need to be transported from field to culture laboratories. The associated transport delays lead to high rates of contamination and false negative culture, particularly in laboratories in low resource settings. Many gaps for the diagnosis and management of RR-TB patients still need to be addressed and the DIAMA project (DIAgnostics for Multidrug resistant tuberculosis in Africa) study aims to address some of them.

Detailed Description
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The proposed DIAMA (DIAgnostics for Multidrug resistant tuberculosis in Africa) study aims to address current gaps in the diagnosis and management of patients with Multi-Drug-Resistant (MDR) tuberculosis. Building on existing networks and research collaborations previously funded by the European & Developing Countries Clinical Trials Partnership (EDCTP), this project involved partners in West, Central, and East Africa. It aims to evaluate and implement rapid and accurate molecular tests for several anti Tuberculosis drugs, to replace the current dependency on phenotypic drug resistance testing, which takes up to 4 months and is technically so demanding that few laboratories can perform it correctly. The project builds on the continuous surveillance of Tuberculosis retreatment patients for rifampicin resistance. Two African partners (Benin and Rwanda) with advanced molecular laboratories are establishing reference laboratories for the 'Deeplex' assay, a novel multiplex deep sequencing-based drug resistance diagnostic platform that simultaneously provides sequence information of genes that confer resistance to several key anti tuberculosis drugs. Partners are recruiting all patients with rifampicin resistant Tuberculosis, and a subset of those with rifampicin sensitive Tuberculosis. In a first phase, sputum will be shipped for the Deeplex assay, for comparison against phenotypic DST, the reference method for detecting resistance to 1st and 2nd line drugs. In addition, since Whole Genome Sequencing is the reference of molecular tests, Deeplex assay will also be validated again this test. In a second phase, Cepheid 2nd line Xpert and Molbio Truenat test, two 'lower tech' tests at the last stages of laboratory validations, will also be validated. The Cepheid Xpert 2nd line cartridge can be implemented in existing Xpert machines used for the Xpert MTB/Rif assays. These tests will be compared versus the Deeplex assay and versus WGS Using the latest advances in DataTocare software developed by one of the project partners, molecular results will be communicated in real time to the National Tuberculosis Programmes, so that Multi Drug Resistant Tuberculosis patients can swiftly start appropriate treatment. The added-value of this system will be evaluated as a pilot study in some sites. Lastly, once patients have initiated MDR treatment, they will be monitored for treatment success by faster alternative approaches to the WHO recommended monthly cultures: serial sputum samples will have Fluorescein DiAcetate (FDA) vital stain microscopy, measurement of the bacterial load using the Xpert MTB/Rif as well as precursor of ribosomal RNA measurement (pre-rRNA). Together, these advances are expected to dramatically improve the currently dismal prognosis of MDR-TB in health systems in resource-poor settings.

Official Title
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Culture Free Diagnosis and Follow-up of Multidrug Resistant Tuberculosis Patients

Conditions
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Tuberculosis, Multidrug-Resistant

Intervention / Treatment
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* Diagnostic Test: Deeplex test, MolBio TrueNat for 2nd line, GeneXpert 2nd line
* Diagnostic Test: Fluorescein DiAcetate (FDA) Microscopy,GeneXpert Ct value, pre-rRNA synthesis


Participation Criteria
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Eligibility Criteria
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Inclusion criteria: Being ≥ 15 year old Having a positive test on GeneXpert (M. tuberculosis) with or without resistance detected to rifampicin Willing and able to provide written informed consent, or for minors: assent from and consent from a legal representative Exclusion Criteria: None

Ages Eligible for Study
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Minimum Age: 15 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Rifampicin resistant and susceptible patients<br>Study 1: Patients detected positive by the GeneXpert Mycobacterium tuberculosis/Rifampicin (susceptible and resistant to rifampicin) | Diagnostic Test: Deeplex test, MolBio TrueNat for 2nd line, GeneXpert 2nd line<br>* Improvement of the diagnosis of Multi Drug Resistant-Tuberculosis patients with culture-free approaches. We have planned to diagnose Tuberculosis resistance to 1st and 2nd line drugs through novel molecular multiplex assays (Study 1) by: Validating the Deeplex test and establish a network for shipment of sputum samples in ethanol to regional reference laboratories (Study 1 - phase 1) Validating the Molbio Truenat test as a point of care test (Study 1 - phase 2) Validating the Cepheid GeneXpert 2nd line cartridge at the district level (Study 1 -phase2)<br>|
| Rifampicin resistant patients<br>Study 2: Follow up of the rifampicin resistant patients included in the study 1 during their treatment | Diagnostic Test: Fluorescein DiAcetate (FDA) Microscopy,GeneXpert Ct value, pre-rRNA synthesis<br>* Improvement of the management of Multi Drug Resistant-Tuberculosis patients with culture-free approaches. We have planned to set up alternative culture-free approaches for the monitoring of patients' response to Multi Drug Resistant-Tuberculosis treatment (Study 2), with: FDA microscopy Measurement of bacterial load by following Cycle threshold (Ct) values in GeneXpert Mycobacterium tuberculosis/Rifampicin Measurement of pre-rRNA synthesis<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Validation of Deeplex test | Concordance between phenotypic Drug Susceptibility Test, WGS and Deeplex results | 4 years | 
| Validation of GeneXpert 2nd line | Concordance between WGS, Deeplex results and GeneXpert 2nd line results | 4 years | 
| Validation of MolBio TrueNat for INH, FQ and BDQ | Concordance between WGS, Deeplex results and MolBioTrueNat results | 4 years | 
| Validation of FDA microscopy | Concordance between Culture results and FDA microscopy results | 4 years | 
| Validation of GeneXpert Ct value | Concordance between Culture results and GeneXpert Ct value results | 4 years | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Estimation of proportion of additional resistance in patients resistant to Rifampicin | Evaluation to be done with the Deeplex test | 4 years | 
| Measurement of the association of specific mutations against some drugs with programmatic treatment outcome | Evaluation to be done with the Deeplex test | 4 years | 
| Evaluation of the add value of Connectivity system in the management of Multi Drug Resistant-Tuberculosis patients | Evaluation to be done with Data2Care connectivity system | 2 years | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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culture-free, tuberculosis, multidrug resistant, diagnosis, follow-up, africa, molecular tools