EDCTP portfolio: Career Development Fellowships

Dr Bugwesa Zablon Katale evaluates whether whole-genome sequencing of multidrug-resistant strains of Mycobacterium tuberculosis will improve the diagnosis and treatment of TB.

Whole-genome sequencing for diagnosis and treatment of MDR-TB

Drug-resistant tuberculosis presents a challenge to global control of tuberculosis. Globally, 45% of the 480,000 cases of multidrug-resistant tuberculosis (MDR-TB) is detected, and at most 70% of these patients receive appropriate drug therapy.

Tanzania has adopted rapid molecular methods for dual detection of Mycobacterium tuberculosis complex (MTBC) and susceptibility to either rifampicin alone or with isoniazid and second-line injectable and fluoroquinolones using Xpert MTB/Rif assay, genotype MTBDRplus and MTBDRsl.

These assays only target predetermined regions of the genome known to predict phenotypic resistance to anti-TB drugs. This leads to the isolate being incorrectly called susceptible. Thus, undetected patients are likely to fail treatment but also spread resistance organisms. A recent retrospective study in Tanzania has found a diversity of mutations, including rrs and gyrB, which code for second-line drugs, suggesting ongoing transmission of MDR-TB strains rather than de novo evolution or importation of drug resistance strains.

The challenge

Dr Katale hypothesises that whole-genome sequencing of MDR-TB strains will improve the diagnosis and treatment of TB in Tanzania while providing precise strain discrimination. The study is designed as a case-control study in which sputum samples will be collected from TB patients attending health services at the TB-dedicated Kibong’oto Hospital, in northern Tanzania.

Cases will be defined as MDR-TB patients when confirmed by culture and drug-susceptibility testing (DST) as having resistance to at least rifampicin and isoniazid. Controls will be patients who are sensitive to rifampicin and isoniazid.

Samples will be processed using the modified Petroff’s method. Culture and identification of MTBC colonies will be performed according to local and CLSI standard operating procedures. Phenotypic DST of the MTBC isolates will be performed using Mycobacteria Growth Indicator Tube DST. Genomic DNA will be extracted using a modified protocol based on Restriction Fragment Length Polymorphism and sequenced using MiseqTM. The whole-genome sequencing and bioinformatic analysis will be performed to determine mutations that predict phenotypic resistance to anti-TB drugs. Immunological and haematological assays will be performed to associate between types of drug-resistance genes, alone or in combination, and TB progression/severity. Patient’s clinical information and outcomes will be obtained and compared to phenotypic and genetic data.

The project

This study will provide insights into the role of whole-genome sequencing in the clinical management of patients and the role of drug-resistance genes in the progression and severity of TB infections.

Impact


test the safety and efficacy of this new formulation in young children

Bringing antiretroviral drugs to children

The CHAPAS trials have ensured that many more children with HIV have benefited
from life-saving antiretrovirals.

EDCTP portfolio: HIV & HIV-associated infections

The challenge

Drug-resistant tuberculosis presents a challenge to global control of tuberculosis. Globally, 45% of the 480,000 cases of multidrug-resistant tuberculosis (MDR-TB) is detected, and at most 70% of these patients receive appropriate drug therapy.

Tanzania has adopted rapid molecular methods for dual detection of Mycobacterium tuberculosis complex (MTBC) and susceptibility to either rifampicin alone or with isoniazid and second-line injectable and fluoroquinolones using Xpert MTB/Rif assay, genotype MTBDRplus and MTBDRsl.

These assays only target predetermined regions of the genome known to predict phenotypic resistance to anti-TB drugs. This leads to the isolate being incorrectly called susceptible. Thus, undetected patients are likely to fail treatment but also spread resistance organisms. A recent retrospective study in Tanzania has found a diversity of mutations, including rrs and gyrB, which code for second-line drugs, suggesting ongoing transmission of MDR-TB strains rather than de novo evolution or importation of drug resistance strains.

Dr Katale hypothesises that whole-genome sequencing of MDR-TB strains will improve the diagnosis and treatment of TB in Tanzania while providing precise strain discrimination. The study is designed as a case-control study in which sputum samples will be collected from TB patients attending health services at the TB-dedicated Kibong’oto Hospital, in northern Tanzania.

Cases will be defined as MDR-TB patients when confirmed by culture and drug-susceptibility testing (DST) as having resistance to at least rifampicin and isoniazid. Controls will be patients who are sensitive to rifampicin and isoniazid.

Samples will be processed using the modified Petroff’s method. Culture and identification of MTBC colonies will be performed according to local and CLSI standard operating procedures. Phenotypic DST of the MTBC isolates will be performed using Mycobacteria Growth Indicator Tube DST. Genomic DNA will be extracted using a modified protocol based on Restriction Fragment Length Polymorphism and sequenced using MiseqTM. The whole-genome sequencing and bioinformatic analysis will be performed to determine mutations that predict phenotypic resistance to anti-TB drugs. Immunological and haematological assays will be performed to associate between types of drug-resistance genes, alone or in combination, and TB progression/severity. Patient’s clinical information and outcomes will be obtained and compared to phenotypic and genetic data.

The project

The later CHAPAS-3 trial compared the efficacy and safety of three fixed-dose combinations including two without stavudine (found to have some long-term side effects in adults, leading to a recommendation that its use be discontinued in children). The trial the first of its kind in Africa studied nearly 500 children at four sites in two African countries.

This study will provide insights into the role of whole-genome sequencing in the clinical management of patients and the role of drug-resistance genes in the progression and severity of TB infections.

ratios forfixed-dose combinations and on appropriatedosage according to weight. 

The CHAPAS-3 trial confirmed the effectiveness of fixed-dose combinations, providing further impetus to the rollout of antiretrovirals to children. Its evidence on abacavir informed the WHO recommendation of abacavir-containing combinations for first-line therapy in children. Trial data have also been used to support applications for regulatory approval for new scored efavirenz tablets.

Impact

L’homme RF et al. Nevirapine, stavudine and lamivudine pharmacokinetics in African children on paediatric fixed-dose combination tablets. AIDS. 2008;22(5):557–65.

Mulenga V et al. Abacavir, zidovudine, or stavudine as paediatric tablets for African HIVinfected children (CHAPAS-3): an open-label, parallel-group, randomised controlled trial. Lancet Infect Dis. 2016;16(2):169–79.

WHO. Guidelines on the use of antiretroviral drugs for treating and preventing HIV infection: recommendations for a public health approach. 2010.

WHO. Consolidated guidelines on the use of antiretroviral drugs
for treating and preventing

HIV infection: Recommendations for a public health approach
(second edition). 2016

Projects: Children with HIV in Africa Pharmacokinetics and Adherence of Simple Antiretroviral Regimens (CHAPAS): CHAPAS-1 and -3

Project lead: Professor Chifumbe Chintu, University Teaching Hospital, Zambia (CHAPAS-1); Dr Veronica Mulenga, University Teaching Hospital, Zambia (CHAPAS-3)

Target population(s): Children with HIV

Sample size: 71 (CHAPAS-1); 480 (CHAPAS-3)

Countries involved: Ireland, the Netherlands, the UK, the USA, Zambia (CHAPAS-1); Uganda, Zambia (CHAPAS-3)

Project duration: 2005–2009 (CHAPAS-1); 2010 –2011 (CHAPAS-3)

EDCTP funding: €1.2M (CHAPAS-1); €4.6M (CHAPAS-3)

Total project funding: €1.2M (CHAPAS-1); €5.0M

About us

The European & Developing Countries Clinical Trials Partnership (EDCTP) is a public–public partnership between 14 European and 16 African countries, supported by the European Union. EDCTP’s vision is to reduce the individual, social and economic burden of poverty-related infectious diseases by affecting sub-Saharan Africa. EDCTP’s mission is to accelerate the development of new or improved medicinal products for the identification, treatment and prevention of infectious diseases, including emerging and re-emerging diseases, through pre- and postregistration clinical studies, with emphasis on phase II and III clinical trials. Our approach integrates conduct of research with development of African clinical research capacity and networking. The second EDCTP programme is implemented by the EDCTP Association supported under Horizon 2020, the European Union’s Framework Programme for Research and Innovation.

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