Current Organisation

Centre for the Aids Programme of Research in South Africa (CAPRISA)

Current Job Title

Post-Doctoral Research Fellow

Biography

Project Title

Optimizing the clinical utility of Whole Genome Sequencing to enhance Drug-Resistant Tuberculosis outcomes (Optim-TB)

EDCTP Project Call

Career Development Fellowship (CDF)

Host Organisation

Project Objectives

Aim 1: To establish a comprehensive evidence based approach for the clinical implementation of WGS-based treatment regimens Aim 2: To optimise an assay for the detection of drug-resistance for M.tuberculosis directly from sputum samples to improve the utility of WGS-based DST Aim 3: To characterise pathogen-specific factors that impact on TB treatment

Study Design

Phase IV interventional Study

Project Summary

Resistance to anti-tuberculosis drugs has emerged as a key public health challenge of modern times. The last decade has seen an unprecedented increase in resistance to rifampicin and isoniazid (defined as multidrugresistance), and has been supplanted by additional resistance to fluoroquinolones and secondline injectable agents: amikacin, kanamycin and capreomycin (defined as extensive resistance). Multidrug resistant TB (MDR-TB) and extensively drug resistant TB (XDR-TB) drive approximately a quarter of the global TB related mortality, are unsustainably costly to treat and pose a major threat to continued transmission of infection. Current treatment options for XDR-TB fail to cure 30-75% of patients with XDRTB, contributing to an emerging public health crisis. The management of drug-resistant TB is challenged by limitations of our current diagnostics, with limited capacity to detect drug resistance and slow turnaround times. The potential benefits associated with individualized therapy based on whole-genome predictions of susceptibility for patients with drug-resistant tuberculosis (DR-TB) has been highlighted significantly in literature over the last decade. Current standard of care practice involves the use of empiric regimens at diagnosis of TB disease, which is later modified as Line Probe Assay (LPA, Hain Life Sciences) based drug susceptibility results become available. Whilst these rapid molecular-based tests are designed to provide rapid information on selected mutations and drugs, initial treatment may contain ineffective and potentially toxic drugs. Whole genome sequencing (WGS) technology has significantly strengthened the TB research landscape, providing valuable insights on the pathogenesis of Mycobacterium tuberculosis. WGS is a powerful tool with the capacity to provide rapid and accurate detection of clinically significant drug resistance mutations, thereby offering a rapid diagnosis of DR-TB. The current study is embedded in the CAPRISA 020 InDEX Study; which leverages on a full genomic resistance profile of the infecting organism to tailor an individualized treatment regimen. The InDEX study, a first-of-its kind in a high-burden TB setting has highlighted significant avenues for improving the potential of WGS to pioneer individualized treatment. In order to address knowledge gap on the associations between genotypic, phenotypic and clinically relevant resistance, we conducted a comprehensive literature review. The review has occurred over the last few years and has been updated during the current reporting period to include the mechanisms of resistance to new drugs. The resulting algorithm which incorporates a stringent grading approach has been tested on 77 patients thus far. The manuscript is in preparation for resubmission. The current study will focus on improving understanding of the development of resistance in patients undergoing treatment and assess the contribution of the various pathogen factors that impact on drugresistant TB outcomes. During this reporting period DNA was extracted from 37 serial samples from 5 patients failing treatment who were failing DR-TB for WGS. MIC testing was conducted on 9 anti-TB drugs. DNA has been extracted from samples for WGS. We anticipate that translation of the science emanating from this study will improve the utility of sequencing technology to provide a robust real-time diagnostic assay. This study will provide a comprehensive algorithm for the inclusion and exclusion of drugs based on clinical relevance of resistance mutations and will improve our understanding on the differential pathogenesis and disease outcomes by certain strain types and inform targeted interventions for interrupting transmission. The implications of such a study are profound and will pave the way for new therapeutic and management approaches for drugresistant TB. In addition to scientific contributions, the proposed project provides training opportunities for junior researchers thereby increasing the critical mass of global health scientists. During this reporting period, two Master's students have successfully completed the lab assays and are about to graduate.

Results & Outcomes