Improved diagnosis of drug-resistant tuberculosis : from implementation of simple phenotypic testing to whole genome sequencing

Abstract: For many years, the diagnosis of tuberculosis (TB) and resistance to anti-TB drugs has relied on standard phenotypic methods, based on the culture of viable mycobacteria. These analyses are expensive and slow, and to contain biohazard, they must be conducted in high containment laboratories, not available in remote low-resource settings. During the last decade, diagnosis of TB has been revolutionized by the development of rapid molecular diagnostic tests, such as Xpert MTB/RIF, now rolled out worldwide. At the time of its endorsement, in 2011, M\ue9decins sans Fronti\ue8res has been one of the early implementers, installing the tests in over eighteen countries. The thesis reports the results of this experience, showing undoubtful increase of TB detection, but also challenges due to logistic constraints, mainly encountered in peripheral laboratories. Despite the improvement of TB diagnosis, the need for phenotypic methods persists, particularly to monitor patients during treatment and to assess resistance to drugs not targeted in rapid molecular assays. This thesis describes the improvement of thin layer agar (TLA) a rapid, simple, and inexpensive phenotypic non-commercial method for simultaneous detection of TB and drug resistance, applicable to low resources setting. In a first phase, the assay was assessed at the Institute of Tropical Medicine, demonstrating very good results. Next, TLA has been evaluated under field conditions in a M\ue9decins sans Fronti\ue8res project in Eswatini. The thesis presents the results, discusses the challenges and limitations, and proposes ways forward for further improvement of this technique. Along with the great advancements in diagnostic tools, new anti-TB drugs have been approved. However, specifically for bedaquiline, results from both molecular and phenotypic susceptibility testing methods remain difficult to interpret. Our research generated data to contribute to closing this knowledge gap. Testing for susceptibility to new drugs before starting treatment, to avoid weak treatments and the risk to contribute to the development of resistance, should become a priority in routine practice. The development of a rapid molecular test however does not seem close, so that in peripheral settings, TLA could be further evaluated to provide rapid and accurate results for these new drugs