Roles and dynamics of genetically encoded drug TOLerance in drug RESistance emergence in Mycobacterium tuberculosis – ResTolTB

The global rise in antimicrobial resistance (AMR) underscores the critical need to target the mechanisms that limit the effectiveness of antibiotics, promote the development of resistance and lead to treatment failures. In addition to classical drug resistance, the effectiveness of antibiotics is also impaired by more complex, so-defined bacterial tolerance mechanisms, which do not increase the minimum concentration of a drug needed to prevent growth, but enhance bacterial survival to transient antibiotic exposure. These mechanisms are also believed to play a key role in the emergence of resistance. We propose to determine the role and dynamics of genetically encoded multidrug tolerance mechanisms in altering synergistic drug interactions and in the emergence of AMR in Mycobacterium tuberculosis, the deadliest infectious bacterium and the first contributor to mortality due to AMR. By gathering strong and complementary experience and multidisciplinary expertise, we propose an ad hoc systemic approach combining genetics and experimental evolution in vitro and in vivo, in silico modeling, phylogenomics and GWAS analyses of circulating strains, as well as analyzes by multi-target deep sequencing and whole genome sequencing (GWS), to determine the evolutionary dynamics of tolerance/ persistence in evolved populations and clones, and to determine its role in the emergence of resistance. Using a new deep sequencing-based prototype test and WGS, we will also assess the detection and association of tolerance and resistance mutations, directly in clinical samples from patients on treatment for multidrug resistant or drug susceptible tuberculosis. The advanced understanding of the dynamic interactions between tolerance and resistance will allow the development of novel diagnostic and therapeutic tools.