Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward

Abstract

SUMMARY The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis. As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis. We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.

How well do routine molecular diagnostics detect rifampicin heteroresistance inMycobacterium tuberculosis?

“…The LPAs and Deeplex-MycTB provide direct information on the occurrence of RIF heteroresistance, whereas Ultra, after informing that RR was detected, may suggest RIF heteroresistance only through additional examination of wild-type and Mut melt probes and corresponding melt peak temperatures in the raw data on the computer screen or in the generated extended report (Supplemental File Figure S3 b-e, f). The clinical importance of heteroresistance is likely substantial (2), akin to ’fixed‘, i.e. 100% resistance.…”

“…Our findings can thus inform and guide TB reference laboratory staff, healthcare providers, and researchers, that the threshold for reporting resistance in case of rifampicin heteroresistance is the highest for Classic Xpert and Ultra, to resolve phenotypic and genotypic discordant rifampicin-resistant TB results. Prospective large-scale clinical studies using next generation sequencing approaches (2, 7) are necessary to establish the proportion of mutants that predicts poor outcome of treatment with the specific drug.…”

“…In 2017, 71% of global RIF resistant-TB (RR-TB) cases were not diagnosed (1). The diagnosis of RR-TB may be complicated by RIF heteroresistance, observed in patient samples where RR and RIF-susceptible (RS) strains co-exist (2, 3), which may be missed and diagnosed as RS because of detection limits. RIF heteroresistance may arise from an existing resistant clonal subpopulation or from a mixed infection of independent strains with RR and RS profiles.…”

“…Such heteroresistance, also known as ‘unfixed’ resistance, precedes full blown resistance (‘fixed’ resistance, 100% RR) as a result of further resistance selection under treatment (3–6). Failure to detect these minority resistant variants can thus result in unsuccessful treatment and potential spread of RR-TB strains (2, 3, 7).…”

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy

“…Apart from this, novel genetic variants may be fixed in the population by the mechanism of hitchhiking or independently [10]. A comprehensive review of these mutations has been recently published and demonstrated that most of these variants occurred in the genes, associated with the compensatory mechanisms, virulence, or relapse and survival, but their consequences remain unclear [11].…”