Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value

Abstract

Rationale: The development of molecular diagnostics that detect both the presence of Mycobacterium tuberculosis in clinical samples and drug resistance-conferring mutations promises to revolutionize patient care and interrupt transmission by ensuring early diagnosis. However, these tools require the identification of genetic determinants of resistance to the full range of antituberculosis drugs.Objectives: To determine the optimal molecular approach needed, we sought to create a comprehensive catalog of resistance mutations and assess their sensitivity and specificity in diagnosing drug resistance.Methods: We developed and validated molecular inversion probes for DNA capture and deep sequencing of 28 drug-resistance loci in M. tuberculosis. We used the probes for targeted sequencing of a geographically diverse set of 1,397 clinical M. tuberculosis isolates with known drug resistance phenotypes. We identified a minimal set of mutations to predict resistance to first-and second-line antituberculosis drugs and validated our predictions in an independent dataset. We constructed and piloted a web-based database that provides public access to the sequence data and prediction tool. Measurements and Main Results:The predicted resistance to rifampicin and isoniazid exceeded 90% sensitivity and specificity but was lower for other drugs. The number of mutations needed to diagnose resistance is large, and for the 13 drugs studied it was 238 across 18 genetic loci.Conclusions: These data suggest that a comprehensive M. tuberculosis drug resistance diagnostic will need to allow for a high dimension of mutation detection. They also support the hypothesis that currently unknown genetic determinants, potentially discoverable by whole-genome sequencing, encode resistance to second-line tuberculosis drugs.

Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State

“…Publicly released in 2008, the TB Drug Resistance Mutation Database (TBDReaMDB) was one of the earliest centralized databases compiling potential resistance-associated mutations from a systematic literature review, providing a valuable resource for molecular M. tuberculosis diagnostics and further research in this field (38). Since the initial release of TBDReaMDB, efforts to build upon this data set to construct curated databases linking genotype data with phenotypic DST results have been undertaken and are critical to improving the accuracy of molecularbased susceptibility profiling (39)(40)(41).…”

Isoniazid-resistant tuberculosis: a cause for concern?

“…Studies in various settings (of which the cited are a few) have demonstrated this to be the case, 25;28;29;49–55 (including enrichment of katG mutations in MDR versus non-MDR INH resistant strains 20;25;28;29;56 ). The ‘spectrum’ of mutations observed in MDR strains varies from setting to setting, however, and may be linked to the dose of INH used for treatment 54 and the clonal spread of different mutations.…”

“…20 Lack of clarity about the association between specific mutations, phenotypic resistance, and treatment outcomes hinders genotyping being used to make rapid treatment decisions. 21;22 inhA mutations are generally associated with lower phenotypic resistance than katG mutations, 23;24 but even within the same gene different mutations can cause differing levels of phenotypic resistance.…”

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis

“…The most frequently observed cause of resistance are SNPs in genes encoding drug targets or converting enzymes, but large deletions might also result in resistance. 71,241 A summary of loci implicated in resistance to antituberculosis drugs is presented in table 4. A review of the loci is not included in this Commission, and for a comprehensive list of resistancecausing mutations (1325 polymorphisms [SNPs and indels] at 992 nucleotide positions from 31 loci, 6 promoters, and 25 coding regions) and corresponding aminoacid changes, we refer the reader to the London School of Hygiene & Tropical Medicine TB Profiler.…”