Added value of whole-genome sequencing for management of highly drug-resistant TB

Abstract

ObjectivesPhenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis takes several weeks to complete and second-line DST is often poorly reproducible, potentially leading to compromised clinical decisions. Following a fatal case of XDR TB, we investigated the potential benefit of using whole-genome sequencing to generate an in silico drug susceptibility profile.MethodsThe clinical course of the patient was reviewed, assessing the times at which phenotypic DST data became available and changes made to the therapeutic regimen. Whole-genome sequencing was performed on the earliest available isolate and variants associated with drug resistance were identified.ResultsThe final DST report, including second-line drugs, was issued 10 weeks after patient presentation and 8 weeks after initial growth of M. tuberculosis. In the interim, the patient may have received a compromised regimen that had the potential to select for further drug resistance. The in silico susceptibility profile, extrapolated from evolving evidence in the literature, provided comparable or superior data to the DST results for second-line drugs and could be generated in a much shorter timeframe.ConclusionsWe propose routine whole-genome sequencing of all MDR M. tuberculosis isolates in adequately resourced settings. This will improve individual patient care, monitor for transmission events and advance our understanding of resistance-associated mutations.

Role of gyrB Mutations in Pre-extensively and Extensively Drug-Resistant Tuberculosis in Thai Clinical Isolates

“…Currently, the clinical applications of whole-genome sequencing are being expanded to produce genotypic drug susceptibility profiles faster than phenotypic susceptibility results can be obtained (50,51). The construction of a database of resistance-related mutations is required for the reliable genotypic prediction of drug resistance.…”

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

“…In the same paper, the potential of shotgun metagenomics, sequencing of DNA from samples without culture, or target-specific amplification was shown (237). Hence, metagenomic analysis might open a new chapter in diagnostics, at least in the case of MDR/XDR strains (238). Furthermore, metagenomic research might yet bring much new information about the evolution of mycobacteria, as it allows the reconstruction of ancient bacterial genomes from skeletal remains, even those that are 1,000 years old (239).…”

Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform: Figure 1.

“…Increasingly, researchers are reporting results from WGS analysis of diverse sets of drug-resistant and -susceptible isolates of Mtb in correlation with phenotypic results [20][21][22]. These studies are valuable for improving our as-yet incomplete understanding of drug resistance, which includes questions surrounding cross-resistance, heteroresistance, additive effects of compensatory mechanisms of resistance, and discrepant analysis.…”