Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools - PubMed (original) (raw)

Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools

Viola Schleusener et al. Sci Rep. 2017.

Abstract

Whole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis (TB). Several recently developed automated software tools promise to standardize the analysis and interpretation of WGS data. We assessed five tools (CASTB, KvarQ, Mykrobe Predictor TB, PhyResSE, and TBProfiler) with regards to DST and phylogenetic lineage classification, which we compared with phenotypic DST, Sanger sequencing, and traditional typing results for a collection of 91 strains. The lineage classifications by the tools generally only differed in the resolution of the results. However, some strains could not be classified at all and one strain was misclassified. The sensitivities and specificities for isoniazid and rifampicin resistance of the tools were high, whereas the results for ethambutol, pyrazinamide, and streptomycin resistance were more variable. False-susceptible DST results were mainly due to missing mutations in the resistance catalogues that the respective tools employed for data interpretation. Notably, we also found cases of false-resistance because of the misclassification of polymorphisms as resistance mutations. In conclusion, the performance of current WGS analysis tools for DST is highly variable. Sustainable business models and a shared, high-quality catalogue of resistance mutations are needed to ensure the clinical utility of these tools.

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Conflict of interest statement

C.U.K. has collaborated with Illumina Inc. on a number of scientific projects and is a consultant for the Foundation for Innovative New Diagnostics. The Bill & Melinda Gates Foundation, PerkinElmer, and Janssen Pharmaceutica covered C.U.K.’s travel and accommodation to present at meetings. The European Society of Mycobacteriology awarded C.U.K. the Gertrud Meissner Award, which is sponsored by Hain Lifescience. S.N. is a consultant for the Foundation for Innovative New Diagnostics.

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Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools - PubMed (original) (raw)