Value of routine whole genome sequencing for Mycobacterium tuberculosis drug resistance detection

Abstract

Routine whole genome sequencing (WGS) of pathogens is becoming more feasible as sequencing costs decrease and access to benchtop sequencing equipment and bioinformatics pipelines increases. This study examined the added value gained from implementing routine WGS of all Mycobacterium tuberculosis isolates in New South Wales, Australia.Drug resistance markers inferred from WGS data were compared to commercial genotypic drug susceptibility testing (DST) assays and conventional phenotypic DST in all isolates sequenced between 2016 and 2019. Of the 1107 clinical M. tuberculosis isolates sequenced, 29 (2.6%) were multi-drug resistant (MDR); most belonged to Beijing (336; 30.4%) or East-African Indian (332; 30%) lineages. Compared with conventional phenotypic DST, WGS identified an additional 1% of isolates which were likely drug resistant, explained by mutations previously associated with treatment failure and mixed bacterial populations. However, WGS provided a 20% increase in drug resistance detection in comparison with commercial genotypic assays by identifying mutations outside of the classic resistance determining regions in rpoB, inhA, katG, pncA and embB genes. Gains in drug resistance detection were significant (p = 0.0137, paired t-test), but varied substantially for different phylogenetic lineages.In low incidence settings, routine WGS of M. tuberculosis provides better guidance for person-centered management of drug resistant tuberculosis than commercial genotypic assays.

Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens

“…While these studies have demonstrated the feasibility of NGS in TB drug resistance diagnosis, the sequencing platforms are either obsoleted (Colman et al, 2016), or the study only focused on AFB positive specimens with limited variability in drug resistance patterns (Smith et al, 2020). More importantly, as most platform focused on whole genome sequencing data, high-quality genomic DNA prepared from MTB isolates are usually required (Lam et al, 2021;Olawoye et al, 2021). The long turnaround time of MTB culture would not be in favor of rapid MTB resistance analysis.…”

Beijing genotype of Mycobacterium tuberculosis is associated with extensively drug-resistant tuberculosis: A global analysis

“…In particular, mutt gene alleles cause drug resistance and alter bacterial morphology [ [57] , [58] , [59] ]. Numerous pieces of evidence have been reported regarding the relationship between the Beijing genotype and MDR-TB so that this genotype can be considered as a biomarker for drug-resistant TB [ [60] , [61] , [62] ]. We showed for the first time in a comprehensive analysis that the Beijing family is the most predominant genotype among the XDR-TB strains.…”

Prevalence and genetic basis of first-line drug resistance ofMycobacterium tuberculosisin Ca Mau, Vietnam

“…Our experience has been that phenotypic isoniazid resistance associated with this mutation is only observed when the broth microdilution method (TREK) is used. 41 In contrast, to these findings with inhA and fabG1, most isolates that demonstrated katG mutations did demonstrate phenotypic isoniazid resistance consistent with its association with high level isoniazid resistance. 33 The high specificity of the katG gene mutation for isoniazid resistance along with the high prevalence of Isoniazid resistance in the general population supports its inclusion in rapid molecular tests that are used for screening for resistance.…”