Investigation of genomic mutations and their association with phenotypic resistance to new and repurposed drugs in Mycobacterium tuberculosis complex clinical isolates

Abstract

Background: WGS has the potential to detect resistance-associated mutations and guide treatment of MDR TB. However, the knowledge base to confidently interpret mutations associated with the new and repurposed drugs is sparse, and phenotypic drug susceptibility testing is required to detect resistance.

Methods: We screened 900 Mycobacterium tuberculosis complex genomes from Ireland, a low TB incidence country, for mutations in 13 candidate genes and assessed their association with phenotypic resistance to bedaquiline, clofazimine, linezolid, delamanid and pretomanid.

Results: We identified a large diversity of mutations in the candidate genes of 195 clinical isolates, with very few isolates associated with phenotypic resistance to bedaquiline (n = 4), delamanid (n = 4) and pretomanid (n = 2). We identified bedaquiline resistance among two drug-susceptible TB isolates that harboured mutations in Rv0678. Bedaquiline resistance was also identified in two MDR-TB isolates harbouring Met146Thr in Rv0678, which dated back to 2007, prior to the introduction of bedaquiline. High-level delamanid resistance was observed in two isolates with deletions in ddn, which were also resistant to pretomanid. Delamanid resistance was detected in two further isolates that harboured mutations in fbiA, but did not show cross-resistance to pretomanid. All isolates were susceptible to linezolid and clofazimine, and no mutations found were associated with resistance.

Conclusions: More studies that correlate genotypic and phenotypic drug susceptibility data are needed to increase the knowledge base of mutations associated with resistance, in particular for pretomanid. Overall, this study contributes to the development of future mutation catalogues for M. tuberculosis complex isolates.

Figure 1.

Phylogenetic tree of 195 M. tuberculosis complex clinical isolates with mutations identified in candidate genes associated with resistance to new and repurposed drugs. The inner track indicates unique mutations most frequently identified (≥5 isolates) in the candidate genes associated with bedaquiline/clofazimine or delamanid/pretomanid resistance. The second track indicates the lineage of each isolate. Phenotypic drug susceptibility for bedaquiline, clofazimine, delamanid and linezolid is indicated by a circle (filled indicates resistant and unfilled indicates susceptible). The outer track shows the drug resistance profile for each isolate. Details of bedaquiline/clofazimine- and delamanid/pretomanid-resistant isolates are shown in Tables 1 and 2. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.