Characterization of Genomic Variants Associated with Resistance to Bedaquiline and Delamanid in Naive Mycobacterium tuberculosis Clinical Strains

Abstract

The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of genetic variants' role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analysed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole genome sequencing (WGS) dataset from a collection of 4795 MTBc clinical isolates from six high-burden countries of tuberculosis (TB). From WGS analysis, we identified 61 and 163 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to the medicines. To characterize the role of mutations, we calculated the free energy variation upon mutations in the available protein structure of Ddn (DLM), Fgd1 (DLM) and Rv0678 (BDQ), and performed minimum inhibitory concentration (MIC) assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural and phenotypic data allowed for cataloging the mutations clearly associated with resistance to BDQ (n = 4) and DLM (n = 35) of which only two were previously described, as well as about a hundred genetic variants without any correlation with resistance. Significantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance to the development of comprehensive molecular diagnostic tools.

Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid

“…2 ). Twenty-one of the remaining SNPs in mmpR5 , including high frequency D5G, V20A, L117R, L32S, G121R, D141H, R90C and N98D, were in the same residue where mutations associated with increments in MIC have been observed; however, mutations V20A and D141H have associated MIC values within a susceptibility range 36 .…”

Comparative Efficacy of the Novel Diarylquinoline TBAJ-587 and Bedaquiline against a Resistant Rv0678 Mutant in a Mouse Model of Tuberculosis

“…Therefore, it is of great concern that Rv0678 variants with reduced susceptibility to BDQ are reported with increasing frequency among patients treated with BDQ or clofazimine, including at least 1 participant treated with BPaL in the Nix-TB trial who relapsed with an Rv0678 mutant (14). In addition, several studies have reported Rv0678 variants among baseline MDR-TB isolates obtained prior to any known BDQ or clofazimine exposure (19,23,24), suggesting that they may be enriched among MDR-TB isolates due to selection by other factors. The results presented here confirm that loss-offunction mutations in Rv0678 significantly reduce the efficacy of BDQ in vivo (19) and show for the first time that they also significantly reduced the efficacy of the novel BPaL regimen.…”

“…Rv0678 are associated with relatively small reductions in susceptibility to BDQ and clofazimine, they are readily selected by BDQ and/or clofazimine treatment in mouse models of TB and also have been selected during clinical use of BDQ, including in the Nix-TB trial (14). Coupled with evidence that Rv0678 variants with reduced BDQ susceptibility have been isolated from MDR-TB patients without known prior exposure to BDQ or clofazimine (19,23,24), these reports raise concern that emergence of Rv0678 variants could undermine the promising clinical efficacy of BDQ-containing regimens.…”

Comparative efficacy of the novel diarylquinoline TBAJ-587 and bedaquiline against a resistant Rv0678 mutant in a mouse model of tuberculosis

“…Therefore, it is of great concern that Rv0678 variants with reduced susceptibility to BDQ are reported with increasing frequency among patients treated with BDQ or clofazimine, including at least 1 participant treated with BPaL in the Nix-TB trial who relapsed with an Rv0678 mutant (14). In addition, several studies have reported Rv0678 variants among baseline MDR-TB isolates obtained prior to any known BDQ or clofazimine exposure (19, 23, 24), suggesting that they may be enriched among MDR-TB isolates due to selection by other factors. The results presented here confirm that loss-of-function mutations in Rv0678 significantly reduce the efficacy of BDQ in vivo (19) and show for the first time that they also significantly reduced the efficacy of the novel BPaL regimen.…”

“…Although mutations in Rv0678 are associated with relatively small reductions in susceptibility to BDQ and clofazimine, they are readily selected by BDQ and/or clofazimine treatment in mouse models of TB and also have been selected during clinical use of BDQ, including in the Nix-TB trial (14). Coupled with evidence that Rv0678 variants with reduced BDQ susceptibility have been isolated from MDR-TB patients without known prior exposure to BDQ or clofazimine (19, 23, 24), these reports raise concern that emergence of Rv0678 variants could undermine the promising clinical efficacy of BDQ-containing regimens.…”