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

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases worldwide. Multidrug and extensively drug-resistant strains are making disease control difficult, and exhausting treatment options. New anti-TB drugs bedaquiline (BDQ), delamanid (DLM) and pretomanid (PTM) have been approved for the treatment of multi-drug resistant TB, but there is increasing resistance to them. Nine genetic loci strongly linked to resistance have been identified (mmpR5, atpE, and pepQ for BDQ; ddn, fgd1, fbiA, fbiB, fbiC, and fbiD for DLM/PTM). Here we investigated the genetic diversity of these loci across >33,000 M. tuberculosis isolates. In addition, epistatic mutations in mmpL5-mmpS5 as well as variants in ndh, implicated for DLM/PTM resistance in M. smegmatis, were explored. Our analysis revealed 1,227 variants across the nine genes, with the majority (78%) present in isolates collected prior to the roll-out of BDQ and DLM/PTM. We identified phylogenetically-related mutations, which are unlikely to be resistance associated, but also high-impact variants such as frameshifts (e.g. in mmpR5, ddn) with likely functional effects, as well as non-synonymous mutations predominantly in MDR-/XDR-TB strains with predicted protein destabilising effects. Overall, our work provides a comprehensive mutational catalogue for BDQ and DLM/PTM associated genes, which will assist with establishing associations with phenotypic resistance; thereby, improving the understanding of the causative mechanisms of resistance for these drugs, leading to better treatment outcomes.

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

“…On the other hand, while the guideline updated in late 2020 included bedaquiline as one of the medications for XDR-TB definition, our current TB-NGS protocol did not include bedaquiline genotypic resistance test due to several reasons. As a new anti-TB drug recommended by WHO in 2016, the exact mechanism for bedaquiline resistance pattern in clinical isolates are still far from fully elucidated (Nguyen et al, 2018;Nieto Ramirez et al, 2020;Gomez-Gonzalez et al, 2021). In addition, the occurrence of bedaquiline resistance TB strains in our locality is still extremely rare.…”

Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications

“…New genomic tools allow for whole-genome sequencing (WGS) with increasing opportunities to use it directly from the sputum [ 8 ]. Together with new analysis methods, WGS data can be used to profile the bacteria for drug resistance [ 5 , 9 , 10 ], characterize ancient and modern lineages and different strain types [ 11 ], and establish who may have transmitted to whom; thus allow targeted resources to hotspot areas to reduce transmission [ 12 ]. These genomic insights are facilitated through advances in health informatics [ 13 ].…”

“…Compared to other pathogen genomes, the M. tuberculosis genome (size: 4.4Mb) is relatively clonal with no horizontal gene transfer, but was historically challenging to sequence due to its high guanine–cytosine (GC) content and repetitive nature [ 15 ]. The Illumina sequencing platform with its paired short reads and low error rates has been employed successfully to analyse almost the entire genome, including drug-resistance loci [ 10 ], with highly variable and GC-rich pe / ppe genes often excluded due to the difficulties in accurately mapping these repetitive regions [ 16–18 ]. Recently, sequencing platforms with long reads (>1 kb) have been applied for the construction of reference genomes and analysis of methylated base modifications [ 19 ], but are too costly for implementation as a high throughput tool.…”

The evolving biology of Mycobacterium tuberculosis drug resistance

“…ddn, fgd1, fbiA, fbiB, fbiC, and fbiD Unknown (Haver et al, 2015;Gomez-Gonzalez et al, 2021) Linezolid (LZD) rrl, rplC Unknown (Hillemann et al, 2008;Beckert et al, 2012) Capreomycin (CAP) A1408G mutation in 16S rRNA gene (rrs)…”