Mycobacterium tuberculosis Strains from Eastern Siberia Resistant to Bedaquiline and Linezolid: Identification of Novel Mutations

Background . The spread of resistance to bedaquiline and linezolid is a global public health issue across all countries. Investigating the molecular mechanisms underlying this resistance is crucial for curbing the spread of extensively drug-resistant (XDR) tuberculosis. The aim of the study was to identify mutations associated with resistance to bedaquiline and linezolid and to determine the genotypes of 26 Mycobacterium tuberculosis strains circulating in the Irkutsk Region and Yakutia in 2024–2025. Materials and methods . From a collection of 183 strain DNA samples, 26 strains exhibiting phenotypic resistance to bedaquiline and/or linezolid were selected. Sanger sequencing identified mutations listed in the WHO catalog. Additionally, SNP and indel analysis was performed using the previously developed BSATool software. Results. Phenotypically, the isolates were resistant to bedaquiline (16) and linezolid (14); 3 were pre-XDR and 15 were XDR, while the remainder were monoor poly-resistant. Four strains were resistant to both bedaquiline and linezolid. Among the 16 bedaquiline-resistant strains, five had loss-of-function (LoF) mutations, while the other nine carried mutations of uncertain significance. Eleven new mutations were identified, ten of which were conclusively classified as LoF mutations. For two bedaquiline-resistant strains where no SNPs were detected upon amplification of the Rv0678 gene, a significant increase in amplicon size was observed. Further analysis demonstrated that the bedaquiline resistance was caused by the insertion of the IS6110 mobile element at positions 179 and 370 of the Rv0678 gene. The strains belonged to different L2.2 subtypes: B0/W148 and CAO. Conclusion . The widespread use of bedaquiline and linezolid in the treatment of tuberculosis over the past 5 years in the study areas has provided selective advantages for strains implementing various molecular mechanisms of resistance to these drugs. When using molecular tests aimed at determining drug resistance, it is necessary to pay attention to a wide range of changes in the genome of the tuberculosis pathogen, including major genomic rearrangements.