Genomic Polymorphisms in Toxin-Antitoxin Systems and Identification of Novel Phylo-SNPs and Polymorphisms Associated with Drug Resistance/Susceptibility in Clinical Isolates of Mycobacterium tuberculosis from Mumbai, India

Toxin-antitoxin (TA) modules are one of the prominent determinants that triggers a persistent state aiding Mycobacterium tuberculosis evasion to host generated stresses. The 79 characterized and putative TA systems described in M. tuberculosis are dominated by the VapBC, MazEF, HigAB, RelBE and ParDE TA families, largely involved in persistence and cell arrest. Hence, there is a need to maintain and conserve the TA loci in the chromosome of the pathogen. It is essential to study the genomic differences of the TA systems in clinical isolates along with its association to drug susceptibility patterns and lineage. In the current study, the TA loci and their promoter sequences were analysed from the whole genome sequence data of 74 clinical isolates. Mykrobe Predictor was used for lineage identification and drug resistance predictions in the clinical isolates. Polymorphisms associated with 79.8% (63/79) TA systems were observed across 72 clinical isolates. Among the TA systems, the isolates had a varying number of polymorphisms localised primarily in the toxin genes (58.7%), antitoxin genes (40.7%) and chaperones (0.6%), due to Single Nucleotide Polymorphism (SNP) resulting in transition (67.3%), transversion or frameshift mutations. Our analysis suggests the presence of novel Phylo-SNPs by establishing high confidence association of specific lineages to polymorphisms in the TA systems. Notably, association of polymorphisms in Rv1838c-1839c (VapBC13), Rv3358-3357 (YefM/YoeB) and Rv0240-0239 (VapBC24) to Delhi/Central Asia lineage. The polymorphic loci of the 3 TA systems is localised in the antitoxin gene of the Delhi/Central Asia strains, with a resultant silent mutation. The assessment of correlation between TA polymorphisms and the drug resistance profile revealed correlation of SNPs in VapBC35 with drug resistant M. tuberculosis strains and SNPs in VapBC24, VapBC13 and YefM/YoeB to drug sensitive strains.