Whole Genome Sequencing and Metabolomic Profiling of Six Clinical Mycobacterium Tuberculosis Isolates Reveal Drug Resistance-Associated Features

Drug-resistant tuberculosis (DR-TB), resulting from newly emerging strains of Mycobacterium tuberculosis (Mtb), and the World Health Organisation (WHO) included it as a top-priority antimicrobial-resistant pathogen. Whole genome sequence analysis (WGS) of clinical Mtb isolates could correlate to their drug resistance phenotype and may also reflect their metabolome. In this report, clinical Mtb isolates (S1, S4, S5, S6, S7, S10) harvested from the sputum of tuberculosis patients were characterized using drug sensitive test (DST), electron microscope, WGS and untargeted Gas chromatography and mass spectrometry (GC-MS) based metabolomics analysis. The majority of these Mtb isolates showed similar size (length: 1.0-3.2 μm; width: 0.32-0.52 μm) to the H37Rv Mtb strain, whereas significant variations were observed in their growth kinetics, WGS and metabolome profiles. In-silico drug resistance prediction, from the WGS data (single-nucleotide polymorphisms (SNP) pattern) of these Mtb isolates, showed resistance to tuberculosis drugs and matched with DST results. Differences in the genes involved in stress response, pathogenicity, and drug efflux pumps were observed between isolates, but genes of the central carbon metabolic pathways and amino acid metabolism were conserved. GC-MS-based metabolite profiling of these clinical isolates identified 291 metabolites involved in various metabolic pathways, and a subset of these metabolites (glutamic acid, aspartic acid and serine) contributed to the drug resistance patterns. These clinical Mtb isolates could be useful as an alternate reagent for understanding host-pathogen interaction. The pipeline used for WGS analysis could be used to predict the drug resistance pattern of new Mtb isolates.