Whole genome sequencing and global metabolome profiling of clinical Mycobacterium tuberculosis isolates provide insights to their drug resistance status

Whole genome sequence analysis of the Mycobacterium tuberculosis (Mtb) isolates show correlation to their drug resistance phenotype which may also reflect in their global 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, whole genome sequencing (WGS) and metabolomics. 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-nulceotide 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, drug efflux pumps were observed between isolates but genes of the central carbon metabolic pathways and amino acid metabolism were conserved. Gas chromatography and mass spectrometry (GC-MS) based metabolite profiling of these clinical isolates identified 291 metabolites involved in various metabolic pathways and a sub set of these metabolites (glutamic acid, aspartic acid and serine) contributed to the drug resistance patterns. These clinical Mtb isolates could be useful as alternate reagent for understanding host pathogen interaction and the pipeline used for WGS analysis could be used to predict drug resistance pattern of new Mtb isolates.