Genome sequence and comparative analysis of Mycobacterium tuberculosis resourced from Pakistan and global lineage strains insights into the virulence and drug resistance

The current study unveiled the drug susceptibility profiling of randomly selected 102 out of 1,323 archives samples of Mycobacterium tuberculosis collected between 2020 to 2022 from the south Punjab province of Pakistan followed by genome sequence, In silico comparative analysis of genome, virulence, and drug resistance genes and analysis of molecular basis of niche adaptation. Out of 102 isolates, 15 (~ 12%) were culture-negative, 71 (69%) were culture-positive, and 16 (~ 15%) were contaminated. The 65 isolates were resistant to at least one drug, while the remaining six were sensitive to all drugs. The genome of M. tuberculosis strain MNPK1 has a size of 4.33 Mbp with greater than 95% similarity to strain H37RV, MNPK, and SWLPK. It encodes 4,321 coding genes including virulent, drug-resistant, PPE/PE, and HSPs associated genes. Molecular structure analysis of GroEL, grpE, and dnaK indicates the most conserved nature except minor differences in loop regions compared to H37Rv confirming evolutionary conservation of HSPs in M. tuberculosis strain MNPK1 and its lineages with reference strain H37Rv. Moreover, differential gene expression of HSPs-associated genes has revealed a significantly higher expression level under host-simulated conditions and sputum compared to growth conditions in 7H9 media revealing the role of HSPs in virulence and niche adaption. Overall, the study unveiled M. tuberculosis strain MNPK1 encodes virulent and MDR features, especially in relation to the Beijing genotype strain H37Rv, SWLPK, and strain MNPK and vital addition in ongoing research focused on therapy and diagnosis of M. tuberculosis not only locally but globally.