Whole genomic sequencing of pre-XDR Mycobacterium tuberculosis isolates in iraq reveals resistance-associated mutations and distinct phylogenetic lineages

Abstract Background Multidrug-resistant (MDR) and preextensively drug-resistant (pre-XDR) Mycobacterium tuberculosis pose major problems to tuberculosis control worldwide. In this study, we combined the phenotypic drug resistance patterns and the whole genome sequencing (WGS) to characterize the resistance profile of M. tuberculosis isolates obtained from Iraqi TB patients. Methods Out of 96 clinical isolates, two pre-XDR strains exhibited fluoroquinolone resistance and were selected for WGS. Results Whole-genomic comparison and SNP-based phylogenetic tree using global reference strains revealed that both strains belonged to distinct evolutionary lineages, with MH-11 belonging to Lineage 3 (East African-Indian) and MM-22 to Lineage 4.3.2 (Euro-American/LAM), referring to lineage diversity within Iraqi TB patients. Both isolates possess well-characterised resistance-conferring mutations in key genes: gyrA (p.Asp94Gly, pAl90Val), rpoB (S450L), and katG (p.Ser315Thr). Notably, a shared upstream variant in the rrS gene (n-187 C˃T) was identified. In addition, the comparative analysis of virulence factors revealed variations in genes correlated with the secretion system, lipid metabolism, and host immune modulation, including structural differences in pks15 and plcA in comparison with the reference strain H37Rv. Moreover, BRIG-based whole-genome comparison identified a notable genomic divergence between the two pre-XDR isolates. Conclusion Our study provides novel genomic insights into pre-XDR M. tuberculosis from Iraq, a region that is inadequately represented in global TB datasets and supports the value of integration of WGS-based surveillance to improve TB management strategies in Iraq.