Whole-genome sequencing to explore genomic profile, pathogenicity, virulence motifs, and pangenome of clinical MRSA isolates.

Multidrug-resistant (MDR) and Methicillin-resistant Staphylococcus aureus (MRSA) are major opportunistic pathogens, particularly in healthcare settings. Despite the importance of such strains as a priority nosocomial pathogen, genomic data on Bangladeshi isolates remain limited. This study presents whole genome sequence (WGS) analysis of three MDR-MRSA strains (SA-18, SA-36, and SA-41) isolated from wound-infected patients in a tertiary care hospital in Bangladesh. Multi-locus sequence typing (MLST) identified SA-18 and SA-36 as sequence type ST6, and SA-41 as ST1930. All isolates carried the mecA gene and SCCmec type IVa were classified as MRSA. A total of 22 antibiotic resistance genes (ARGs) were identified, including blaZ, erm(C), norA, and sdrM. Pathogenicity prediction classified all isolates as human pathogens, with SA-41 showing the highest pathogenic potential (98%). Virulence analysis revealed 75 virulence factor genes (VFGs), such as hla, spa, icaA-D, and PVL. Mobile genetic elements (MGEs), plasmids, and an intact 50.9 kb prophage region were detected, with the ebp gene identified within the prophage in SA-41. Pangenome analysis revealed 3764 gene clusters, indicating an open and diverse pangenome. The findings of the present study highlight the importance of WGS in antimicrobial stewardship programs by rapidly identifying resistant genes and spread of multidrug-resistant MRSA strains in Bangladesh which will allow better infection control, rational use of antibiotics and developing effective public health policies.