A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan

This study used a metagenomics-based approach to characterize the hospital surface microbiome and antimicrobial resistome and to infer potential transmission routes of healthcare associated antimicrobial resistance (AMR) within a tertiary-care hospital in Pakistan. Environmental swab samples were collected from multiple clinical settings, including the intensive care unit, surgical ward, cardiac wards, and the operating theater. We combined 16S rRNA gene sequencing and shotgun metagenomics to profile microbial communities, identify antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), and evaluate ward-to-ward microbial source sink relationships. The resulting datasets provide baseline genomic evidence for environmental AMR reservoirs and support metagenomics-informed infection control and surveillance strategies in resource limited healthcare settings.