Genome-resolved metagenomics uncovers antimicrobial resistance gene carriers in hospital and municipal wastewater environments

This study used wastewater-based epidemiology (WBE) and genome-resolved metagenomics to analyse antimicrobial resistance (AMR) patterns across Wales, UK. From national wastewater samples, researchers reconstructed 3,978 microbial genomes, revealing a diverse bacterial community that varied by season and source. About 13.6% of genomes carried antimicrobial resistance genes (ARGs), mainly against tetracycline and oxacillin. Importantly, the team uncovered previously unknown microbes (“microbial dark matter”) carrying clinically relevant ARGs. Resistance profiles differed between untreated and treated wastewater and across treatment types, showing how wastewater processing shapes ARG dynamics. This first comprehensive genomic survey of hospital and municipal wastewater in Wales underscores the value of integrating genome-resolved metagenomics into national AMR surveillance to detect emerging threats and guide public health actions.