Whole Genome Sequencing of E. coli for antimicrobial resistance surveillance

The growing issue of Antimicrobial Resistance or AMR calls for effective surveillance and careful use of antimicrobials. One promising method is wastewater based epidemiology, where Next Generation Sequencing technologies are used to identify pathogens and their resistance genes. This report explores the use of Escherichia coli in wastewater for AMR surveillance. E. coli isolates from wastewater samples of hospital and community sites were analyzed using whole genome sequencing Oxford Nanopores MinION Mk1C and Genotypics Commander Software. Antimicrobial resistance genes were screened with ABRicate and CARD. Phenotypic testing showed similar resistance patterns in both hospital and community wastewater, but hospital wastewater had higher resistance rates. Genotypic analysis found resistance genes in samples, with all isolates having genes for resistance to at least one drug class, most showing resistance to three or more classes. This method, using E. coli as an indicator, provides a valuable tool for monitoring AMR in different environments. Continued research and adoption of such strategies are vital to addressing the global threat of AMR.