Quantification of Cefotaxime-Resistant Escherichia coli and Class 1 Integron Integrase Genes as Key Indicators of Antimicrobial Resistance in Urban Wastewater in Two Cities in Japan

Antimicrobial resistance (AMR) is a pressing global health threat. Wastewater surveillance is a promising approach to comprehensively evaluate the prevalence of antimicrobial resistant bacteria and antimicrobial resistance genes in the urban areas. Although cefotaxime-resistant E. coli and class 1 integron integrase gene were proposed as key indicators of AMR, their levels in wastewater in Japan remain unknown. This study quantified these parameters in wastewater samples collected every two months from two cities in Japan. Metagenomic analysis with hybrid capture enrichment identified dominant genes conferring resistance to tetracyclines, aminoglycosides, beta-lactams, and macrolides, with a particular focus on ESBL, carbapenemase, and colistin resistance genes.