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

Antimicrobial resistance in human, veterinary, and agricultural sectors 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 urban areas. Although cefotaxime-resistant E. coli and class 1 integron integrase gene (intI1) 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 (A and B) in Japan. Cefotaxime-resistant E. coli and intI1 genes were consistently detected in wastewater from both cities, with relative abundances of cefotaxime-resistant E. coli/total E. coli ranging from 0.3%–2.5% in City A and 1.2%–2.5% in City B, and intI1/16S rRNA gene ratios ranging from 1.0 × 10−2–3.3 × 10−2 in City A and 3.0 × 10−3–2.2 × 10−2 in City B. The cefotaxime-resistant E. coli isolates harbored extended-spectrum β-lactamase genes including blaCTX-M-1 group, blaCTX-M-9 group, and blaTEM. Metagenomic analysis with hybrid capture enrichment identified dominant genes conferring resistance to tetracyclines, aminoglycosides, β-lactams, and macrolides. The relative abundances of some extended-spectrum β-lactamase, carbapenemase, and colistin resistance genes was higher in wastewater samples from City B than those in City A.