Cross-regional metagenomic insights into clinical and stable resistomes in urban wastewater systems

Antimicrobial resistance (AMR) is a growing global threat, with elevating risks in low- and middle-income countries due to inadequate infrastructure and limited regulation. However, comprehensive analyses on AMR profiles in these regions remain scarce. We compared AMR risks across full-scale wastewater treatment plants (WWTPs) in Egypt (Cairo) and China (Xiamen), utilizing shotgun metagenomic sequencing, bioinformatics, and multivariate analysis. Our results indicated that while influent samples exhibited comparable AMR risk levels, the activated sludge and effluent from Egyptian WWTPs showed significantly higher risks, characterized by greater clinical ARG abundance, enhanced mobility potential, and more diverse pathogenic hosts. We identified 51 stable ARGs that persisted across WWTPs, seasons and treatment units. These stable ARGs showed strong association with pathogen community and were detected across a broader range of pathogenic hosts, and were predominantly plasmids-borne. Plasmids were the primary vectors of horizontal gene transfer (HGT) of clinical ARGs, whereas viruses showed selective associations with stable ARGs. Key pathogens facilitating HGT of both clinical and stable ARGs included Alcaligenes faecalis and Shigella spp., with cross-domain putative HGT events also being detected. These findings address a critical knowledge gap in underrepresented regions and provide risk-based strategies to mitigate ARG dissemination in urban wastewater systems.