Genomic Surveillance and Epidemiological Modeling of Antimicrobial Resistance (AMR) in Urban Hospital Effluents

Abstract

Antimicrobial resistance (AMR) constitutes one of the most pressing global health crises, with hospital wastewater (HWW) serving as a critical environmental hotspot for the emergence, selection, and dissemination of multi-drug resistant (MDR) pathogens. This review synthesizes recent advances in genomic surveillance and epidemiological modeling of AMR in urban hospital effluents, focusing on high-income and low- and middle-income settings. Whole-genome sequencing (WGS) and metagenomic approaches reveal high abundances of clinically relevant resistance genes (blaNDM, blaOXA-48, mcr-1, qnrS) and mobile genetic elements (integrons, transposons, plasmids) in effluents, often mirroring patient case rates and mirroring hospital antibiotic usage patterns. Longitudinal sampling combined with phylogenetic analysis demonstrates clonal transmission of MDR Enterobacterales (e.g., carbapenem-resistant Klebsiella pneumoniae, ESBL-producing E. coli) from hospitals to downstream urban waterways and agricultural irrigation systems. Epidemiological models integrating compartmental SIR frameworks, agent-based simulations, and One Health network analysis quantify transmission risks, estimate secondary infection burdens, and evaluate intervention efficacy (advanced wastewater treatment, antibiotic stewardship). Key findings highlight the disproportionate contribution of HWW to regional resistome expansion and underscore the urgent need for routine genomic surveillance, point-of-care diagnostics, and integrated wastewater-based epidemiology to inform national action plans and interrupt AMR dissemination cycles.