Antimicrobial Resistance Across the Urban Wastewater Continuum: A One Health Assessment Using High-Throughput qPCR

Background: Wastewater systems provide an integrated One Health perspective on antimicrobial resistance but remain uneven globally, with limited data from rapidly urbanizing and highly connected regions such as the Arabian Gulf. Methods: An eight-month prospective study was conducted in Dubai, United Arab Emirates, with monthly sampling from nine community and two hospital nodes and two wastewater treatment plants (WWTP). Samples were analysed using high-throughput quantitative PCR (HT-qPCR; Resistomap, Finland) with a 72-target One Health gene panel. Results: Across the 120 samples analyzed, the number of detected gene targets ranged from 26 to 68 genes, with the highest diversity in hospital wastewater and the lowest in WWTP effluent. Pathogen-associated markers were detected in all sources, with enterococci, Escherichia coli, and Klebsiella pneumoniae predominant. Hospital wastewater showed broader pathogen-associated gene markers, including those linked to Acinetobacter baumannii and Pseudomonas aeruginosa. Antibiotic resistance genes (ARGs) associated with macrolide-lincosamide-streptogramin B, tetracycline, and aminoglycoside resistance were widespread. Community and influent samples were dominated by msrE, tet(M), and aminoglycoside resistance genes, whereas hospital wastewater showed the highest ARG burden, including enrichment of aac(6')-Ib, qnrS2, bla_GES, bla_TEM, bla_KPC-2, and bla_IMP-1. Several ARGs, including mcr-1, persisted in WWTP effluent. Mobile genetic elements (MGEs) were ubiquitous, with integron-associated markers prominent in WWTP effluent. ARG-MGE network analysis demonstrated extensive co-occurrence, with MGEs as central hubs linking multiple ARGs. Conclusions: Wastewater captures distinct resistome profiles across urban compartments, supporting its role for AMR surveillance. The persistence of ARGs and MGEs in WWTP effluent highlights the potential for environmental dissemination, through reuse of treated wastewater.