Hotspots of Resistance: Screening of Antimicrobial Resistant Genes In Poultry-Related Water Sources and Wastewater Treatment Plants by A Culture-Independent Technique

Antimicrobial resistance genes (ARGs) are emerging micropollutants that spread widely yet remain difficult to control. Wastewater treatment plants (WWTPs) are central to contaminant removal, but their role in ARG dissemination remains limited, especially in Egypt under a One Health framework. This study investigated ARG prevalence in WWTPs and poultry-associated waters (n=33) within the Greater Cairo Metropolitan Area (GCMA). Twenty-five clinically and environmentally relevant ARGs were screened using direct resistome PCR across three WWTPs (Zenin, Belqas, and El-Berka) and adjacent waters, alongside water quality analyses. Zenin WWTP (Giza) showed the highest ARG richness (mean=12.8, ±1.3 SE) across treatment steps. Activated sludge (66.6%) emerged as a hotspot for ARG persistence, whereas clarifiers showed lower counts. Shared ARG profiles across influent, sludge, and effluent were recorded: Belqas, Zenin, and El-Berka harbored 8, 6, and 1 shared genes, respectively. Several water quality parameters, including temperature, TSS, TP, TN, COD, MLSS, SRT, and HRT were positively correlated with ARG richness and counts in sludge and effluents. All environmental samples amplified at least one ARG: agricultural and fecal waters contained 19/25 genes (76%), while drinking water harbored 10/25 (40%). Geographically, ARGs were most frequent in Giza (16), followed by Cairo (10) and Kalyoubia (4). To the best of our knowledge, our study is the first survey in Egypt to provide a snapshot of 25 ARGs across WWTPs and poultry-associated waters using direct PCR. It highlights treatment processes and environmental interfaces as drivers of ARG spread in the GCMA and calls for One Health strategies to mitigate AMR risks.