Metagenomics-Based Characterization of Antibiotic Resistance Genes in Effluents from Tertiary Hospital Sewage Treatment Plants in Abuja, FCT

Hospital sewage treatment plants are recognized as critical hotspots for the concentration and dissemination of antibiotic resistance genes (ARGs) into receiving water bodies. Conventional culture-based methods underestimate the full resistome present in complex environmental matrices, making metagenomics a more comprehensive analytical approach. This study applied shotgun metagenomics to characterize the antibiotic resistome in influent and effluent samples from sewage treatment plants of three tertiary hospitals in Abuja, FCT, North Central Nigeria. DNA was extracted from water filter membranes and sequenced on the Illumina NovaSeq platform. Bioinformatics analysis using ResFinder, CARD database, and ARG-OAP pipeline identified ARG classes, subtypes, and their mobile genetic element associations. Results revealed 287 unique ARG subtypes across all samples, with beta-lactamase, aminoglycoside, and tetracycline resistance genes most abundant. Effluent samples retained 78 percent of the influent ARG diversity despite sewage treatment, indicating inadequate ARG removal by conventional activated sludge processes. blaNDM-1 and mcr-1 (colistin resistance) genes were detected in effluent from all three hospitals. Mobile integrons and plasmid-associated ARGs constituted 46 percent of identified resistance elements. These findings demonstrate that hospital sewage treatment in Abuja is insufficient to eliminate clinically significant resistance genes and call for advanced treatment technologies including ozonation or UV-based systems. Keywords: antibiotic resistance genes, metagenomics, hospital sewage, resistome, Abuja.