Biogeography of Antibiotic Resistance in Nigeria’s Major River Systems: A Longitudinal Environmental Metagenomics Study with Human Health Risk Assessment

Nigeria's major river systems including the Niger, Benue, Imo, and Cross Rivers serve as critical ecological conduits for antibiotic resistance gene dissemination, yet the resistome biogeography of these rivers and associated human health risk pathways remain undescribed. This longitudinal environmental metagenomics study characterized resistome composition and human health-associated risk across five spatially distributed sampling zones on each of four major river systems over 18 months, encompassing three sampling periods representing dry season, early wet season, and peak wet season. Water, sediment, and biofilm samples were collected at upstream, midstream, industrial discharge, hospital effluent, and downstream agricultural zones. Shotgun metagenomics followed by resistance gene identification, taxonomic host assignment, and quantitative risk assessment using WHO hazard quotient methodology were performed. Hospital effluent discharge zones demonstrated the highest resistome density across all rivers. blaNDM-1 and mcr-1 genes were detected in downstream drinking water intake zones, below hospital effluent entry points, in 60 and 40 percent of wet-season samples respectively. Agricultural zones downstream of animal husbandry activities showed elevated tetracycline and sulfonamide resistance gene abundance. Seasonal analysis revealed wet season peak resistome enrichment averaging 3.8-fold above dry season levels in hospital proximity zones. Human health risk assessment indicated unacceptable hazard quotients for carbapenem resistance exposure at three of twenty downstream drinking water intakes. This study provides a national-scale river system resistome atlas and identifies priority risk zones for urgent environmental and public health intervention. Keywords: environmental resistome, river systems, metagenomics, health risk assessment, Nigeria.