Citywide metagenomics reveals microbial community and resistome dynamics in urban wastewater

Urban wastewater systems connect hospitals, residential communities, transport hubs, and wastewater treatment plants, creating opportunities for the dissemination of microorganisms and antibiotic resistance genes (ARGs). Here, we conduct a three-month, citywide metagenomic survey of wastewater in Xiamen, China, comprising 252 samples from seven hospital sites (n = 16), 27 residential sites (n = 55), 16 wastewater treatment plant sites (n = 159), and individual international flights (n = 22). Genome-resolved analyses reveal source-specific microbial community structures, resistome profiles, lineage-sharing patterns, and associations between ARGs and mobile genetic elements across wastewater sources. Hospital wastewater harbors the most diverse resistome, while international flight wastewater introduces microbial taxa and ARGs absent from local wastewater networks. Wastewater treatment plants accumulate ARGs from multiple upstream sources, exhibiting frequent lineage sharing and signals of potential horizontal gene transfer. Compared with within-environment sharing, cross-environment lineage sharing is associated with lower nucleotide diversity, consistent with possible genetic bottlenecks. Among potential correlates, pH shows strong non-linear associations with microbial diversity and resistome composition. These findings indicate that urban wastewater systems function as interconnected networks for microbial and ARG dissemination and identify potential hotspots for targeted antimicrobial resistance surveillance. In this study, the authors conducted a citywide metagenomics survey of urban wastewater and revealed widespread co-occurrence of microbes and antibiotic resistance genes that suggest potential transmission across hospitals, residential pipelines, international flights, and wastewater treatment plants.