Mobile genetic elements drive the assembly of high-risk resistance and virulence configurations at the riverine water–sediment interface

Riverine ecosystems are major conduits and repositories for microplastics, heavy metals and antibiotics yet how these co-occurring stressors jointly shape resistance and virulence risks across water and sediments remains unclear. Here we combined shotgun metagenomics with pollutant profiling along a representative rural-to-urban gradient during the dry season to resolve the distribution, mobility and drivers of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), virulence factors (VFs) and mobile genetic elements (MGEs) in paired surface waters and surficial sediments. Bacterial communities were dominated by Pseudomonadota and Actinomycetota while fungal communities were dominated by Ascomycota and Uroviricota respectively with stronger land-use effects observed in water than in sediments. Across all samples we detected 36 ARG classes and 1589 subtypes where multidrug and efflux or target alteration mechanisms predominated. Furthermore ARG richness, abundance and diversity increased from rural to urban reaches in both media. MGEs were dominated by transposases where ARG-MGE co-localization on 1474 contigs revealed dense transposase-centered networks in urban sediments that linked multidrug, peptide, glycopeptide and tetracycline resistance. Crucially we identified contigs co-harboring ARGs, MRGs, and VFs as multi-trait risk gene carriers. Urban reaches hosted diverse carrier lineages whereas rural reaches were dominated by the high abundance of specific carriers. SourceTracker and partial least squares path modeling together indicated that rural sediments are the principal upstream sources of microbes and risk genes while MGEs in urban sediments translate multi-pollutant stress into enlarged and more mobile risk gene pools. These findings highlight the need to jointly manage agricultural inputs and urban sediments under multi-stressor conditions.