From city waste to river risk: tracking AMR and pathogenic potential in urban water gradient of the Kathajodi river

This first metagenomic assessment of the Kathajodi River in eastern India demonstrates how urban pollution reshapes riverine microbial ecosystems and accelerates antimicrobial resistance (AMR) dynamics along an upstream–catchment–downstream gradient. While the relatively pristine upstream site showed low species richness and a modest resistome adapted to natural biogeochemical cycles, the urban wastewater-impacted catchment emerged as a hotspot with markedly higher microbial diversity, abundant antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes, and virulence factors, driven by heavy metals and organic pollution that create strong selective pressure. Downstream sites showed partial ecological recovery but retained high-risk ARGs and virulence genes, indicating persistent contamination and adaptation. Functional and network analyses revealed that pollution shifts microbial communities toward stress-response pathways and that MGEs play a central role in horizontal gene transfer and co-selection of resistance and virulence traits, underscoring the public health risks of untreated urban waste discharge and the urgent need for integrated environmental management and policy action to curb environmental AMR spread.