City-scale resistome-mobilome architecture and mobility-associated ARG backbones across a megacity watershed

Antimicrobial resistance (AMR) in urban watersheds is shaped by diverse anthropogenic inputs, and linking reads-level resistome-mobilome associations to local antibiotic resistance gene (ARG) genetic contexts can strengthen environmental surveillance. Here, we analyzed 63 deeply sequenced shotgun metagenomes from a Chongqing megacity watershed spanning surface water, river sediments, wastewater treatment activated sludge, livestock wastewater, and hospital wastewater. Reads-based profiling revealed strong habitat structuring of ARG subtypes and MobileElementFinder-derived mobilome families, and total ARG loads co-varied with mobile genetic element (MGE), biocide resistance, and metal resistance axes. To add sequence-resolved context, we surveyed 8,043 ARG-carrying contigs and integrated element-level MGE calls with open reading frame (ORF)-level mobility functions to define putative mobility tiers. Wastewater-impacted habitats showed higher representation of contigs carrying conjugation-related mobility signals, whereas sediments exhibited high ARG and MGE loads but weaker ARG-MGE coupling. This megacity-scale framework prioritizes mobility-associated and co-selection genetic contexts for environmental AMR monitoring and mitigation.