Coordinated resistance–virulence organization across urban microbiomes reveals context-dependent ecological structuring

Microbial communities in built environments are shaped by functional traits associated with persistence, ecological interaction, and pathogenic potential. While antimicrobial resistance (AMR) genes and virulence factors (VFs) are typically studied independently, their coordinated organization may contribute to ecological structuring across urban microbiomes. Here, we investigated coordinated resistance–virulence organization across hospital settings, ambulances, hospital sewage, and public transport systems using genome-resolved metagenomics. We show that microbial communities differed not only in taxonomic composition, but also in the ecological organization of coordinated resistance- and virulence-associated functional mechanisms. Integration of functional diversity, multivariate ecological differentiation, and recurrent mechanism-level enrichment patterns indicated that ambulances more frequently exhibited persistence-associated ecological tendencies, whereas hospital sewage and public transport more frequently exhibited interaction-associated and multifunctional ecological tendencies, with substantial overlap across environments. Coordinated functional profiles accurately predicted environmental origin, while synthetic perturbation analyses revealed non-linear transition dynamics, intermediate ecological states, and variable instability landscapes across environments. Together, these findings support an ecological framework in which coordinated resistance–virulence organization is associated with functional differentiation, transition behavior, and ecological structuring across urban microbiomes