Urban water systems as reservoirs of antimicrobial resistance genes: sources, microbiological mechanisms, and implications for environmental monitoring

Antimicrobial resistance (AMR) is increasingly recognized as an environmental concern, and antibiotic resistance genes (ARGs) represent its genetic basis in microbial systems. Urban water systems play an essential role as reservoirs and pathways for these genes. Wastewater collection systems, treatment plants, and surface waters receive continuous inputs of microorganisms and genetic materials from human activities, allowing ARG to persist and spread. This review summarizes current knowledge on the sources, occurrence, and environmental behavior of ARGs in urban water systems, with emphasis on microbial, genetic, and environmental processes that control their persistence and dissemination. The roles of microbial communities, mobile genetic elements, and extracellular DNA are discussed, along with the influence of hydrological conditions, chemical stressors, and treatment processes. Common molecular methods for ARG detection are reviewed, highlighting that measured ARG levels depend on environmental context and do not always indicate biological activity. In addition, standardized and context-aware monitoring approaches are needed to improve the environmental assessment of antimicrobial resistance.