Tracking antimicrobial resistance in river waters: Sources, key microbes, and detection techniques

Abstract

Antimicrobial resistance (AMR) poses a critical and escalating threat to global health, driven largely by the dissemination of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) across environmental matrices. Among these, river waters—frequently contaminated by municipal, hospital, industrial, and abattoir effluents—serve as key reservoirs and conduits for ARG and ARB propagation. The coexistence of antibiotics, heavy metals, and microbial communities in such waters fosters horizontal gene transfer and amplifies the spread of resistance. This review focuses on the prevalence, diversity, and persistence of ARGs in riverine ecosystems, emphasizing the role of environmental factors and anthropogenic inputs in shaping AMR dynamics. It further examines current molecular tools, including quantitative PCR, metagenomic sequencing, and fluorescence-activated cell sorting, used to detect and characterize ARGs and ARB in aquatic environments. Despite technological advances, major gaps remain in standardizing ARG quantification methods, defining threshold levels for risk assessment, and establishing effective monitoring and remediation strategies. This review outlines a strategic research roadmap, advocating for harmonized protocols, the development of ARG/ARB monitoring surrogates, and integration of molecular data into environmental risk management. Strengthening river water surveillance and mitigation efforts is essential to interrupt AMR transmission pathways and safeguard public and environmental health.