The mobile resistome in the water–soil–air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes

Abstract

The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes (ARGs) present in pathogenic and non-pathogenic micro-organisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water-soil-air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.