Riverine antibiotic resistome along an anthropogenic gradient

The introduction of antibiotic-resistant bacteria into riverine systems through the discharge of wastewater treatment plant (WWTP) effluent and agricultural waste poses significant health risks. Even when not pathogenic, these bacteria can act as reservoirs for antibiotic resistance genes (ARGs), transferring them to pathogens that infect humans and animals. In this study, we used fluorescence <i>in situ</i> hybridization, qPCR, and metagenomics to investigate how anthropogenic activities affect microbial abundance and the resistome along the Holtemme River, a small river in Germany, from near-pristine to human-impacted sites. Our results showed higher bacterial abundance, a greater absolute and relative abundance of ARGs, and a more diverse ARG profile at the impacted sites. Overall, the ARG profiles at these sites reflected antibiotic usage in Germany, with genes conferring resistance to drug classes such as beta-lactams, aminoglycosides, folate biosynthesis inhibitors, and tetracyclines. There were also variations in the ARG profiles of the impacted sites. Notably, there was a high abundance of the oxacillin resistance gene <i>OXA-4</i> at the downstream site in the river. In the metagenome assembly, this gene was associated with a contig homologous to small plasmids previously identified in members of the <i>Thiotrichaceae</i>. The likely in-situ host of the putative plasmid was a close relative of <i>Thiolinea</i> (also known as <i>Thiothrix</i>) <i>eikelboomii</i>, a prominent member of WWTP microbiomes worldwide. Our results show that the effluent from WWTPs can introduce bacteria into the environment that act as shuttle systems for clinically relevant ARG.