Ripples of Resistance: Unveiling Antimicrobial Resistance Dynamics Along Switzerland’s Aare River

• First survey of antimicrobial resistance along the Aare River, Switzerland’s longest river and a major tributary of the Rhine: Absolute and relative abundance of resistance genes and fluxes. • Wastewater of urban centres is the main source of AMR in the Aare, leading to an accumulation of AMR along its course. • Where the river passes through lakes, AMR levels are strongly reduced, even when lake water residence time is low: Lakes act as AMR sinks. • ARGs are highly correlated with other indicators of anthropogenic influences, such as nutrients, trace metals, and fecal source tracking marker crAssphage: AMR is a marker of anthropogenic impact. The global spread of antimicrobial resistance (AMR) is a serious public health concern, driven by widespread antibiotic use and the global environmental circulation of antibiotic-resistant bacteria and resistance genes (ARGs). Wastewater treatment plants (WWTPs) are important sources of anthropogenic AMR entering large rivers, which serve as vital water resources but facilitate downstream dissemination. The drivers and dynamics of AMR propagation along river systems remain poorly understood. As Switzerland’s longest and one of its largest rivers, the Aare, situated in the upper Rhine watershed, plays a central role in the ‘water castle of Europe’. This study examines the impact of WWTP discharges, some receiving high loads of hospital effluent, on ARG distribution along the 288 km Aare river-continuum. Using quantitative PCR targeting 14 ARGs conferring resistance to eight antibiotic classes, combined with 16S rRNA gene amplicon sequencing, we conducted a high-resolution spatial survey to assess shifts in the riverine ARG content and microbiome. Concentrations of trace metals and nutrients were analyzed as tracers of anthropogenic inputs. Results revealed a progressive increase in ARG abundance downstream, driven by WWTP effluents enriched in ARGs. Effluents had 70-fold higher mean ARG concentrations than upstream waters, raising downstream levels up to 141-fold. Major tributaries such as the Reuss and Limmat sustained elevated ARG levels, while passage through lakes markedly reduced concentrations. This study provides the first detailed baseline for ARG prevalence along a large river system, from pristine headwaters to pollution-affected lower reaches and insights into aquatic AMR dynamics and guidance for future monitoring.