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bioRxiv · 10.64898/2026.09.08.750159

Rapid Antimicrobial Resistance Decline Coupled with Microbial Community Shifts in Sewage Polluted River Mesocosms

Kashyap, A.·Sonkar, V.·Graham, D. W.·Kreft, J.-U.·Thatikonda, S.
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Abstract

Antimicrobial resistance poses a global health threat, yet the fate of antimicrobial resistance genes (ARGs) and microbial communities from wastewaters in receiving rivers is rarely quantified. This study investigated the degradation kinetics of ARGs in sewage-polluted river water mesocosms and under sulfamethoxazole and copper stress, separately and in combination. Seven clinically relevant ARGs (blaCTX-M, blaNDM, qnrS, sul2, tetW, ermF, and aph(3'')-Ib), a mobile genetic element marker (intI1) and bacterial marker genes (uidA, 16S rDNA) were quantified by qPCR. Bacterial community changes were monitored using 16S rDNA amplicon sequencing. All target genes decayed with approximately first-order kinetics in all conditions, with qnrS (half-life: 8.0 h) and blaCTX-M (8.4 h) declining most rapidly and intI1 (32.5 h) and sul2 (46.5 h) declining most slowly. Ordination showed that ARG composition shifted primarily over time rather than by antibiotic/metal treatment. Bacterial communities shifted from initially Campylobacterota dominated ([≥] 90%) to Pseudomonadota, Bacillota, and Actinomycetota dominated communities over 168 h. Quantitative microbiome profiling showed a 95% reduction in ASV richness. PICRUSt2 analysis suggested progressive enrichment of aerobic and several metabolic pathways, as the mesocosms transitioned from highly polluted anoxic conditions to oxygenated conditions. Shifts in microbial community composition were coupled with changes in the resistome as identified by Procrustes analyses (r = 0.841, p = 0.001) and other analyses. Together, results show that river self-purification can rapidly reduce ARG loads, at least in warmer climates. This study provides approximate kinetic parameters for mathematical models to predict the fate of ARGs in rivers.

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Kashyap, A., Sonkar, V., Graham, D. W., Kreft, J.-U., Thatikonda, S.. 2026-09-09. Rapid Antimicrobial Resistance Decline Coupled with Microbial Community Shifts in Sewage Polluted River Mesocosms. https://doi.org/10.64898/2026.09.08.750159

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