Comparative genomic surveillance of fluoroquinolone resistance markers across major riverine hotspots by leveraging public metagenomes.

OBJECTIVE

The global surge in fluoroquinolone resistance (FQR) underscores the urgent need for robust environmental surveillance. From a One Health perspective, rivers serve as critical conduits and hotspots for antimicrobial resistance (AMR) dissemination.

METHODS

To address this issue, we conducted a systematic metagenomic surveillance of FQR across spatially prioritized freshwater ecosystems using distribution data of five major markers (gyr, par, qnr, aac, and qep) retrieved from the National Center for Biotechnology Information Pathogen Detection Isolate Browser.

RESULTS

Among 164 riverine metagenomic datasets, 31 high-quality datasets from the Mississippi, Yukon, Saint Lawrence, Yangtze, and Pearl Rivers were analysed. FQR genes were detected in 12 datasets, with normalized abundances ranging from 0.01 to 1.22 copies per bacterial cell. Plasmid-mediated qnrS2 and efflux pump genes (qepA2 and AbaQ) emerged as the most prevalent determinants. Multivariate analyses revealed river-specific clustering patterns and strong correlations with metal resistance genes, highlighting co-selection pressures. The predominance of conjugative mobile genetic elements indicated an elevated potential for horizontal gene transfer. Taxonomic profiling further revealed enrichment of clinically important and World Health Organization priority pathogens. Community structure analyses (permutational multivariate analysis, R² = 0.7598, P = 0.003) confirmed significant microbial variations across rivers.

CONCLUSIONS

Collectively, this integrative approach identifies environmental reservoirs of FQR genes, supporting river-based AMR surveillance. These insights are pivotal for shaping evidence-driven mitigation strategies and informing both national and global AMR policies.