Metagenomic sequencing reveals the abundance and diversity of antimicrobial resistant genes (ARGs) in Butuanon River, Cebu, Philippines
Lead Researcher(s): Britney Ann Yu, Edrine Durante, Hans Diether Tolabing, Fleurdeliz Maglangit, Brisneve Edullantes, Eukene Bensig
Status: Published
Abstract/summary: Antimicrobial resistance (AMR) poses a significant public health threat, impacting the future of modern medicine. Antimicrobial resistance genes (ARGs) facilitate AMR spread through horizontal gene transfer. Although aquatic systems serve as reservoirs, limited studies have been conducted to detect ARG occurrence. This study assessed the abundance and diversity of ARGs across ten sampling points in the upstream, midstream, and downstream sections of the Butuanon River, and examined their relationship with physicochemical parameters. Water samples were collected from the sampling sites across the river stretch during the northeast monsoon. eDNA was extracted and sequenced using shotgun metagenomic sequencing. Following de novo assembly, probing for ARGs was determined through RGI (Resistance Gene Identifier) based on the Comprehensive Antibiotic Resistance Database (CARD). Overall, a total of 153 ARGs resistant to 17 antibiotic drug classes were found. ARG richness and alpha diversity increase from upstream to downstream, with an average alpha diversity of 1.78 to 3.76, respectively. Composition varies significantly between the three streams, with ARGs resistant to beta-lactamases and aminoglycosides dominating midstream and downstream, while glycopeptides are prevalent in the upstreams. While sul1 and sul2 have a significantly positive correlation with one another (p < 0.05, R = 0.65), no physicochemical variables had any correlation with either of the genes. Only pH and temperature had significant relationships with the total abundance of rifamycin, quinolone, and MLS. Risk ranking reveals thirteen (13) Rank I ARGs and three (3) Rank II ARGs. Several members of the Enterobacteriaceae family were detected as pathogen sources for selected ARGs. Profiling the antimicrobial resistance will serve as the baseline for monitoring the ecological health status of aquatic systems.
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