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Antimicrobial-resistant bacterial populations and antimicrobial resistance genes obtained from environments impacted by livestock and municipal waste

Getahun E. Agga, Terrance M. Arthur, Lisa M. Durso, Dayna M. Harhay, John W. Schmidt
Plos One 2015 v.10 no.7 pp. e0132586
DNA, Enterococcus, Escherichia coli, Salmonella enterica, animal wastes, antibiotic resistance, bacteria, beta-lactamase, cattle, erythromycin, feedlots, fluoroquinolones, genes, humans, lakes, metagenomics, municipal solid waste, municipal wastewater, ponds, population, runoff, sulfamethoxazole, swine, trimethoprim, waste lagoons, wastewater treatment, watersheds
This study compared the populations of antimicrobial-resistant bacteria and the repertoire of antimicrobial resistance genes in four environments: effluent of three municipal waste water treatment facilities, three cattle feedlot runoff catchment ponds, three swine waste lagoons, and two "low impact" environments (a municipal lake and a relict prairie). Multiple liquid and solid samples were collected from each environment. The prevalences and concentrations of antimicrobial-resistant (AMR) Gram-negative (Escherichia coli and Salmonella enterica) and Salmonella prevalences of 83 antimicrobial resistance genes in metagenomic DNA isolated from samples pooled (n= 44) by collection date, location, and sample type were determined. The prevalences and concentrations of AMR E. coli and S. Salmonella were similar among the livestock and municipal sample sources. The levels of erythromycin-resistant enterococci were significantly higher in cattle runoff and swine waste lagoon liquid samples compared to municipal samples, but not significantly different in solid samples. Similarly, trimethoprim/sulfamethoxazole-resistant E. coli concentrations were significantly higher in swine liquid than in municipal liquid samples, but there was no difference in solid samples. Individual antimicrobial resistance genes were significantly clustered within livestock, low impact, and municipal samples, with municipal samples harboring the highest number of antimicrobial resistance genes. The numbers of class A beta-lactamase, class C beta-lactamase, and fluoroquinolone resistance genes detected were significantly higher (P < 0.05) in municipal samples than in cattle runoff or swine lagoon samples. In conclusion, we report that AMR is a very widespread phenomenon and that similar prevalences and concentrations of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes exist in cattle, human, and swine waste streams, but a higher diversity of antimicrobial resistance genes are present in human waste streams.