Abstract
The dissemination of antimicrobial-resistant bacteria in environmental water is an emerging concern in medical and industrial settings. Here, we analysed the antimicrobial resistance of Escherichia coli isolates from river water and sewage by the use of a combined experimental phenotypic and whole-genome-based genetic approach. Among the 283 tested strains, 52 were phenotypically resistant to one or more antimicrobial agents. The E. coli isolates from the river and sewage samples were phylogenetically indistinguishable, and the antimicrobial-resistant strains were dispersedly distributed in a whole-genome-based phylogenetic tree. The prevalence of antimicrobial-resistant strains as well as the number of antimicrobials to which they were resistant were higher in sewage samples than in river samples. Antimicrobial resistance genes were more frequently detected in strains from sewage samples than in those from river samples. We also found that 16 river isolates that were classified as Escherichia cryptic clade V were susceptible to all the antimicrobials tested and were negative for antimicrobial resistance genes. Our results suggest that E. coli strains may acquire antimicrobial resistance genes more frequently and/or antimicrobial-resistant E. coli strains may have higher rates of accumulation and positive selection in sewage than in rivers, irrespective of their phylogenetic distribution.
Highlights
The dissemination of antimicrobial-resistant bacteria in environmental water is an emerging concern in medical and industrial settings
We isolated and analysed more than 300 E. coli strains from two river and two sewage samples
The whole-genome-based phylogenetic tree revealed great phylogenetic diversity among E. coli isolates from water samples. Even though both phenotypically and genotypically antimicrobial-resistant strains were dispersedly distributed in the whole-genome-based tree, resistant strains were detected more frequently in the sewage samples than in the river samples
Summary
The dissemination of antimicrobial-resistant bacteria in environmental water is an emerging concern in medical and industrial settings. We analysed the antimicrobial resistance of Escherichia coli isolates from river water and sewage by the use of a combined experimental phenotypic and whole-genome-based genetic approach. E. coli strains are traditionally classified into phylogroups (A, B1, B2, C, D, E, F and G) and cryptic Escherichia clades (clades I to V) by PCR-based phylotyping[17,18,19] or into sequence types (STs) by multilocus sequence typing (MLST)[20,21] Using these typing methods, antimicrobial-resistant E. coli strains from water environments have been analysed to determine the clonal structure of these s trains[22,23,24]. No systematic whole-genome-based study has focused on the difference in the prevalence and characteristics of antimicrobial-resistant E. coli strains between sewage and river water
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