A monitoring method to evaluate the accumulation of antimicrobial-resistance genes on plasmids harbored by antimicrobial-resistant bacteria distributed in environmental water.

Antimicrobial-resistant bacteria (AMRB) distributed in the environment can cause human refractory infections. Frequently performed environmental metagenomics could not provide information on what types of AMRB accumulate what types of antimicrobial resistance genes (ARGs). Assuming to monitor AMRB in the environment, we selected 910 AMRB isolates using cefotaxime and ciprofloxacin from Vietnamese environmental water samples and subjected to 16S rRNA sequencing. It indicated that Escherichia coli (36.0%), Citrobacter freundii (21.4%), Acinetobacter baumannii (20.6%), and Klebsiella pneumoniae (19.7%) were dominant. Using E. coli as a model, we further analyzed AMRB isolates by phylogenetic analysis and whole-genome sequencing (WGS). The sequenced full-length fimH of the isolates were plotted with the already published fimH sequences on a phylogenetic tree. Considering phylogeny, 14 strains were subjected to WGS that indicated not only the number and type of ARGs but also the order of ARGs on the plasmid were confirmed in the analyzed E. coli isolates. More importantly, 3 of the 14 strains were blaNDM-5-positive, i.e., carbapenem-resistant E. coli. These results suggest that our analytical procedure in this study is applicable as a monitoring method to understand in detail genetic characteristics of AMRB isolates in environmental water samples.