Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River (Japan) were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six (14.3%) were multidrug resistant (MDR), 66 (12.4%) were non-susceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing using Illumina technology on selected strains. In total, genome sequences of 155 strains were analyzed for their antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n=66), ST155 complex (n=9), ST10 complex (n=9), and ST69 complex (n=7) were prevalent. Among potential extraintestinal pathogenic E. coli (ExPEC) strains (n=58), clinically important clonal groups, namely ST95 complex (n=18), ST127 complex (n=8), ST12 complex (n=6), ST14 complex (n=6), and ST131 complex (n=6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis revealed no significant difference between environmental and clinical ST95 complex strains. The results indicate that environmental waters can be reservoirs of E. coli strains belonging to clinically important clonal groups, increasing the risk of waterborne disease.