title: Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water.
abstract: Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531Escherichia coliisolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for 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), sequence type 155 (ST155) complex (n= 9), ST10 complex (n= 9), and ST69 complex (n= 7) were prevalent. Among extraintestinal pathogenicE. 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. Typing of thefimH(type 1 fimbrial adhesin) gene revealed that ST131 complex strains carriedfimH22orfimH41, and no strains belonging to thefimH30subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters byE. colistrains belonging to clinically important clonal groups.IMPORTANCEThe prevalence of antimicrobial-resistant and pathogenicE. colistrains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters byE. colistrains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.
authors.affiliation: Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
authors.forename: Ryota
authors.initials: R
authors.lastname: Gomi
authors.affiliation: Research Center for Environmental Quality Management, Kyoto University, Otsu, Japan matsuda.tomonari.8z@kyoto-u.ac.jp.
authors.forename: Tomonari
authors.initials: T
authors.lastname: Matsuda
authors.affiliation: Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
authors.forename: Yasufumi
authors.identifier: http://orcid.org/0000-0001-8595-8944
authors.initials: Y
authors.lastname: Matsumura
authors.affiliation: Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Yamamoto
authors.affiliation: Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
authors.forename: Michio
authors.initials: M
authors.lastname: Tanaka
authors.affiliation: Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ichiyama
authors.affiliation: Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
authors.forename: Minoru
authors.initials: M
authors.lastname: Yoneda
mesh_terms: D000818:Animals; D044822:Biodiversity; D004269:DNA, Bacterial / Q000235:genetics; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D004783:Environmental Microbiology; D004927:Escherichia coli Infections / Q000382:microbiology; D000072282:Extraintestinal Pathogenic Escherichia coli / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D007564:Japan; D008826:Microbial Sensitivity Tests; D058889:Molecular Typing; D009154:Mutation; D010802:Phylogeny; D045483:Rivers / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D014774:Virulence / Q000235:genetics; D037521:Virulence Factors / Q000235:genetics; D014871:Water Microbiology; D014876:Water Pollution
chemical_list: D004269:DNA, Bacterial; D037521:Virulence Factors
keywords: Escherichia coli; ExPEC; antimicrobial resistance; whole-genome sequencing