Molecular Characteristics of Extraintestinal Pathogenic E. coli (ExPEC), Uropathogenic E. coli (UPEC), and Multidrug Resistant E. coli Isolated from Healthy Dogs in Spain. Whole Genome Sequencing of Canine ST372 Isolates and Comparison with Human Isolates Causing Extraintestinal Infections.

Saskia-Camille Flament-Simon,Marie-Hélène Nicolas-Chanoine,Miguel Blanco,Vanesa García,Ana Goicoa,Jesús E Blanco,Jorge Blanco,María Pilar Alonso,María De Toro,Juan Díaz-González

doi:10.3390/microorganisms8111712

Abstract

Under a one health perspective and the worldwide antimicrobial resistance concern, we investigated extraintestinal pathogenic Escherichia coli (ExPEC), uropathogenic E. coli (UPEC), and multidrug resistant (MDR) E. coli from 197 isolates recovered from healthy dogs in Spain between 2013 and 2017. A total of 91 (46.2%) isolates were molecularly classified as ExPEC and/or UPEC, including 50 clones, among which (i) four clones were dominant (B2-CH14-180-ST127, B2-CH52-14-ST141, B2-CH103-9-ST372 and F-CH4-58-ST648) and (ii) 15 had been identified among isolates causing extraintestinal infections in Spanish and French humans in 2015 and 2016. A total of 28 (14.2%) isolates were classified as MDR, associated with B1, D, and E phylogroups, and included 24 clones, of which eight had also been identified among the human clinical isolates. We selected 23 ST372 strains, 21 from healthy dogs, and two from human clinical isolates for whole genome sequencing and built an SNP-tree with these 23 genomes and 174 genomes (128 from canine strains and 46 from human strains) obtained from public databases. These 197 genomes were segregated into six clusters. Cluster 1 comprised 74.6% of the strain genomes, mostly composed of canine strain genomes (p < 0.00001). Clusters 4 and 6 also included canine strain genomes, while clusters 2, 3, and 5 were significantly associated with human strain genomes. Finding several common clones and clone-related serotypes in dogs and humans suggests a potentially bidirectional clone transfer that argues for the one health perspective.

Highlights

IntroductionE. coli is the main bacterial pathogen responsible for extraintestinal infections in humans and dogs, including urinary tract infections (UTIs) [1,2,3,4,5]
Escherichia coli is a common commensal of the gastrointestinal tract
The prevalence hypothesis postulates that most urinary tract infections (UTIs) are opportunistic infections caused by bacteria that predominate in the faecal microbiota, whereas the special pathogenicity hypothesis suggests that most UTI are caused by pathogenic strains that possess appropriate virulence factor (VF)-encoding genes [5,6]

Summary

Introduction

E. coli is the main bacterial pathogen responsible for extraintestinal infections in humans and dogs, including urinary tract infections (UTIs) [1,2,3,4,5]. The two theories for the origin of uropathogenic isolates are the “prevalence” and the “special pathogenicity”. More than 50 E. coli genes associated with extraintestinal infections have been identified, encoding adhesins, toxins, siderophores, capsular antigens, and invasines [7,8]. Isolates are designed presumptively as extraintestinal pathogenic E. coli (ExPEC) if they contained ≥2 of 5 of the following VF-encoding genes: papAH and/or papC, sfa/focDE, afa/draBC, kpsM II, and iutA [7], and as uropathogenic E. coli (UPEC) if they are positive for ≥3 of the four following VF-encoding genes: chuA, fyuA, vat, and yfcV [8]

Methods

Results

Discussion

Conclusion