Multidrug resistance in pathogenic Escherichia coli isolates from urinary tract infections in dogs, Spain

Abstract

Escherichia coli (E. coli) is a pathogen frequently isolated in cases of urinary tract infections (UTIs) in both humans and dogs and evidence exists that dogs are reservoirs for human infections. In addition, E. coli is associated to increasing antimicrobial resistance rates. This study focuses on the analysis of antimicrobial resistance and the presence of selected virulence genes in E. coli isolates from a Spanish dog population suffering from UTI. This collection of isolates showed an extremely high level of phenotypic resistance to 1st-3rd generation cephalosporins, followed by penicillins, fluoroquinolones and amphenicols. Apart from that, 13.46% of them were considered extended-spectrum beta-lactamase producers. An alarmingly high percentage (71.15%) of multidrug resistant isolates were also detected. There was a good correlation between the antimicrobial resistance genes found and the phenotypic resistance expressed. Most of the isolates were classified as extraintestinal pathogenic E. coli, and two others harbored virulence factors related to diarrheagenic pathotypes. A significant relationship between low antibiotic resistance and high virulence factor carriage was found, but the mechanisms behind it are still poorly understood. The detection of high antimicrobial resistance rates to first-choice treatments highlights the need of constant antimicrobial resistance surveillance, as well as continuous revision of therapeutic guidelines for canine UTI to adapt them to changes in antimicrobial resistance patterns.

Keywords: Escherichia coli; dog; multidrug resistance; urinary tract infection; virulence factors.

Figure 1

Prevalence of resistance to different antimicrobial categories found in E. coli isolates from dog urine.

Figure 2

Phylogenetic tree including the sequenced E. coli isolates. Metadata was added using Phandango web application (60).

Figure 3

Comparison of E. coli K12 reference genome with sequenced isolates. The annotation of selected antimicrobial resistance genes was carried out on Proksee Server from the Stothard Research Group (University of Alberta, Canada) that uses BLAST analysis to illustrate conserved and missing genomic sequences (available online: https://proksee.ca/).

Figure 4

Selected contigs of different isolates containing antimicrobial resistance genes as well as MGE annotated with Prokka (56). (A) Organization of a fragment of contig 27 in isolate 266.493, which contains aadA5, dfrA17, qacE, sul1, and mphA genes. (B) Organization of contig 42 in isolate 269.901, which contains aph(6)-Id, aph(3″)-Ib and sul2 genes. (C) Organization of a fragment of contig 11 in isolate 258.883, which contains bla_CTX-M-55 gene. (D) Organization of a fragment of contig 36 in isolate 271.960, which contains several resistance genes, such as aadA1, sul2 and tet(A). (E) Organization of a fragment of isolate 263.715, which contains tet(M) resistance gene.