Molecular epidemiology of multi-drug resistant Escherichia coli in companion animal species

Abstract

This study focused on a group of multi-drug resistant (MDR) E. coli collected between 2002 and 2011 at the Small Animal Hospital, Royal (Dick) Veterinary School; isolated from urinary tract infections in dogs. The MDR E. coli isolates were compared against a group of fully susceptible E. coli, also collected from canine urinary tract infections. The MDR isolates were notable for their AmpC β-lactamase resistance phenotype (12/18) and resistance genotype (blaCMY-2, 8/12). Phylogenetic comparisons between the MDR and susceptible groups of isolates showed a large degree of separation between the two groups. Susceptible isolates strongly associated the the pathogenic B2 phylogroup (67%), which was expected. The MDR group was much more mixed, with isolates more associated with commensal A (28%) and B1 (22%) phylogroups. Virulence marker abundance, evaluated using an Identibac microarray, showed a much reduced presence of virulence markers in the MDR group, as compared with the susceptible isolates. An infection model, using Galleria mellonella larvae, was used to better test the phenotypic virulence of the MDR and susceptible E. coli isolates. An asymptomatic bacteriurea strain (ABU83972) and a virulent pyelonephritis strain (CFT073) were used as non-virulent and virulent control strains of uropathogenic E. coli. The model produced consistent and expected differences in lethality between ABU8392 (non-lethal) and CFT073 (lethal) strains. However, the model showed no differences between the MDR and susceptible isolates. Second generation Illumina short-read sequencing and third generation single-molecule real-time sequencing were used to further dissect the genetic background of both the E. coli and the MDR genotype. Core-genomic sequence comparisons of the E. coli showed no clonal relatedness amongst the different MDR and susceptible strains. Most strikingly, sequencing revealed extensive plasmid carriage of the MDR genotype. Plasmid mediated blaCMY-2 was associated with a clonal group of IncI1 plasmids. The IncI1 plasmids show favorable sequence comparisons to a plasmid backbone previously reported in dogs and other animals, with a global distribution. The remaining resistance genes were associated with a group of IncFII plasmid sequences. This study highlights a broader range of commensal E. coli, which have resulted in opportunistic infections in their canine hosts. As such, they act as a potential reservoir of resistance, which is as yet uncharacterized.