Phylogeny and antibiotic resistance profile (resistome) of urinary E. coli isolated from individual dogs at different time points were investigated to gain a better understanding of recurrent or persistent E. coli UTI. The microbiology database of the U-Vet Werribee Animal Hospital was screened for urinary E. coli isolated from dogs with at least two positive urine cultures. Comorbidities on the date of the respective urine culture were retrieved from the dogs' medical records. E. coli strains were recovered from frozen storage banks and subjected to whole genome sequencing. The core genome of study strains was compared to reference strain ABU83097 and multi-locus sequence types (MLST) were identified. Strain resistomes were determined by searching genomes for 38 known antibiotic resistance genes. Seventy-six E. coli strains from 19 dogs were analysed. All dogs had conditions that predisposed to UTI and were treated with antibiotics after positive urine cultures. The number of examined E. coli strains per individual dog ranged from 2 to 8 (median 3.5); they had originally been recovered over a median time span of 146.5 days (range 9–2450 days). Overall, E. coli were phylogenetically diverse; 25 different MLST were recorded. Core genomes were 73.9–95.2% similar to the reference. None of the E. coli isolated had identical core genomes. However, in 18/19 dogs, 2 to 6 (median 2.5) E. coli with highly similar core genomes (with single nucleotide differences ranging from 25 to 457) were identified. These highly similar E. coli had originally been cultured from urine of affected dogs over a median time span of 84 days (range 7 to 602 days) and in 15/18 cases, all highly similar strains had identical resistomes over time. In 10 dogs, at least one strain that was phylogenetically different was also present; in 3 dogs, these strains were cultured between episodes with 2 highly similar strains. Thirty-five of 76 strains (46%) were phenotypically multi-drug-resistant (MDR). Up to 13 different antibiotic resistance genes (median 2.5) were identified. There was no apparent correlation between time point of strain isolation (i.e., late or early in disease) and MDR status. Results of this study suggest that the majority of E. coli isolated from the urine of dogs with comorbidities either belong to one evolving lineage, or that several highly similar lineages co-exist in any given dog. Changes in resistome were uncommon.

Disclosures

Disclosures to report:

Dr Bulach is affiliated with Doherty Applied Microbial Genomics, The Doherty Institute, Melbourne, Australia. The laboratory work for this abstract was performed at the Doherty Institute, which is affiliated with the University of Melbourne.