Bacterial Isolates

Escherichia coli isolates were obtained from companion animal clinical specimens submitted to the Microbiology Diagnostic Laboratory, Liverpool Institute of Veterinary Science between January 2010 and August 2016. Clinical specimens, mainly originated from animals admitted to the University of Liverpool Small Animal and Equine Referral Hospitals, included urine samples collected by cystocentesis, body fluids, tissue biopsy samples, bile and/or liver biopsy, swabs from skin infections and otitis externa cases, fecal samples from diarrheic patients or animals suspected of GI disease. These were plated out aerobically on culture media following site-specific culture protocols, including 5% sheep blood agar (Oxoid, Basingstoke, United Kingdom) and were incubated at 37°C for 1–7 days. Clinical isolates presumptively identified as E. coli based on a positive reaction on Eosin Methylene Blue Agar (EMBA; Oxoid, Basingstoke, United Kingdom) and which showed reduced susceptibility to cefpodoxime (10 μg) and/or cefoxitin, were selected for this study. Species identification of clinical isolates was performed using API 20E identification kits (Biomerieux, France) and also by PCR detection of the uidA gene for confirmation of E. coli (McDaniels et al., 1996). Bacterial culture data, including specimen site, the type of bacterial growth obtained (pure or mixed, repeat E. coli isolation from the same case) and the number of bacterial species isolated from each specimen were recorded in the Veterinary Diagnostic Laboratory database.