Pandemic human-associated extended-spectrum β-lactamase-producing Escherichia coli lineages of ST38, ST131 and ST141 identified in Viennese dogs

Abstract

Objectives: To assess the prevalence of ESBL Enterobacteriaceae among dogs attending a veterinary clinic in Vienna, characterize the isolates in terms of antimicrobial resistance, virulence and phylogenetic relationships.

Methods: Faecal samples of 88 dogs were streaked on selective plates, species were identified by MALDI-ToF MS, tested for resistance by a combination disk test and VITEK 2®, whole genome-sequenced, bioinformatically genotyped, phylogenetically analysed and screened for resistance and virulence genes.

Results: ESBL Escherichia coli carriage rate was 14.8% (95% CI: [8.1-23.9]). No carbapenem resistance was found, but 53.8% of the isolates were classified genotypically as multi-drug resistant. Phylogenetic analyses revealed that half of the isolates belonged to animal and environment-associated phylogroups, while another half was human-associated, and included high-risk international clones of ST38, ST131 and ST141, which clustered primarily with human isolates. All isolates harboured various virulence-associated genes, including four isolates that encoded exotoxins, of which two were from the pandemic ST131 and emerging ST141 lineages.

Conclusions: Dogs in Vienna carry ESBL E. coli with high rates of multi-drug resistance and virulence, and a highly diverse population structure that includes pandemic human-associated lineages.

Figure 1.

Genotypic and phenotypic resistance patterns observed in the ESBL isolates (a) and virulence-associated genes identified within the WGS of the ESBL isolates, grouped into functional categories (b). PIP, piperacillin; PIP/TAZ, piperacillin/tazobactam; CTX, cefotaxime; CAZ, ceftazidime; CFP, cefepime; ATM, aztreonam; IMI, imipenem; MEM, meropenem; AMK, amikacin; GEN, gentamicin; TOB, tobramycin; CIP, ciprofloxacin; TG, tigecycline; FOS, fosfomycin; TMP/SMX, trimethoprim/sulfamethoxazole.