Antimicrobial Resistance Genes and Diversity of Clones among Faecal ESBL-Producing Escherichia coli Isolated from Healthy and Sick Dogs Living in Portugal

Abstract

The purpose of this study was to analyse the prevalence and genetic characteristics of ESBL and acquired-AmpC (qAmpC)-producing <i>Escherichia coli</i> isolates from healthy and sick dogs in Portugal. Three hundred and sixty-one faecal samples from sick and healthy dogs were seeded on MacConkey agar supplemented with cefotaxime (2 µg/mL) for cefotaxime-resistant (CTX^R) <i>E. coli</i> recovery. Antimicrobial susceptibility testing for 15 antibiotics was performed and the ESBL-phenotype of the <i>E. coli</i> isolates was screened. Detection of antimicrobial resistance and virulence genes, and molecular typing of the isolates (phylogroups, multilocus-sequence-typing, and specific-ST131) were performed by PCR (and sequencing when required). CTX^R<i>E. coli</i> isolates were obtained in 51/361 faecal samples analysed (14.1%), originating from 36/234 sick dogs and 15/127 healthy dogs. Forty-seven ESBL-producing <i>E. coli</i> isolates were recovered from 32 sick (13.7%) and 15 healthy animals (11.8%). Different variants of <i>bla</i>_CTX-M genes were detected among 45/47 ESBL-producers: <i>bla</i>_CTX-M-15 (<i>n</i> = 26), <i>bla</i>_CTX-M-1 (<i>n</i> = 10), <i>bla</i>_CTX-M-32 (<i>n</i> = 3), <i>bla</i>_CTX-M-55 (<i>n</i> = 3), <i>bla</i>_CTX-M-14 (<i>n</i> = 2), and <i>bla</i>_CTX-M-variant (<i>n</i> = 1); one ESBL-positive isolate co-produced CTX-M-15 and CMY-2 enzymes. Moreover, two additional CTX^R ESBL-negative <i>E. coli</i> isolates were CMY-2-producers (qAmpC). Ten different sequence types were identified (ST/phylogenetic-group/β-lactamase): ST131/B2/CTX-M-15, ST617/A/CTX-M-55, ST3078/B1/CTX-M-32, ST542/A/CTX-M-14, ST57/D/CTX-M-1, ST12/B2/CTX-M-15, ST6448/B1/CTX-M-15 + CMY-2, ST5766/A/CTX-M-32, ST115/D/CMY-2 and a new-ST/D/CMY-2. Five variants of CTX-M enzymes (CTX-M-15 and CTX-M-1 predominant) and eight different clonal complexes were detected from canine ESBL-producing <i>E. coli</i> isolates. Although at a lower rate, CMY-2 β-lactamase was also found. Dogs remain frequent carriers of ESBL and/or qAmpC-producing <i>E. coli</i> with a potential zoonotic role.