Genome analysis of enterobacteriaceae with non-wild type susceptibility to third-generation cephalosporins recovered from diseased dogs and cats in Europe

Background: Extended-spectrum-(3-lactamases (ESBL) and plasmid-mediated cephalosporinases (pAmpC)-producing Enterobacteriaceae isolates are now reported worldwide in humans, animals, and in the environment. We identified the determinants of resistance to fi-lactams and associated resistance genes as well as phylogenetic diversity of 53 ESBL- or pAmpC-producing Enterobacteriaceae isolated from dogs and cats in Europe. Materials/methods: Of a collection of 842 Enterobacteriaceae isolates that were recovered in 2013 and 2014 from 842 diseased and untreated dogs and cats, for 242 ampicillin or amoxicillin resistant isolates (MIC 16 mg/L), cefotaxime (CTX) and ceftazidime (CAZ) MICs were determined. Isolates with CTX and/or CAZ MIC 1 mg/L (n = 63) were selected, and their genomes were fully sequenced using Illumina Technology. Genomic data were explored to identify the resistance determinants, the plasmid incompatibility groups, and the sequence types (STs). Plasmid location of b/aEsa and b/aA,pc was evaluated for all isolates based on the co-localization of resistance and plasmid incompatibility group genes on the same contig. Phylogenetic trees were constructed using core-genome MLST. Results: Of the 63 sequenced isolates, 53 isolates harbored a blaEsm, or b/aA,,,c gene. Ten CTX and/or CAZ nonwild type isolates had neither blaEsm, nor b/aA, pc. Among the 63 isolates, 44 (69.8 %) were Escherichia coli, 11 (17.5 %) were Klebsiella pneumoniae, and 8 (12.7 %) were Proteus mirabilis. Fifty-one (80.9 %) isolates originated from dogs and 12 (19.1 %) from cats. Isolates were sampled from urinary tract (n = 36), skin and soft tissue (n = 22) and respiratory tract infections (n = 5). Thirty-two isolates (32/53, 60.4 %) carried b/aEsm, genes, including 12/acrx.,,15 (n = 12), blacrx-m-14 (n = 6), b/acrx.m-i (n = 5), blacix-m-2 (n = 3), blacrx-m-27 (n = 3), bias' iv.28 (n = 4), bias! iv.12 (n = 2), and blaveB-6 (n = 1). Four isolates of K. pneumoniae had both b/ac–rx.m.15 and bias! iv_28. Twenty-one isolates (21/53, 39.6 %) carried genes encoding pAmpC, including blacmy.2 (n = 19) and blant (n = 2). Thirteen E. coli isolates harbored both blaEsm, or blaA,,,c genes and plasmids of incompatibility groups IncIB (9/13), Inch (8/13), and IncF11 (6/13). In addition to the reduced susceptibility to CTX and/or CAZ, reduced susceptibility or evidence of acquired resistance to at least one other relevant class of antibiotics was observed for all 63 isolates. E. colt: isolates clustered in 23 STs, including B2 virulent clones from humans such as ST131 (n = 5), K. pneumoniae isolates mostly clustered in 3 STs: ST11 (n = 4), ST307 (n = 3), and ST16 (n = 2). Phylogenetic analysis identified the spread of E. coli ST131 b/am.m.27, and of K. pneumoniae ST307 harboring biac-nc.m.is and blasiiv-28 or ST11 biacrx-m-isConclusions: We report here a 6.3 % prevalence of ESBL/pAmpC producing Enterobacteriaceae in diseased dogs and cats. This EU survey confirms that dogs and cats can be infected with epidemic multidrug resistant clones that may also spread in humans.