Novel sequence types of extended-spectrum and acquired ampc beta-lactamase producing Escherichia coli and Escherichia clade V isolated from wild mammals

Abstract

The closer contact with wildlife due to the growing human population and the destruction of natural habitats emphasizes the need of gaining insight into the role of animals as source of antimicrobial resistance. Here, we aim at characterizing the antimicrobial resistance genes and phylogenetic distribution of commensal E. coli from 62 wild mammals. Isolates exhibiting resistance to ≥ 1 antibiotic were detected in 25.8% of the animals and 6.4% carried an ESBL/AmpC-producing E. coli. Genetic mechanisms involved in third-generation cephalosporin resistance were: i) hyperproduction of chromosomal AmpC (hedgehog), ii) production of acquired CMY-2 β-lactamase (hedgehog), iii) production of SHV-12 and CTX-M-14 ESBLs (n = 2, mink and roe-deer). ESBL genes were transferable by conjugation and bla_CMY-2 was mobilized by a 95kb IncI1 plasmid. The distribution of the phylogenetic groups in the E. coli collection studied was B1 (44.6%), B2 (24.6%), E (15.4%), A (4.6%) and F (3.1%). Five isolates (7.7%) were cryptic Escherichia clades (clade IV, 4 mice; clade V, 1 mink). ESBL/AmpC-E. coli isolates showed different STs: ST1128/B1, ST4564/B1 (new), ST4996/B1 (new), and a non registered ST. This study contributes to better understand the E. coli population and antimicrobial resistance flow in wildlife and reports new AmpC-E. coli sequence types and a first described ESBL-producing Escherichia clade V isolate.

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