Characterization of plasmids harboring bla(CTX-M) and bla(CMY) genes in E. coli from French broilers

Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010–2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids contained the bla(CTX-M-1) gene and belonged to the IncI1/ST3 type, with 27 and 20 of them carrying the sul2 or tet(A) genes respectively. Despite their diverse origins, several plasmids showed very high percentages of identity. None of the bla(CTX-M-1)-containing plasmid contained APEC virulence genes, although some of them were detected in the parental strains. Three plasmids had the bla(CMY-2) gene, but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB replicon types. The bla(CMY-2) IncFIA/FIB plasmid was obtained from a strain isolated from a diseased broiler and also containing a bla(CTX-M-1) IncI1/ST3 plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT, etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the bla(CMY-2) plasmid. In conclusion, our results show the dominance and high similarity of bla(CTX-M-1) IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a bla(CMY-2) plasmid.