Genomic Characterization of Extended-Spectrum Cephalosporin-Resistant in the Colombian Poultry Chain.

serovars have been isolated from Colombian broilers and broiler meat. The aim of this study was to investigate the diversity of ESBL/pAmpC genes in extended-spectrum cephalosporin resistant and the phylogeny of ESBL/pAmpC-carrying using Whole Genome Sequencing (WGS). A total of 260 cefotaxime resistant isolates, obtained between 2008 and 2013 from broiler farms, slaughterhouses and retail, were included. Isolates were screened by PCR for ESBL/pAmpC genes. Gene and plasmid subtyping and strain Multi Locus Sequence Typing was performed for a selection of fully sequenced isolates. Core-genome-based analyses were performed per ST encountered. was carried in 168 isolates, 52 carried group, 7 , 5 a combination of - and 3 a combination of - group. In 25 isolates no ESBL/pAmpC genes that were screened for were found. WGS characterization of 36 selected strains showed plasmid-encoded in 21, in 11 and in 7 strains. These genes were mostly carried on IncI1/ST12, IncQ1, and IncI1/ST231 plasmids, respectively. Finally, 17 strains belonged to . Heidelberg ST15, 16 to . Paratyphi B variant Java ST28, 1 to . Enteritidis ST11, 1 to . Kentucky ST152 and 1 to . Albany ST292. Phylogenetic comparisons with publicly available genomes showed separate clustering of Colombian . Heidelberg and . Paratyphi B var. Java. In conclusion, resistance to extended-spectrum cephalosporins in from Colombian poultry is mainly encoded by and genes. These genes are mostly associated with IncI1/ST12 and IncQ1 plasmids, respectively. Evolutionary divergence is observed between Colombian . Heidelberg and . Paratyphi B var. Java and those from other countries.