AUTHOR=Castellanos Luis Ricardo , van der Graaf-van Bloois Linda , Donado-Godoy Pilar , León Maribel , Clavijo Viviana , Arévalo Alejandra , Bernal Johan F. , Mevius Dik J. , Wagenaar Jaap A. , Zomer Aldert , Hordijk Joost 

TITLE=Genomic Characterization of Extended-Spectrum Cephalosporin-Resistant Salmonella enterica in the Colombian Poultry Chain

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.02431

DOI=10.3389/fmicb.2018.02431

ISSN=1664-302X

ABSTRACT=<p><italic>Salmonella enterica</italic> 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 <italic>Salmonella enterica</italic> and the phylogeny of ESBL/pAmpC-carrying <italic>Salmonella</italic> using Whole Genome Sequencing (WGS). A total of 260 cefotaxime resistant <italic>Salmonella</italic> 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 <italic>in silico</italic> for a selection of fully sequenced isolates. Core-genome-based analyses were performed per ST encountered. <italic>bla</italic><sub>CMY−2−like</sub> was carried in 168 isolates, 52 carried <italic>bla</italic><sub>CTX−M−2</sub> group, 7 <italic>bla</italic><sub>SHV</sub>, 5 a combination of <italic>bla</italic><sub>CMY−2−like</sub>-<italic>bla</italic><sub>SHV</sub> and 3 a combination of <italic>bla</italic><sub>CMY−2−like</sub>-<italic>bla</italic><sub>CTX−M−2</sub> group. In 25 isolates no ESBL/pAmpC genes that were screened for were found. WGS characterization of 36 selected strains showed plasmid-encoded <italic>bla</italic><sub>CMY−2</sub> in 21, <italic>bla</italic><sub>CTX−M−165</sub> in 11 and <italic>bla</italic><sub>SHV−12</sub> in 7 strains. These genes were mostly carried on IncI1/ST12, IncQ1, and IncI1/ST231 plasmids, respectively. Finally, 17 strains belonged to <italic>S</italic>. Heidelberg ST15, 16 to <italic>S</italic>. Paratyphi B variant Java ST28, 1 to <italic>S</italic>. Enteritidis ST11, 1 to <italic>S</italic>. Kentucky ST152 and 1 to <italic>S</italic>. Albany ST292. Phylogenetic comparisons with publicly available genomes showed separate clustering of Colombian <italic>S</italic>. Heidelberg and <italic>S</italic>. Paratyphi B var. Java. In conclusion, resistance to extended-spectrum cephalosporins in <italic>Salmonella</italic> from Colombian poultry is mainly encoded by <italic>bla</italic><sub>CMY−2</sub> and <italic>bla</italic><sub>CTX−M−165</sub> genes. These genes are mostly associated with IncI1/ST12 and IncQ1 plasmids, respectively. Evolutionary divergence is observed between Colombian <italic>S</italic>. Heidelberg and <italic>S</italic>. Paratyphi B var. Java and those from other countries.</p>