Clonal and Plasmid-mediated Flow of ESBL/AmpC Genes in Escherichia Coli in a Commercial Laying Hen Farm

Resistance to third- and fourth-generation cephalosporins in Escherichia coli is mainly due to extended-spectrum beta-lactamases (ESBL) and AmpC cephalosporinases, which have been increasingly reported, mainly in isolates from humans and poultry. The aim of this study was to address the flow of antimicrobial resistance determinants in the full laying hen production cycle (four batches followed from day-old chicks to 83/84-week-old layers), using cephalosporin-resistant E. coli as a model and their characterization using whole genome sequencing (WGS). Fifteen out of 22 samples analysed yielded growth on MacConkey agar with cefotaxime (1 mg/L). Of these, 141 isolates were identified as E. coli and 47 were characterized by WGS. Genes detected were three ESBL (bla (n = 19); bla (n = 1); and bla (n = 9)) and one AmpC (bla (n = 13)). Some isolates only harboured bla (n = 2) or bla (n = 1). IncI1 plasmids were the main platform for ESBL/AmpC genes. In addition, five clones were identified harbouring bla (two), bla (one) and bla (two), drawing a clone-plasmid mixed flow model. Gene bla was found in the chromosomal DNA of clone 1 over 14 months, and in IncI1/ST3 plasmids over six months; over six months bla was found harboured by clone 3 (IncI1/ST26 plasmids), and 15 months later in a non-replicon detected plasmid. Finally, bla spread for at least 16 months, mainly by IncK2 (including clone 4) and IncI1/ST12 (clone 5) plasmids. Proper use of antimicrobials should be combined with other farm management strategies for the effective control of cephalosporin-resistant E. coli isolates in commercial layer farms.