Whole-genome sequence analysis of extended spectrum beta-lactamase producing E. coli strains from poultry and humans

Extended-spectrum β-lactamases (ESBLs) or AmpC β-lactamases are an increasing concern for public health. In a previous study, contact with broilers was identified as a risk factor for ESBL/pAmpC-producing Escherichia coli (ESBL-E) carriage for humans working or living on a broiler farm. Dissemination of ESBL/pAmpC-producing genes within and between sources can occur via clonal transmission, horizontal plasmid transmission, and mobilisation of the gene e.g. from a plasmid to the chromosome. In the present study, possible transmission events were investigated using a combination of short (illumina) reads and long (PacBio) reads.