Origin and development of two Escherichia coli clones vertically transferred in broiler production

Investigation of clonal development of dominant persistent clones of avian pathogenic <i>Escherichia coli</i> (APEC) is important to understand their evolution and to gain knowledge to improve their control in poultry production. Whole-genomic sequencing, including hybrid assembled genomes of short and long reads, was used to analyse clonal persistence and evolution of APEC. Two vertically transferred <i>E. coli</i> clones, represented by ten isolates from sequence type (ST) 95-PFGE type 65 and eight isolates from ST131-PFGE type 47, were selected to identify genomic variations. The isolates had been sampled in broiler production during a period of 9 months in a previous study. The main differences among strains within each clone were related to plasmids, transposases, incomplete phage elements and amino acid substitutions which by far exceeded the genetic variation related to core-genome SNPs (cgSNPs). Fourier-transform infrared spectroscopy was, for the most part, only able to trace clones within the same ST. The genome-wide mutation rate was equivalent to 1.48 mutations per genome per year for ST95-PFGE65 and 2.86 for ST131-PFGE47, respectively. The most recent common ancestors were estimated back to 2009 for ST95-PFGE65 and to 2011 for ST131-PFGE47, with further divergence occurring in years until sampling in 2014-2015. The methodology introduced is able to trace the temporal origin of APEC clones. The conventional threshold of ten or fewer cgSNPs to include strains in the same clone did not consider any gain or loss of plasmids for the strains compared. On average, one plasmid transfer event was predicted every second year. For strains expected to be vertically transferred during the long production periods of great-grandparents over grandparents and parents to broilers, one to two plasmid transfers are therefore predicted, and several cgSNPs may be introduced, whereas up to one cgSNP is expected to be manifested during a broiler production cycle and rarely involving plasmid transfer.