Phylogenomic comparison of 18 clinical Escherichia coli strains belonging to serogroups O5 and O118 isolated from bovine and human

In developed countries enterohaemorrhagic Escherichia coli (EHEC) are responsible for small- or large-scale outbreaks of uncomplicated diarrhoea, haemorrhagic colitis and/or haemolytic–uraemic syndrome (HUS) in human and cattle. If the two major EHEC serotypes in Europe well studied and characherized, several subdominant serotypes such as O5 and O118 are present in cattle and can act as a reservoir for potential outbreaks.
This study present the phylogenomic comparison of 10 O118 and 8 O5 clinical E. coli strains that were isolated from cattle and human diarrhea. Genomic DNA was isolated from an active growing colony and sequenced on a MySeq apparatus.
The raw sequences from the 18 genomes were assembled into scaffolds using an in-house pipeline and subjected to a quick automated annotation pipeline. The metabolic models of the strains were elaborated and compared. We used the contigs data to determine the MLST sequence types and virulotypes. A scheme of 20 houskeeping and virulence determinents were concatenated and used to select the most ancestral strains for both serotypes. This ancestral strain was selected for another run of sequencing and used as the anchor for a phylogenomic analysis of the 18 strains. The phylogenomic tree allowed us to analyse if the source parameter (human or bovine) could be used to cluster strains. This study shows that genomic sequencing has become a quick and efficient tool that can be used to replace numerous existing typing analysis methods by an unique analysis scheme.