Whole Genome Sequencing of an Unusual Serotype of Shiga Toxin–producing Escherichia coli

Tim Dallman, Lisa Cross, Chloe Bishop, Neil Perry, Bente Olesen, Kathie A. Grant, and Claire Jenkins

Author affiliations: Health Protection Agency, London, UK (T. Dallman, L. Cross, C. Bishop, N. Perry, K.A. Grant, C. Jenkins); Hillerød Hospital, Hillerød, Denmark (B. Olesen)

Abstract

Shiga toxin–producing Escherichia coli serotype O117:K1:H7 is a cause of persistent diarrhea in travelers to tropical locations. Whole genome sequencing identified genetic mechanisms involved in the pathoadaptive phenotype. Sequencing also identified toxin and putative adherence genes flanked by sequences indicating horizontal gene transfer from Shigella dysenteriae and Salmonella spp., respectively.

There are > 400 serotypes of Shiga toxin–producing Escherichia coli (STEC), and > 100 of these are known to be associated with severe disease in humans (1). STEC are defined by the presence of 1 or both phage-encoded Shiga toxin genes stx1 and stx2. However, those serotypes associated with more severe disease generally harbor additional virulence genes, such as eae (intimin), which is encoded on the locus of enterocyte effacement, or virulence regulation genes, such as aggR, which is located on the aggregative adherence plasmid. Both of these genes mediate attachment of the bacteria to the host gut mucosa (2). The stx1 gene is also found in Shigella dysenteriae serotype 1.
A range of molecular typing methods show that the shigellae belong within the Escherichia coli species (3). Peng et al. (4) described an evolutionary path of Shigella spp. from E. coli involving gene acquisition (virulence plasmid and pathogenicity islands) and gene loss (pathoadaptivity). Gene loss, or loss of gene function, may result from changes to bacterial biosynthesis pathways driven by the abundance of resources in the host or because the genes may encode proteins adverse to bacterial virulence.
Olesen et al. (5) described a strain of STEC serotype O117:K1:H7 found in travelers from Denmark who returned from tropical locations. The strain was unusual because it was negative for the production of lysine decarboxylase and β-galactosidase (ortho-nitrophenol test) and positive only for stx1.
Since 2004, 19 isolates of STEC O117:K1:H7 have been submitted to the Gastrointestinal Bacteria Reference Unit at the Health Protection Agency in London, UK, from frontline diagnostic microbiology laboratories in England and Wales for confirmation of identification and typing (Table). All isolates were originally misidentified by the submitting laboratory as Shigella sonnei or Shigella spp., probably because of the unusual biochemical phenotype exhibited by this strain. The purpose of this study was to use whole genome sequencing to investigate the evolutionary origins, putative virulence genes, and pathoadaptive mechanisms of this unusual STEC serotype.