Large-scale Molecular Risk Assessment of Shiga Toxin-producing Escherichia coli (STEC) by Whole Genome Sequencing

Introduction: Shiga toxin-producing Escherichia coli (STEC) are potentially lethal zoonotic pathogens with a clinical spectrum including non-bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). The most common STEC serotype associated with human disease is O157:H7, but there is a growing recognition of over a hundred non-O157 STEC serotypes that also may cause human illness. The large variation of serotypes and genetic contents of STEC associated with severe disease results in the current inability of designating individual strains as pathogens, which has negative impact for both clinical care and food safety measures.

Purpose: To predictively classify the clinical and/or epidemic potential of a STEC isolate it is crucial to associate its virulence and other distinctive features to the ability to cause disease. This study aimed at identifying associations between serotype, virulence factors, phylogeny, isolation source and severity of disease in order to gain an increased understanding on the complex epidemiology of STEC infections.

Methods: Nearly 400 STEC isolates (including clinical, animal and food isolates of multiple serotypes) were whole-genome-sequenced and serotypes, phylogenetic groups, MLST, and virulence profiles were determined in silico from the assembled genomes and used in a multi-dimensional scaling (principal component analysis).

Results: The results clearly showed distinct groups of STEC based on their virulence profiles, with STEC isolated from pigs, plants and imported meat being clearly separated from the group of clinical human isolates. These non-clinical isolates lacked many of the known STEC virulence markers. Interestingly, the classical Karmali´s seropathotype classification is visible in the multidimensional scaling based on the virulence profiles. In contrast to the virulence profiles, the phylogeny based on single-nucleotide-polymorphisms (SNPs) was not informative for the risk analysis.

Significance: WGS followed by in silico virulence profiling provides ample opportunities to assess the potential public health risk associated with STEC strains.