Purpose: This study had two major goals. First, the genomic comparison of STEC O157 isolates belonging to similar LSPA6 lineages from The Netherlands and the US. Second, developing a molecular risk assessment (MRA) approach to discriminate between STEC of high and lower human health risk.
Methods: Eighteen Dutch human STEC O157 isolates (5 LSPA6 lineage I, 8 lineage I/II, 5 lineage II) were subjected to whole genome sequencing using the Illumina MiSeq platform and compared with STEC O157 Sakai as a reference strain. Based on a published single nucleotide polymorphism (SNPs) list from sequenced U.S. isolates (Bono 2012), phylogenetic comparisons were made. A set of 225 non-O157 strains isolated from humans, food and cattle were screened for a large number of virulence genes. In addition, these strains were phylotyped and grouped in different seropathotypes (Karmali 2003).
Results: Phylogenetic analysis of SNP lists generated from the genome sequences revealed that Dutch and U.S. isolates belonging to the same LSPA6 lineage cluster together, suggesting no major differences between isolates from both geographic locations. Further analysis of the genome sequences and SNPs of the Dutch strains is ongoing. With respect to the non-O157 STEC, cluster analysis based on the presence/absence of virulence genes showed that STEC seropathotype A and B (including the top 5 relevant STEC serotypes in the EU) clustered together and were separated from seropathotype D and E. The majority of the isolates belonged to Escherichia coli phylogroup B1 (60%) and A (20%). Genes responsible for the differentiation between the seropathotypes include eae, efa1, and nleB. The latter determinant was strongly associated with isolates from hospitalized patients.
Significance: These results increase the understanding in cross-boundary STEC epidemiology and provide a framework for STEC risk assessment.