Purpose: The purpose of the study was to examine the eae gene in a collection of STEC strains from humans to identify informative regions to detect, subtype and predict the serogroup to facilitate the response to public health events caused by these STECs.
Methods: We examined full length eae sequences extracted from the whole genome sequences of over 100 sporadic and outbreak-associated STEC isolates from serogroups O26, O45, O103, O111, O121, O145 and O157. As controls we included 18 eae sequences from other Escherichia coli and E. albertii deposited at NCBI. Meta-data and eae sequences from these serogroups were visualized and analyzed using Geneious and CLC genomics software to detect 1) conserved regions for broad detection of eae-positive strains 2) fixed SNPs for prediction of serogroup and 3) variable SNPs for discrimination between outbreak and non-outbreak isolates.
Results: Among the strains tested, conserved regions within the first two-thirds of the eae gene were identified that could detect all eae-positive STEC, and fixed SNPs in the latter third of the gene were identified that could predict the serogroup. No outbreak-specific SNPs were identified among the strains tested.
Significance: This study is an initial step toward the development of highly discriminatory genotyping assays for use in future detection or subtyping strategies. Improved diagnostic and tracking methods will directly impact our ability to identify and control outbreaks of existing and emerging virulent clones of this pathogen in a timely fashion.