Genomic anatomy of Escherichia coli O157:H7 outbreaks

Abstract

The rapid emergence of Escherichia coli O157:H7 from an unknown strain in 1982 to the dominant hemorrhagic E. coli serotype in the United States and the cause of widespread outbreaks of human food-borne illness highlights a need to evaluate critically the extent to which genomic plasticity of this important enteric pathogen contributes to its pathogenic potential and its evolution as well as its adaptation in different ecological niches. Aimed at a better understanding of the evolution of the E. coli O157:H7 pathogenome, the present study presents the high-quality sequencing and comparative phylogenomic analysis of a comprehensive panel of 25 E. coli O157:H7 strains associated with three nearly simultaneous food-borne outbreaks of human disease in the United States. Here we present a population genetic analysis of more than 200 related strains recovered from patients, contaminated produce, and zoonotic sources. High-resolution phylogenomic approaches allow the dynamics of pathogenome evolution to be followed at a high level of phylogenetic accuracy and resolution. SNP discovery and study of genome architecture and prophage content identified numerous biomarkers to assess the extent of genetic diversity within a set of clinical and environmental strains. A total of 1,225 SNPs were identified in the present study and are now available for typing of the E. coli O157:H7 lineage. These data should prove useful for the development of a refined phylogenomic framework for forensic, diagnostic, and epidemiological studies to define better risk in response to novel and emerging E. coli O157:H7 resistance and virulence phenotypes.

Phylogenetic characterization of Escherichia coli O157 : H7 based on IS629 distribution and Shiga toxin genotype

“…Sixteen additional strains from disparate sources were included in order to increase the diversity of the strain set: including three lineage-prototype strains (EDL933 for lineage I, EC869 for lineage II and EC4115 for lineage I/II), four spinach outbreak strains, strain Sakai and six Wisconsin dairy-farm isolates (Table 1). The analysis of strains EC869, EC4115 and EC4206 was based on their published genomic sequences (Eppinger et al, 2011b), while the other 28 strains were characterized using conventional PCR. The genomic sequences of strains EDL933, EC869 and EC4115 were used to identify lineage-specific IS629 markers as described in detail below.…”

“…Typical lineage I strains carry shiga toxin genes stx1 and stx2a, while lineage II strains usually carry stx1 and stx2c. Lineage I/II strains typically carry both stx2a and stx2c (Eppinger et al, 2011b). In addition, two alternative integration sites of stx2a-encoding phage have been identified, wrbA and argW.…”

“…For example, three spinach outbreak strains shared an identical IDP confirming their clonal nature (Eppinger et al, 2011b). EC4115 was previously defined as an outlier among the outbreak isolates based upon SNP analysis (Eppinger et al, 2011b) and had an IDP that differed from the clonal group IDP by three IS629 markers (see Fig.…”

“…Multiple subtyping methods have been developed, including high-resolution genotyping based on single nucleotide polymorphisms (SNPs) (Manning et al, 2008;Eppinger et al, 2011b), octamer-based genome scanning (Kim et al, 1999) and comparative genome hybridization (Zhang et al, 2007). However, these methods are labour intensive and not feasible for high throughput.…”

Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing

“…However, the studies associated with these sequences make no mention of the possibility of multiple alleles (17,18,19,20). The presence of multiple alleles of the same stx type has been previously identified by WGS (21), however this is the first study to present a large sale comparison of this method with PCR subtyping. Some of the ambiguous positions in sequences in the NCBI database were the same positions in stx as the mixed positions observed in this study, supporting the evidence that multiple alleles exist and are present in the same strain.…”