Identification of Common Subpopulations of Non-Sorbitol-Fermenting, β-Glucuronidase-Negative Escherichia coli O157:H7 from Bovine Production Environments and Human Clinical Samples

Abstract

Non-sorbitol-fermenting, ␤-glucuronidase-negative Escherichia coli O157:H7 strains are regarded as a clone complex, and populations from different geographical locations are believed to share a recent common ancestor. Despite their relatedness, high-resolution genotyping methods can detect significant genome variation among different populations. Phylogenetic analysis of high-resolution genotyping data from these strains has shown that subpopulations from geographically unlinked continents can be divided into two primary phylogenetic lineages, termed lineage I and lineage II, and limited studies of the distribution of these lineages suggest there could be differences in their propensity to cause disease in humans or to be transmitted to humans. Because the genotyping methods necessary to discriminate the two lineages are tedious and subjective, these methods are not particularly suited for studying the large sets of strains that are required to systematically evaluate the ecology and transmission characteristics of these lineages. To overcome this limitation, we have developed a lineage-specific polymorphism assay (LSPA) that can readily distinguish between the lineage I and lineage II subpopulations. In the studies reported here, we describe the development of a six-marker test (LSPA-6) and its validation in a side-by-side comparison with octamer-based genome scanning. Analysis of over 1,400 O157:H7 strains with the LSPA-6 demonstrated that five genotypes comprise over 91% of the strains, suggesting that these subpopulations may be widespread.

Genetic diversity of Shiga toxin-producing Escherichia coli O157 : H7 recovered from human and food sources

“…Molecular typing and microbial genomics have facilitated the characterization and comparison of E. coli O157 : H7 strains recovered from different isolation sources demonstrating non-random distribution of genotypes among clinical and non-clinical strains (Besser et al, 2008;Franz et al, 2012;Hartzell et al, 2011;Lee et al, 2011;Whitworth et al, 2010;Yang et al, 2004;Yokoyama et al, 2011;Zhang et al, 2010;Ziebell et al, 2008). In addition, several epidemiological studies supported the growing evidence of substantial variability in the virulence of E. coli O157 : H7 genotypes implicated in different outbreaks and variation in patient symptoms (Besser et al, 2008;Grant et al, 2008;Manning et al, 2008).…”

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

“…The LSPA lineage type of all 31 strains was determined using 6 polymorphism markers (Yang et al, 2004). LSPA-6 alleles were defined using the reference table provided by Yang et al (2004). Isolates that possessed LSPA-6 genotype 111111 were classified as lineage I, isolates that possessed 222222 or 222223 were classified as lineage II, while all others were assigned to lineage I/II (211111 and 211211).…”

“…The LSPA lineage type of all 31 strains was determined using 6 polymorphism markers (Yang et al, 2004). LSPA-6 alleles were defined using the reference table provided by Yang et al (2004).…”

“…Isolates that possessed LSPA-6 genotype 111111 were classified as lineage I, isolates that possessed 222222 or 222223 were classified as lineage II, while all others were assigned to lineage I/II (211111 and 211211). Previously defined PCR conditions were used (Yang et al, 2004) and amplicons were resolved by agarose (4.0 %) gel electrophoresis run overnight at 75 V.…”

Geographically Distinct Escherichia coli O157 Isolates Differ by Lineage, Shiga Toxin Genotype, and Total Shiga Toxin Production

“…The identification of markers that occur at different frequencies in cattle and human isolates represents an established strategy for identifying E. coli O157 genotypes of increased public health risk. In recent years, phylogenetics has proven particularly useful in identifying host-specific (cattle/human) associations among E. coli O157 populations (1,(5)(6)(7)(8)(9)(10).…”