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

Abstract

Shiga toxin (stx)-producing Escherichia coli O157 : H7 is a prominent food-borne pathogen. Symptoms in human infections range from asymptomatic to haemorrhagic colitis and haemolytic uraemic syndrome, and there is a need for methods that yield information that can be used to better predict clinical and epidemiological outcomes. IS629 is an insertion sequence notable for its prevalence and variable distribution in the chromosome of E. coli O157 : H7, which has been exploited for subtyping and strain characterization. In particular, IS629 distribution is closely aligned with the major phylogenetic lineages that are known to be distinctive in their genome structure and virulence potential. In the present study, a comprehensive subtyping method in which IS629-typing was combined with stx genotyping was developed using a conventional PCR approach. This method consisted of a set of 32 markers based on the unique distribution of IS629 in the three major phylogenetic lineages of E. coli O157 : H7 and six additional markers to determine the stx genotype, a key virulence signature associated with each lineage. The analysis of IS629 loci variation with the 32 markers allowed us to determine the IS629 distribution profile (IDP), phylogenetic lineage and genetic relatedness of the 31 E. coli O157 : H7 strains examined. An association between IDP typing and stx genotype was observed. The use of both IDP and the stx genotype for strain characterization provided confirmative and complementary data in support of lineage placement of closely related strains. In addition, IS629/stx profiles were in agreement with strain segregation based on LSPA-6 (lineage-specific polymorphism assay) and PFGE subtyping, demonstrating its potential as a subtyping and strain tracking method.

Simultaneous Presence of Insertion Sequence Excision Enhancer and Insertion Sequence IS 629 Correlates with Increased Diversity and Virulence in Shiga Toxin-Producing Escherichia coli

“…These results show that the presence of IEE and IS629 appears to be related to a strain H-type (lineage specific) and that this IEE and IS629 combination appears to be associated mostly with serotypes related to high pathogenicity and human disease (SPT A and B). This supports other findings by Stanton et al, who found an association between the presence of IS629 and elements with an effect on virulence and phage production (32).…”

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

“…These results supported recent epidemiological studies that demonstrated higher association between stx 2a and clinical outcome, as compared to stx 2c (Andersson et al, 2011;Beutin et al, 2007;Persson et al, 2007). In the present study, a strong correlation between stx 2a /stx 2c genotypes and LSPA-6 genotypes was observed, supporting a recent postulation that both lineage types, together with stx genotype, may be informative surrogate markers for epidemiological and evolutionary investigations (Stanton et al, 2014).…”

“…To assess the public health risks associated with E. coli O157 : H7, it is crucial to understand the phenotypic and genotypic differences among strains from clinical illness, as well as from their sources of infection, that might enable better prediction of clinical and epidemiological outcomes (Stanton et al, 2014). 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).…”

Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes

“…Pathogenome Architecture and Virulence Profiles of Stx (−) NSF O157:H7 and SF O157:NM Alterations in genome size and architecture in EHEC O157:H7/NM are driven by the individual prophage complement, particularly Stx-phages Eppinger et al, 2011b;Shaaban et al, 2016) and dynamics of other MGEs (Eppinger et al, 2011b;Yokoyama et al, 2011;Stanton et al, 2014;Toro et al, 2015). We compared the chromosomes of the Stx (−) NSF O157:H7 and SF O157:NM strains with BRIG (Alikhan et al, 2011) using Stx (+) strain EC4115 (stx1−, stx2a+, stx2c+) as reference (Eppinger et al, 2011b).…”