Octamer-based genome scanning distinguishes a unique subpopulation of
            <i>Escherichia coli</i>
            O157:H7 strains in cattle

Kim, Jae-Hyoung; Nietfeldt, Joseph; Benson, Andrew K.

doi:10.1073/pnas.96.23.13288

Cited by 172 publications

(214 citation statements)

References 33 publications

(23 reference statements)

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“…As the population of EHEC O157 strains has increased in frequency and spread geographically, it has genetically diversified. Isolates of EHEC O157 from clinical and bovine sources have been shown to be genotypically diverse by different methods, including PFGE (26), octomer-based genome scanning (42), and multilocus variable number of tandem repeats analysis (43). Studies of prophage and prophage remnants in EHEC O157 strains have indicated that genotypic diversity is largely attributable to bacteriophage-related insertions, deletions, and duplications of variable sizes of DNA fragments (24,25,44).…”

Section: Discussionmentioning

confidence: 99%

Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks

Manning

Motiwala

Springman

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

410

612

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Escherichia coli O157:H7, a toxin-producing food and waterborne bacterial pathogen, has been linked to large outbreaks of gastrointestinal illness for more than two decades. E. coli O157 causes a wide range of clinical illness that varies by outbreak, although factors that contribute to variation in disease severity are poorly understood. Several recent outbreaks involving O157 contamination of fresh produce (e.g., spinach) were associated with more severe disease, as defined by higher hemolytic uremic syndrome and hospitalization frequencies, suggesting that increased virulence has evolved. To test this hypothesis, we developed a system that detects SNPs in 96 loci and applied it to >500 E. coli O157 clinical strains. Phylogenetic analyses identified 39 SNP genotypes that differ at 20% of SNP loci and are separated into nine distinct clades. Differences were observed between clades in the frequency and distribution of Shiga toxin genes and in the type of clinical disease reported. Patients with hemolytic uremic syndrome were significantly more likely to be infected with clade 8 strains, which have increased in frequency over the past 5 years. Genome sequencing of a spinach outbreak strain, a member of clade 8, also revealed substantial genomic differences. These findings suggest that an emergent subpopulation of the clade 8 lineage has acquired critical factors that contribute to more severe disease. The ability to detect and rapidly genotype O157 strains belonging to such lineages is important and will have a significant impact on both disease diagnosis and treatment guidelines.pathogens ͉ polymorphisms ͉ population genetics E nterohemorrhagic Escherichia coli (EHEC) includes a diverse population of Shiga toxin-producing E. coli that causes outbreaks of food and waterborne disease (1-3). EHEC often resides in bovine reservoirs and is transmitted via many food vehicles including cooked meat, such as hamburger (4) and salami (5), and raw vegetables, such as lettuce (6, 7) and spinach (8). In North America, E. coli O157:H7 is the most common EHEC serotype contributing to Ͼ75,000 human infections (9) and 17 outbreaks (3) per year.It is not clear why outbreaks of EHEC O157 vary dramatically in the severity of illness and the frequency of the most serious complication, hemolytic uremic syndrome (HUS) (10-12). The 1993 outbreak in western North America (4) and the large 1996 outbreak in Japan (13) had low rates of hospitalization and HUS (14, 15), whereas the 2006 North American spinach outbreak (8) had high rates of both hospitalization (Ͼ50%) and HUS (Ͼ10%). One hypothesis is that outbreak strains differ in virulence as a result of variation in the presence and expression of different Shiga toxin (Stx) gene combinations (16)(17)(18)(19).To assess the genetic diversity and variability in virulence among E. coli O157 strains, we developed a real-time PCR system for identifying synonymous and nonsynonymous mutations as SNPs (20-23). Although molecular subtyping methods, such as pulsedfield gel electrophoresis (PFGE), ...

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Section: Discussionmentioning

confidence: 99%

Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks

Manning

Motiwala

Springman

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

410

612

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“…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.…”

Section: Introductionmentioning

confidence: 99%

“…Shringi et al, 2012;Boerlin et al, 1999). Genome analysis by octamer-based genomic scanning and microarraybased comparative genomic hybridization (Kim et al, 1999;Zhang et al, 2007) has shown that E. coli O157 : H7 can be assigned to three main phylogenetic lineages: termed lineages I, II and I/II. Typically, lineage I isolates originate from human clinical and bovine sources; whereas, lineage II strains predominantly have a bovine origin, while I/II strains are associated with human infection and include a hyper-virulent group consisting of the multistate 'spinach' outbreak strains Kulasekara et al, 2009;Laing et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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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.

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“…Early multi-locus enzyme electrophoresis (MLEE) analyses suggested a clonal inheritance for O157:H7 [9] and subsequent multilocus sequence typing (MLST) of selected housekeeping genes indeed showed a marked similarity among E. coli O157:H7 strains that were distinguishable by www.elsevier.com/locate/forsciint Forensic Science International 168 (2007) [183][184][185][186][187][188][189][190][191][192][193][194][195][196][197][198][199] Abbreviations: SNP, single-nucleotide polymorphism; MNP, multi-nucleotide polymorphism; CNP, copy number polymorphismpulsed-field gel electrophoresis (PFGE) patterns [10]. A much richer genetic diversity within E. coli O157:H7 has been depicted by a variety of other molecular analyses, nonetheless, including octamer-based genome scanning [11], extensions of pulsed-field gel electrophoresis (PFGE) [12], whole genome PCR scanning [13], and comparative genomic microarray [14]. The inherent plasticity of the E. coli O157:H7 genome coupled with the transiting of prophages would suggest that other, yet unidentified, loci have likely contributed to the ultimate pathogenesis of this organism.…”

Section: Introductionmentioning

confidence: 99%

Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays

Jackson

Mammel

Patel

et al. 2007

Forensic Science International

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Here, we describe a novel microarray-based approach for investigating the genomic diversity of Escherichia coli O157:H7 in a semi-high throughput manner using a high density, oligonucleotide-based microarray. This microarray, designed to detect polymorphisms at each of 60,000 base-pair (bp) positions within an E. coli genome, is composed of overlapping 29-mer oligonucleotides specific for 60 equally spaced, 1000-bp loci of the E. coli O157:H7 strain EDL933 chromosome. By use of a novel 12-well microarray that permitted the simultaneous investigation of 12 strains, the genomes of 44 individual isolates of E. coli O157:H7 were interrogated. These analyses revealed more than 150 single nucleotide polymorphisms (SNPs) and several deletions and amplifications in the test strains. Pyrosequencing was used to confirm the usefulness of the novel SNPs by determining their allelic frequency among a collection of diverse isolates of E. coli O157:H7. The tiling DNA microarray system would be useful for the tracking and identification of individual strains of E. coli O157:H7 needed for forensic investigations. #

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Octamer-based genome scanning distinguishes a unique subpopulation of Escherichia coli O157:H7 strains in cattle

Cited by 172 publications

References 33 publications

Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks

Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks

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

Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays

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