Probing genomic diversity and evolution of <i>Escherichia coli</i> O157 by single nucleotide polymorphisms

Zhang, Wei; Qi, Weihong; Albert, Thomas; Motiwala, Alifiya S.; Alland, David; Hyytiä-Trees, Eija; Ribot, Efrain M.; Fields, Patricia I.; Whittam, Thomas S.; Swaminathan, Bala

doi:10.1101/gr.4759706

Cited by 125 publications

(94 citation statements)

References 69 publications

(109 reference statements)

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“…More sensitive means have subsequently been applied to study the evolution of plasmid pO157. By using pO157 from the Sakai strain as a reference for the resequencing and mapping of pO157 from multiple strains, Zhang et al found that differences between pO157 plasmids ranged from few to many at the SNP level (198). Such results reinforce the idea that SNP analysis can be applied on a plasmid genome scale as a more sensitive means for examining the evolution of closely related plasmid genomes.…”

Section: Ehec and Stec Virulence Plasmidssupporting

confidence: 62%

Pathogenomics of the Virulence Plasmids ofEscherichia coli

Johnson

Nolan

2009

Microbiol Mol Biol Rev

372

369

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SUMMARY Bacterial plasmids are self-replicating, extrachromosomal elements that are key agents of change in microbial populations. They promote the dissemination of a variety of traits, including virulence, enhanced fitness, resistance to antimicrobial agents, and metabolism of rare substances. Escherichia coli, perhaps the most studied of microorganisms, has been found to possess a variety of plasmid types. Included among these are plasmids associated with virulence. Several types of E. coli virulence plasmids exist, including those essential for the virulence of enterotoxigenic E. coli, enteroinvasive E. coli, enteropathogenic E. coli, enterohemorrhagic E. coli, enteroaggregative E. coli, and extraintestinal pathogenic E. coli. Despite their diversity, these plasmids belong to a few plasmid backbones that present themselves in a conserved and syntenic manner. Thanks to some recent research, including sequence analysis of several representative plasmid genomes and molecular pathogenesis studies, the evolution of these virulence plasmids and the implications of their acquisition by E. coli are now better understood and appreciated. Here, work involving each of the E. coli virulence plasmid types is summarized, with the available plasmid genomic sequences for several E. coli pathotypes being compared in an effort to understand the evolution of these plasmid types and define their core and accessory components.

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Section: Ehec and Stec Virulence Plasmidssupporting

confidence: 62%

Pathogenomics of the Virulence Plasmids ofEscherichia coli

Johnson

Nolan

2009

Microbiol Mol Biol Rev

372

369

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“…coli O157:H7 strains associated with outbreaks and severe epidemicity have been shown to represent a single phylogenetic branch when they are grouped by MLST (using seven housekeeping genes), comprising 100% of the seropathotype A strains (40,50,51). It has been postulated that over the last 50 years, the pathogenic O157 lineage has evolved from an enteropathogenic E. coli O55:H7 group with the acquisition of verotoxin-converting phages and an O157 rfb (O-antigen subunit) gene cluster (3).…”

Section: Discussionmentioning

confidence: 99%

Genomic O Island 122, Locus for Enterocyte Effacement, and the Evolution of Virulent Verocytotoxin-ProducingEscherichia coli

et al. 2008

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The locus of enterocyte effacement (LEE) and genomic O island 122 (OI-122) are pathogenicity islands in verocytotoxin-producing Escherichia coli (VTEC) serotypes that are associated with outbreaks and serious disease. Composed of three modules, OI-122 may occur as "complete" (with all three modules) or "incomplete" (with one or two modules) in different strains. OI-122 encodes two non-LEE effector (Nle) molecules that are secreted by the LEE type III secretion system, and LEE and OI-122 are cointegrated in some VTEC strains. Thus, they are functionally linked, but little is known about the patterns of acquisition of these codependent islands. To examine this, we conducted a population genetics analysis, using multilocus sequence typing (MLST), with 72 VTEC strains (classified into seropathotypes A to E) and superimposed on the results the LEE and OI-122 contents of these organisms. The wide distribution of LEE and OI-122 modules among MLST clonal groups corroborates the hypothesis that there has been lateral transfer of both pathogenicity islands. Sequence analysis of a pagC-like gene in OI-122 module 1 also revealed two nonsynonymous single-nucleotide polymorphisms that could help discriminate a subset of seropathotype C strains and determine the presence of the LEE. A nonsense mutation was found in this gene in five less virulent strains, consistent with a decaying or inactive gene. The modular nature of OI-122 could be explained by the acquisition of modules by lateral transfer, either singly or as a group, and by degeneration of genes within modules. Correlations between clonal group, seropathotype, and LEE and OI-122 content provide insight into the role of genomic islands in VTEC evolution.Verocytotoxin-producing Escherichia coli (VTEC) and Shiga toxin-producing E. coli (STEC) are emerging zoonotic pathogens consisting of multiple serotypes, over 200 of which have been isolated from cases of human disease (48). Human infection by some VTEC serotypes, notably O157:H7, is associated with significant outbreaks and may lead to serious complications, such as hemorrhagic colitis and the hemolytic-uremic syndrome (HUS) (23,25,34). Karmali et al. (24) have classified VTEC into five seropathotype groups based on the relative frequency with which the serotypes are associated with serious and epidemic human disease (Table 1). There is a strong association between VTEC seropathotypes A and B that cause serious or epidemic disease and the presence of two genomic islands, the locus of enterocyte effacement (LEE), which is associated with the characteristic "attaching and effacing" lesions (20, 34), and genomic O island 122 (OI-122) (24).All of the virulence factors necessary for the formation of the attaching and effacing lesions in VTEC are encoded by the LEE pathogenicity island (18,20,34,47), which encodes the structural, accessory, and effector molecules of this type III secretion system (4,12,13,18,19). The LEE of VTEC serotype O157:H7 reference strain EDL 933, which is ϳ43.4 kb long, contains 41 open reading fram...

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“…We acknowledge a Department of Homeland Security IAG #224-04-2806 for supporting work on the discrimination of E. [31,32].…”

Section: Acknowledgementsmentioning

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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Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms

Cited by 125 publications

References 69 publications

Pathogenomics of the Virulence Plasmids ofEscherichia coli

Pathogenomics of the Virulence Plasmids ofEscherichia coli

Genomic O Island 122, Locus for Enterocyte Effacement, and the Evolution of Virulent Verocytotoxin-ProducingEscherichia coli

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

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