Ancestral Divergence, Genome Diversification, and Phylogeographic Variation in Subpopulations of Sorbitol-Negative, β-Glucuronidase-Negative Enterohemorrhagic
            <i>Escherichia coli</i>
            O157

Kim, Jae-Hyoung; Nietfeldt, Joseph; Ju, Jingliang; Wise, John Pierce; Fegan, Narelle; Desmarchelier, Patricia; Benson, Andrew K.

doi:10.1128/jb.183.23.6885-6897.2001

Cited by 83 publications

(93 citation statements)

References 36 publications

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“…Identifying the underlying factors that lead to enhanced virulence and the successful transmission of EHEC O157 in contaminated food and water is imperative. Similarly, conducting large-scale molecular epidemiologic studies is necessary to assess the actual distribution of SGs, clades, and Stx variants in environmental reservoirs and broad geographic scales (50). The development and deployment of a rapid, inexpensive molecular test that can identify more virulent O157 subtypes also would be useful for clinical laboratories to identify patients with an increased likelihood of developing HUS.…”

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.

406

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.

406

612

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“…These observations suggested that the various types of PSC in a genome were the result of Herein, we propose that both the quantity and quality of PSC may be important for bacterial genome evolution. The Ohno theory of evolution by genome expansion is widely accepted (4,15,18). Genome expansion by DNA recombinations would create a repertoire of redundant genes.…”

Section: Discussionmentioning

confidence: 99%

Role of Premature Stop Codons in Bacterial Evolution

et al. 2008

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When the stop codons TGA, TAA, and TAG are found in the second and third reading frames of a protein-encoding gene, they are considered premature stop codons (PSC). Deinococcus radiodurans disproportionately favored TGA more than the other two triplets as a PSC. The TGA triplet was also found more often in noncoding regions and as a stop codon, though the bias was less pronounced. We investigated this phenomenon in 72 bacterial species with widely differing chromosomal GC contents. Although TGA and TAG were compositionally similar, we found a great variation in use of TGA but a very limited range of use of TAG. The frequency of use of TGA in the gene sequences generally increased with the GC content of the chromosome, while the frequency of use of TAG, like that of TAA, was inversely proportional to the GC content of the chromosome. The patterns of use of TAA, TGA and TAG as real stop codons were less biased and less influenced by the GC content of the chromosome. Bacteria with higher chromosomal GC contents often contained fewer PSC trimers in their genes. Phylogenetically related bacteria often exhibited similar PSC ratios. In addition, metabolically versatile bacteria have significantly fewer PSC trimers in their genes. The bias toward TGA but against TAG as a PSC could not be explained either by the preferential usage of specific codons or by the GC contents of individual chromosomes. We proposed that the quantity and the quality of the PSC in the genome might be important in bacterial evolution.

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“…These changes in PFGE type are interpreted as changes in an XbaI restriction site or the addition or deletion of a large block(s) of DNA; the latter has been observed in E. coli O157:H7 (19). Selection of nonhousekeeping genes, hypervariable regions for MLST, PCR of variable-length tandem repeat loci, octamer-based genome scanning, and PCR/sequence-based methods have been used for subpopulations of E. coli O157:H7 and yielded high diversity indexes (15,16,25). The addition of two antibiotic resistance genes, in particular the shv gene, where the most variability was observed, increased the discriminatory index to 0.956.…”

Section: Discussionmentioning

confidence: 99%

Multilocus Sequence Typing versus Pulsed-Field Gel Electrophoresis for Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates

Nemoy

Kotetishvili²,

Tigno

et al. 2005

J Clin Microbiol

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Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains are emerging pathogens. Molecular typing of ESBL-producing E. coli is useful for surveillance purposes, to monitor outbreaks and track nosocomial spread. Although pulsed-field gel electrophoresis (PFGE) is the current "gold standard" for bacterial molecular typing, multilocus sequence typing (MLST) may offer advantages. Forty ESBL-producing E. coli isolates were selected at random from a cohort of intensive care unit patients who had active surveillance perirectal cultures done. PFGE identified 19 unique PFGE types (PT) among the 40 isolates; MLST identified 22 unique sequence types. MLST had greater discriminatory ability than PFGE for ESBL-producing E. coli. Simpson's indices of diversity for PFGE and MLST were 0.895 and 0.956, respectively. There were five clonal complexes (CCs) (isolates with differences of no more than two loci) that each contained multiple PT, but each PT was found in only one CC, indicating genetic consistency within a CC. MLST has clear utility in studies of ESBL-producing E. coli, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains.Pulsed-field gel electrophoresis (PFGE) is the most widely used tool for molecular typing of bacterial strains (1), but new DNA fingerprinting techniques, including multilocus sequence typing (MLST), are emerging as alternatives, particularly when information regarding evolutionary history is needed (30). MLST is a relatively new technique where multiple genes (loci) are sequenced to measure genetic relatedness and analyze sequence variation between alleles from many strains (20). MLST has already been used to characterize a number of pathogenic bacteria, including Neisseria meningitidis, Enterococcus spp., Staphylococcus aureus, and Campylobacter spp. (3,4,7,21). In studies comparing MLST to PFGE among Salmonella spp., Vibrio cholerae, Enterococcus faecalis, and S. aureus isolates, MLST has been found to have similar or greater discriminatory ability than PFGE (17,18,21,27). However, these results may not be generalizable to all species, since a study comparing MLST to PFGE in Escherichia coli O157:H7 found that PFGE had a greater discriminatory ability than MLST did (26).MLST has not yet been used to characterize extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates. ESBL production, which confers resistance to all penicillins and cephalosporins, is found in E. coli and other members of the family Enterobacteriaceae. In the United States, the prevalence of ESBL carriage ranges between 0 and 25%, with a national average of approximately 6%, and these numbers are increasing (2, 24). ESBL-producing E. coli bacteria cause nosocomial infections, including bloodstream infections, urinary tract infections, and pneumonias, and are associated with increased patient morbidity and mortality (29). Molecular typing of ESBL-producing E. coli is useful as a framework for hospital epidemiologist...

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Ancestral Divergence, Genome Diversification, and Phylogeographic Variation in Subpopulations of Sorbitol-Negative, β-Glucuronidase-Negative Enterohemorrhagic Escherichia coli O157

Cited by 83 publications

References 36 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

Role of Premature Stop Codons in Bacterial Evolution

Multilocus Sequence Typing versus Pulsed-Field Gel Electrophoresis for Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates

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