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Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis.


ABSTRACT: The current pathogen-typing methods have suboptimal sensitivities and specificities. DNA sequencing offers an opportunity to type pathogens with greater degrees of discrimination using single nucleotide polymorphisms (SNPs) than with pulsed-field gel electrophoresis (PFGE) and other methodologies. In a recent cluster of Escherichia coli O157:H7 infections attributed to salad bar exposures and romaine lettuce, a subset of cases denied exposure to either source, although PFGE and multiple-locus variable-number tandem-repeat analysis (MLVA) suggested that all isolates had the same recent progenitor. Interrogation of a preselected set of 3,442,673 nucleotides in backbone open reading frames (ORFs) identified only 1 or 2 single nucleotide differences in 3 of 12 isolates from the cases who denied exposure. The backbone DNAs of 9 of 9 and 3 of 3 cases who reported or were unsure about exposure, respectively, were isogenic. Backbone ORF SNP set sequencing offers pathogen differentiation capabilities that exceed those of PFGE and MLVA.

SUBMITTER: Turabelidze G 

PROVIDER: S-EPMC3838074 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis.

Turabelidze George G   Lawrence Steven J SJ   Gao Hongyu H   Sodergren Erica E   Weinstock George M GM   Abubucker Sahar S   Wylie Todd T   Mitreva Makedonka M   Shaikh Nurmohammad N   Gautom Romesh R   Tarr Phillip I PI  

Journal of clinical microbiology 20130918 12


The current pathogen-typing methods have suboptimal sensitivities and specificities. DNA sequencing offers an opportunity to type pathogens with greater degrees of discrimination using single nucleotide polymorphisms (SNPs) than with pulsed-field gel electrophoresis (PFGE) and other methodologies. In a recent cluster of Escherichia coli O157:H7 infections attributed to salad bar exposures and romaine lettuce, a subset of cases denied exposure to either source, although PFGE and multiple-locus va  ...[more]

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