Precise dissection of an escherichia coli o157:H7 outbreak by single nucleotide polymorphism analysis

George Turabelidze, Steven J. Lawrence, Hongyu Gao, Erica Sodergren, George M. Weinstock, Sahar Abubucker, Todd Wylie, Makedonka Mitreva, Nurmohammad Shaikh, Romesh Gautom, Phillip I. Tarr

Research output: Contribution to journalArticle

28 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)3950-3954
Number of pages5
JournalJournal of clinical microbiology
Volume51
Issue number12
DOIs
StatePublished - Dec 2013

ASJC Scopus subject areas

  • Microbiology (medical)

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    Turabelidze, G., Lawrence, S. J., Gao, H., Sodergren, E., Weinstock, G. M., Abubucker, S., Wylie, T., Mitreva, M., Shaikh, N., Gautom, R., & Tarr, P. I. (2013). Precise dissection of an escherichia coli o157:H7 outbreak by single nucleotide polymorphism analysis. Journal of clinical microbiology, 51(12), 3950-3954. https://doi.org/10.1128/JCM.01930-13