title: Putative classification of clades of enterohemorrhagic Escherichia coli O157 using an IS-printing system.
abstract: Enterohemorrhagic Escherichia coli O157 (O157) strains can be classified in clades by single nucleotide polymorphisms (SNPs), but this analysis requires significant laboratory effort. As the distribution of insertion sequence (IS) 629 insertions has been reported to be biased among different clades, O157 isolates can be putatively classified in clades by comparison with an IS629 distribution database. A database of the IS629 distribution in O157 strains isolated in Chiba Prefecture and their classification in clades was determined by SNP analysis and IS-printing, an easy and quick analytical tool for IS629 in the O157 genome. The IS629 distribution in O157 strains isolated in Fukuoka and Yamagata Prefectures was determined by IS-printing. These strains were putatively classified in clades by Relative Likelihood calculations that compared the IS-printing data and the IS629 distribution database. Concordance Ratios were calculated, which compared the number of strains putatively classified in a clade by Relative Likelihood to the number of strains classified in that clade by SNP analysis. For the Fukuoka and Yamagata strains, the Concordance Ratios for clades 3, 6 and 8 were 97-100%, for clade 7 about 88%, and for clades 2 and 12 over 90%. In conclusion, O157 clade 2, 3, 6, 7, 8 and 12 strains could be putatively classified by IS-printing.
  
  
  CONCLUSIONS
  This study demonstrated that enterohemorrhagic E. coli O157 (O157) strains could be putatively classified in clades using an IS-printing system. IS-printing was previously developed as a relatively quick and easy tool for analysis of insertion sequence 629 in the O157 genome. Since most local government public health institutes in Japan carry out IS-printing for early detection of O157 outbreaks, these data should be useful for putative classification of O157 strains in each area.
authors.affiliation: Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.|Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Hirai
authors.affiliation: Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
authors.forename: E
authors.initials: E
authors.lastname: Yokoyama
authors.affiliation: Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Etoh
authors.affiliation: Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Seto
authors.affiliation: Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Ichihara
authors.affiliation: Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan.
authors.forename: E
authors.initials: E
authors.lastname: Maeda
authors.affiliation: Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan.
authors.forename: N
authors.initials: N
authors.lastname: Sera
authors.affiliation: Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Horikawa
authors.affiliation: Chiba Prefectural Institute of Public Health, Chiba, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Sato
authors.affiliation: Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Yamamoto
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D004196:Disease Outbreaks / Q000517:prevention & control; D004927:Escherichia coli Infections / Q000453:epidemiology*; D019453:Escherichia coli O157 / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D007564:Japan; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide
chemical_list: D004251:DNA Transposable Elements
keywords: IS-printing system; Relative Likelihood; enterohemorrhagic Escherichia coli O157; population genetic analysis; putative classification of clades