Tadasuke Ooka, Kazuko Seto, Kimiko Kawano, Hideki Kobayashi, Yoshiki Etoh, Sachiko Ichihara, Akiko Kaneko, Junko Isobe, Keiji Yamaguchi, Kazumi Horikawa, Tânia A.T. Gomes, Annick Linden, Marjorie Bardiau, Jacques G. Mainil, Lothar Beutin, Yoshitoshi Ogura, and Tetsuya Hayashi
Author affiliations: University of Miyazaki, Miyazaki, Japan (T. Ooka, Y. Ogura, T. Hayashi); Osaka Prefectural Institute of Public Health, Osaka, Japan (K. Seto); Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki (K. Kawano); National Institute of Animal Health, Ibaraki, Japan (H. Kobayashi); Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan (Y. Etoh, S. Ichihara, K. Horikawa); Yamagata Prefectural Institute of Public Health, Yamagata, Japan (A. Kaneko); Toyama Institute of Health, Toyama, Japan (J. Isobe); Hokkaido Institute of Public Health, Hokkaido, Japan (K. Yamaguchi); Universidade Federal de São Paulo, São Paulo, Brazil (T.A.T. Gomes); University of Liège, Liège, Belgium (A. Linden, M. Bardiau, J.G. Mainil); Federal Institute for Risk Assessment, Berlin, Germany (L. Beutin)
Figure 1. Phylogenies of the intimin subtypes and the cdtB genes of 275 eae-positive strains from humans, animals, and the environment that had been originally identified by routine diagnostic protocols as enteropathogenic or enterohemorrhagic Escherichia coli. A) Neighbor-joining tree constructed based on the amino acid sequences of 30 known intimin subtypes and previously undescribed 5 intimin subtypes (N1–N5) that were identified. The sequences of the N1–N5 alleles are substantially divergent from any of the known intimin subtypes (<95% sequence identity). Three variants of N1 (N1.1–N1.3) exhibit >95% homology to each other. B) Neighbor-joining tree constructed by using the partial amino acid sequences of the cytolethal distending toxin B subunit encoded by the cdtB gene. Boldface indicates reference sequences (and strain names) for 5 subtypes; underlining indicates alleles identified and names of the strains from which each allele was identified. The alleles that were amplified by the s2/as2 primer pair were classified into the I/IV subtype group, and those amplified by the s1/as1 primer pair were classified into the II/III/V subtype group (see Technical Appendix for primer information). Among the 3 alleles classified into the latter group, 1 was identified as a second copy in 2 Escherichia albertii strains (E2675–2 and HIPH08472–2), but the others were from either 1 E. coli strain (94037) or 8 E. coli strains (e.g., Bird 10). All alleles classified into the II/III/V subtype group were from E. albertii strains. Scale bars indicate amino acid substitutions (%) per site.
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