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.