Percentages of 100,000 simulated sequences with SNPs, as functions of ORFs sampled, and of clusters of origin of strains. A total of 50, 100, 300, and 500 the backbone concatenome ORFs were randomly selected in 100,000 independent simulations. We compared the 2 genomically sequenced clinical isolates in cluster 1 (A) and the 2 genomically sequenced clinical isolates strains in cluster 3 (B) to model how many ORFs one would need to sequence to find differentiating SNPs. The distribution of ORFs that contained SNPs in pairwise interpathogen comparisons are portrayed as curves, with each curve representing a different number of ORFs sampled. x axis depicts numbers of SNPs identified. The y axis depicts percentage of simulation.

Evolutionary scenario for EHEC 1 pathogens. E. coli O55:H7 belongs to the most ancestral subgroup of the EHEC 1 clade (subgroup A). The gray sphere depicts a probably extinct intermediate between O55:H7 and E. coli expressing the O157 lipopolysaccharide, with subgroup B consisting of the SF O157:H⁻ and subgroup C consisting of E. coli O157:H7. Critical intraclade events are noted. Intracluster ovals represent genomically sequenced strains (dark-pink), strains used for SNP consensus sampling (green), inferred founders (pale-pink), and postulated organisms that are immediate progenitors to the next cluster or subgroup (white). Screened strains were assigned to the main branch if they had each of the 3 signature SNPs among the 111 shared SNPs (38/48), and the minor branch if they lacked this SNPs (10/48). More extensive evolutionary detail is provided in Fig. S1. Distances not drawn to scale.

Possible scenarios underlying constrained radiation observed in cluster 1. (A) Many different radiations of similarly virulent O157:H7s extend from the cluster 1 founder, until a bottleneck (selective sweep) eliminated all descendants of the founder except for one that had sustained the 111 shared SNPs between the red symbols in Fig. 1 and Fig. S1. The descendants of the survivor of this event flourished, and randomly spillover to human populations today. (B) Heterogeneous cluster 1 O157:H7s reside in their natural reservoir (different colored bacilli), but only a small minority (red bacilli) are capable of injuring an incidentally infected human (source sink dynamics). (C) Many different radiations of similarly virulent O157:H7s extend from the cluster 1 founder. A mutation that conferred a selective advantage occurred in an O157:H7 at or immediately before the node in Fig. 1 and Fig. S1. The descendants of this advantaged mutant flourished and randomly spillover to human populations today.

SNP clusterings, E. coli O55:H7 strain TB182A versus founder of E. coli O157:H7 cluster 1. Percentage of single nucleotide differences in each backbone ORF in the subgroup C the backbone concatenome, comparing ORFs in strain TB182A and the founder of subgroup C, cluster 1. The y axis portrays percentage of ORF nucleotides that differ from counterpart in descendant E. coli O157:H7 in the most closely related cluster. The x axis portrays concatenated ORFs. The 160,818 nucleotide region between hisG and yehL has 39,295 O-island and 121,523 backbone nucleotides. The backbone part of this region in strain TB182A has 1,337 SNPs that are not found in the founder of E. coli O157:H7 cluster 1 or in strain 493/89, whereas the remaining 3,190,617 EHEC 1 the backbone concatenome nucleotides have only 1,764 SNPs. This 161-kb region includes the O55 gnd gene and the O55 rfb cluster, which encodes the lipopolysaccharide side chain (Fig. S3). (Inset) Noted are several ORFs relevant to this region, including cross-over sites designated by GENECONV (amn and yehL) and by Wang, et al. (amn-hisG and galF) (3). The backbone region encoding ECs2830–2847, which spans gnd, rfb genes, and galF, was not included in this pairwise comparison because of <95% similarity (gnd) or unequal lengths (galF) between orthologues, or absence of genes from K-12 (rfb cluster). However, we have included their relative position between included backbone ORFs in this region.