Figure 1.
Phylogeny of E.coli and Salmonella genomes.
Maximum-likelihood phylogenies (A) of all E. coli and Salmonella strains for which genome data is available and (B) of selected O104:H4 strains and their closest non-O104:H4 strain, 55989. Font coloring, red: O104:H4 strains; blue: EAEC of non-O104:H4 serotype; green: EHEC strains. Phylogroups B1, A and E [7] are shown with blue, green and violet boxes, respectively. The probable insertions of prophages, genomic islands and plasmids are indicated. Bootstrap support higher than 70 (out of 100) is shown. To improve readability of the tree in panel A, bootstraps are not shown in the clade that is also depicted in panel B. (C) Inferred lateral transfers of virulence factors between phylogroups A, B1 and E.
Table 1.
SNPs between E112/10 and the E. coli outbreak German isolates.
Table 2.
Summary of the number of SNPs between E112/10 and the E. coli outbreak German isolates.
Figure 2.
Comparison of the genomes and plasmids of E.coli strains.
Comparisons of (A) chromosomes and (B–C) plasmids pTY1 and pTY2. Each circle corresponds to the alignment of one strain relative to TY2482. Numbering on the outside corresponds to the position on the genome of TY2482 after rotation to put the start of the sequence at the same position as in 55989 and K12. The chromosomal regions of difference between 55989 and TY2482 (Dataset S1) are shown in red boxes and numbered. For strains for which a full genome is available, regions are shown in white, pale or dark color if the identity between the regions is, respectively, lower than 95%, between 95% and 98%, and over 98%. For strains for which raw reads are available, regions are shown in white if the coverage in the alignment to TY2482 is lower than a standard deviation of the coverage distribution, in pale color if between this and the median coverage minus one standard deviation, and in dark color if above.
Figure 3.
Comparison of the agg genes in the outbreak strains and in other EAEC strains.
Blast hits between the plasmids are shown in grey. agg genes are shown by blue arrows, mobile genes (transposases, transposons and IS elements) are in green, and other genes in grey. The shorter agg3C gene in E92/11 is probably due to a sequencing error. The scale is indicated in the lower right corner.
Figure 4.
Comparison of the second large putative plasmid found in E112/10 with related plasmids.
Comparisons are shown as in Figure 3. The two last plasmids (pHE603110 and pTY1) are shown in reverse orientation. Genes are shown by grey arrows, except for mobile genes (transposases, transposons and IS elements) (green). The scale is indicated in the lower right corner.
Figure 5.
Comparison of the gene order structures of pathogenicity island 1 (PAI1).
Genes located inside PAI1 are shown as blue arrows. Genes shown as green arrows are mobile genes (transposases, transposons and IS sequences). Four regions are defined with colors, and contain the iha gene (blue-grey), the microcin operon (pink), the tellurium resistance cluster (green) and the flu genes (yellow). Comparisons are shown as in Figure 3. The maximum-likelihood phylogenies of these regions are represented next to the gene map. Colors represent different subsets of strains, as in Figure 1.
Figure 6.
Comparison of the gene order structures of pathogenicity island 2 (PAI2).
Genes located inside PAI2 are shown as blue arrows. Genes shown as green arrows are mobile genes (transposases, transposons and IS sequences). Two regions are defined with colors, and contain an antibiotic resistance cluster (light brown) and the 3′ region of the PAI (grey). The location of the integrase (int), ethidium bromide resistance gene (ebr), the streptomycin resistance genes, the tetramycin resistance gene (tetA) and the toxin-antitoxin genes yeeU-yeeV are shown. Comparisons are shown as in Figure 3. The maximum-likelihood phylogenies of the second regions is represented next to the gene map. The phylogeny of the first region was not inferred, due to too many rearrangements in this region. Colors represent different subsets of strains, as in Figure 1.
Figure 7.
Comparison of the gene order structures of the VT2 phages.
Genes located inside the prophage are shown as blue arrows. A transposase in O157:H7 Sakai is indicated in green. Two sub-regions have been defined and are shown in green and orange. The gene into which the insertion site is located, wrbA, is indicated in red. The location of the integrase (int), exonuclease (exo) and the Shiga toxin genes (stx2A, stx2B) are shown. For 01-09591, a contig containing wrbA is shown next to the contigs containing the prophage. Comparisons are shown as in Figure 3. The maximum-likelihood phylogeny of two sub-regions is shown below the map. Colors represent different subsets of strains, as in Figure 1.