Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics

Abstract

The evolutionary relationships of 46 Shigella strains representing each of the serotypes belonging to the four traditional Shigella species (subgroups), Dysenteriae, Flexneri, Boydii, and Sonnei, were determined by sequencing of eight housekeeping genes in four regions of the chromosome. Analysis revealed a very similar evolutionary pattern for each region. Three clusters of strains were identified, each including strains from different subgroups. Cluster 1 contains the majority of Boydii and Dysenteriae strains (B1-4, B6, B8, B10, B14, and B18; and D3-7, D9, and D11-13) plus Flexneri 6 and 6A. Cluster 2 contains seven Boydii strains (B5, B7, B9, B11, B15, B16, and B17) and Dysenteriae 2. Cluster 3 contains one Boydii strain (B12) and the Flexneri serotypes 1-5 strains. Sonnei and three Dysenteriae strains (D1, D8, and D10) are outside of the three main clusters but, nonetheless, are clearly within Escherichia coli. Boydii 13 was found to be distantly related to E. coli. Shigella strains, like the other pathogenic forms of E. coli, do not have a single evolutionary origin, indicating convergent evolution of Shigella phenotypic properties. We estimate the three main Shigella clusters to have evolved within the last 35,000 to 270,000 years, suggesting that shigellosis was one of the early infectious diseases of humans.

Figure 1

Alignment of the informative sites for the four regions sequenced. Note that for B13, D1, D8, D10, and Sonnei, which have very divergent sequences, the use of informative sites leads only to omission of many polymorphic sites.

Figure 2

Phylogenetic trees generated by the neighbor-joining method for the four regions sequenced, showing different placement of the three clusters among ECOR set strains. The three major clusters are identified by numbers 1, 2, and 3 respectively. For detailed branching within each cluster, see Supplementary Fig. 4. Bootstrap values are percentages of 1000 replications and are indicated at the nodes. LT2 is used as the outgroup.

Figure 3

Combined phylogenetic tree generated by the neighbor-joining method. Includes the sequences from the four regions sequenced to give a total of 7160 bp. F, Flexneri; B, Boydii; D, Dysenteriae; SS, Sonnei, followed by the serotype number. Bootstrap values are percentages of 1000 replications and are indicated at the nodes. LT2 is used as the outgroup.