Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp

Abstract

Enteroinvasive Escherichia coli (EIEC), a distinctive pathogenic form of E. coli causing dysentery, is similar in many properties to bacteria placed in the four species of Shigella. Shigella has been separated as a genus but in fact comprises several clones of E. coli. The evolutionary relationships of 32 EIEC strains of 12 serotypes have been determined by sequencing of four housekeeping genes and two plasmid genes which were used previously to determine the relationships of Shigella strains. The EIEC strains were grouped in four clusters with one outlier strain, indicating independent derivation of EIEC several times. Three of the four clusters contain more than one O antigen type. One EIEC strain (an O112ac:H- strain) was found in Shigella cluster 3 but is not identical to the Shigella cluster 3 D2 and B15 strains with the same O antigen. Two forms of the virulence plasmid pINV have been identified in Shigella strains by using the sequences of ipgD and mxiA genes, and all but two of our EIEC strains have pINV A. The EIEC strains were grouped in two subclusters with a very low level of variation, generally not intermingled with Shigella pINV A strains. The EIEC clusters based on housekeeping genes were reflected in the plasmid gene sequences, with some exceptions. Two strains were found in the pINV B form by using the ipgD sequence, with one strain having an mxiA sequence similar to the divergent sequence of D1. Clearly, EIEC and Shigella spp. form a pathovar of E. coli.

FIG. 1.

Informative bases for the thrB, purN, trpB, and mdh-argR gene regions for EIEC strains. The numbers at the top of the figure, reading vertically, are base positions. The phylogenetic grouping of each strain is indicated in the left column. O and H antigens are shown in parentheses after the strain name.

FIG. 2.

Phylogenetic tree generated by the neighbor-joining method for the combined data for the purN, thrB, trpB, and mdh-argR regions sequenced to give a total of 3,390 bp. Strain names prefixed with M are EIEC and are followed by serotype and biochemical properties for mucate and acetate if negative as M- and A-respectively; for Shigella strains, F denotes S. flexneri, D denotes S. dysenteriae; B denotes S. boydii, and SS denotes S. sonnei, followed by the serotype number. Bootstrap values are percentages of 1,000 replications and, if 50% or greater, are indicated at the nodes. LT2 is used as the outgroup.

FIG. 3.

Informative sites for the ipgD and mxiA gene for EIEC strains. Note that for some strains, where no sequence was obtained, the corresponding region appears blank. The numbers at the top of the figure, reading vertically, are base positions.

FIG. 4.

Phylogenetic tree generated by the neighbor-joining method for the combined data for plasmid genes ipgD and mxiA. Strain names are prefixed with M for EIEC, F for S. flexneri, B for S. boydii, and D for S. dysenteriae, followed by serotype number and relevant cluster number. M2339 is shown twice on the tree. Its alternative position (marked by a dotted line) is based on the mxiA sequence. Bootstrap values are percentages of 1,000 replications and, if 50% or greater, are indicated at the nodes.