All Shigella and enteroinvasive Escherichia coli (EIEC) strains carry a 230-kb virulence plasmid (pINV) which is essential for their invasiveness. There are two sequence forms, pINV A and pINV B, of the plasmid (R. Lan, B. Lumb, D. Ryan, and P. R. Reeves, Infect. Immun. 69:6303-6309, 2001), and the recently sequenced pINV plasmid from Shigella flexneri serotype 5 is a pINV B form. In this study we sequenced the majority of the coding region of the pINV A form from S. flexneri serotype 6 other than insertion sequence or related sequences and compared it with the pINV B form. More than half of the genes sequenced appear to be under positive selection based on their low ratio of synonymous to nonsynonymous substitutions. This high proportion of selected differences indicates that the two pINV forms have functional differences, and comparative studies of pathogenicity in different Shigella-EIEC strains could be informative. There are also genes absent in the S. flexneri serotype 6 plasmid, including the sepA gene encoding serine protease, the major secreted protein of S. flexneri serotype 2a, and the stbAB genes, which encode one of the two partition systems found in S. flexneri serotype 5. The incompatibility of the two pINV forms appears to be due to either small differences in the mvpAT postsegregational killing system or the presence of an unknown system in pINVA.Shigella strains are the causative agent of shigellosis or bacillary dysentery, a diarrheal disease of humans (1). Molecular evidence derived from studies involving DNA hybridization, multilocus enzyme electrophoresis, and sequencing of housekeeping genes indicates that Escherichia coli and all members of the genus Shigella belong to the same species (8,30,35). Enteroinvasive E. coli (EIEC) and Shigella have long been known to be similar (28) and can in fact be treated as comprising a single pathovar of E. coli (21). Most Shigella strains fall into three clusters (clusters 1, 2, and 3) based on the sequence of housekeeping genes (36), but Shigella dysenteriae serotypes 1, 8, and 10 and Shigella sonnei are not in any of the clusters while Shigella boydii serotype 13 is outside E. coli.The pathogenesis of EIEC and Shigella involves invasion of mucosal epithelial cells of the large intestine (1, 34). Virulence in Shigella strains is dependent on the presence of a large 210-to 230-kb plasmid. The virulence plasmids pWR100 in S. flexneri serotype 5, pMYSH6000 in S. flexneri serotype 2a, and pSS120 in S. sonnei, together with those of other Shigella bacteria, have been shown to carry determinants for invasiveness and the ability to cause disease. These large plasmids are collectively termed pINV plasmids (13), which are also present in EIEC strains. The cell invasion capacity of Shigella-EIEC is determined by a cluster of 38 genes within a 32-kb segment of the pINV plasmid, often referred to as the entry or invasion region, which includes genes for invasins, molecular chaperones, motility, regulation, and a specialized type III secretion apparatus (32).In a p...