The enterobacterial "species" Escherichia coli and Shigella can be grouped into a phylogenetic cluster which diverged from other members of the c-subdivision of gram-negative purple bacteria around the time of the emergence of mammalian organisms [1]. Shigella and E. coli are closely related, and it is becoming more and more clear that both could be considered as members of one species as their distinction is only based on the pathogenic character of the bacteria. Their chromosomal organization shares more than 90% homology according to DNA-DNA reassociation experiments [2]. E. coli and Shigella populations are clonal. E. coli isolates can be grouped into particular clones that have evolved under competition as distinct genetic types. They can be classified according to their pathotype and their host [3-7]. These clones arose in parallel by both the loss and the ordered gain of genetic information. The clones are maintained during adaptation to their respective niches, and because of horizontal gene transfer, their further evolution is constantly in progress, thus resulting in very dynamic and diverse genome structures.

In the case of E. coli K-12 strain MG1655, about 18% of the genome has been estimated to represent horizontally acquired sequences [8]. The stepwise acquisition of "foreign DNA" from distantly related organisms as well as the loss of DNA regions (genome reduction) resulted in different metabolic and pathogenic features that distinguish the different genera, strains, and pathotypes. Arising from a nonpathogenic E. coli ancestor, the loss of the ompTand cadA gene in combination with the acquisition of two pathogenicity islands and one virulence plasmid led to the evolution of pathogenic Shigella [9]. The parallel gain and loss of mobile genetic elements, such as bacteriophages, plasmids, and the LEE ("locus of enter-ocyte effacement") pathogenicity island, in different lineages of pathogenic E. coli enabled the evolution of separate clones which belong to different E. coli pathotypes [6]. Accordingly, there is growing evidence that the genome of E. coli and Shigella can be considered as being composed of a conserved core of genes providing the backbone of genetic information required for essential cellular processes.

In addition, a flexible gene pool exists which is not common for all strains and consists of an individual assortment of strain-specific genetic information which may provide additional properties enabling these strains to adapt to special environmental conditions. Therefore, differences in genome size reflect the size variation of the flexible gene pool and are mainly due to the acquisition and loss of genomic DNA. A surprisingly large proportion of the flexible gene pool consists of uncharacterized unknown open reading frames (ORFs) without any obvious function. Another major constituent of the flexible gene pool is the group of accessory genetic elements, e.g., plasmids, transposons, insertion sequence elements, prophages, nonfunctional fragments thereof, and genomic islands. They can either be integrated into the chromosome or replicate independently as extrachromosomal elements. Several types of these elements can be laterally transferred and are present in probably all of the major bacterial phylogenetic groups, thus contributing to the inter- and intraspecies variability in genome content [9-11].

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