Shigella genomes: a tale of convergent evolution and specialization through IS-expansion and genome reduction

Although all Shigella species share similar pathogenic properties, each species exhibits peculiar epidemiological characteristics. S. dysenteriae, S. flexneri, and S. boydii are most common in developing countries, whereas S. sonnei is more prevalent in developed countries. A remarkable difference between Shigella and E. coli genomes is the presence of pseudogenes in the former. The second remarkable feature of the Shigella genome is the presence of enormous copies of IS elements, which are likely the cause of genomic rearrangements, including deletions, inversions, and translocations that may effectively disrupt the colinearity among different Shigella genomes. After the acquisition of the ancestral forms of the virulence plasmid by Shigella/enteroinvasive E. coli (EIEC), genome reduction by inactivation of the pathway-specific antivirulence loci (AVL) is vital for adaptation in the cytosolic niche. Similar to obligate pathogens, reduced selection pressure might have played an important role in Shigella genome reduction, which may have further accelerated terminal evolution and resulted in the increased host specificity. Numerous genes responsible for cell motility cell envelope, carbohydrate transport, and metabolism that are present in E. coli were frequently lost in Shigella. A combination of various strategies using the basic information provided by genomic research will be helpful in efficient control and prevention of Shigella infections.