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Background   Shigella  bacteria cause dysentery, which remains a significant threat to public health.  Shigella flexneri  is the most common species in both developing and developed countries. Five  Shigella  genomes have been sequenced, revealing dynamic and diverse features. To investigate the intra-species diversity of  S. flexneri  genomes further, we have sequenced the complete genome of  S. flexneri  5b strain 8401 (abbreviated Sf8401) and compared it with  S. flexneri  2a (Sf301).    Results  The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of Sf301, mainly because the former lacks the SHI-1 pathogenicity island (PAI). Compared with Sf301, there are 6 inversions and one translocation in Sf8401, which are probably mediated by insertion sequences (IS). There are clear differences in the known PAIs between these two genomes. The bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from Sf8401 but a specific related protein is found next to the  pheV  locus. SHI-2 is involved in one intra-replichore inversion near the origin of replication, which may change the expression of  iut/iuc  genes. Moreover, genes related to the glycine-betaine biosynthesis pathway are present only in Sf8401 among the known  Shigella  genomes.    Conclusion  Our data show that the two  S. flexneri  genomes are very similar, which suggests a high level of structural and functional conservation between the two serotypes. The differences reflect different selection pressures during evolution. The ancestor of  S. flexneri  probably acquired SHI-1 and SHI-2 before SHI-O was integrated and the serotypes diverged. SHI-1 was subsequently deleted from the  S. flexneri  5b genome by recombination, but stabilized in the  S. flexneri  2a genome. These events may have contributed to the differences in pathogenicity and epidemicity between the two serotypes of  S. flexneri .

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a