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Background  Outbreak of  V. parahaemolyticus  infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of  V. parahaemolyticus . In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of  V. parahaemolyticus .    Results  Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5), and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested ( trh  - ,  tdh  +  and GS-PCR + ), while C2 contained 12 pre-1996 'old' O3:K6 strains ( trh  + ,  tdh  -  and GS-PCR - ) tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18) might be emerged from the old-O3:K6 clone, which was promoted by acquisition of  toxRS /new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade ( trh  - ,  tdh  -  and GS-PCR + ) was identified between the pandemic and old-O3:K6 clones.    Conclusion  A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of  V. parahaemolyticus  and an evolutionary history of the pandemic group (clone) of this pathogen.

Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'