is the aetiological agent of the deadly diarrhoeal disease cholera. In this study the 7·5 kb seventh pandemic island-II (VSP-II) that is unique to El Tor and O139 serogroups was analysed and it was found to be part of a novel 26·9 kb genomic island (GEI) encompassing VC0490–VC0516. The low-GC-content VSP-II encompassed 24 predicted ORFs, including DNA repair and methyl-accepting chemotaxis proteins, a group of hypothetical proteins and a bacteriophage-like integrase adjacent to a tRNA gene. Interestingly, ORFs VC0493–VC0498, VC0504–VC0510 and VC0516, which encodes an integrase, were homologous to strain YJ016 ORFs VV0510–VV0516, VV0518–VV0525 and VV0560, which also encodes an integrase, respectively. Some ORFs showed amino acid identities greater than 90 % between the two species in these regions. In strain YJ016, a 43·4 kb low-GC-content (43 %) GEI encompassing ORFs VV0509–VV0560 was identified and named island-I (VVI-I). The 52 ORFs of VVI-I included a phosphotransferase system gene cluster, genes required for sugar metabolism and transposase genes. There was synteny and homology between the 5′ region of VSP-II and the 5′ region of VVI-I; however, VVI-I contained an additional 31·5 kb of DNA between VV0526 and VV0560 in strain YJ016. A second strain, CMCP6, did not contain the 43·4 kb VVI-I; in this strain two ORFs were found between the 5′ and 3′ flanking genes VV10636 and VV10632, showing 100 % identity to VV0508 and VV0561, respectively, which flank VVI-I.


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