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Cholera is a devastating diarrhoeal disease caused by certain strains of serogroup O1/O139  Vibrio cholerae . Mobile genetic elements such as genomic islands (GIs) have been pivotal in the evolution of O1/O139  V. cholerae . Perhaps the most important GI involved in cholera disease is the  V. cholerae  pathogenicity island 1 (VPI-1). This GI contains the toxin-coregulated pilus (TCP) gene cluster that is necessary for colonization of the human intestine as well as being the receptor for infection by the cholera-toxin bearing CTX phage. In this study, we report a GI (designated GI Vch S12) from a non-O1/O139 strain of  V. cholerae  that is present in the same chromosomal location as VPI-1, contains an integrase gene with 94% nucleotide and 100% protein identity to the VPI-1 integrase, and attachment ( att ) sites 100% identical to those found in VPI-1. However, instead of TCP and the other accessory genes present in VPI-1, GI Vch S12 contains a CRISPR-Cas element and a type VI secretion system (T6SS). GIs similar to GI Vch S12 were identified in other  V. cholerae  genomes, also containing CRISPR-Cas elements and/or T6SS’s. This study highlights the diversity of GIs circulating in natural  V. cholerae  populations and identifies GIs with VPI-1 recombination characteristics as a propagator of CRISPR-Cas and T6SS modules.

A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules