Abstract
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 GIVchS12) 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, GIVchS12 contains a CRISPR-Cas element and a type VI secretion system (T6SS). GIs similar to GIVchS12 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.
Highlights
Cholera is a devastating diarrhoeal disease caused by certain strains of serogroup O1/O139 Vibrio cholerae
There have been seven pandemics of cholera, with the current seventh pandemic caused by O1 strains of the El Tor biotype and the sixth and presumably the previous five pandemics caused by O1 strains of the classical biotype[1]
The evolution of pandemic strains has been greatly influenced by lateral gene transfer (LGT), which led to the acquisition of many novel virulence factors[3]
Summary
Growth conditions, and molecular biology methods. The non-O1/O139 V. cholerae S12 strain was isolated from the Georges River (Sydney, Australia) in 200927 and routinely cultured on LuriaBertani medium at 37 °C. Analysis of GIVchS12 on contig 000009 identified three assembly gaps between ORFs 13 and 15 due to a putative repeat of ORF14 (annotated as ORF14a and ORF14b). To confirm this repeat, a PCR with primers Gap_F1 and Gap_R1 that anneal outside of this repeat region (see Fig. 1) resulted in an expected ~2.5 kb product (as opposed to a ~1.3–1.5 kb product if only one copy of ORF14 was present). The raw Illumina HiSeq sequencing reads are available under accession number ERR063652 and the improved draft genome assembly of V. cholerae S12 can be accessed at MDST00000000
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