Genome Sequence of Vibrio cholerae G4222, a South African Clinical Isolate

Abstract

Vibrio cholerae, a Gram-negative pathogen autochthonous to the aquatic environment, is the causative agent of cholera. Here, we report the complete genome sequence of V. cholerae G4222, a clinical isolate from South Africa.

GENOME ANNOUNCEMENT

Vibrio cholerae is the causative agent of cholera, a severe diarrheal disease that remains a socioeconomic burden in many developing countries (1). As such, the species, also widely regarded as a model organism for studies pertaining to water-borne pathogens, has received much attention (2). Among other foci, emphasis has been placed on defining serotypes and biotypes in an attempt to understand this rapidly evolving pathogen (3). However, with the discoveries of intraspecies serogroup transfer and contradicting biotype-related phenotypes, the focus has shifted away from classic diagnostic markers to genome-based comparisons with an emphasis on mobile elements (3, 4). To this end, the genome sequence of V. cholerae G4222, a clinical O1 isolate obtained in South Africa during the 2000-2001 epidemic, was determined. This represents the first genome of a South African V. cholerae strain. In light of the dearth of African V. cholerae strain sequences and the recent discovery of new recombinant V. cholerae biotypes in southern Africa, this genome might provide valuable insights into the evolution of this pathogen (5, 6). Furthermore, the genome sequence of this strain may contribute to the understanding of the V. cholerae mobilome.

The genome was sequenced using a Roche 454 GS-FLX sequencer at Inqaba Biotec, South Africa. A total of 201,286 reads with an average read length of 236 bp were obtained, giving a total of 47,503,496 nucleotides and genome coverage of 11.6×. The reads were assembled into 280 contigs using Newbler assembler v2.6 (454 Life Sciences). These contigs were then scaffolded by alignment against the complete genome sequences of V. cholerae MJ-1236 (7) and V. cholerae O1 biovar El Tor strain N16961 (8) with the NCBI Genomic (NG) Aligner tool of the NCBI Genome Workbench v2.5.5. A further 38 gaps were closed by PCR amplification and Sanger sequencing. This resulted in the assembly of the V. cholerae G4222 genome sequence into a total of 21 contigs. Protein-coding sequence (CDS) prediction and functional annotation of the predicted proteins were done using the Rapid Annotations using Subsystems Technology (RAST) Web server (9) before manual curation was performed.

The V. cholerae G4222 contigs could be scaffolded into two distinct chromosomes, as is typical of V. cholerae strains (10). Chromosome I consists of 14 contigs amounting to a total length of 3,139,654 bp, with an average G+C content of 47.72% and 2,809 annotated CDS. Chromosome II consists of seven contigs with a total length of 1,061,058 bp and a G+C content of 46.88%, with 1,051 CDS annotated. The chromosome sizes and G+C compositions correlate well with those of other V. cholerae strains (6, 8). An ~150-kb integrative conjugative element (ICE), belonging to the SXT family, is located on chromosome I of V. cholerae G4222 and carries the genes involved in multiple-drug resistance. Given that an African origin for SXT-related ICEs in V. cholerae strains has been proposed, the genome of V. cholerae G4222 provides further opportunity to investigate the evolution of SXT elements (11). The strain might also provide insights into the biology of South African epidemic V. cholerae strains.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ANNB00000000. The version described in this paper is the first version, ANNB01000000.