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Review
. 2014:379:211-29.
doi: 10.1007/82_2014_366.

Genomic science in understanding cholera outbreaks and evolution of Vibrio cholerae as a human pathogen

Affiliations
Review

Genomic science in understanding cholera outbreaks and evolution of Vibrio cholerae as a human pathogen

William P Robins et al. Curr Top Microbiol Immunol. 2014.

Abstract

Modern genomic and bioinformatic approaches have been applied to interrogate the V. cholerae genome, the role of genomic elements in cholera disease, and the origin, relatedness, and dissemination of epidemic strains. A universal attribute of choleragenic strains includes a repertoire of pathogenicity islands and virulence genes, namely the CTXφ prophage and Toxin Co-regulated Pilus (TCP) in addition to other virulent genetic elements including those referred to as Seventh Pandemic Islands. During the last decade, the advent of Next Generation Sequencing (NGS) has provided highly resolved and often complete genomic sequences of epidemic isolates in addition to both clinical and environmental strains isolated from geographically unconnected regions. Genomic comparisons of these strains, as was completed during and following the Haitian outbreak in 2010, reveals that most epidemic strains appear closely related, regardless of region of origin. Non-O1 clinical or environmental strains may also possess some virulence islands, but phylogenic analysis of the core genome suggests they are more diverse and distantly related than those isolated during epidemics. Like Haiti, genomic studies that examine both the Vibrio core and pan-genome in addition to Single Nucleotide Polymorphisms (SNPs) conclude that a number of epidemics are caused by strains that closely resemble those in Asia, and often appear to originate there and then spread globally. The accumulation of SNPs in the epidemic strains over time can then be applied to better understand the evolution of the V. cholerae genome as an etiological agent.

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Figures

Fig. 1
Fig. 1
Genome blast atlas created with CMG Biotools (Vesth et al. 2013) showing the aligned genomes of a panel of V. cholerae clinical and environmental isolates using the 2010 Haiti epidemic strain as reference. Genomes are colored by both biotype and source and also match genomes analyzed in the Fig. 2. Seventh pandemic islands and Superintegron are labeled on both chromosomes
Fig. 2
Fig. 2
The bootstrap consensus tree (Neighbor-Joining) inferred from 500 replicates for a small diverse sample of O1 and non-O1 strains (a) and for a collection of clinical and environmental strains (b). Core genomes were extrapolated using CMG-biotools 2.2, aligned using MAAFT (vs 7.127), and trees were calculated and produced using MEGA (vs 5.10). Genomes are colored by biotype and source. CMG Biotools (vs 2.2, Vesth et al. 2013), MAAFT (vs 7.127, Katoh and Standely 2013) MEGA (vs 5.10, Hall 2013)
Fig. 3
Fig. 3
Different arrangement of CTX/RS1 region in El Tor, classical and variant strains (a). The amino acid variation in ctxB gene (b) is used to generate phylogenic tree based on the alignment of ctxB variants (c)

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