Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa - PubMed (original) (raw)

. 2011 Nov;17(11):2113-21.

doi: 10.3201/eid1711.110794.

Gary Van Domselaar, Steven Stroika, Matthew Walker, Heather Kent, Cheryl Tarr, Deborah Talkington, Lori Rowe, Melissa Olsen-Rasmussen, Michael Frace, Scott Sammons, Georges Anicet Dahourou, Jacques Boncy, Anthony M Smith, Philip Mabon, Aaron Petkau, Morag Graham, Matthew W Gilmour, Peter Gerner-Smidt; V. cholerae Outbreak Genomics Task Force

Collaborators, Affiliations

Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa

Aleisha R Reimer et al. Emerg Infect Dis. 2011 Nov.

Abstract

Cholera was absent from the island of Hispaniola at least a century before an outbreak that began in Haiti in the fall of 2010. Pulsed-field gel electrophoresis (PFGE) analysis of clinical isolates from the Haiti outbreak and recent global travelers returning to the United States showed indistinguishable PFGE fingerprints. To better explore the genetic ancestry of the Haiti outbreak strain, we acquired 23 whole-genome Vibrio cholerae sequences: 9 isolates obtained in Haiti or the Dominican Republic, 12 PFGE pattern-matched isolates linked to Asia or Africa, and 2 nonmatched outliers from the Western Hemisphere. Phylogenies for whole-genome sequences and core genome single-nucleotide polymorphisms showed that the Haiti outbreak strain is genetically related to strains originating in India and Cameroon. However, because no identical genetic match was found among sequenced contemporary isolates, a definitive genetic origin for the outbreak in Haiti remains speculative.

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Figures

Figure 1

Figure 1

Whole-genome neighbor-joining tree of Vibrio cholerae isolate from cholera outbreak in Haiti, fall 2010; concurrent clinical isolates with pulsed-field gel electrophoresis pattern-matched combinations; reference isolates sequenced in this study; and available reference sequences. Sequence alignments of quality draft or complete genomes were performed by using Progressive Mauve (16) and visualized by using PhyML version 3.0 (17). Whole-genome relationship of Haiti isolates with closest genetic relatives is shown in the inset. Scale bar indicates nucleotides substitutions per site.

Figure 2

Figure 2

BLAST (

http://blast.ncbi.nlm.gov/Blast.cgi

) atlas of predicted protein homologies mapped against the closed genome of Haiti Vibrio cholerae outbreak type isolate 2010EL-1786, fall 2010. Full color saturation represents 100% sequence homology, and gaps indicate regions of divergence. Gaps in the innermost (red) circle for reference isolate 2010EL-1786 represent gaps between coding sequences, not genetic diversity. A) Chromosome I; B) chromosome II. From center: Haiti/Dominican Republic isolates 2010EL-1786, 2010EL-1961, 2011EL-1089, 2010EL-2010N, 2010EL-2010H, 2011V-1021, 2010EL-1798, 2010EL-1792, and 2011EL-1133; Cameroon isolate 2010EL-1749; India isolates 2009V-1085, 2009V-1096, 2009V-1131, 3546–06, and 3500–05; Nepal isolate 3554–08; Pakistan isolates 3582–05, 2009V-1046, 2010-V1014, and 2009V-1116; South Africa isolate 2011EL-1137; Bangladesh isolates CIRS101, MJ-1236 and N16961; and other isolates C6706, M66–2, and 3569–08.

Figure 3

Figure 3

Genetic structure of cholera toxin (CTX) prophage and associated elements in Haiti cholera outbreak Vibrio cholerae isolate 2010EL-1786, fall 2010. The toxin-linked cryptic (TLC) element is not drawn to scale. Black arrows indicate the direction of transcription for each coding region. Red, forward transcription; blue, reverse transcription; gray, predicted open reading frame with no experimental evidence.

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References

    1. Feng L, Reeves PR, Lan R, Ren Y, Gao C, Zhou Z, et al. A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS ONE. 2008;3:e4053. 10.1371/journal.pone.0004053 - DOI - PMC - PubMed
    1. Safa A, Nair GB, Kong RY. Evolution of new variants of Vibrio cholerae O1. Trends Microbiol. 2010;18:46–54. 10.1016/j.tim.2009.10.003 - DOI - PubMed
    1. Nguyen BM, Lee JH, Cuong NT, Choi SY, Hien NT, Anh DD, et al. Cholera outbreaks caused by an altered Vibrio cholerae O1 El Tor biotype strain producing classical cholera toxin B in Vietnam in 2007 to 2008. J Clin Microbiol. 2009;47:1568–71. 10.1128/JCM.02040-08 - DOI - PMC - PubMed
    1. Grim CJ, Hasan NA, Taviani E, Haley B, Chun J, Brettin TS, et al. Genome sequence of hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and comparative genomics with V. cholerae. J Bacteriol. 2010;192:3524–33. 10.1128/JB.00040-10 - DOI - PMC - PubMed
    1. Pan American Health Organization. Cholera and post-earthquake response in Haiti, 2011. Jul 25 [cited 2011 Aug 6]. http://www.who.int/hac/crises/hti/sitreps/haiti_health_cluster_bulletin_....

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