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Volume 17, Number 11—November 2011


THEME ISSUE
CHOLERA IN HAITI
Research

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

Aleisha R. Reimer, Gary Van Domselaar, Steven Stroika, Matthew Walker, Heather Kent, Cheryl Tarr, Deborah Talkington, Lori A. Rowe, Melissa Olsen-Rasmussen, Michael Frace, Scott A. Sammons, Georges Anicet Dahourou, Jacques Boncy, Anthony M. Smith, Philip Mabon, Aaron Petkau, Morag Graham, Matthew W. Gilmour, Peter Gerner-SmidtComments to Author , and the V. cholerae Outbreak Genomics Task Force
Author affiliations: Author affiliations: Public Health Agency of Canada, Winnipeg, Manitoba, Canada (A.R. Reimer, G. Van Domselaar, M. Walker, H. Kent, P. Mabon, A. Petkau, M. Graham, M.W. Gilmour); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S. Stroika, C. Tarr, D. Talkington, L. Rowe, M. Olsen-Rasmussen, M. Frace, S. Sammons, P. Gerner-Smidt); Centers for Disease Control and Prevention, Port-au-Prince, Haiti (G.A. Dahourou); Ministry of Public Health and Population, Port-au-Prince (J. Boncy); National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith)

Main Article

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 re

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.

Main Article

References
  1. Feng  L, Reeves  PR, Lan  R, Ren  Y, Gao  C, Zhou  Z, A recalibrated molecular clock and independent origins for the cholera pandemic clones. PLoS ONE. 2008;3:e4053. DOIPubMedGoogle Scholar
  2. Safa  A, Nair  GB, Kong  RY. Evolution of new variants of Vibrio cholerae O1. Trends Microbiol. 2010;18:46–54. DOIPubMedGoogle Scholar
  3. Nguyen  BM, Lee  JH, Cuong  NT, Choi  SY, Hien  NT, Anh  DD, 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. DOIPubMedGoogle Scholar
  4. Grim  CJ, Hasan  NA, Taviani  E, Haley  B, Chun  J, Brettin  TS, 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. DOIPubMedGoogle Scholar
  5. 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_25july2011.pdf.
  6. Centers for Disease Control and Prevention. Update on cholera—Haiti, Dominican Republic, and Florida, 2010. MMWR Morb Mortal Wkly Rep. 2010;59:1637–41.PubMedGoogle Scholar
  7. Gilmour  MW, Martel-Laferrière  V, Lévesque  S, Gaudreau  C, Bekal  S, Nadon  C, Vibrio cholerae in traveler from Haiti to Canada. Emerg Infect Dis. 2011;17:1124–5.PubMedGoogle Scholar
  8. Talkington  D, Bopp  C, Tarr  C, Parsons  MB, Dahourou  G, Freeman  M, Characterization of toxigenic Vibrio cholerae from Haiti, 2010–2011. Emerg Infect Dis. 2011;17:2122–9.
  9. Chin  CS, Sorenson  J, Harris  JB, Robins  WP, Charles  RC, Jean-Charles  RR, The origin of the Haitian cholera outbreak strain. N Engl J Med. 2011;364:33–42. DOIPubMedGoogle Scholar
  10. Archer  BN, Cengimbo  A, De Jong  GM, Keddy  KH, Smith  AM, Sooka  A, Cholera outbreak in South Africa: preliminary descriptive epidemiology on laboratory-confirmed cases, 15 November 2008 to 30 April 2009. Communicable Diseases Surveillance Bulletin. 2009;7:3–8.
  11. Sakazaki  R, Shimada  T. Serovars of Vibrio cholerae identified during 1970–1975. Jpn J Med Sci Biol. 1977;30:279–82.PubMedGoogle Scholar
  12. Sakazaki  R, Tamura  K, Gomez  CZ, Sen  R. Serological studies on the cholera group of vibrios. Jpn J Med Sci Biol. 1970;23:13–20.PubMedGoogle Scholar
  13. Heidelberg  JF, Eisen  JA, Nelson  WC, Clayton  RA, Gwinn  ML, Dodson  RJ, DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000;406:477–83. DOIPubMedGoogle Scholar
  14. Delcher  AL, Bratke  KA, Powers  EC, Salzberg  SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23:673–9. DOIPubMedGoogle Scholar
  15. Meyer  F, Goesmann  A, McHardy  AC, Bartels  D, Bekel  T, Clausen  J, GenDB–an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003;31:2187–95. DOIPubMedGoogle Scholar
  16. Darling  AE, Mau  B, Perna  NT. Progressive Mauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5:e11147. DOIPubMedGoogle Scholar
  17. Guindon  S, Delsuc  F, Dufayard  JF, Gascuel  O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol. 2009;537:113–37. DOIPubMedGoogle Scholar
  18. Thompson  JD, Higgins  DG, Gibson  TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673–80. DOIPubMedGoogle Scholar
  19. Anisimova  M, Gascuel  O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 2006;55:539–52. DOIPubMedGoogle Scholar
  20. Petkau  A, Stuart-Edwards  M, Stothard  P, Van Domselaar  G. Interactive microbial genome visualization with GView. Bioinformatics. 2010;26:3125–6. DOIPubMedGoogle Scholar
  21. Mason  PR. Zimbabwe experiences the worst epidemic of cholera in Africa. J Infect Dev Ctries. 2009;3:148–51. DOIPubMedGoogle Scholar
  22. Chun  J, Grim  CJ, Hasan  NA, Je  HL, Seon  YC, Haley  BJ, Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A. 2009;106:15442–7. DOIPubMedGoogle Scholar
  23. Olsvik  O, Wahlberg  J, Petterson  B, Uhlen  M, Popovic  T, Wachsmuth  IK, Use of automated sequencing of polymerase chain reaction–generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains. J Clin Microbiol. 1993;31:22–5.PubMedGoogle Scholar
  24. Gilmour  MW, Graham  M, Van Domselaar  G, Tyler  S, Kent  H, Trout-Yakel  KM, High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics. 2010;11:120.PubMedGoogle Scholar
  25. Gardy  JL, Johnston  JC, Ho Sui  SJ, Cook  VJ, Shah  L, Brodkin  E, Whole genome sequencing and social network analysis of a tuberculosis outbreak. N Engl J Med. 2011;364:730–9. DOIPubMedGoogle Scholar
  26. Taboada  EN, van Belkum  A, Yuki  N, Acedillo  RR, Godschalk  PC, Koga  M, Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity. BMC Genomics. 2007;8:359. DOIPubMedGoogle Scholar
  27. Cho  YJ, Yi  H, Lee  JH, Kim  DW, Chun  J. Genomic evolution of Vibrio cholerae. Curr Opin Microbiol. 2010;13:646–51. DOIPubMedGoogle Scholar
  28. Croucher  NJ, Harris  SR, Fraser  C, Quail  MA, Burton  J, van der Linden  M, Rapid pneumococcal evolution in response to clinical interventions. Science. 2011;331:430–4. DOIPubMedGoogle Scholar
  29. Goel  AK, Jain  M, Kumar  P, Bhadauria  S, Kmboj  DV, Singh  L. A new variant of Vibrio cholerae O1 El Tor causing cholera in India. J Infect. 2008;57:280–1. DOIPubMedGoogle Scholar
  30. Quilici  ML, Massenet  D, Gake  B, Bwalki  B, Olson  DM. Vibrio cholerae O1 variant with reduced susceptibility to ciprofloxacin, western Africa. Emerg Infect Dis. 2010;16:1804–5.PubMedGoogle Scholar

Main Article

1Members of the V. cholerae Outbreak Genomics Task Force are Arunmozhi Balajee, Shanna Bolcen, Cheryl A. Bopp, John Besser, Ifeoma Ezeoke, Patricia Fields, Molly Freeman, Lori Gladney, Dhwani Govil, Michael S. Humphrys, Maria Sjölund-Karlsson, Karen H. Keddy, Elizabeth Neuhaus, Michele M. Parsons, Efrain Ribot, Maryann Turnsek, Shaun Tyler, Jean M. Whichard, Anne Whitney, and the authors.

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