title: The origin of the Haitian cholera outbreak strain.
abstract: BACKGROUND
  Although cholera has been present in Latin America since 1991, it had not been epidemic in Haiti for at least 100 years. Recently, however, there has been a severe outbreak of cholera in Haiti.
  
  
  METHODS
  We used third-generation single-molecule real-time DNA sequencing to determine the genome sequences of 2 clinical Vibrio cholerae isolates from the current outbreak in Haiti, 1 strain that caused cholera in Latin America in 1991, and 2 strains isolated in South Asia in 2002 and 2008. Using primary sequence data, we compared the genomes of these 5 strains and a set of previously obtained partial genomic sequences of 23 diverse strains of V. cholerae to assess the likely origin of the cholera outbreak in Haiti.
  
  
  RESULTS
  Both single-nucleotide variations and the presence and structure of hypervariable chromosomal elements indicate that there is a close relationship between the Haitian isolates and variant V. cholerae El Tor O1 strains isolated in Bangladesh in 2002 and 2008. In contrast, analysis of genomic variation of the Haitian isolates reveals a more distant relationship with circulating South American isolates.
  
  
  CONCLUSIONS
  The Haitian epidemic is probably the result of the introduction, through human activity, of a V. cholerae strain from a distant geographic source. (Funded by the National Institute of Allergy and Infectious Diseases and the Howard Hughes Medical Institute.).
authors.affiliation: Pacific Biosciences, Menlo Park, CA, USA.
authors.forename: Chen-Shan
authors.initials: CS
authors.lastname: Chin
authors.forename: Jon
authors.initials: J
authors.lastname: Sorenson
authors.forename: Jason B
authors.initials: JB
authors.lastname: Harris
authors.forename: William P
authors.initials: WP
authors.lastname: Robins
authors.forename: Richelle C
authors.initials: RC
authors.lastname: Charles
authors.forename: Roger R
authors.initials: RR
authors.lastname: Jean-Charles
authors.forename: James
authors.initials: J
authors.lastname: Bullard
authors.forename: Dale R
authors.initials: DR
authors.lastname: Webster
authors.forename: Andrew
authors.initials: A
authors.lastname: Kasarskis
authors.forename: Paul
authors.initials: P
authors.lastname: Peluso
authors.forename: Ellen E
authors.initials: EE
authors.lastname: Paxinos
authors.forename: Yoshiharu
authors.initials: Y
authors.lastname: Yamaichi
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Calderwood
authors.forename: John J
authors.initials: JJ
authors.lastname: Mekalanos
authors.forename: Eric E
authors.initials: EE
authors.lastname: Schadt
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Waldor
mesh_terms: D002771:Cholera / Q000453:epidemiology / Q000382:microbiology*; D002874:Chromosome Mapping; D004196:Disease Outbreaks; D005243:Feces / Q000382:microbiology; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D006205:Haiti / Q000453:epidemiology; D049671:History, 18th Century; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012703:Serotyping; D014734:Vibrio cholerae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D041241:Vibrio cholerae O1 / Q000235:genetics