The Origin of the Haitian Cholera Outbreak Strain

TLDR

Cholera has circulated in Latin America since 1991 but had not caused an epidemic in Haiti for at least a century. The authors sequenced the genomes of two Haitian outbreak isolates, a 1991 Latin American strain, and two South Asian strains using third‑generation single‑molecule real‑time sequencing, then compared these and 23 additional V. cholerae genomes to trace the outbreak’s origin. Genomic analysis shows the Haitian isolates are closely related to Bangladeshi El Tor O1 strains from 2002 and 2008, but only distantly related to South American strains, indicating the epidemic likely arose from a human‑mediated introduction of a distant strain.

Abstract

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.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.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.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.).