The Origin of the Haitian Cholera Outbreak Strain

By Chen-Shan Chin, J. Sorenson, J. Harris, W. Robins, R. Charles, Roger R Jean-Charles, James H. Bullard, Dale R. Webster, Andrew Kasarskis, P. Peluso and 6 more. New England Journal of Medicine, 2010

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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.)

Subfields: Endocrinology, Genetics, Molecular Biology

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Citations in the corpus

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The Pangenome: Diversity, Dynamics and Evolution of Genomes (2020, background): “A pangenomic analysis revealed that the epidemic was caused by strains originated in Southeast Asia (Reimer et al. 2011; Hendriksen et al. 2011; Chin et al. 2011; Mutreja et al. 2011; Orata et al. 2014; Hasan et al. 2012).”
PBSIM: PacBio reads simulator - toward accurate genome assembly (2013, methodology): “In addition, we conducted hybrid error correction and assembly tests for datasets simulated by PBSIM, suggesting that a CLR coverage depth of at least 15 in combination with a CCS coverage depth of at least 30 achieved extensive assembly results.”
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Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels (2012, background): “5–5% [20,21,25,28] on Roche, Illumina, and Applied Biosystems platforms to 18% on the Pacific Biosciences platform [23].”
Evidence for multiple waves of global transmission within the seventh cholera pandemic (2011, methodology): “we followed the rationale: (1) For CTX-1 to CTX-2, because there was a shift of rstR Tor to rstR, rstA Tor to rstA 1 El Tor and ctxB Tor to ctxB, we called it CTX-2; (2) for CTX-1 to CTX-3, because there was a shift of ctxB Tor to ctxB, we called it CTX-3; (3) for CTX-3 to CTX-3b, because there was ”
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