High Depth, Whole-Genome Sequencing of Cholera Isolates from Haiti and the Dominican Republic

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High Depth, Whole-Genome Sequencing of Cholera Isolates from Haiti and the Dominican Republic

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dc.contributor.author Sealfon, Rachel
dc.contributor.author Gire, Stephen
dc.contributor.author Ellis, Crystal Nicole
dc.contributor.author Calderwood, Stephen Beaven
dc.contributor.author Qadri, Firdausi
dc.contributor.author Hensley, Lisa
dc.contributor.author Kellis, Manolis
dc.contributor.author Ryan, Edward Thomas
dc.contributor.author Larocque, Regina Celes
dc.contributor.author Harris, Jason B.
dc.contributor.author Sabeti, Pardis Christine
dc.date.accessioned 2012-11-13T18:53:11Z
dc.date.issued 2012
dc.identifier.citation Sealfon, Rachel, Stephen Gire, Crystal Ellis, Stephen Calderwood, Firdausi Qadri, Lisa Hensley, Manolis Kellis, et al. 2012. High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic. BMC Genomics 13:468. en_US
dc.identifier.issn 1471-2164 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:9891816
dc.description.abstract Background: Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole- genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced. Results: Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Conclusions: Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic. en_US
dc.description.sponsorship Organismic and Evolutionary Biology en_US
dc.language.iso en_US en_US
dc.publisher BioMed Central en_US
dc.relation.isversionof doi:10.1186/1471-2164-13-468 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pubmed/22963323 en_US
dash.license OAP
dc.subject whole-genome sequencing en_US
dc.subject Vibrio cholerae en_US
dc.subject Haitian cholera epidemic en_US
dc.subject microbial evolution en_US
dc.title High Depth, Whole-Genome Sequencing of Cholera Isolates from Haiti and the Dominican Republic en_US
dc.type Journal Article en_US
dc.description.version Accepted Manuscript en_US
dc.relation.journal BMC Genomics en_US
dash.depositing.author Sabeti, Pardis Christine
dc.date.available 2012-11-13T18:53:11Z

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  • FAS Scholarly Articles [7362]
    Peer reviewed scholarly articles from the Faculty of Arts and Sciences of Harvard University

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