{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T11:10:23Z","timestamp":1791285023708,"version":"4.1.0"},"reference-count":44,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2013,7,2]],"date-time":"2013-07-02T00:00:00Z","timestamp":1372723200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"},{"start":{"date-parts":[[2013,8,30]],"date-time":"2013-08-30T00:00:00Z","timestamp":1377820800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2013,8,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of\n                    <jats:named-content content-type=\"genus-species\">Vibrio cholerae<\/jats:named-content>\n                    O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and &gt;7,500 deaths in the first two\u00a0years of the epidemic. We applied whole-genome sequencing to a temporal series of\n                    <jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>\n                    isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of\n                    <jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>\n                    O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent\n                    <jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>\n                    isolates, each expressed\n                    <jats:italic>hapR<\/jats:italic>\n                    and possessed a functional quorum-sensing system. Continued monitoring of\n                    <jats:named-content content-type=\"genus-species\">V. cholerae<\/jats:named-content>\n                    in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:bold>IMPORTANCE<\/jats:bold>\n                    <jats:named-content content-type=\"genus-species\">Vibrio cholerae<\/jats:named-content>\n                    is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of\n                    <jats:named-content content-type=\"genus-species\">Vibrio cholerae<\/jats:named-content>\n                    O1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.\n                  <\/jats:p>","DOI":"10.1128\/mbio.00398-13","type":"journal-article","created":{"date-parts":[[2013,7,3]],"date-time":"2013-07-03T00:39:14Z","timestamp":1372811954000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":106,"title":["Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti"],"prefix":"10.1128","volume":"4","author":[{"given":"Lee S.","family":"Katz","sequence":"first","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron","family":"Petkau","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Beaulaurier","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaun","family":"Tyler","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena S.","family":"Antonova","sequence":"additional","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryann A.","family":"Turnsek","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Guo","sequence":"additional","affiliation":[{"name":"Pacific Biosciences, Menlo Park, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Wang","sequence":"additional","affiliation":[{"name":"Pacific Biosciences, Menlo Park, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellen E.","family":"Paxinos","sequence":"additional","affiliation":[{"name":"Pacific Biosciences, Menlo Park, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabini","family":"Orata","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lori M.","family":"Gladney","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Stroika","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason P.","family":"Folster","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lori","family":"Rowe","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly M.","family":"Freeman","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Knox","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Frace","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Boncy","sequence":"additional","affiliation":[{"name":"National Public Health Laboratory, Port-au-Prince, Haiti"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morag","family":"Graham","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian K.","family":"Hammer","sequence":"additional","affiliation":[{"name":"School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Boucher","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Bashir","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, New York, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William P.","family":"Hanage","sequence":"additional","affiliation":[{"name":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard University, Boston, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary","family":"Van Domselaar","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheryl L.","family":"Tarr","sequence":"additional","affiliation":[{"name":"Centers for Disease Control and Prevention, Atlanta, Georgia, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.272.5270.1910"},{"key":"e_1_3_2_3_2","first-page":"1001","article-title":"Cholera","volume":"58","author":"Pollitzer R","year":"1959","unstructured":"PollitzerR SwaroopS BurrowsW . 1959. Cholera. Monogr. S. World Health Organ. 58:1001\u20131019.","journal-title":"Monogr. S. World Health Organ."},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10392"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1711.110958"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1204927"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1012928"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1711.110794"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.2012.03841.x"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00157-11"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1207359109"},{"key":"e_1_3_2_12_2","first-page":"309","article-title":"Notes from the field: identification of Vibrio cholerae serogroup O1, serotype Inaba, biotype El Tor strain\u2014Haiti, March 2012","volume":"61","author":"Centers for Disease Control and Prevention","year":"2012","unstructured":"Centers for Disease Control and Prevention . 2012. Notes from the field: identification of Vibrio cholerae serogroup O1, serotype Inaba, biotype El Tor strain\u2014Haiti, March 2012. MMWR Morb. Mortal. Wkly. Rep. 61:309.","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.7.2566"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1120096"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2011.02328.x"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.2012.11-0435"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000786"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1711.110720"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0907787106"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/35012500"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00452-12"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02040-08"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00040-10"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2008.06.015"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0056477"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2009.10.003"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1711.110805"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.64.7.2853-2856.1996"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1106920"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq284"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.074492.107"},{"key":"e_1_3_2_32_2","first-page":"313","article-title":"SMALT\u2014a new mapper for DNA sequencing reads","volume":"1","author":"Ponstingl H","year":"2010","unstructured":"PonstinglH NingZ . 2010. SMALT\u2014a new mapper for DNA sequencing reads. F1000 Posters 1:313.","journal-title":"F1000 Posters"},{"key":"e_1_3_2_33_2","unstructured":"GarrisonE\nMarthG\n. 2012. Haplotype-based variant detection from short-read sequencing. arXiv 1207.3907."},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syq010"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mss075"},{"key":"e_1_3_2_37_2","unstructured":"RambautA\n. 2009. Path-O-Gen. http:\/\/tree.bio.ed.ac.uk\/software\/pathogen."},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2474"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2288"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2280"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-13-238"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msr121"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12054"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(02)00829-2"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.00398-13","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.00398-13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T20:51:15Z","timestamp":1646686275000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mBio.00398-13"}},"subtitle":[],"editor":[{"given":"John","family":"Mekalanos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,8,30]]},"references-count":44,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2013,8,30]]}},"alternative-id":["10.1128\/mBio.00398-13"],"URL":"https:\/\/doi.org\/10.1128\/mbio.00398-13","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.718105125.793484432","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.718105125.793483554","asserted-by":"object"}]},"ISSN":["2161-2129","2150-7511"],"issn-type":[{"value":"2161-2129","type":"print"},{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,8,30]]},"assertion":[{"value":"2013-05-24","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-06-03","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-07-02","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00398-13"}}