{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T12:03:33Z","timestamp":1791633813018,"version":"4.3.4"},"update-to":[{"DOI":"10.1371\/journal.pntd.0007330","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,11]],"date-time":"2019-06-11T00:00:00Z","timestamp":1560211200000}}],"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T00:00:00Z","timestamp":1559174400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1148763"],"award-info":[{"award-number":["OPP1148763"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wellcome Trust","award":["098051"],"award-info":[{"award-number":["098051"]}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"DOI":"10.1371\/journal.pntd.0007330","type":"journal-article","created":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T17:24:51Z","timestamp":1559237091000},"page":"e0007330","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper"],"prefix":"10.1371","volume":"13","author":[{"given":"Ang\u00e8le H. M.","family":"B\u00e9nard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Etienne","family":"Guenou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Fookes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerome","family":"Ateudjieu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Watipaso","family":"Kasambara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Siever","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5099-1947","authenticated-orcid":true,"given":"Stanislas","family":"Rebaudet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Boncy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Adrien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renaud","family":"Piarroux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Sack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Thomson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4006-073X","authenticated-orcid":true,"given":"Amanda K.","family":"Debes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,5,30]]},"reference":[{"key":"ref1","unstructured":"A New Way to Calculate Costs of Infectious Diseases [Internet]. [cited 2018 Mar 23]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.centerforhealthsecurity.org\/about-the-center\/pressroom\/press_releases\/2013-05-07_ID_Cost_Calculator.html\" xlink:type=\"simple\">http:\/\/www.centerforhealthsecurity.org\/about-the-center\/pressroom\/press_releases\/2013-05-07_ID_Cost_Calculator.html<\/ext-link>"},{"issue":"6364","key":"ref2","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1126\/science.aad5901","article-title":"Genomic history of the seventh pandemic of cholera in Africa","volume":"358","author":"F-X Weill","year":"2017","journal-title":"Science"},{"issue":"6364","key":"ref3","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1126\/science.aao2136","article-title":"Integrated view of Vibrio cholerae in the Americas","volume":"358","author":"D Domman","year":"2017","journal-title":"Science"},{"key":"ref4","article-title":"Networking of Public Health Microbiology Laboratories Bolsters Europe\u2019s Defenses against Infectious Diseases","author":"B Albiger","year":"2018","journal-title":"Front Public Health"},{"issue":"5964","key":"ref5","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1126\/science.1182395","article-title":"Evolution of MRSA during hospital transmission and intercontinental spread","volume":"327","author":"SR Harris","year":"2010","journal-title":"Science"},{"issue":"7","key":"ref6","first-page":"474","article-title":"Molecular epidemiology of infectious diseases: a case for increased surveillance","volume":"81","author":"SE Hasnain","year":"2003","journal-title":"Bull World Health Organ"},{"issue":"8","key":"ref7","doi-asserted-by":"crossref","first-page":"e0181496","DOI":"10.1371\/journal.pone.0181496","article-title":"Antibiotics resistance in El Tor Vibrio cholerae 01 isolated during cholera outbreaks in Mozambique from 2012 to 2015","volume":"12","author":"LC Dengo-Baloi","year":"2017","journal-title":"PloS One"},{"issue":"3","key":"ref8","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1080\/21645515.2016.1245250","article-title":"Achievements and challenges for the use of killed oral cholera vaccines in the global stockpile era","volume":"04","author":"SN Desai","year":"2017","journal-title":"Hum Vaccines Immunother"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/infdis\/jiy283","article-title":"Micro-Hotspots of Risk in Urban Cholera Epidemics","volume":"218","author":"AS Azman","year":"2018","journal-title":"J Infect Dis"},{"issue":"10133","key":"ref10","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1016\/S0140-6736(17)33050-7","article-title":"Mapping the burden of cholera in sub-Saharan Africa and implications for control: an analysis of data across geographical scales","volume":"12","author":"J Lessler","year":"2018","journal-title":"Lancet Lond Engl"},{"issue":"3","key":"ref11","doi-asserted-by":"crossref","first-page":"537","DOI":"10.4269\/ajtmh.15-0496","article-title":"Clinical and Environmental Surveillance for Vibrio cholerae in Resource Constrained Areas: Application during a 1-Year Surveillance in the Far North Region of Cameroon","volume":"94","author":"AK Debes","year":"2016","journal-title":"Am J Trop Med Hyg"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"e0004307","DOI":"10.1371\/journal.pntd.0004307","article-title":"Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings","volume":"10","author":"AK Debes","year":"2016","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"ref13","doi-asserted-by":"crossref","first-page":"251","DOI":"10.4269\/ajtmh.16-0246a","article-title":"Direct Dried Stool Sampling on Filter Paper for Molecular Analyses of Cholera","volume":"95","author":"S Rebaudet","year":"2016","journal-title":"Am J Trop Med Hyg"},{"issue":"11","key":"ref14","doi-asserted-by":"crossref","first-page":"4145","DOI":"10.1128\/JCM.38.11.4145-4151.2000","article-title":"Rapid method for species-specific identification of Vibrio cholerae using primers targeted to the gene of outer membrane protein OmpW","volume":"38","author":"B Nandi","year":"2000","journal-title":"J Clin Microbiol"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1111\/j.1574-695X.1998.tb01128.x","article-title":"Development and evaluation of a multiplex PCR assay for rapid detection of toxigenic Vibrio cholerae O1 and O139","volume":"20","author":"K Hoshino","year":"1998","journal-title":"FEMS Immunol Med Microbiol"},{"key":"ref16","unstructured":"Wood EJ. Molecular cloning. A laboratory manual by T Maniatis, E F Fritsch and J Sambrook. pp 545. Cold Spring Harbor Laboratory, New York. 1982. $48 ISBN 0-87969-136-0. Biochem Educ [Internet]. 1983 [cited 2019 Jan 18];11(2):82\u201382. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1016\/0307-4412%2883%2990068-7\" xlink:type=\"simple\">https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1016\/0307-4412%2883%2990068-7<\/ext-link>"},{"key":"ref17","unstructured":"SMALT | Wellcome Sanger Institute [Internet]. [cited 2018 Mar 9]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.sanger.ac.uk\/science\/tools\/smalt-0\" xlink:type=\"simple\">http:\/\/www.sanger.ac.uk\/science\/tools\/smalt-0<\/ext-link>"},{"key":"ref18","unstructured":"Picard Tools\u2014By Broad Institute [Internet]. [cited 2018 Mar 9]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/broadinstitute.github.io\/picard\/\" xlink:type=\"simple\">http:\/\/broadinstitute.github.io\/picard\/<\/ext-link>"},{"issue":"14","key":"ref19","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"D1","key":"ref20","doi-asserted-by":"crossref","first-page":"D130","DOI":"10.1093\/nar\/gkr1079","article-title":"NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy","volume":"40","author":"KD Pruitt","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"16","key":"ref21","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref22","unstructured":"Bcftools by samtools [Internet]. [cited 2018 Mar 9]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/samtools.github.io\/bcftools\/\" xlink:type=\"simple\">https:\/\/samtools.github.io\/bcftools\/<\/ext-link>"},{"issue":"10","key":"ref23","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: sequence visualization and annotation","volume":"16","author":"K Rutherford","year":"2000","journal-title":"Bioinforma Oxf Engl"},{"issue":"16","key":"ref24","first-page":"3422","article-title":"ACT: the Artemis comparison tool. Bioinformatics","volume":"21","author":"TJ Carver","year":"2005","journal-title":"ACT: the Artemis comparison tool. Bioinformatics"},{"issue":"5","key":"ref25","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J Comput Biol J Comput Mol Cell Biol"},{"key":"ref26","unstructured":"ABACAS [Internet]. [cited 2018 Mar 9]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/abacas.sourceforge.net\/\" xlink:type=\"simple\">http:\/\/abacas.sourceforge.net\/<\/ext-link>"},{"key":"ref27","article-title":"metaSPAdes: a new versatile metagenomic assembler","author":"S Nurk","year":"2017","journal-title":"Genome Res"},{"issue":"7","key":"ref28","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1093\/bioinformatics\/btv697","article-title":"MetaQUAST: evaluation of metagenome assemblies","volume":"32","author":"A Mikheenko","year":"2016","journal-title":"Bioinforma Oxf Engl"},{"issue":"7","key":"ref29","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"DH Parks","year":"2015","journal-title":"Genome Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"DE Wood","year":"2014","journal-title":"Genome Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: Rapid Annotations using Subsystems Technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"BD Ondov","year":"2016","journal-title":"Genome Biol"},{"key":"ref33","article-title":"mashtree: Create a tree using Mash distances","author":"L Katz","year":"2018"},{"issue":"11","key":"ref34","doi-asserted-by":"crossref","first-page":"e000093","DOI":"10.1099\/mgen.0.000093","article-title":"Microreact: visualizing and sharing data for genomic epidemiology and phylogeography","volume":"2","author":"S Argim\u00f3n","year":"2016","journal-title":"Microb Genomics"},{"issue":"9","key":"ref35","doi-asserted-by":"crossref","first-page":"3296","DOI":"10.1128\/JCM.40.9.3296-3299.2002","article-title":"New Variants of Vibrio cholerae O1 Biotype El Tor with Attributes of the Classical Biotype from Hospitalized Patients with Acute Diarrhea in Bangladesh","volume":"40","author":"GB Nair","year":"2002","journal-title":"J Clin Microbiol"},{"issue":"2","key":"ref36","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1128\/IAI.74.2.927-930.2006","article-title":"Activation of the Vibrio cholerae SOS Response Is Not Required for Intestinal Cholera Toxin Production or Colonization","volume":"74","author":"M Quinones","year":"2006","journal-title":"Infect Immun"},{"issue":"24","key":"ref37","doi-asserted-by":"crossref","first-page":"6992","DOI":"10.1128\/JB.182.24.6992-6998.2000","article-title":"CTX Prophages in Classical Biotype Vibrio cholerae: Functional Phage Genes but Dysfunctional Phage Genomes","volume":"182","author":"BM Davis","year":"2000","journal-title":"J Bacteriol"},{"issue":"2","key":"ref38","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.bbadis.2004.06.006","article-title":"Lipopolysaccharides of Vibrio cholerae: II. Genetics of biosynthesis","volume":"1690","author":"SN Chatterjee","year":"2004","journal-title":"Biochim Biophys Acta BBA\u2014Mol Basis Dis"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.3389\/fmicb.2016.01250","article-title":"Phenotypic and Genetic Heterogeneity in Vibrio cholerae O139 Isolated from Cholera Cases in Delhi, India during 2001\u20132006","volume":"7","author":"R Ghosh","year":"2016","journal-title":"Front Microbiol"},{"issue":"5","key":"ref40","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.4269\/ajtmh.17-0296","article-title":"Molecular Epidemiology of Cholera Outbreaks during the Rainy Season in Mandalay, Myanmar","volume":"97","author":"A Roobthaisong","year":"2017","journal-title":"Am J Trop Med Hyg"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.3389\/fmicb.2015.01040","article-title":"Molecular tools in understanding the evolution of Vibrio cholerae","volume":"6","author":"MH Rahaman","year":"2015","journal-title":"Front Microbiol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1757-4749-5-1","article-title":"Metagenomic profile of gut microbiota in children during cholera and recovery","volume":"5","author":"S Monira","year":"2013","journal-title":"Gut Pathog"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0007330","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,11]],"date-time":"2019-06-11T00:00:00Z","timestamp":1560211200000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pntd.0007330","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,16]],"date-time":"2020-12-16T06:10:37Z","timestamp":1608099037000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0007330"}},"subtitle":[],"editor":[{"given":"Nicholas","family":"Feasey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,5,30]]},"references-count":42,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,5,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0007330","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pntd.0007330","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,30]]}}}