{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T10:11:44Z","timestamp":1790417504423,"version":"4.1.0"},"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2011,9,13]],"date-time":"2011-09-13T00:00:00Z","timestamp":1315872000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"DOI":"10.1371\/journal.pntd.0001319","type":"journal-article","created":{"date-parts":[[2011,9,13]],"date-time":"2011-09-13T17:18:14Z","timestamp":1315934294000},"page":"e1319","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":75,"title":["Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar"],"prefix":"10.1371","volume":"5","author":[{"given":"Amy J.","family":"Vogler","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabien","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Roumagnac","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judy","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roxanne","family":"Nera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Eppinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"Ravel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lila","family":"Rahalison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno W.","family":"Rasoamanana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen M.","family":"Beckstrom-Sternberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Achtman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne","family":"Chanteau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Keim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2011,9,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1038\/ng.705","article-title":"<italic>Yersinia pestis<\/italic> genome sequencing identifies patterns of global phylogenetic diversity.","volume":"42","author":"G Morelli","year":"2010","journal-title":"Nat Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1128\/CMR.10.1.35","article-title":"<italic>Yersinia pestis<\/italic>-etiologic agent of plague.","volume":"10","author":"RD Perry","year":"1997","journal-title":"Clin Microbiol Rev"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"225","DOI":"10.3201\/eid0802.010164","article-title":"Public health assessment of potential biological terrorism agents.","volume":"8","author":"LD Rotz","year":"2002","journal-title":"Emerging infectious diseases"},{"key":"ref4","first-page":"40","article-title":"Human plague: review of regional morbidity and mortality, 2004\u20132009.","volume":"85","year":"2010","journal-title":"Wkly Epidemiol Rec"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1056\/NEJM199709043371004","article-title":"Multidrug resistance in <italic>Yersinia pestis<\/italic> mediated by a transferable plasmid.","volume":"337","author":"M Galimand","year":"1997","journal-title":"N Engl J Med"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e309","DOI":"10.1371\/journal.pone.0000309","article-title":"Multiple antimicrobial resistance in plague: an emerging public health risk.","volume":"2","author":"TJ Welch","year":"2007","journal-title":"PLoS One"},{"key":"ref7","first-page":"9","article-title":"Epid\u00e9miologie de la peste \u00e0 Madagascar.","volume":"35","author":"ER Brygoo","year":"1966","journal-title":"Arch Inst Pasteur Madagascar"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"101","DOI":"10.3201\/eid0401.980114","article-title":"Plague, a reemerging disease in Madagascar.","volume":"4","author":"S Chanteau","year":"1998","journal-title":"Emerg Infect Dis"},{"key":"ref9","first-page":"1","article-title":"The black rat&apos;s role in spreading human plague in Madagascar.","volume":"131","author":"JM Duplantier","year":"2001","journal-title":"L'Institut de recherche pour le d\u00e9veloppement Scientific Bulletin"},{"key":"ref10","first-page":"441","article-title":"The rodent problem in Madagascar: agricultural pest and threat to human health.","author":"JM Duplantier","year":"1999"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S1286-4579(00)00289-6","article-title":"Current epidemiology of human plague in Madagascar.","volume":"2","author":"S Chanteau","year":"2000","journal-title":"Microbes Infect"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1111\/j.1365-3156.2006.01677.x","article-title":"Epidemiological trends for human plague in Madagascar during the second half of the 20th century: a survey of 20,900 notified cases.","volume":"11","author":"R Migliani","year":"2006","journal-title":"Trop Med Int Health"},{"key":"ref13","first-page":"1","article-title":"Epid\u00e9mie de peste \u00e0 Majunga en 1991.","volume":"1991","author":"S Laventure","year":"1991","journal-title":"Rapport de mission de l'Institut Pasteur de Madagascar"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"311","DOI":"10.3201\/eid0803.010250","article-title":"Epidemiologic features of four successive annual outbreaks of bubonic plague in Mahajanga, Madagascar.","volume":"8","author":"P Boisier","year":"2002","journal-title":"Emerg Infect Dis"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1111\/j.1365-3156.1997.tb00163.x","article-title":"Urban epidemic of bubonic plague in Majunga, Madagascar: epidemiological aspects.","volume":"2","author":"P Boisier","year":"1997","journal-title":"Trop Med Int Health"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1016\/S0140-6736(95)92944-4","article-title":"Plague in Majunga, Madagascar.","volume":"346","author":"M Rasolomaharo","year":"1995","journal-title":"Lancet"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1051\/vetres:2005007","article-title":"From the recent lessons of the Malagasy foci towards a global understanding of the factors involved in plague reemergence.","volume":"36","author":"JM Duplantier","year":"2005","journal-title":"Vet Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"14043","DOI":"10.1073\/pnas.96.24.14043","article-title":"<italic>Yersinia pestis<\/italic>, the cause of plague, is a recently emerged clone of <italic>Yersinia pseudotuberculosis<\/italic>.","volume":"96","author":"M Achtman","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"17837","DOI":"10.1073\/pnas.0408026101","article-title":"Microevolution and history of the plague bacillus, <italic>Yersinia pestis<\/italic>.","volume":"101","author":"M Achtman","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1128\/JB.01518-09","article-title":"Genome sequence of the deep-rooted <italic>Yersinia pestis<\/italic> strain Angola reveals new insights into the evolution and pangenome of the plague bacterium.","volume":"192","author":"M Eppinger","year":"2010","journal-title":"J Bacteriol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1128\/JCM.32.3.634-641.1994","article-title":"Plague pandemics investigated by ribotyping of <italic>Yersinia pestis<\/italic> strains.","volume":"32","author":"A Guiyoule","year":"1994","journal-title":"J Clin Microbiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1128\/jb.184.4.1019-1027.2002","article-title":"Genetic variability of <italic>Yersinia pestis<\/italic> isolates as predicted by PCR-based IS<italic>100<\/italic> genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (<italic>glpD<\/italic>).","volume":"184","author":"VL Motin","year":"2002","journal-title":"J Bacteriol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1128\/jb.174.7.2078-2086.1992","article-title":"Determination of genome size, macrorestriction pattern polymorphism, and nonpigmentation-specific deletion in <italic>Yersinia pestis<\/italic> by pulsed-field gel electrophoresis.","volume":"174","author":"TS Lucier","year":"1992","journal-title":"J Bacteriol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2826","DOI":"10.1128\/JCM.35.11.2826-2833.1997","article-title":"Recent emergence of new variants of <italic>Yersinia pestis<\/italic> in Madagascar.","volume":"35","author":"A Guiyoule","year":"1997","journal-title":"J Clin Microbiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1128\/JCM.40.4.1164-1173.2002","article-title":"Genotyping of a homogeneous group of <italic>Yersinia pestis<\/italic> strains isolated in the United States.","volume":"40","author":"XZ Huang","year":"2002","journal-title":"J Clin Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e2166","DOI":"10.1371\/journal.pone.0002166","article-title":"Different region analysis for genotyping <italic>Yersinia pestis<\/italic> isolates from China.","volume":"3","author":"Y Li","year":"2008","journal-title":"PLoS ONE"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e2652","DOI":"10.1371\/journal.pone.0002652","article-title":"Insight into microevolution of <italic>Yersinia pestis<\/italic> by clustered regularly interspaced short palindromic repeats.","volume":"3","author":"Y Cui","year":"2008","journal-title":"PLoS ONE"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1007\/s10482-009-9347-2","article-title":"Genotyping of Indian <italic>Yersinia pestis<\/italic> strains by MLVA and repetitive DNA sequence based PCRs.","volume":"96","author":"JJ Kingston","year":"2009","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"714","DOI":"10.4269\/ajtmh.2009.09-0174","article-title":"Spatial variation of <italic>Yersinia pestis<\/italic> from Yunnan Province of China.","volume":"81","author":"Z Zhang","year":"2009","journal-title":"Am J Trop Med Hyg"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"3179","DOI":"10.1128\/JCM.39.9.3179-3185.2001","article-title":"Identification and characterization of variable-number tandem repeats in the <italic>Yersinia pestis<\/italic> genome.","volume":"39","author":"AM Klevytska","year":"2001","journal-title":"J Clin Microbiol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1471-2180-4-22","article-title":"Tandem repeats analysis for the high resolution phylogenetic analysis of <italic>Yersinia pestis<\/italic>.","volume":"4","author":"C Pourcel","year":"2004","journal-title":"BMC Microbiol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"8408","DOI":"10.1073\/pnas.0401561101","article-title":"Differential plague-transmission dynamics determine <italic>Yersinia pestis<\/italic> population genetic structure on local, regional, and global scales.","volume":"101","author":"JM Girard","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e6000","DOI":"10.1371\/journal.pone.0006000","article-title":"Genotyping and phylogenetic analysis of <italic>Yersinia pestis<\/italic> by MLVA: insights into the worldwide expansion of Central Asia plague foci.","volume":"4","author":"Y Li","year":"2009","journal-title":"PLoS One"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1099\/mic.0.29059-0","article-title":"Phenotypic and molecular characterizations of <italic>Yersinia pestis<\/italic> isolates from Kazakhstan and adjacent regions.","volume":"153","author":"JL Lowell","year":"2007","journal-title":"Microbiology"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/1471-2180-9-205","article-title":"MLVA distribution characteristics of <italic>Yersinia pestis<\/italic> in China and the correlation analysis.","volume":"9","author":"X Zhang","year":"2009","journal-title":"BMC Microbiol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.meegid.2004.02.005","article-title":"Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales.","volume":"4","author":"P Keim","year":"2004","journal-title":"Infect Genet Evol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e461","DOI":"10.1371\/journal.pone.0000461","article-title":"Global genetic population structure of <italic>Bacillus anthracis<\/italic>.","volume":"2","author":"MN Van Ert","year":"2007","journal-title":"PLoS One"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"2474","DOI":"10.1128\/JB.01786-08","article-title":"Phylogeography of <italic>Francisella tularensis<\/italic>: global expansion of a highly fit clone.","volume":"191","author":"AJ Vogler","year":"2009","journal-title":"J Bacteriol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"13536","DOI":"10.1073\/pnas.0403844101","article-title":"Phylogenetic discovery bias in <italic>Bacillus anthracis<\/italic> using single-nucleotide polymorphisms from whole-genome sequencing.","volume":"101","author":"T Pearson","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/35097083","article-title":"Genome sequence of <italic>Yersinia pestis<\/italic>, the causative agent of plague.","volume":"413","author":"J Parkhill","year":"2001","journal-title":"Nature"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"e220","DOI":"10.1371\/journal.pone.0000220","article-title":"A North American <italic>Yersinia pestis<\/italic> draft genome sequence: SNPs and phylogenetic analysis.","volume":"2","author":"JW Touchman","year":"2007","journal-title":"PLoS One"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"e770","DOI":"10.1371\/journal.pone.0000770","article-title":"<italic>Yersinia pestis<\/italic> evolution on a small timescale: comparison of whole genome sequences from North America.","volume":"2","author":"RK Auerbach","year":"2007","journal-title":"PLoS One"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1128\/JB.00124-06","article-title":"Complete genome sequence of <italic>Yersinia pestis<\/italic> strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen.","volume":"188","author":"PS Chain","year":"2006","journal-title":"J Bacteriol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"4601","DOI":"10.1128\/JB.184.16.4601-4611.2002","article-title":"Genome sequence of <italic>Yersinia pestis<\/italic> KIM.","volume":"184","author":"W Deng","year":"2002","journal-title":"J Bacteriol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"7628","DOI":"10.1128\/JB.01227-09","article-title":"Draft genome sequences of <italic>Yersinia pestis<\/italic> isolates from natural foci of endemic plague in China.","volume":"191","author":"M Eppinger","year":"2009","journal-title":"J Bacteriol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/978-0-387-72124-8_2","article-title":"Pestoides F, an atypical <italic>Yersinia pestis<\/italic> strain from the former Soviet Union.","volume":"603","author":"E Garcia","year":"2007","journal-title":"Adv Exp Med Biol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/dnares\/11.3.179","article-title":"Complete genome sequence of <italic>Yersinia pestis<\/italic> strain 91001, an isolate avirulent to humans.","volume":"11","author":"Y Song","year":"2004","journal-title":"DNA Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1093\/nar\/30.11.2478","article-title":"Fast algorithms for large-scale genome alignment and comparison.","volume":"30","author":"AL Delcher","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1101\/gr.8.3.175","article-title":"Base-calling of automated sequencer traces using <italic>phred<\/italic>. I. Accuracy assessment.","volume":"8","author":"B Ewing","year":"1998","journal-title":"Genome Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1093\/bioinformatics\/17.12.1244","article-title":"MEGA2: molecular evolutionary genetics analysis software.","volume":"17","author":"S Kumar","year":"2001","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1111\/j.1442-9993.1993.tb00438.x","article-title":"Non-parametric multivariate analyses of changes in community structure.","volume":"18","author":"KR Clarke","year":"1993","journal-title":"Aust J Ecol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"5808","DOI":"10.1128\/JB.186.17.5808-5818.2004","article-title":"Worldwide genetic relationships among <italic>Francisella tularensis<\/italic> isolates determined by multiple-locus variable-number tandem repeat analysis.","volume":"186","author":"A Johansson","year":"2004","journal-title":"J Bacteriol"},{"key":"ref53","first-page":"115","article-title":"[Resurgence of the plague in the Ikongo district of Madagascar in 1998. 1. Epidemiological aspects in the human population].","volume":"94","author":"R Migliani","year":"2001","journal-title":"Bull Soc Pathol Exot"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1139\/Z07-083","article-title":"Genetic structure of black rat populations in a rural plague focus in Madagascar.","volume":"85","author":"A Gilabert","year":"2007","journal-title":"Can J Zool"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1089\/vbz.2009.0019","article-title":"Study on the movement of <italic>Rattus rattus<\/italic> and evaluation of the plague dispersion in Madagascar.","volume":"10","author":"S Rahelinirina","year":"2010","journal-title":"Vector Borne Zoonotic Dis"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1007\/s10393-010-0312-3","article-title":"Susceptibility to <italic>Yersinia pestis<\/italic> experimental infection in wild <italic>Rattus rattus<\/italic>, reservoir of plague in Madagascar.","volume":"7","author":"C Tollenaere","year":"2010","journal-title":"Ecohealth"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nrmicro2219","article-title":"Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases.","volume":"7","author":"PS Keim","year":"2009","journal-title":"Nat Rev Microbiol"}],"container-title":["PLoS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pntd.0001319","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,23]],"date-time":"2020-06-23T15:46:23Z","timestamp":1592927183000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0001319"}},"subtitle":[],"editor":[{"given":"Mathieu","family":"Picardeau","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2011,9,13]]},"references-count":57,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2011,9,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0001319","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.13373038.14743169","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,9,13]]}}}