{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T16:59:32Z","timestamp":1790873972313,"version":"4.1.0"},"reference-count":52,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2013,10,1]],"date-time":"2013-10-01T00:00:00Z","timestamp":1380585600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2018,4,17]],"date-time":"2018-04-17T00:00:00Z","timestamp":1523923200000},"content-version":"vor","delay-in-days":1659,"URL":"https:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"name":"Heilongjiang Innovation Endowment Award","award":["YJSCX2012-197HLJ"],"award-info":[{"award-number":["YJSCX2012-197HLJ"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["NSFC30970078"],"award-info":[{"award-number":["NSFC30970078"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["NSFC30970119"],"award-info":[{"award-number":["NSFC30970119"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["81030029"],"award-info":[{"award-number":["81030029"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["81271786"],"award-info":[{"award-number":["81271786"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["NSFC-NIH 81161120416"],"award-info":[{"award-number":["NSFC-NIH 81161120416"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province of China","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2013,10]]},"DOI":"10.1016\/j.ygeno.2013.07.014","type":"journal-article","created":{"date-parts":[[2013,8,6]],"date-time":"2013-08-06T16:29:16Z","timestamp":1375806556000},"page":"331-337","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":14,"title":["Genetic boundaries to delineate the typhoid agent and other Salmonella serotypes into distinct natural lineages"],"prefix":"10.1016","volume":"102","author":[{"given":"Le","family":"Tang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun-Xiao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song-Ling","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Randal N.","family":"Johnston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gui-Rong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu-Lin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ygeno.2013.07.014_bb0005","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/j.1462-2920.2011.02668.x","article-title":"Bacterial species may exist, metagenomics reveal","volume":"14","author":"Caro-Quintero","year":"2012","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0010","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1101\/gr.5512906","article-title":"A bimodal pattern of relatedness between the Salmonella paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?","volume":"17","author":"Didelot","year":"2007","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0015","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1101\/gr.086645.108","article-title":"On the origin of prokaryotic species","volume":"19","author":"Doolittle","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0020","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1093\/ajcp\/22.7_ts.692","article-title":"A simplification of the Kauffmann\u2013White schema","volume":"22","author":"Edwards","year":"1952","journal-title":"Am. J. Clin. Pathol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0025","doi-asserted-by":"crossref","first-page":"e59427","DOI":"10.1371\/journal.pone.0059427","article-title":"Genomic comparison between Salmonella Gallinarum and Pullorum: differential pseudogene formation under common host restriction","volume":"8","author":"Feng","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0030","series-title":"Omics, Microbial Modeling, and Technologies for Food-borne Pathogens","first-page":"43","article-title":"Pathogenic Salmonella","author":"Feng","year":"2011"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0035","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1128\/JB.06507-11","article-title":"Complete genome sequence of Salmonella enterica serovar Pullorum RKS5078","volume":"194","author":"Feng","year":"2012","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0040","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1126\/science.6771870","article-title":"The phylogeny of prokaryotes","volume":"209","author":"Fox","year":"1980","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0045","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1097\/MOG.0b013e3282f21388","article-title":"Pathogenesis of enteric Salmonella infections","volume":"24","author":"Grassl","year":"2008","journal-title":"Curr. Opin. Gastroenterol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0050","first-page":"434","article-title":"Enteric fever caused by Salmonella paratyphi C in South and South West Africa","volume":"54","author":"Jacobs","year":"1978","journal-title":"S. Afr. Med. J."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0055","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1128\/JB.41.2.127-140.1941","article-title":"A typhoid variant and a new serological variation in the Salmonella group","volume":"41","author":"Kauffmann","year":"1941","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0060","first-page":"171","article-title":"International Salmonella centre","volume":"3","author":"Kauffmann","year":"1950","journal-title":"Bull. World Health Organ."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0065","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1111\/j.1699-0463.1953.tb00291.x","article-title":"On the antigenic structure of Salmonella paratyphi A","volume":"32","author":"Kauffmann","year":"1953","journal-title":"Acta Pathol. Microbiol. Scand."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0070","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1111\/j.1699-0463.1957.tb01021.x","article-title":"A revised, simplified Kauffmann\u2013White schema","volume":"41","author":"Kauffmann","year":"1957","journal-title":"Acta Pathol. Microbiol. Scand."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0075","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S1567-1348(02)00089-8","article-title":"Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000years old","volume":"2","author":"Kidgell","year":"2002","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0080","first-page":"1100","article-title":"Paratyphoid C fever. 1 case","volume":"8","author":"Laurent","year":"1979","journal-title":"Nouv. Presse Med."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0085","series-title":"Bergey's Manual of Systematic Bacteriology","first-page":"427","article-title":"Genus III. Salmonella","author":"Le Minor","year":"1984"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0090","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1007\/BF01963091","article-title":"Typing of Salmonella species","volume":"7","author":"Le Minor","year":"1988","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0095","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1099\/00207713-37-4-465","article-title":"Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella","volume":"37","author":"Le Minor","year":"1987","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0100","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/molbev\/msj042","article-title":"Genome plasticity and ori-ter rebalancing in Salmonella typhi","volume":"23","author":"Liu","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0105","series-title":"ASM 2nd Conference on Salmonella: From Pathogenesis to Therapeutics","first-page":"97","article-title":"Near complete conservation of endonuclease cleavage sites to define the basic phylogenetic unit of Salmonella","author":"Liu","year":"2006"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0110","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1128\/JB.184.10.2626-2633.2002","article-title":"The evolving genome of Salmonella enterica serovar Pullorum","volume":"184","author":"Liu","year":"2002","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0115","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/978-1-59745-512-1_3","article-title":"Physical mapping of Salmonella genomes","volume":"394","author":"Liu","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0120","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1128\/jb.176.4.1014-1024.1994","article-title":"The XbaI\u2013BlnI\u2013CeuI genomic cleavage map of Salmonella paratyphi B","volume":"176","author":"Liu","year":"1994","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0125","doi-asserted-by":"crossref","first-page":"4104","DOI":"10.1128\/jb.175.13.4104-4120.1993","article-title":"The XbaI\u2013BlnI\u2013CeuI genomic cleavage map of Salmonella typhimurium LT2 determined by double digestion, end labelling, and pulsed-field gel electrophoresis","volume":"175","author":"Liu","year":"1993","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0130","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1128\/jb.174.5.1662-1672.1992","article-title":"A physical map of the Salmonella typhimurium LT2 genome made by using XbaI analysis","volume":"174","author":"Liu","year":"1992","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0135","doi-asserted-by":"crossref","first-page":"6585","DOI":"10.1128\/jb.177.22.6585-6592.1995","article-title":"The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG","volume":"177","author":"Liu","year":"1995","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0140","doi-asserted-by":"crossref","first-page":"5099","DOI":"10.1128\/jb.177.17.5099-5107.1995","article-title":"Genomic cleavage map of Salmonella typhi Ty2","volume":"177","author":"Liu","year":"1995","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0145","doi-asserted-by":"crossref","first-page":"3355","DOI":"10.1128\/jb.177.11.3355-3357.1995","article-title":"I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium","volume":"177","author":"Liu","year":"1995","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0150","doi-asserted-by":"crossref","first-page":"10303","DOI":"10.1073\/pnas.93.19.10303","article-title":"Highly plastic chromosomal organization in Salmonella typhi","volume":"93","author":"Liu","year":"1996","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0155","doi-asserted-by":"crossref","first-page":"6747","DOI":"10.1128\/JB.181.21.6747-6755.1999","article-title":"Bacterial phylogenetic clusters revealed by genome structure","volume":"181","author":"Liu","year":"1999","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0160","doi-asserted-by":"crossref","first-page":"e4510","DOI":"10.1371\/journal.pone.0004510","article-title":"Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi","volume":"4","author":"Liu","year":"2009","journal-title":"PLoS One"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0165","series-title":"Systematics and the Origin of Species from the Viewpoint of a Zoologist, New York","author":"Mayr","year":"1944"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0170","first-page":"262","article-title":"What is a species, and what is not?","volume":"63","author":"Mayr","year":"1996","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0175","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1038\/ng1470","article-title":"Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid","volume":"36","author":"McClelland","year":"2004","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0180","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/35101614","article-title":"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2","volume":"413","author":"McClelland","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0185","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1146\/annurev.med.52.1.259","article-title":"Salmonella: a model for bacterial pathogenesis","volume":"52","author":"Ohl","year":"2001","journal-title":"Annu. Rev. Med."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0190","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1038\/35101607","article-title":"Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18","volume":"413","author":"Parkhill","year":"2001","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0195","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.1056\/NEJMra020201","article-title":"Typhoid fever","volume":"347","author":"Parry","year":"2002","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0200","series-title":"Bergey's Manual of Systematic Bacteriology","first-page":"764","article-title":"Genus XXXIII. Salmonella","author":"Popoff","year":"2005"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0205","first-page":"260","article-title":"Clinical pathogenesis of typhoid fever","volume":"2","author":"Raffatellu","year":"2008","journal-title":"J. Infect. Dev. Ctries."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0210","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1128\/JCM.27.2.313-320.1989","article-title":"Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov.","volume":"27","author":"Reeves","year":"1989","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0215","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1126\/science.1134933","article-title":"Evolutionary history of Salmonella typhi","volume":"314","author":"Roumagnac","year":"2006","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0220","series-title":"Bacterial Pathogenesis","author":"Salyers","year":"2002"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0225","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1126\/science.1229224","article-title":"A Rab32-dependent pathway contributes to Salmonella typhi host restriction","volume":"338","author":"Span\u00f2","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0230","first-page":"1043","article-title":"Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology","volume":"52","author":"Stackebrandt","year":"2002","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0235","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0240","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1101\/gr.077404.108","article-title":"Comparative genome analysis of Salmonella enteritidis PT4 and Salmonella gallinarum 287\/91 provides insights into evolutionary and host adaptation pathways","volume":"18","author":"Thomson","year":"2008","journal-title":"Genome Res."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0245","doi-asserted-by":"crossref","first-page":"88","DOI":"10.4161\/gmic.18602","article-title":"Typhoid fever: \u201cyou can't hit what you can't see\u201d","volume":"3","author":"Wangdi","year":"2012","journal-title":"Gut Microbes"},{"key":"10.1016\/j.ygeno.2013.07.014_bb0250","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1073\/pnas.87.12.4576","article-title":"Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya","volume":"87","author":"Woese","year":"1990","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0255","doi-asserted-by":"crossref","first-page":"4720","DOI":"10.1128\/JB.187.14.4720-4727.2005","article-title":"The genome of Salmonella enterica serovar Gallinarum: distinct insertions\/deletions and rare rearrangements","volume":"187","author":"Wu","year":"2005","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.ygeno.2013.07.014_bb0260","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1186\/1471-2164-11-729","article-title":"SPC-P1: a pathogenicity-associated prophage of Salmonella paratyphi C","volume":"11","author":"Zou","year":"2010","journal-title":"BMC Genomics"}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754313001511?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0888754313001511?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,8,1]],"date-time":"2020-08-01T14:14:31Z","timestamp":1596291271000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0888754313001511"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":52,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["S0888754313001511"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2013.07.014","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2013,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genetic boundaries to delineate the typhoid agent and other Salmonella serotypes into distinct natural lineages","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2013.07.014","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2013 Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}]}}