{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T23:25:00Z","timestamp":1792020300769,"version":"4.4.0"},"reference-count":42,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2017,12,1]],"date-time":"2017-12-01T00:00:00Z","timestamp":1512086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2017,12,1]],"date-time":"2017-12-01T00:00:00Z","timestamp":1512086400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"funder":[{"name":"VIROGENESIS Project","award":["634650"],"award-info":[{"award-number":["634650"]}]},{"name":"Medical Research Council (MRC) of the Republic of South Africa","award":["MRC-RFA-FSP-01-2013\/UKZN HIVEPI"],"award-info":[{"award-number":["MRC-RFA-FSP-01-2013\/UKZN HIVEPI"]}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Veterinary Microbiology"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1016\/j.vetmic.2017.11.001","type":"journal-article","created":{"date-parts":[[2017,11,20]],"date-time":"2017-11-20T06:16:21Z","timestamp":1511158581000},"page":"80-86","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":29,"special_numbering":"C","title":["Molecular and phylogenetic analyses of Salmonella Gallinarum trace the origin and diversification of recent outbreaks of fowl typhoid in poultry farms"],"prefix":"10.1016","volume":"212","author":[{"given":"Silvia","family":"De Carli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiago","family":"Gr\u00e4f","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Di\u00e9ssy","family":"Kipper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda Kieling Moreira","family":"Lehmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Zanetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franciele Maboni","family":"Siqueira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Cibulski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9 Salvador Kazantzi","family":"Fonseca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nilo","family":"Ikuta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vagner Ricardo","family":"Lunge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.vetmic.2017.11.001_bib0005","doi-asserted-by":"crossref","first-page":"e1002776","DOI":"10.1371\/journal.ppat.1002776","article-title":"S. enterica MLST Study Group. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica","volume":"8","author":"Achtman","year":"2012","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0010","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics","volume":"30","author":"Baele","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/03079457.2010.542575","article-title":"Pullorum disease and fowl typhoid-new thoughts on old diseases: a review","volume":"40","author":"Barrow","year":"2011","journal-title":"Avian Pathol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0020","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1128\/genomeA.00028-14","article-title":"Draft genome sequence of Salmonella enterica subsp. enterica Serovar Gallinarum Biovar Pullorum Strain FCAV198, a Brazilian chicken pathogen","volume":"2","author":"Batista","year":"2014","journal-title":"Genome Announc."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0025","first-page":"25","article-title":"A evolu\u00e7\u00e3o da avicultura industrial brasileira e seus efeitos territoriais","volume":"2","author":"Belusso","year":"2010","journal-title":"Rev. Percurso"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0030","series-title":"Doen\u00e7as das aves. Campinas","article-title":"Salmoneloses","author":"Berchieri J\u00fanior","year":"2010"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0035","series-title":"Manual de Legisla\u00e7\u00e3o: programas nacionais de sa\u00fade animal do Brasil\/Minist\u00e9rio da Agricultura, Pecu\u00e1ria e Abastecimento. Secretaria de Defesa Agropecu\u00e1ria","first-page":"171","article-title":"PNSA: Programa Nacional de Sanidade Av\u00edcola","author":"Brasil, Minist\u00e9rio da Agricultura, Pecu\u00e1ria e Abastecimento","year":"2009"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0040","doi-asserted-by":"crossref","first-page":"422","DOI":"10.2307\/1589326","article-title":"The history of avian medicine in the U.S. II. pullorum disease and fowl typhoid","volume":"21","author":"Bullis","year":"1977","journal-title":"Avian Dis."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0045","first-page":"1","article-title":"Further investigations on the epidemiology of fowl typhoid in Brazil","volume":"1","author":"Celis-Estupi\u00f1an","year":"2017","journal-title":"Avian Pathol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0050","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/genomeA.00019-16","article-title":"Draft genome sequence of a Salmonella enteric subsp. Enteric Serovar Gallinarum bv. Gallinarum isolate associated with fowl typhoid outbreaks in Brazil","volume":"4","author":"De Carli","year":"2016","journal-title":"Genome Announc."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0055","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.3201\/eid2009.131095","article-title":"Genomic epidemiology of Salmonella enterica serotype enteritidis based on population structure of prevalent lineages","volume":"20","author":"Deng","year":"2014","journal-title":"Emerg. Infec. Dis."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0060","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"Drummond","year":"2012","journal-title":"Mol. Biol. Evol."},{"issue":"10","key":"10.1016\/j.vetmic.2017.11.001_bib0065","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/ng.3644","article-title":"Distinct Salmonella enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings","volume":"48","author":"Feasey","year":"2016","journal-title":"Nat. Genet."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0070","first-page":"1","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.vetmic.2017.11.001_bib0075","series-title":"Diseases of Poultry","first-page":"619","article-title":"Bacterial diseases: Salmonella infection","author":"Gast","year":"2008"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0080","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.prevetmed.2016.11.018","article-title":"The application of epidemiology in national veterinary services: challenges and threats in Brazil","volume":"137","author":"Gon\u00e7alves","year":"2017","journal-title":"Prev. Vet. Med."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0085","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/genetics\/165.3.951","article-title":"Genomic Rearrangements at rrn Operons in Salmonella","volume":"165","author":"Helm","year":"2003","journal-title":"Genetics"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0090","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1128\/JCM.38.9.3429-3435.2000","article-title":"Automated 5\u2019 nuclease PCR assay for identification of Salmonella enterica","volume":"38","author":"Hoorfar","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0095","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.resmic.2014.07.004","article-title":"Supplement 2008\u20132010 (no. 48) to the White-Kauffmann-Le minor scheme","volume":"165","author":"Issenhuth-Jeanjean","year":"2014","journal-title":"Res. Microbiol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0100","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0104984","article-title":"Solving the problem of comparing whole bacterial genomes across different sequencing platforms","volume":"9","author":"Kaas","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0105","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.vetmic.2010.05.039","article-title":"Differential identification of Salmonella enterica subsp: enteric serovar Gallinarum biovars Gallinarum and Pullorum based on polymorphic regions of glgC and speC genes","volume":"147","author":"Kang","year":"2011","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0110","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.vetmic.2012.05.041","article-title":"Differential identification of Salmonella enteric serovar Gallinarum biovars Gallinarum and Pullorum and the biovar Gallinarum live vaccine strain 9R","volume":"160","author":"Kang","year":"2012","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0115","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0120","doi-asserted-by":"crossref","first-page":"236","DOI":"10.3382\/ps.2009-00420","article-title":"Prevalence and characterization of Salmonella Gallinarum in the chicken in Korea during 2000 to 2008","volume":"89","author":"Kwon","year":"2014","journal-title":"Poult. Sci."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0125","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1073\/pnas.1416707112","article-title":"Patterns of genome evolution that have accompanied host adaptation in Salmonella","volume":"112","author":"Langridge","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0130","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1080\/03079450500180895","article-title":"Safety and efficacy of Salmonella gallinarum 9R vaccine in young laying chickens","volume":"34","author":"Lee","year":"2005","journal-title":"Avian Pathol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0135","doi-asserted-by":"crossref","first-page":"2516","DOI":"10.1128\/AEM.03821-15","article-title":"Global genomic epidemiology of Salmonella enterica Serovar Typhimurium DT104","volume":"82","author":"Leekitcharoenphon","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0140","doi-asserted-by":"crossref","first-page":"606","DOI":"10.4014\/jmb.1406.06031","article-title":"Complete genome sequence of Salmonella enterica serovar Pullorum multidrug resistance strain S06004 from China","volume":"25","author":"Li","year":"2015","journal-title":"J. Microbiol. Biotechnol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0145","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0013503","article-title":"Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars","volume":"5","author":"Matthews","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0150","series-title":"Fowl Typhoid","author":"OIE \u2013 World Organization for Animal Health","year":"2016"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0155","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1093\/molbev\/msn083","article-title":"jModelTest: phylogenetic model averaging","volume":"25","author":"Posada","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0160","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1111\/lam.12110","article-title":"Assignment of serotype to Salmonella enterica isolates obtained from poultry and their environment in southern Brazil","volume":"57","author":"Pulido-Land\u00ednez","year":"2013","journal-title":"Lett. Appl. Microbiol."},{"issue":"1","key":"10.1016\/j.vetmic.2017.11.001_bib0165","first-page":"2","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"9","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0170","doi-asserted-by":"crossref","first-page":"3162","DOI":"10.1128\/JB.00394-11","article-title":"Genome sequences of Salmonella enterica serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well-defined virulence in food-producing animals","volume":"193","author":"Richardson","year":"2011","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0175","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1080\/03079457.2015.1086975","article-title":"ERIC-PCR genotyping of field isolates of Salmonella enterica subsp. enterica serovar Gallinarum biovars Gallinarum and Pullorum","volume":"44","author":"Secundo de Souza","year":"2015","journal-title":"Avian Pathol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0180","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0185","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 intoation pathways","volume":"18","author":"Thomson","year":"2008","journal-title":"Genome Res."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0190","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/genomeA.01221-15","article-title":"First draft genome sequence of Salmonella enterica serovar Gallinarum strain VTCCBAA614, isolated from chicken in India","volume":"3","author":"Vaid","year":"2015","journal-title":"Genome Announc."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0195","doi-asserted-by":"crossref","first-page":"4940","DOI":"10.1016\/j.vaccine.2013.08.033","article-title":"Salmonella Gallinarum field isolates from laying hens are related to the vaccine strain SG9R","volume":"31","author":"Van Immerseel","year":"2013","journal-title":"Vaccine"},{"key":"10.1016\/j.vetmic.2017.11.001_bib0200","first-page":"1","article-title":"Salmonella enterica serovar Gallinarum: addressing fundamental questions in bacteriology sixty years on from the 9R vaccine","volume":"9457","author":"Wigley","year":"2016","journal-title":"Avian Pathol."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0205","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/genomeA.01599-15","article-title":"Complete genome and methylome sequences of two Salmonella enterica spp","volume":"4","author":"Yao","year":"2016","journal-title":"Genome Announc."},{"key":"10.1016\/j.vetmic.2017.11.001_bib0210","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/genomeA.01718-15","article-title":"Draft whole-genome sequences of 25 Salmonella enterica strains representing 24 Serovares","volume":"4","author":"Yoshida","year":"2016","journal-title":"Genome Announc."}],"updated-by":[{"DOI":"10.1016\/j.vetmic.2017.12.001","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000}}],"container-title":["Veterinary Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S037811351730384X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S037811351730384X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T22:59:32Z","timestamp":1759877972000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S037811351730384X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":42,"alternative-id":["S037811351730384X"],"URL":"https:\/\/doi.org\/10.1016\/j.vetmic.2017.11.001","relation":{},"ISSN":["0378-1135"],"issn-type":[{"value":"0378-1135","type":"print"}],"subject":[],"published":{"date-parts":[[2017,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Molecular and phylogenetic analyses of Salmonella Gallinarum trace the origin and diversification of recent outbreaks of fowl typhoid in poultry farms","name":"articletitle","label":"Article Title"},{"value":"Veterinary Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.vetmic.2017.11.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2017 Elsevier B.V. All rights reserved.","name":"copyright","label":"Copyright"}]}}