{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T02:46:00Z","timestamp":1761965160145,"version":"3.37.3"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T00:00:00Z","timestamp":1583712000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["GenomePT (ref. POCI-01-0145-FEDER-022184)"],"award-info":[{"award-number":["GenomePT (ref. POCI-01-0145-FEDER-022184)"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0229863","type":"journal-article","created":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T17:27:04Z","timestamp":1583774824000},"page":"e0229863","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["Genome\u2013scale approach to study the genetic relatedness among Brucella melitensis strains"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4770-9079","authenticated-orcid":true,"given":"Ana","family":"Pelerito","sequence":"first","affiliation":[]},{"given":"Alexandra","family":"Nunes","sequence":"additional","affiliation":[]},{"given":"Maria Sofia","family":"N\u00fancio","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o Paulo","family":"Gomes","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,3,9]]},"reference":[{"issue":"2","key":"pone.0229863.ref001","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S1473-3099(06)70382-6","article-title":"The new global map of human brucellosis","volume":"6","author":"G Pappas","year":"2006","journal-title":"Lancet Infect Dis"},{"key":"pone.0229863.ref002","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2014.00213","article-title":"Retrospective and prospective perspectives on zoonotic brucellosis","volume":"5","author":"E Moreno","year":"2014","journal-title":"Frontiers in Microbiology"},{"issue":"2","key":"pone.0229863.ref003","doi-asserted-by":"crossref","first-page":"213","DOI":"10.3201\/eid0302.970219","article-title":"Brucellosis: an overview","volume":"3","author":"MJ Corbel","year":"1997","journal-title":"Emerg Infect Dis"},{"key":"pone.0229863.ref004","article-title":"Brucella papionis sp. nov. isolated from baboons (Papio spp.)","volume":"9","author":"AM Whatmore","year":"2014","journal-title":"Int J Syst Evol Microbiol"},{"issue":"Pt 4","key":"pone.0229863.ref005","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1099\/ijs.0.011148-0","article-title":"Brucella inopinata sp. nov., isolated from a breast implant infection","volume":"60","author":"HC Scholz","year":"2010","journal-title":"Int J Syst Evol Microbiol"},{"issue":"5","key":"pone.0229863.ref006","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1099\/ijsem.0.000998","article-title":"Brucella vulpis sp. nov., isolated from mandibular lymph nodes of red foxes. (Vulpes vulpes)","volume":"66","author":"HC Scholz","year":"2016","journal-title":"Int J Syst Evol Microbiol"},{"key":"pone.0229863.ref007","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.meegid.2017.11.016","article-title":"Identification of genetic variations of Brucella spp. through genome\u2014wide association studies","volume":"56","author":"J Sankarasubramanian","year":"2017","journal-title":"Infect Genet Evol"},{"issue":"1","key":"pone.0229863.ref008","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1073\/pnas.221575398","article-title":"The genome of the facultative intracellular pathogen Brucella melitensis","volume":"99","author":"VG Del Vecchio","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"pone.0229863.ref009","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1471-2180-6-13","article-title":"Molecular targets for rapid identification of Brucella spp","volume":"22","author":"VG Ratushna","year":"2006","journal-title":"BMC Microbiol"},{"issue":"19","key":"pone.0229863.ref010","doi-asserted-by":"crossref","DOI":"10.1093\/femsle\/fnx199","article-title":"Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon","volume":"364","author":"N Abou Zaki","year":"2017","journal-title":"FEMS Microbiol Lett"},{"key":"pone.0229863.ref011","article-title":"Genetic Characterization and Comparative Genome Analysis of Brucella melitensis isolates from India","author":"S Azam","year":"2016","journal-title":"Int J Genomics"},{"key":"pone.0229863.ref012","doi-asserted-by":"crossref","first-page":"24","DOI":"10.3389\/fmicb.2016.00024","article-title":"Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata","volume":"7","author":"JA Hammerl","year":"2016","journal-title":"Front Microbiol"},{"issue":"3\u20134","key":"pone.0229863.ref013","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.vetmic.2014.10.015","article-title":"Brucellosis outbreak in a Swedish kennel in 2013: determination of genetic markers for source tracing","volume":"174","author":"R Kaden","year":"2014","journal-title":"Vet Microbiol"},{"key":"pone.0229863.ref014","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0378-1119(93)90236-V","article-title":"Sequence and characterization of an insertion sequence, IS711, from brucella ovis","volume":"133","author":"SM Halling","year":"1993","journal-title":"Gene"},{"issue":"5","key":"pone.0229863.ref015","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1128\/JB.01091-13","article-title":"Comparative phylogenomics and evolution of the Brucellae reveal a path to virulence","volume":"196","author":"AR Wattam","year":"2014","journal-title":"J Bacteriol"},{"key":"pone.0229863.ref016","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.meegid.2018.10.021","article-title":"Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp","volume":"67","author":"J Sankarasubramanian","year":"2019","journal-title":"Infection, genetics and Evolution"},{"key":"pone.0229863.ref017","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1128\/JCM.00517-18","article-title":"Core Genome Multilocus Sequence Typing and Single Nucleotide polymorphism Analysis in the epidemiology of Brucella melitensis infections","volume":"56","author":"A Janowicz","year":"2018","journal-title":"J Clin Microbiol"},{"key":"pone.0229863.ref018","unstructured":"Doen\u00e7as de Declara\u00e7\u00e3o Obrigat\u00f3ria 2012\u20132015. Dire\u00e7\u00e3o Geral de Sa\u00fade."},{"key":"pone.0229863.ref019","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1371\/journal.pone.0042514","article-title":"MLVA 16 Typing of Portuguese Human and Animal Brucela melitensis and Brucela abortus Isolates","volume":"7","author":"AC Ferreira","year":"2012","journal-title":"PLOS One"},{"issue":"7","key":"pone.0229863.ref020","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0179667","article-title":"Human Brucellosis in Portugal\u2014Retrosptective analysis of suspected clinical cases of infection from 2009 to 2016","volume":"12","author":"A Pelerito","year":"2017","journal-title":"Plos One"},{"volume-title":"Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria","year":"2016","author":"CLSI. Guideline M45","key":"pone.0229863.ref021"},{"issue":"15","key":"pone.0229863.ref022","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0229863.ref023","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"},{"issue":"11","key":"pone.0229863.ref024","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PLoS ONE"},{"issue":"W1","key":"pone.0229863.ref025","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gkw359","article-title":"PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees","volume":"44","author":"B Ribeiro-Gon\u00e7alves","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pone.0229863.ref026","first-page":"142","article-title":"INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens","author":"AK Llarena","year":"2018","journal-title":"EFSA supporting publication"},{"key":"pone.0229863.ref027","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets","volume":"33","author":"S Kumar","year":"2016","journal-title":"Molecular Biology and Evolution"},{"key":"pone.0229863.ref028","first-page":"406","article-title":"The neighbor-joining method: A new method for reconstructing phylogenetic trees","volume":"4","author":"N Saitou","year":"1987","journal-title":"Molecular Biology and Evolution"},{"key":"pone.0229863.ref029","doi-asserted-by":"crossref","first-page":"11030","DOI":"10.1073\/pnas.0404206101","article-title":"Prospects for inferring very large phylogenies by using the neighbor-joining method","volume":"101","author":"K Tamura","year":"2004","journal-title":"Proceedings of the National Academy of Sciences (USA)"},{"key":"pone.0229863.ref030","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1111\/j.1558-5646.1985.tb00420.x","article-title":"Confidence limits on phylogenies: An approach using the bootstrap","volume":"39","author":"J Felsenstein","year":"1985","journal-title":"Evolution"},{"issue":"6","key":"pone.0229863.ref031","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.1128\/JCM.02039-05","article-title":"Identification and characterization of variable-number tandem-repeat markers for typing of Brucella spp","volume":"44","author":"AM Whatmore","year":"2006","journal-title":"J Clin Microbiol"},{"key":"pone.0229863.ref032","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.3389\/fmicb.2016.02049","article-title":"Extended Multilocus Sequence Analysis to Describe the Global Population Structure of the Genus Brucella: Phylogeography and Relationship to Biovars","volume":"7","author":"AM Whatmore","year":"2016","journal-title":"Front Microbiol"},{"key":"pone.0229863.ref033","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/1471-2105-10-152","article-title":"Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach","volume":"10","author":"AP Francisco","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pone.0229863.ref034","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.mimet.2006.12.015","article-title":"Evaluation of Brucella MLVA Typing for Human Brucellosis","volume":"69","author":"S AL Dahouk","year":"2007","journal-title":"J Microbiol Methods"},{"key":"pone.0229863.ref035","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s12864-015-1294-x","article-title":"Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis","volume":"16","author":"KK Tan","year":"2015","journal-title":"BMC Genomics"},{"issue":"1","key":"pone.0229863.ref036","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1186\/s12864-018-4762-2","article-title":"Global evolution and phylogeography of Brucella melitensis strains","volume":"19","author":"SV Pisarenko","year":"2018","journal-title":"BMC Genomics"},{"issue":"1","key":"pone.0229863.ref037","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-26906-3","article-title":"Whole\u2014Genome Sequencing and Antimicrobial Resistance in Brucella melitensis from a Norwegian Perspective","volume":"8","author":"TB Johansen","year":"2018","journal-title":"Sci Rep"},{"issue":"4","key":"pone.0229863.ref038","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0175425","article-title":"Whole genome sequencing of Brucella melitensis isolated from 57 patients in Germany reveals high diversity in strains from Middle East","volume":"12","author":"E Georgi","year":"2017","journal-title":"Plos One"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0229863","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T17:27:23Z","timestamp":1583774843000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0229863"}},"subtitle":[],"editor":[{"given":"Roy Martin","family":"Roop","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,3,9]]},"references-count":38,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0229863","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2020,3,9]]}}}