{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:59:33Z","timestamp":1792061973845,"version":"4.4.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011538","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,8,10]],"date-time":"2023-08-10T00:00:00Z","timestamp":1691625600000}}],"reference-count":105,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2023,7,31]],"date-time":"2023-07-31T00:00:00Z","timestamp":1690761600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000155","name":"Social Sciences and Humanities Research Council of Canada","doi-asserted-by":"publisher","award":["20008499"],"award-info":[{"award-number":["20008499"]}],"id":[{"id":"10.13039\/501100000155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007631","name":"Canadian Institute for Advanced Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007631","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2020-05733"],"award-info":[{"award-number":["RGPIN-2020-05733"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012773","name":"Fondation J. Armand Bombardier","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012773","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT2017197"],"award-info":[{"award-number":["GNT2017197"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>Brucellosis is a disease caused by the bacterium<jats:italic>Brucella<\/jats:italic>and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species\u2014<jats:italic>Brucella melitensis<\/jats:italic>. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient<jats:italic>B. melitensis<\/jats:italic>draft genome from the kidney stone of a 14<jats:sup>th<\/jats:sup>-century Italian friar. The ancient strain contained fewer core genes than modern<jats:italic>B. melitensis<\/jats:italic>isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient<jats:italic>B. melitensis<\/jats:italic>genome fell as a basal sister lineage to a subgroup of<jats:italic>B. melitensis<\/jats:italic>strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between<jats:italic>B. melitensis<\/jats:italic>and<jats:italic>B. abortus<\/jats:italic>is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14<jats:sup>th<\/jats:sup>CE and suggest that its divergence was due to human and ruminant co-migration.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011538","type":"journal-article","created":{"date-parts":[[2023,7,31]],"date-time":"2023-07-31T17:33:42Z","timestamp":1690824822000},"page":"e1011538","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9088-9848","authenticated-orcid":true,"given":"George S.","family":"Long","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Hider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana T.","family":"Duggan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Klunk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Eaton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emil","family":"Karpinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina","family":"Giuffra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Ventura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tracy L.","family":"Prowse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Fornaciari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gino","family":"Fornaciari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. Brian","family":"Golding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendrik N.","family":"Poinar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,7,31]]},"reference":[{"key":"ppat.1011538.ref001","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1056\/NEJMra050570","article-title":"Brucellosis","volume":"352","author":"G Pappas","year":"2005","journal-title":"N Engl J Med"},{"key":"ppat.1011538.ref002","first-page":"1500846","article-title":"Comparisons of brucellosis between human and veterinary medicine","volume":"8","author":"NC Hull","year":"2018","journal-title":"Infect Ecol Epidemiol"},{"key":"ppat.1011538.ref003","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":"ppat.1011538.ref004","doi-asserted-by":"crossref","first-page":"213","DOI":"10.3389\/fmicb.2014.00213","article-title":"Retrospective and prospective perspectives on zoonotic brucellosis","volume":"5","author":"E Moreno","year":"2014","journal-title":"Front Microbiol"},{"key":"ppat.1011538.ref005","doi-asserted-by":"crossref","first-page":"e1163","DOI":"10.1002\/cti2.1163","article-title":"Systematic analysis of disease-specific immunological signatures in patients with febrile illness from Saudi Arabia","volume":"9","author":"YW Kam","year":"2020","journal-title":"Clin Transl Immunology"},{"key":"ppat.1011538.ref006","first-page":"e06971","article-title":"The European Union One Health 2020 Zoonoses Report","volume":"19","author":"E European Food Safety Authority","year":"2021","journal-title":"EFSA J"},{"key":"ppat.1011538.ref007","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1017\/S095026881000097X","article-title":"Origin, evolution and paleoepidemiology of brucellosis","volume":"139","author":"R D\u2019Anastasio","year":"2011","journal-title":"Epidemiol Infect"},{"issue":"5","key":"ppat.1011538.ref008","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1002\/(SICI)1099-1212(199909\/10)9:5<277::AID-OA489>3.0.CO;2-0","article-title":"Brucellosis at Herculaneum (79 AD)","volume":"9","author":"L Capasso","year":"1999","journal-title":"International Journal of Osteoarchaeology"},{"key":"ppat.1011538.ref009","volume-title":"Identification of pathological conditions in human skeletal remains","author":"DJ Ortner","year":"2003"},{"key":"ppat.1011538.ref010","doi-asserted-by":"crossref","first-page":"421","DOI":"10.2169\/internalmedicine.50.4700","article-title":"Osteoarticular involvement among 202 brucellosis cases identified in Central Anatolia region of Turkey","volume":"50","author":"H Turan","year":"2011","journal-title":"Intern Med"},{"key":"ppat.1011538.ref011","doi-asserted-by":"crossref","first-page":"e469","DOI":"10.1016\/j.ijid.2009.06.031","article-title":"Clinical manifestations and complications in 1028 cases of brucellosis: a retrospective evaluation and review of the literature","volume":"14","author":"T Buzgan","year":"2010","journal-title":"Int J Infect Dis"},{"issue":"1","key":"ppat.1011538.ref012","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1002\/oa.2837","article-title":"Approaching ancient disease from a One Health perspective: Interdisciplinary review for the investigation of zoonotic brucellosis","volume":"30","author":"R Bendrey","year":"2020","journal-title":"International Journal of Osteoarchaeology"},{"key":"ppat.1011538.ref013","first-page":"e01337","article-title":"Recovery of a medieval Brucella melitensis genome using shotgun metagenomics","volume":"5","author":"GL Kay","year":"2014","journal-title":"mBio"},{"key":"ppat.1011538.ref014","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1002\/ajpa.21643","article-title":"Osteological and molecular identification of Brucellosis in ancient Butrint, Albania","volume":"147","author":"MJ Mutolo","year":"2012","journal-title":"Am J Phys Anthropol"},{"issue":"34 (1)","key":"ppat.1011538.ref015","article-title":"\u00c0 propos de deux cas de brucellose dans le sud de la France aux \u00e9poques m\u00e9di\u00e9vale et moderne (Abbaye Saint-Sauveur, Aniane; La Closeraie, Aix-en-Provence)","volume":"34","author":"A Meffray","year":"2022","journal-title":"Bulletins et m\u00e9moires de la Soci\u00e9t\u00e9 d\u2019Anthropologie de Paris BMSAP"},{"key":"ppat.1011538.ref016","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.ijpp.2022.08.002","article-title":"Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis","volume":"39","author":"J Hider","year":"2022","journal-title":"International Journal of Paleopathology"},{"issue":"5","key":"ppat.1011538.ref017","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1016\/j.jas.2004.11.014","article-title":"The limits of biomolecular palaeopathology: ancient DNA cannot be used to study venereal syphilis","volume":"32","author":"AS Bouwman","year":"2005","journal-title":"Journal of Archaeological Science"},{"issue":"12","key":"ppat.1011538.ref018","doi-asserted-by":"crossref","first-page":"2091","DOI":"10.1016\/j.jas.2007.02.007","article-title":"Digging deeper into the limits of ancient DNA research on syphilis","volume":"34","author":"TE von Hunnius","year":"2007","journal-title":"Journal of Archaeological Science"},{"key":"ppat.1011538.ref019","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.meegid.2013.06.021","article-title":"Investigating genetic diversity of Brucella abortus and Brucella melitensis in Italy with MLVA-16","volume":"19","author":"G Garofolo","year":"2013","journal-title":"Infect Genet Evol"},{"key":"ppat.1011538.ref020","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"},{"key":"ppat.1011538.ref021","doi-asserted-by":"crossref","first-page":"521","DOI":"10.20506\/rst.33.2.2290","article-title":"The quest for a true One Health perspective of brucellosis","volume":"33","author":"J Godfroid","year":"2014","journal-title":"Rev Sci Tech"},{"key":"ppat.1011538.ref022","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s13690-017-0207-7","article-title":"Brucellosis in livestock and wildlife: zoonotic diseases without pandemic potential in need of innovative one health approaches","volume":"75","author":"J Godfroid","year":"2017","journal-title":"Arch Public Health"},{"key":"ppat.1011538.ref023","article-title":"Production and consumption of animals in Roman Italy: integrating the zooarchaeological and textual evidence","volume":"54","author":"M MacKinnon","year":"2004","journal-title":"Journal of Roman archaeology"},{"issue":"3","key":"ppat.1011538.ref024","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.smallrumres.2005.08.012","article-title":"Mediterranean sheep and goats production: An uncertain future","volume":"62","author":"M De Rancourt","year":"2006","journal-title":"Small Ruminant Research"},{"key":"ppat.1011538.ref025","doi-asserted-by":"crossref","first-page":"11597","DOI":"10.1073\/pnas.0801317105","article-title":"Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact","volume":"105","author":"MA Zeder","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1011538.ref026","article-title":"Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy","volume":"6","author":"A Janowicz","year":"2020","journal-title":"Microb Genom"},{"key":"ppat.1011538.ref027","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"},{"key":"ppat.1011538.ref028","first-page":"658","article-title":"The Paleopathology of the EB-MB and Middle Bronze Age Remains from Jericho (1957-58) Excavations","author":"D Brothwell","year":"1965","journal-title":"Kenyon KM Excavations at Jericho II London"},{"key":"ppat.1011538.ref029","unstructured":"Rashidi J, Ortner D, Frohlich B, Jonsdottir B. Brucellosis in Early Bronze Age Jordan and Bahrain: an analysis of possible cases of Brucella Spondylitits. In: American Journal of Physical Anthropology. WILEY-LISS DIV JOHN WILEY & SONS INC, 605 THIRD AVE, NEW YORK, NY 10158-0012 USA; 2001. p. 122\u2013123."},{"key":"ppat.1011538.ref030","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1126\/science.1170587","article-title":"Revealing the history of sheep domestication using retrovirus integrations","volume":"324","author":"B Chessa","year":"2009","journal-title":"Science"},{"key":"ppat.1011538.ref031","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.tig.2013.01.003","article-title":"A population genetics view of animal domestication","volume":"29","author":"G Larson","year":"2013","journal-title":"Trends Genet"},{"key":"ppat.1011538.ref032","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s12711-020-00545-7","article-title":"On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools","volume":"52","author":"E Ciani","year":"2020","journal-title":"Genet Sel Evol"},{"key":"ppat.1011538.ref033","doi-asserted-by":"crossref","first-page":"4085","DOI":"10.1016\/j.cub.2020.07.077","article-title":"Paternal Origins and Migratory Episodes of Domestic Sheep","volume":"30","author":"J Deng","year":"2020","journal-title":"Curr Biol"},{"key":"ppat.1011538.ref034","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/s41467-018-03206-y","article-title":"Convergent genomic signatures of domestication in sheep and goats","volume":"9","author":"FJ Alberto","year":"2018","journal-title":"Nat Commun"},{"key":"ppat.1011538.ref035","doi-asserted-by":"crossref","DOI":"10.3390\/genes13040613","article-title":"Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes","volume":"13","author":"K Machova","year":"2022","journal-title":"Genes (Basel)"},{"key":"ppat.1011538.ref036","doi-asserted-by":"crossref","first-page":"e0175425","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"},{"key":"ppat.1011538.ref037","doi-asserted-by":"crossref","first-page":"e0010404","DOI":"10.1371\/journal.pntd.0010404","article-title":"Human brucellosis: Widespread information deficiency hinders an understanding of global disease frequency","volume":"16","author":"CG Laine","year":"2022","journal-title":"PLoS Negl Trop Dis"},{"key":"ppat.1011538.ref038","doi-asserted-by":"crossref","first-page":"104865","DOI":"10.1016\/j.meegid.2021.104865","article-title":"Emerging diversity and ongoing expansion of the genus Brucella","volume":"92","author":"AM Whatmore","year":"2021","journal-title":"Infect Genet Evol"},{"key":"ppat.1011538.ref039","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/1471-2180-7-34","article-title":"Characterisation of the genetic diversity of Brucella by multilocus sequencing","volume":"7","author":"AM Whatmore","year":"2007","journal-title":"BMC Microbiol"},{"key":"ppat.1011538.ref040","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":"ppat.1011538.ref041","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/B978-0-12-809738-0.00011-9","volume-title":"Ortner\u2019s Identification of Pathological Conditions in Human Skeletal Remains (Third Edition)","author":"Charlotte A Roberts","year":"2019","edition":"3"},{"issue":"2","key":"ppat.1011538.ref042","doi-asserted-by":"crossref","first-page":"54","DOI":"10.5312\/wjo.v10.i2.54","article-title":"Osteoarticular manifestations of human brucellosis: a review","volume":"10","author":"SM Esmaeilnejad-Ganji","year":"2019","journal-title":"World journal of orthopedics"},{"key":"ppat.1011538.ref043","unstructured":"Ventura L, Arrizza L, Urbani V, Miranda G. Indagini macroscopiche, radiologiche e di laboratorio dei resti del Beato Sante Brancorsini (1343-1394); 2015."},{"key":"ppat.1011538.ref044","doi-asserted-by":"crossref","first-page":"e20983","DOI":"10.7554\/eLife.20983","article-title":"A molecular portrait of maternal sepsis from Byzantine Troy","volume":"6","author":"AM Devault","year":"2017","journal-title":"eLife"},{"key":"ppat.1011538.ref045","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/s42003-022-03527-1","article-title":"A 16(th) century Escherichia coli draft genome associated with an opportunistic bile infection","volume":"5","author":"GS Long","year":"2022","journal-title":"Commun Biol"},{"key":"ppat.1011538.ref046","doi-asserted-by":"crossref","first-page":"9822","DOI":"10.1038\/s41598-018-28091-9","article-title":"Differential preservation of endogenous human and microbial DNA in dental calculus and dentin","volume":"8","author":"AE Mann","year":"2018","journal-title":"Sci Rep"},{"key":"ppat.1011538.ref047","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1475-2859-5-13","article-title":"Brucella spp noncanonical LPS: structure, biosynthesis, and interaction with host immune system","volume":"5","author":"PG Cardoso","year":"2006","journal-title":"Microb Cell Fact"},{"key":"ppat.1011538.ref048","doi-asserted-by":"crossref","DOI":"10.3390\/ijms21207749","article-title":"Brucella Genomics: Macro and Micro Evolution","volume":"21","author":"M Suarez-Esquivel","year":"2020","journal-title":"Int J Mol Sci"},{"key":"ppat.1011538.ref049","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1111\/j.1574-6976.1998.tb00370.x","article-title":"Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?","volume":"22","author":"E Moreno","year":"1998","journal-title":"FEMS Microbiol Rev"},{"key":"ppat.1011538.ref050","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens11030377","article-title":"Pathogenicity and Its Implications in Taxonomy: The Brucella and Ochrobactrum Case","volume":"11","author":"E Moreno","year":"2022","journal-title":"Pathogens"},{"key":"ppat.1011538.ref051","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"J Robertson","year":"2018","journal-title":"Microb Genom"},{"key":"ppat.1011538.ref052","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"A Rambaut","year":"2016","journal-title":"Virus Evol"},{"key":"ppat.1011538.ref053","doi-asserted-by":"crossref","first-page":"e10216","DOI":"10.1371\/journal.pone.0010216","article-title":"Transcriptome analysis of the Brucella abortus BvrR\/BvrS two-component regulatory system","volume":"5","author":"C Viadas","year":"2010","journal-title":"PLoS One"},{"key":"ppat.1011538.ref054","doi-asserted-by":"crossref","first-page":"556795","DOI":"10.3389\/fmicb.2020.556795","article-title":"Outer Membrane Vesicles From Brucella melitensis Modulate Immune Response and Induce Cytoskeleton Rearrangement in Peripheral Blood Mononuclear Cells","volume":"11","author":"ED Avila-Calderon","year":"2020","journal-title":"Front Microbiol"},{"key":"ppat.1011538.ref055","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"D Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011538.ref056","doi-asserted-by":"crossref","first-page":"151","DOI":"10.21307\/pjm-2018-029","article-title":"Brucella\u2014Virulence Factors, Pathogenesis and Treatment","volume":"67","author":"P G\u0142owacka","year":"2018","journal-title":"Pol J Microbiol"},{"issue":"D1","key":"ppat.1011538.ref057","first-page":"D517","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"BP Alcock","year":"2020","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"ppat.1011538.ref058","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1146\/annurev.bi.42.070173.002351","article-title":"Mechanisms of antibiotic resistance in bacteria","volume":"42","author":"R Benveniste","year":"1973","journal-title":"Annual Review of Biochemistry"},{"issue":"8","key":"ppat.1011538.ref059","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1038\/nrmicro1464","article-title":"Multidrug-resistance efflux pumps? not just for resistance","volume":"4","author":"LJ Piddock","year":"2006","journal-title":"Nature Reviews Microbiology"},{"issue":"22","key":"ppat.1011538.ref060","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ppat.1011538.ref061","doi-asserted-by":"crossref","first-page":"8538","DOI":"10.1038\/s41598-018-26906-3","article-title":"Whole-genome sequencing and antimicrobial resistance in Brucella melitensis from a Norwegian perspective","volume":"8","author":"TB Johansen","year":"2018","journal-title":"Sci Rep"},{"key":"ppat.1011538.ref062","doi-asserted-by":"crossref","first-page":"6310","DOI":"10.1093\/nar\/gkx361","article-title":"A new model for ancient DNA decay based on paleogenomic meta-analysis","volume":"45","author":"L Kistler","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011538.ref063","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.3389\/fimmu.2019.01759","article-title":"Immune Response to Mucosal Brucella Infection","volume":"10","author":"R Lopez-Santiago","year":"2019","journal-title":"Front Immunol"},{"key":"ppat.1011538.ref064","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":"ppat.1011538.ref065","doi-asserted-by":"crossref","first-page":"e631","DOI":"10.1371\/journal.pone.0000631","article-title":"Brucella abortus uses a stealthy strategy to avoid activation of the innate immune system during the onset of infection","volume":"2","author":"E Barquero-Calvo","year":"2007","journal-title":"PLoS One"},{"key":"ppat.1011538.ref066","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.jgar.2022.02.005","article-title":"Antimicrobial resistance profiles of human Brucella melitensis isolates in three different microdilution broths: the first multicentre study in Bosnia and Herzegovina","volume":"29","author":"J Arapovic","year":"2022","journal-title":"J Glob Antimicrob Resist"},{"key":"ppat.1011538.ref067","doi-asserted-by":"crossref","first-page":"e1253","DOI":"10.1111\/tbed.14502","article-title":"The perspective of antibiotic therapeutic challenges of brucellosis in the Middle East and North African countries: Current situation and therapeutic management","volume":"69","author":"G Wareth","year":"2022","journal-title":"Transbound Emerg Dis"},{"key":"ppat.1011538.ref068","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s12711-018-0422-x","article-title":"Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes","volume":"50","author":"L Colli","year":"2018","journal-title":"Genet Sel Evol"},{"key":"ppat.1011538.ref069","first-page":"133","article-title":"A review of the Late Mesolithic in Italy and its implications for the Neolithic transition","author":"P Biagi","year":"2003","journal-title":"The widening harvest"},{"key":"ppat.1011538.ref070","first-page":"157","volume-title":"The widening harvest: the neolithic transition in Europe: looking back, looking forward","author":"R Skeates","year":"2003"},{"key":"ppat.1011538.ref071","first-page":"46","volume-title":"Agriculture, Pastoralism, and Mediterranean Landscapes in Prehistory","author":"G Barker","year":"2005"},{"key":"ppat.1011538.ref072","unstructured":"Rowley-Conwy P. Early domestic animals in Europe: imported or locally domesticated? In: Ammerman A, Biagi P, editors. The widening harvest: the neolithic transition in Europe: looking back, looking forward. vol. AIA Colloquia and Conference Papers; 6. Boston: Archaeological Institute of America; 2003. p. 99\u2013117. Available from: http:\/\/dro.dur.ac.uk\/3840\/."},{"issue":"9","key":"ppat.1011538.ref073","doi-asserted-by":"crossref","first-page":"4909","DOI":"10.1007\/s12520-019-00856-x","article-title":"Approaching sheep herds origins and the emergence of the wool economy in continental Europe during the Bronze Age","volume":"11","author":"S Sabatini","year":"2019","journal-title":"Archaeological and Anthropological Sciences"},{"key":"ppat.1011538.ref074","volume-title":"Fonti storiche della vita e risultati scientifici della ricognizione del corpo del Beato Sante","author":"Giancarlo Mandolini","year":"2015"},{"key":"ppat.1011538.ref075","volume-title":"Beato Sante Brancorsini e il Santuario di Mombaroccio","author":"Silvano Bracci","year":"2015"},{"key":"ppat.1011538.ref076","doi-asserted-by":"crossref","first-page":"3215","DOI":"10.1093\/nar\/gkp159","article-title":"New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains","volume":"37","author":"C Schwarz","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011538.ref077","first-page":"201314445","article-title":"Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments","author":"J Dabney","year":"2013","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ppat.1011538.ref078","article-title":"Extending the spectrum of DNA sequences retrieved from ancient bones and teeth","author":"I Glocke","year":"2017","journal-title":"Genome Research"},{"key":"ppat.1011538.ref079","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"S Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ppat.1011538.ref080","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"DE Wood","year":"2019","journal-title":"Genome Biol"},{"key":"ppat.1011538.ref081","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"R Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"ppat.1011538.ref082","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"VA Schneider","year":"2017","journal-title":"Genome Res"},{"issue":"14","key":"ppat.1011538.ref083","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"24","key":"ppat.1011538.ref084","doi-asserted-by":"crossref","first-page":"3407","DOI":"10.1016\/j.cub.2016.10.061","article-title":"17th century variola virus reveals the recent history of smallpox","volume":"26","author":"AT Duggan","year":"2016","journal-title":"Current Biology"},{"key":"ppat.1011538.ref085","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler","volume":"70","author":"A Prjibelski","year":"2020","journal-title":"Curr Protoc Bioinformatics"},{"issue":"1","key":"ppat.1011538.ref086","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"46","key":"ppat.1011538.ref087","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.21105\/joss.01990","article-title":"NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases","volume":"5","author":"K Eaton","year":"2020","journal-title":"Journal of Open Source Software"},{"issue":"14","key":"ppat.1011538.ref088","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":"13","key":"ppat.1011538.ref089","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.1093\/bioinformatics\/btt193","article-title":"mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters","volume":"29","author":"H J\u00f3nsson","year":"2013","journal-title":"Bioinformatics"},{"key":"ppat.1011538.ref090","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Y Benjamini","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011538.ref091","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.1038\/nbt.3704","article-title":"Measurement of bacterial replication rates in microbial communities","volume":"34","author":"CT Brown","year":"2016","journal-title":"Nat Biotechnol"},{"issue":"3","key":"ppat.1011538.ref092","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"NJ Croucher","year":"2015","journal-title":"Nucleic acids research"},{"issue":"5","key":"ppat.1011538.ref093","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"BQ Minh","year":"2020","journal-title":"Molecular Biology and Evolution"},{"key":"ppat.1011538.ref094","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"issue":"1","key":"ppat.1011538.ref095","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-018-2164-8","article-title":"Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity","volume":"19","author":"F Menardo","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"ppat.1011538.ref096","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","article-title":"SRST2: Rapid genomic surveillance for public health and hospital microbiology labs","volume":"6","author":"M Inouye","year":"2014","journal-title":"Genome Med"},{"key":"ppat.1011538.ref097","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","author":"KA Jolley","year":"2018","journal-title":"Wellcome Open Res"},{"key":"ppat.1011538.ref098","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1073\/pnas.78.1.454","article-title":"Estimation of evolutionary distances between homologous nucleotide sequences","volume":"78","author":"M Kimura","year":"1981","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ppat.1011538.ref099","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/sysbio\/syv068","article-title":"Fast Dating Using Least-Squares Criteria and Algorithms","volume":"65","author":"TH To","year":"2016","journal-title":"Systematic Biology"},{"issue":"1","key":"ppat.1011538.ref100","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"MA Suchard","year":"2018","journal-title":"Virus evolution"},{"key":"ppat.1011538.ref101","doi-asserted-by":"crossref","first-page":"3363","DOI":"10.1093\/molbev\/msaa163","article-title":"Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations","volume":"37","author":"S Duchene","year":"2020","journal-title":"Mol Biol Evol"},{"key":"ppat.1011538.ref102","doi-asserted-by":"crossref","first-page":"D274","DOI":"10.1093\/nar\/gkaa1018","article-title":"COG database update: focus on microbial diversity, model organisms, and widespread pathogens","volume":"49","author":"MY Galperin","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011538.ref103","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/B978-0-444-87877-9.50039-X","article-title":"Clustering large data sets","author":"L Kaufman","year":"1986","journal-title":"Pattern Recognition in Practice"},{"key":"ppat.1011538.ref104","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: A graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"PJ Rousseeuw","year":"1987","journal-title":"Journal of Computational and Applied Mathematics"},{"key":"ppat.1011538.ref105","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1017\/9781316686942.012","volume-title":"Human Dispersal and Species Movement: From Prehistory to the Present","author":"MA Zeder","year":"2017"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1011538","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,8,10]],"date-time":"2023-08-10T00:00:00Z","timestamp":1691625600000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011538","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T05:33:21Z","timestamp":1702877601000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011538"}},"subtitle":[],"editor":[{"given":"D. Ashley","family":"Robinson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,7,31]]},"references-count":105,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2023,7,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1011538","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1011538","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,31]]}}}