{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T19:11:34Z","timestamp":1785784294683,"version":"3.56.0"},"reference-count":45,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2021,5,1]],"date-time":"2021-05-01T00:00:00Z","timestamp":1619827200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,5,1]],"date-time":"2021-05-01T00:00:00Z","timestamp":1619827200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,4,9]],"date-time":"2021-04-09T00:00:00Z","timestamp":1617926400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["2901391021"],"award-info":[{"award-number":["2901391021"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["390870439"],"award-info":[{"award-number":["390870439"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CRC 1266"],"award-info":[{"award-number":["CRC 1266"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EXC 2150 \\u2013 ROOTS"],"award-info":[{"award-number":["EXC 2150 \\u2013 ROOTS"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2021,5]]},"DOI":"10.1016\/j.isci.2021.102419","type":"journal-article","created":{"date-parts":[[2021,4,21]],"date-time":"2021-04-21T00:13:57Z","timestamp":1618964037000},"page":"102419","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":20,"title":["Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city L\u00fcbeck"],"prefix":"10.1016","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3677-1504","authenticated-orcid":false,"given":"Magdalena","family":"Haller","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3170-8514","authenticated-orcid":false,"given":"Kimberly","family":"Callan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian","family":"Susat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna Lena","family":"Flux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Immel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andre","family":"Franke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1176-1166","authenticated-orcid":false,"given":"Alexander","family":"Herbig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"Krause","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5237-1899","authenticated-orcid":false,"given":"Anne","family":"Kupczok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerhard","family":"Fouquet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Hummel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9867-4219","authenticated-orcid":false,"given":"Dirk","family":"Rieger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Almut","family":"Nebel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9435-2872","authenticated-orcid":false,"given":"Ben","family":"Krause-Kyora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2021.102419_bib1","doi-asserted-by":"crossref","first-page":"e1002776","DOI":"10.1371\/journal.ppat.1002776","article-title":"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.isci.2021.102419_bib2","doi-asserted-by":"crossref","first-page":"e1007261","DOI":"10.1371\/journal.pgen.1007261","article-title":"A genomic overview of the population structure of Salmonella","volume":"14","author":"Alikhan","year":"2018","journal-title":"PLoS Genet."},{"key":"10.1016\/j.isci.2021.102419_bib3","doi-asserted-by":"crossref","first-page":"3683","DOI":"10.1016\/j.cub.2017.10.025","article-title":"The stone age plague and its persistence in Eurasia","volume":"27","author":"Andrades Valtue\u00f1a","year":"2017","journal-title":"Curr. Biol."},{"key":"10.1016\/j.isci.2021.102419_bib4","series-title":"The Black Death, 1346\u20131353: The Complete History","author":"Benedictow","year":"2017"},{"key":"10.1016\/j.isci.2021.102419_bib5","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/S0140-6736(05)67181-4","article-title":"Typhoid and paratyphoid fever","volume":"366","author":"Bhan","year":"2005","journal-title":"Lancet"},{"key":"10.1016\/j.isci.2021.102419_bib6","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.crpv.2008.02.002","article-title":"Environment and excavation. Pre-lab impacts on ancient DNA analyses","volume":"7","author":"Bollongino","year":"2008","journal-title":"Comptes. Rendus. Palevol."},{"key":"10.1016\/j.isci.2021.102419_bib7","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature10549","article-title":"A draft genome of Yersinia pestis from victims of the Black Death","volume":"478","author":"Bos","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.isci.2021.102419_bib10","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1111\/1475-4754.t01-1-00071","article-title":"The survival of organic matter in bone: a review","volume":"44","author":"Collins","year":"2002","journal-title":"Archaeometry"},{"key":"10.1016\/j.isci.2021.102419_bib11","doi-asserted-by":"crossref","first-page":"5482","DOI":"10.1126\/science.289.5482.1139b","article-title":"Ancient DNA. Do it right or not at all","volume":"289","author":"Cooper","year":"2000","journal-title":"Science"},{"key":"10.1016\/j.isci.2021.102419_bib12","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1086\/649541","article-title":"Global trends in typhoid and paratyphoid fever","volume":"50","author":"Crump","year":"2010","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.isci.2021.102419_bib13","series-title":"Die Hanse","author":"Dollinger","year":"1998"},{"key":"10.1016\/j.isci.2021.102419_bib14","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":"Duggan","year":"2016","journal-title":"Curr. Biol."},{"key":"10.1016\/j.isci.2021.102419_bib15","series-title":"Katastrophen im Sp\u00e4tmittelalter","author":"Fouquet","year":"2011"},{"key":"10.1016\/j.isci.2021.102419_bib16","series-title":"Die Arch\u00e4ologie des Mittelalters und Bauforschung im Hanseraum","first-page":"217","article-title":"Und das Wasser flie\u00dft in R\u00f6hren. Wasserversorgung und Wasserk\u00fcnste in L\u00fcbeck","author":"Grabowski","year":"1993"},{"key":"10.1016\/j.isci.2021.102419_bib17","series-title":"Das Hansische Kontor zu Bergen und die L\u00fcbecker Bergenfahrer: International Workshop L\u00fcbeck 2003","author":"Gra\u00dfmann","year":"2005"},{"key":"10.1016\/j.isci.2021.102419_bib18","doi-asserted-by":"crossref","first-page":"e1001134","DOI":"10.1371\/journal.ppat.1001134","article-title":"Distinct clones of Yersinia pestis caused the black death","volume":"6","author":"Haensch","year":"2010","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.isci.2021.102419_bib19","series-title":"H\u00e4user und H\u00f6fe in L\u00fcbeck. Historische, arch\u00e4ologische und baugeschichtliche Beitr\u00e4ge zur Geschichte der Hansestadt im Sp\u00e4tmittelalter und in der fr\u00fchen Neuzeit","author":"Hammel-Kiesow","year":"2006"},{"key":"10.1016\/j.isci.2021.102419_bib20","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/s13059-019-1903-0","article-title":"HOPS: automated detection and authentication of pathogen DNA in archaeological remains","volume":"20","author":"H\u00fcbler","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2021.102419_bib21","series-title":"Kieler Werkst\u00fccke: Reihe A, Beitr\u00e4ge zur schleswig-holsteinischen und skandinavischen Geschichte 12","article-title":"Die Pest in Schleswig-Holstein von 1350 bis 1547\/48: Eine sozialgeschichtliche Studie \u00fcber eine wiederkehrende Katastrophe","author":"Ibs","year":"1994"},{"key":"10.1016\/j.isci.2021.102419_bib22","first-page":"97","article-title":"Die Pest als Interpretationsproblem mittelalterlicher und fr\u00fchneuzeitlicher Massengr\u00e4ber","volume":"13","author":"Kahlow","year":"2007","journal-title":"Bulletin der Schweizerischen Gesellschaft f\u00fcr Anthropologie"},{"key":"10.1016\/j.isci.2021.102419_bib23","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1038\/s41559-020-1106-9","article-title":"Emergence of human-adapted Salmonella enterica is linked to the Neolithization process","volume":"4","author":"Key","year":"2020","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.isci.2021.102419_bib8","series-title":"Die Chroniken der nieders\u00e4chsischen St\u00e4dte. L\u00fcbeck. Band 1","author":"Koppmann","year":"1884"},{"key":"10.1016\/j.isci.2021.102419_bib9","series-title":"Die Chroniken der nieders\u00e4chsischen St\u00e4dte. L\u00fcbeck. Band 2","author":"Koppmann","year":"1899"},{"key":"10.1016\/j.isci.2021.102419_bib24","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1038\/s41467-018-03857-x","article-title":"Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans","volume":"9","author":"Krause-Kyora","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2021.102419_bib25","doi-asserted-by":"crossref","first-page":"e36666","DOI":"10.7554\/eLife.36666","article-title":"Neolithic and medieval virus genomes reveal complex evolution of hepatitis B","volume":"7","author":"Krause-Kyora","year":"2018","journal-title":"Elife"},{"key":"10.1016\/j.isci.2021.102419_bib26","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.isci.2021.102419_bib27","series-title":"Arch\u00e4ologie in L\u00fcbeck. Erkenntnisse von Arch\u00e4ologie und Bauforschung zur Geschichte und Vorgeschichte der Hansestadt 3","first-page":"97","article-title":"Vom Brunnenwasser zum \"Kunstwasser\" \u2013 die Wasserversorgung im mittelalterlichen und fr\u00fchneuzeitlichen L\u00fcbeck","author":"L\u00fcdecke","year":"1980"},{"key":"10.1016\/j.isci.2021.102419_bib28","series-title":"L\u00fcbecker Schriften zu Arch\u00e4ologie und Kulturgeschichte 26","first-page":"139","article-title":"Arch\u00e4ologische Untersuchungen der Massenbestattungen am Heiligen-Geist-Hospital zu L\u00fcbeck: Auswertung der Befunde und Funde","author":"L\u00fctgert","year":"2002"},{"key":"10.1016\/j.isci.2021.102419_bib30","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O'Leary","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2021.102419_bib31","series-title":"L\u00fcbecker Schriften zu Arch\u00e4ologie und Kulturgeschichte 24","first-page":"323","article-title":"Anthropologische Untersuchungen der Skelettreste aus einem Pestmassengrab am Heiligen-Geist-Hospital zu L\u00fcbeck","author":"Prechel","year":"1996"},{"key":"10.1016\/j.isci.2021.102419_bib32","series-title":"L\u00fcbecker Schriften zu Arch\u00e4ologie und Kulturgeschichte 26","first-page":"245","article-title":"Eine L\u00fcbecker Population von 1350 \u2013 Krankheiten und Mangelerscheinungen","author":"Prechel","year":"2002"},{"key":"10.1016\/j.isci.2021.102419_bib33","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.tmaid.2011.11.001","article-title":"Salmonella infections: an update on epidemiology, management, and prevention","volume":"9","author":"S\u00e1nchez-Vargas","year":"2011","journal-title":"Trav. Med. Infect. Dis."},{"key":"10.1016\/j.isci.2021.102419_bib34","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1126\/science.1238286","article-title":"Genome-wide comparison of medieval and modern Mycobacterium leprae","volume":"341","author":"Schuenemann","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.isci.2021.102419_bib35","doi-asserted-by":"crossref","first-page":"e1006997","DOI":"10.1371\/journal.ppat.1006997","article-title":"Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe","volume":"14","author":"Schuenemann","year":"2018","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.isci.2021.102419_bib36","series-title":"Daily Life in Medieval Europe","author":"Singman","year":"1999"},{"key":"10.1016\/j.isci.2021.102419_bib37","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1016\/j.chom.2016.05.012","article-title":"Historical Y. pestis genomes reveal the European black death as the source of ancient and modern plague pandemics","volume":"19","author":"Spyrou","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.isci.2021.102419_bib38","doi-asserted-by":"crossref","first-page":"4470","DOI":"10.1038\/s41467-019-12154-0","article-title":"Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes","volume":"10","author":"Spyrou","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2021.102419_bib39","doi-asserted-by":"crossref","first-page":"14628","DOI":"10.1038\/s41598-020-71530-9","article-title":"Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic","volume":"10","author":"Susat","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2021.102419_bib40","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1017\/S0950268899004379","article-title":"Host adapted serotypes of Salmonella enterica","volume":"125","author":"Uzzau","year":"2000","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.isci.2021.102419_bib41","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/s41559-017-0446-6","article-title":"Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico","volume":"2","author":"V\u00e5gene","year":"2018","journal-title":"Nat. Ecol. Evol."},{"key":"10.1016\/j.isci.2021.102419_bib42","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev-genom-091416-035526","article-title":"A robust framework for microbial archaeology","volume":"31","author":"Warinner","year":"2017","journal-title":"Annu. Rev. Genomics Hum. Genet."},{"key":"10.1016\/j.isci.2021.102419_bib43","first-page":"153","volume":"93","author":"World Health Organization","year":"2018"},{"key":"10.1016\/j.isci.2021.102419_bib44","doi-asserted-by":"crossref","first-page":"12973","DOI":"10.1038\/s41598-017-13481-2","article-title":"Trade routes and plague transmission in pre-industrial Europe","volume":"7","author":"Yue","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.isci.2021.102419_bib45","doi-asserted-by":"crossref","first-page":"2420","DOI":"10.1016\/j.cub.2018.05.058","article-title":"Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive para C lineage for millennia","volume":"28","author":"Zhou","year":"2018","journal-title":"Curr. Biol."},{"key":"10.1016\/j.isci.2021.102419_bib46","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004221003874?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004221003874?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T02:44:51Z","timestamp":1778899491000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004221003874"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5]]},"references-count":45,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,5]]}},"alternative-id":["S2589004221003874"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2021.102419","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2021,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city L\u00fcbeck","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2021.102419","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s).","name":"copyright","label":"Copyright"}],"article-number":"102419"}}