title: Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus.
abstract: The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.
authors.affiliation: Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.|Max Planck Institute for the Science of Human History, Jena, Germany.
authors.forename: Kirsten I
authors.initials: KI
authors.lastname: Bos
authors.affiliation: Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.|Max Planck Institute for the Science of Human History, Jena, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Herbig
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States.
authors.forename: Jason
authors.initials: J
authors.lastname: Sahl
authors.affiliation: Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Waglechner
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.|Charles Perkins Centre, The University of Sydney, Sydney, Australia.|School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.|Sydney Medical School, The University of Sydney, Sydney, Australia.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Fourment
authors.affiliation: Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Forrest
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.|Department of Biology, McMaster University, Hamilton, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Klunk
authors.affiliation: Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.
authors.forename: Verena J
authors.initials: VJ
authors.lastname: Schuenemann
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.
authors.forename: Debi
authors.initials: D
authors.lastname: Poinar
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.
authors.forename: Melanie
authors.initials: M
authors.lastname: Kuch
authors.affiliation: Department of Biology, McMaster University, Hamilton, Canada.
authors.forename: G Brian
authors.initials: GB
authors.lastname: Golding
authors.affiliation: Laboratoire d'anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, PACEA, Université Bordeaux, Bordeaux, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Dutour
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States.
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States.
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.|Charles Perkins Centre, The University of Sydney, Sydney, Australia.|School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.|Sydney Medical School, The University of Sydney, Sydney, Australia.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.|Max Planck Institute for the Science of Human History, Jena, Germany.
authors.forename: Johannes
authors.identifier: http://orcid.org/0000-0001-9144-3920
authors.initials: J
authors.lastname: Krause
authors.affiliation: Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.|McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.|Department of Biology, McMaster University, Hamilton, Canada.|Department of Biochemistry, McMaster University, Hamilton, Canada.
authors.forename: Hendrik N
authors.initials: HN
authors.lastname: Poinar
mesh_terms: D005060:Europe / Q000453:epidemiology; D016680:Genome, Bacterial; D005838:Genotype; D049668:History, 15th Century; D049669:History, 16th Century; D049670:History, 17th Century; D049671:History, 18th Century; D017720:Molecular Epidemiology; D010930:Plague / Q000453:epidemiology* / Q000266:history*; D015010:Yersinia pestis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*
keywords: ancient DNA; epidemiology; global health; human history; infectious disease; microbial evolution; microbiology; pathogen genomics; yersinia pestis