title: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death.
abstract: Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348-1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.
authors.affiliation: Institut für Naturwissenschaftliche Archäologie, University of Tübingen, 72072 Tübingen, Germany.
authors.forename: Verena J
authors.initials: VJ
authors.lastname: Schuenemann
authors.forename: Kirsten
authors.initials: K
authors.lastname: Bos
authors.forename: Sharon
authors.initials: S
authors.lastname: DeWitte
authors.forename: Sarah
authors.initials: S
authors.lastname: Schmedes
authors.forename: Joslyn
authors.initials: J
authors.lastname: Jamieson
authors.forename: Alissa
authors.initials: A
authors.lastname: Mittnik
authors.forename: Stephen
authors.initials: S
authors.lastname: Forrest
authors.forename: Brian K
authors.initials: BK
authors.lastname: Coombes
authors.forename: James W
authors.initials: JW
authors.lastname: Wood
authors.forename: David J D
authors.initials: DJ
authors.lastname: Earn
authors.forename: William
authors.initials: W
authors.lastname: White
authors.forename: Johannes
authors.initials: J
authors.lastname: Krause
authors.forename: Hendrik N
authors.initials: HN
authors.lastname: Poinar
mesh_terms: D000328:Adult; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D001842:Bone and Bones / Q000378:metabolism / Q000382:microbiology; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D005060:Europe / Q000453:epidemiology; D005260:Female; D014644:Genetic Variation; D049691:History, Medieval; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D058873:Pandemics / Q000266:history; D010930:Plague / Q000453:epidemiology / Q000235:genetics / Q000382:microbiology*; D010957:Plasmids / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014070:Tooth / Q000378:metabolism / Q000382:microbiology; D014774:Virulence / Q000235:genetics; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D004269:DNA, Bacterial; D004272:DNA, Mitochondrial