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. 2011 Sep 20;108(38):E746-52.
doi: 10.1073/pnas.1105107108. Epub 2011 Aug 29.

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

Verena J Schuenemann  1 , Kirsten Bos, Sharon DeWitte, Sarah Schmedes, Joslyn Jamieson, Alissa Mittnik, Stephen Forrest, Brian K Coombes, James W Wood, David J D Earn, William White, Johannes Krause, Hendrik N Poinar
Affiliations

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

Verena J Schuenemann et al. Proc Natl Acad Sci U S A. .

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
The excavation at ES from 1986 to 1988 (A) and sampling at the Museum of London (B). Photos reproduced courtesy of the Museum of London.
Fig. 2.
Fig. 2.
Positional relationship of the sequences reported for medieval Y. pestis. (A) Quantitative PCR assay for the caf1M locus of the pMT1 plasmid. (B) Chromosomal sequence data for s19 (9) showing positions of two synonymous substitutions in the DNA helicase II gene and absence of the CTA SNP required for branch 2 designation (boxed nucleotides). (C) Solexa consensus (minimum of two-fold coverage) compared with 14 modern Y. pestis variants shown with positional information for genes on the PCP1 plasmid (rop, plasmid replication regulatory protein; pim, pesticin immunity protein; pst, pesticin; pla, plasminogen activator gene). Transcriptional polarity (45) is indicated by arrows. Identity is shown in green; the region between 3,000 and 4,200 is not considered (in the text). (D) Alignment of the medieval Y. pestis pPCP1 consensus against 14 modern variants showing presence of an indel common to branch 2 and ancestral isolates.
Fig. 3.
Fig. 3.
GC content and DNA coverage for the consensus sequences of mtDNA, Y. pestis pPCP1 (1–9,612 bp), pPCP1 (4,200–9,612 and 1–3,000 bp), and the excluded region pPCP1 (3,000–4,200 bp).
Fig. 4.
Fig. 4.
Nucleotide misincorporation patterns for both the ES mtDNA consensus sequences and the complete pPCP1 (1–9,612 bp), including the section showing alignment to contaminating modern vector DNA (3,000–4,200 bp), and the entire pPCP1, excluding the mismapping region (1–3,000 and 4,200–9,612 bp).
Fig. 5.
Fig. 5.
Graphical depiction of length distribution vs. number of fragments for different target regions.
Fig. P1.
Fig. P1.
(A) Skeletons removed from East Smithfield Gravesite in 1986–1988. (B) Our sampling strategy was to remove molars from the jaws, extract the powdered roots for DNA, and replace the molars back into the appropriate positions.
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References

    1. Wheelis M. Biological warfare at the 1346 siege of Caffa. Emerg Infect Dis. 2002;8:971–975. - PMC - PubMed
    1. World Health Organization Zoonotic Infections. 2011. Available at www.who.int/vaccine_research/diseases/zoonotic/en/index3.html. Accessed August 11, 2011.
    1. Stenseth NC, et al. Plague: Past, present, and future. PLoS Med. 2008;5:e3. - PMC - PubMed
    1. Twigg G. The Black Death: A Biological Reappraisal. London: Batsford Academic; 1984.
    1. Scott S, Duncan CJ. The Biology of Plagues. Cambridge, UK: Cambridge University Press; 2001. - PubMed

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