Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

Kirsten I Bos^{1

2}, Alexander Herbig^{1

2}, Jason Sahl³, Nicholas Waglechner⁴, Mathieu Fourment^{5

6

7

8}, Stephen A Forrest¹, Jennifer Klunk^{9

10}, Verena J Schuenemann¹, Debi Poinar⁹, Melanie Kuch⁹, G Brian Golding¹⁰, Olivier Dutour¹¹, Paul Keim³, David M Wagner³, Edward C Holmes^{5

6

7

8}, Johannes Krause^{1

2}, Hendrik N Poinar^{4

9

10

12}

Affiliations

¹ Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.
² Max Planck Institute for the Science of Human History, Jena, Germany.
³ Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States.
⁴ Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.
⁵ Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.
⁶ Charles Perkins Centre, The University of Sydney, Sydney, Australia.
⁷ School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.
⁸ Sydney Medical School, The University of Sydney, Sydney, Australia.
⁹ McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.
¹⁰ Department of Biology, McMaster University, Hamilton, Canada.
¹¹ Laboratoire d'anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, PACEA, Université Bordeaux, Bordeaux, France.
¹² Department of Biochemistry, McMaster University, Hamilton, Canada.

PMID: 26795402
PMCID: PMC4798955
DOI: 10.7554/eLife.12994

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

Kirsten I Bos et al. Elife. 2016.

. 2016 Jan 21:5:e12994.

doi: 10.7554/eLife.12994.

Authors

Affiliations

¹ Department of Archeological Sciences, University of Tübingen, Tübingen, Germany.
² Max Planck Institute for the Science of Human History, Jena, Germany.
³ Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States.
⁴ Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.
⁵ Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.
⁶ Charles Perkins Centre, The University of Sydney, Sydney, Australia.
⁷ School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.
⁸ Sydney Medical School, The University of Sydney, Sydney, Australia.
⁹ McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.
¹⁰ Department of Biology, McMaster University, Hamilton, Canada.
¹¹ Laboratoire d'anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, PACEA, Université Bordeaux, Bordeaux, France.
¹² Department of Biochemistry, McMaster University, Hamilton, Canada.

PMID: 26795402
PMCID: PMC4798955
DOI: 10.7554/eLife.12994

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.

Keywords: ancient DNA; epidemiology; global health; human history; infectious disease; microbial evolution; microbiology; pathogen genomics; yersinia pestis.

PubMed Disclaimer

Conflict of interest statement

The authors declare that no competing interests exist.

Figures

**Figure 1.. Photograph of rescue excavations at l’Observance in Marseille, France.**
LAPMO Université de Provence – URA 164 CNRS/AFAN. **DOI:** http://dx.doi.org/10.7554/eLife.12994.003

**Figure 2.. Coverage plots for all reconstructed Observance core genomes.**
Inner ring: GC content from low (brown, <30%) to high (orange, >55%). Outer concentric rings: from inner to outer, coverage plots of OBS107, 110, 116, 124, and 137 on a logarithmic scale. Axes are at 30x and 100x. Dots: SNPs (black = non-synonymous, grey = synonymous, white = intergenic). Outer ring (larger dots) is SNPs shared by all five strains. Inner rings (smaller dots) are associated with the strain immediately outside and are SNPs that are not shared by all five strains (but may be shared by 2–4 strains). Krzywinski, M. *et al.* Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639–1645 **DOI:** http://dx.doi.org/10.7554/eLife.12994.006

**Figure 3.. Phylogenetic tree for *Yersinia pestis*.**
(A) Maximum likelihood phylogeny of *Y. pestis* genomic SNPs showing the position of the Observance (OBS) lineage (red) relative to those of 130 modern (black) and three ancient strains (Black Death in green and Justinian Plague in blue). Modern strains from the third pandemic are shown in purple to highlight their close genetic relatedness. Monophyletic groups of sequences have been collapsed to improve clarity and are shown as triangles. The tree is rooted using single strain of *Y. pseudotuberculosis* (IP32953), with all derived SNPs removed to assist scaling, with branch lengths reflecting the number of nucleotide substitutions/SNP site. The length of the branch leading to the 0.PE3_Angola (AFR) lineage was reduced because its excessive length adversely affected the scaling of the tree. Location abbreviations are as follows: CNH (China), GEO (Georgia), FSU (Former Soviet Union), MNG (Mongolia), NPL (Nepal), IRN (Iran), AFR (Africa), USA (United States of America), MDG (Madagascar), IND (India). (B) Expanded phylogeny schematic to show the relative positions of the Black Death and the Observance lineages. Numbers on branches correspond to SNPs. **DOI:** http://dx.doi.org/10.7554/eLife.12994.007

See this image and copyright information in PMC

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Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

Affiliations

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

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MeSH terms

LinkOut - more resources

Full Text Sources

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Medical