A draft genome of Yersinia pestis from victims of the Black Death

Kirsten I. Bos, Verena J. Schuenemann, G. Brian Golding, Hernãn A. Burbano, Nicholas Waglechner, Brian K. Coombes, Joseph B. McPhee, Sharon N. Dewitte, Matthias Meyer, Sarah Schmedes, James William Wood, David J.D. Earn, D. Ann Herring, Peter Bauer, Hendrik N. Poinar, Johannes Krause

Research output: Contribution to journalArticle

312 Citations (Scopus)

Abstract

Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.

Original languageEnglish (US)
Pages (from-to)506-510
Number of pages5
JournalNature
Volume478
Issue number7370
DOIs
StatePublished - Oct 27 2011

Fingerprint

Yersinia pestis
Plague
Genome
Microbial Genetics
Yersinia Infections
Infection
DNA Sequence Analysis
England
Communicable Diseases
Virulence
Phenotype
Mortality
Research

All Science Journal Classification (ASJC) codes

  • General

Cite this

Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., ... Krause, J. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-510. https://doi.org/10.1038/nature10549
Bos, Kirsten I. ; Schuenemann, Verena J. ; Golding, G. Brian ; Burbano, Hernãn A. ; Waglechner, Nicholas ; Coombes, Brian K. ; McPhee, Joseph B. ; Dewitte, Sharon N. ; Meyer, Matthias ; Schmedes, Sarah ; Wood, James William ; Earn, David J.D. ; Herring, D. Ann ; Bauer, Peter ; Poinar, Hendrik N. ; Krause, Johannes. / A draft genome of Yersinia pestis from victims of the Black Death. In: Nature. 2011 ; Vol. 478, No. 7370. pp. 506-510.
@article{7a93c4124a754019b5716244ded9f490,
title = "A draft genome of Yersinia pestis from victims of the Black Death",
abstract = "Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.",
author = "Bos, {Kirsten I.} and Schuenemann, {Verena J.} and Golding, {G. Brian} and Burbano, {Hern{\~a}n A.} and Nicholas Waglechner and Coombes, {Brian K.} and McPhee, {Joseph B.} and Dewitte, {Sharon N.} and Matthias Meyer and Sarah Schmedes and Wood, {James William} and Earn, {David J.D.} and Herring, {D. Ann} and Peter Bauer and Poinar, {Hendrik N.} and Johannes Krause",
year = "2011",
month = "10",
day = "27",
doi = "10.1038/nature10549",
language = "English (US)",
volume = "478",
pages = "506--510",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7370",

}

Bos, KI, Schuenemann, VJ, Golding, GB, Burbano, HA, Waglechner, N, Coombes, BK, McPhee, JB, Dewitte, SN, Meyer, M, Schmedes, S, Wood, JW, Earn, DJD, Herring, DA, Bauer, P, Poinar, HN & Krause, J 2011, 'A draft genome of Yersinia pestis from victims of the Black Death', Nature, vol. 478, no. 7370, pp. 506-510. https://doi.org/10.1038/nature10549

A draft genome of Yersinia pestis from victims of the Black Death. / Bos, Kirsten I.; Schuenemann, Verena J.; Golding, G. Brian; Burbano, Hernãn A.; Waglechner, Nicholas; Coombes, Brian K.; McPhee, Joseph B.; Dewitte, Sharon N.; Meyer, Matthias; Schmedes, Sarah; Wood, James William; Earn, David J.D.; Herring, D. Ann; Bauer, Peter; Poinar, Hendrik N.; Krause, Johannes.

In: Nature, Vol. 478, No. 7370, 27.10.2011, p. 506-510.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A draft genome of Yersinia pestis from victims of the Black Death

AU - Bos, Kirsten I.

AU - Schuenemann, Verena J.

AU - Golding, G. Brian

AU - Burbano, Hernãn A.

AU - Waglechner, Nicholas

AU - Coombes, Brian K.

AU - McPhee, Joseph B.

AU - Dewitte, Sharon N.

AU - Meyer, Matthias

AU - Schmedes, Sarah

AU - Wood, James William

AU - Earn, David J.D.

AU - Herring, D. Ann

AU - Bauer, Peter

AU - Poinar, Hendrik N.

AU - Krause, Johannes

PY - 2011/10/27

Y1 - 2011/10/27

N2 - Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.

AB - Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.

UR - http://www.scopus.com/inward/record.url?scp=80054987989&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80054987989&partnerID=8YFLogxK

U2 - 10.1038/nature10549

DO - 10.1038/nature10549

M3 - Article

C2 - 21993626

AN - SCOPUS:80054987989

VL - 478

SP - 506

EP - 510

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7370

ER -

Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature. 2011 Oct 27;478(7370):506-510. https://doi.org/10.1038/nature10549