Yersinia pestis, ancient DNA and the Black Death


The Black Death is the name given to a pandemic which killed up to a third of the European population between 1347 and 1352. Over the next three hundred years this pandemic was followed by further plagues of lesser mortality. These are historically ascribed to bubonic plague whose aetiological agent is the bacterium Yersinia pestis.

Recently, DNA specific for Y. pestis was amplified from 16th and 18th century human teeth believed to be French plague victims (Drancourt et al., 1998) and 14th century French Black Death victims (Raoul et al, 2000). The lead authors of these reports now believe that the consideration of any cause for the Black Death other than Y. pestis is now speculative.

Ancient DNA analysis:

The study of aDNA involves the extraction and analysis of DNA from the remains of organisms preserved as fossils, skeletons or mummified tissues. Studies are hampered by extremely low levels of preservation, often coupled by the presence of much greater levels of modern contaminants. Characteristically only short aDNA fragments can be amplified and easy amplification of longer fragments is an indication that contamination has occurred.

In the case of Y. pestis, fatal infection would not be expected to leave any specific bony changes, so no osteological confirmation is available and any retrospective diagnosis is completely DNA-based. Two studies from the same research group reported the successful extraction and sequencing of Y. pestis-specific DNA retrieved from the dental pulp cavities of plague victims. Findings that pathogen-specific DNA can be recovered from this source in systemically infected animals have led Drancourt et al (1998) to hypothesise that teeth provide a lasting, contamination-free refuge where pathogen aDNA may survive.


  • Previous extraction techniques are unsuited to preventing bacterial contamination of the DNA extract. Dental enamel is extremely resistant to diagenesis, but may be permeable to contaminating DNA using both the ‘ground’ and the ‘scraped’ methodologies. Encasing teeth in silicone appears to act as a barrier to movement of DNA between the tooth and the gloved hand and this may explain the reduction in contamination with this method.
  • No evidence of surviving Y. pestis DNA was found in this study, despite the examination of a large number of samples from five mass graves, including two well-documented plague pits and several other probable plague-victim burial sites.
  • Previous studies reported successful direct sequencing from ancient teeth. This implies a low-level of contaminating non-Y. pestis bacterial DNA, despite using a dentine extraction method demonstrated to be contamination prone. This raises two questions:
    1. why such levels of contaminating DNA from other bacteria were found in this study, and
    2. why it was not possible to amplify Y. pestis-specific DNA from samples of plague victims that yield what appears to be authentic human DNA.
  • It is possible that diagenetic conditions in the relatively drier and warmer Southern French locations were more conducive to ancient DNA survival than those of north-western Europe. However, aDNA studies have repeatedly demonstrated an inverse correlation between average temperature, humidity and aDNA retrieval. It is, therefore, surprising that warmer locations would be more successful.
  • An alternative environmental variable is groundwater. An inverse correlation has been noted between sample survival and exposure to water. However the ability to amplify host DNA suggests survival is not an issue.
  • A further explanation is that the individuals from whom the samples derive were either infected by a Y. pestis strain lacking the plasmid-located sites for amplification or not infected with Y. pestis (because they were not victims of the Black Death, or because the infection did not seed the pulp cavity, or because the Black Death and subsequent plagues were not caused by Y. pestis). The first hypothesis is unlikely as the plasmid containing the pla gene is a consistent feature of contemporary isolates. The second hypothesis is plausible. There is no guarantee that bacteria causing a systemic infection entered the teeth. It is, therefore, possible that Y. pestis may not have been present in the teeth specimens but that infection by this bacteria caused death. The third hypothesis is controversial, but cannot immediately be discounted.


Gilbert, M.T.P, Cuccui, J. White, W, Lynnerup, N, Titball, R.W, Cooper, A and Prentice, M.B. 2004. Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology 150: 341-354.

2 responses to “Yersinia pestis, ancient DNA and the Black Death

  1. Pingback: Vidi XI « Archaeoastronomy

  2. Pingback: Love in Mendel’s Garden | Bitesize Bio

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