The paper for 22nd May journal club presents the genome of a Yersinia pestis strain isolated from a victim of the Black Death from the 14th century.

The authors developed a novel capture array to fish out bacterial DNA from the dental pulp of a plague victim buried in London’s East Smithfield cemetery.  The captured sequences were then sequenced and mapped to a contemporary Y. pestis strain. Differences in gene content and synteny, as well as polymorphic sites, were investigated through a combination of BLAST searches and reference-guided assembly of sequence reads.  The study concludes that the 14th century strain does not contain any unique polymorphisms, or significant genetic changes, that would make it more virulent than modern strains.

The authors go on to place the 14th century strain in the phylogenetic context of other Yersinia strains, and show that it sits “close to the ancestral node of all extant human pathogenic Y. pestis strains”.  Using a Bayesian coalescent method, they estimate a date for the emergence of human-associated Y. pestis to between 1282–1343 AD, calling into question the commonly accepted hypothesis that the earlier Justinian Plague was caused by the same pathogen.

The authors feel that the study of ancient pathogens can inform the study of mechanisms of host adaptation and pandemic spread of modern pathogens.  The authors close by stating “At our current resolution, we posit that molecular changes in pathogens are but one component of a constellation of factors contributing to changing infectious disease prevalence and severity, where genetics of the host population, climate, vector dynamics, social conditions and synergistic interactions with concurrent diseases should be foremost in discussions of population susceptibility to infectious disease and host–pathogen relationships with reference to Y. pestis infections.”

Discussion points

  • What are the drawbacks of the capture array/sequencing method used?
  • Is the method used sufficient to support the conclusions the authors have drawn?
  • Do you feel that the study of ancient pathogens is useful for informing the study of contemporary strains?
  • Is the conclusion that the causative agent of the Black Death is distinct from earlier supposed plagues convincing?

Links to other relevant discussions

The paper received quite a bit of coverage when it was published, thought I’d link to the NY Times article and the TWiM podcast that discussed a bit about the previous work done.