Phylogenetic Analysis of the Black Plague Microbiology

Phylogenetic Analysis of the Black Plague

Microbiology Article Review

The first successful sequencing of an ancient bacterial pathogen was reported in the October 27, 2011 issue of Nature (Bos et al., 2011). Samples of Yersinia pestis, otherwise known as the Black Death, the Black Plague, or the bubonic plague, were recovered from the teeth and bones of victims interred in a 14th century burial ground outside of London, England.

Y. pestis DNA was recovered from five teeth and the authors found a C. To T. damage pattern previously shown to be characteristic of endogenous ancient DNA. The recovered DNA fragment length averaged around 55.5 base pairs, which is also consistent with ancient DNA. These findings help to confirm the recovered samples had not been contaminated with extant strains of Y. pestis.

After validating the technical approach, which was a capture-based array method, the authors were faced with aligning the very short reads in order to compare gene locations in the ancient genome to extant Y. pestis strains. To limit complications that could arise from mixing Y. pestis genomes from multiple victims, the authors sequenced samples from only one victim. Of the 2,105 contigs matching the reference strain (CO92), 10 revealed altered gene arrangements. One of the ancient contigs having an altered arrangement matched Y. pseudotuberculosis and the Mictrotus 91001, Angola, Pestoides F. And B42003004 Y. pestis strain, which are both ancestral to all Y. pestis strains known to infect humans.

The Y. pestis genome contains a parent genome of around 4.6 megabases, along with three plasmids (pCD1, pMT1, and pPCP1) that were acquired during evolution. Two of these plasmids, pMT1 and pPCP1, confer special tools for infecting mammals. When compared to the Y. pestis reference sequence (CO92) a total of 97 single nucleotide differences were found in the genome, but only 2 and 4 differences in pCD1 and pMT1. This finding suggests Y. pestis has been under strong evolutionary pressure for the past 660 years that has helped maintain a high degree of conservation.

Of the 97 single nucleotide differences identified, 27 have never been found in contemporary strains of Y. pestis. A comparison between the ancestral Y. pseudotuberculosis genome and the ancient Y. pestis revealed complete sequence identity at the 97 positions, which suggests these single nucleotide differences have emerged during this past 660 years.

Phylogenetic analysis using 1,694 nucleotide positions previously identified as useful for this purpose revealed that the ancient Y. pestis genome differed from all 17 extant strains at only 2 of these positions for 3 of the 4 victims, while the fourth victim differed at 3 positions. This places the ancient strain from these victims into branch 1 Y. pestis. This finding suggests multiple strains were ravaging London at the time, or microevolutionary changes were occurring during the outbreak. Support for a microevolutionary mechanism was found when one nucleotide position known to be polymorphic in extant Y. pestis strains was found to also be polymorphic in a single victim, and between victims, from 660 years ago. Another 18 positions were found have sequence unique to the ancient genome and are not polymorphic in the extant strains, which could be of considerable interest because the ancient genome is suspected of being considerably more virulent.