Yersinia pestis. How immediate our reaction can be to the species name of this bacterium, making us conjure up images of pestilence. As its discoverer, Alexander Yersin, wrote in 1894 of an outbreak of bubonic plague in Hong Kong, this is the "bacille de la peste." (Working independently, Kitasato Shibasaburo also characterized the plague bacterium at nearly the exact same time.) Currently, there are relatively few human plague cases but human history records three devastating plague pandemics: the first from 541 to 750, the second reached Europe in 1348 – often called the Medieval Black Death – and lasted until late in the 18th century. The third, starting in the 1890s, led to the identification of Y. pestis. Written descriptions of the Black Death suggested Y. pestis was the infectious agent. Yet, some historians challenged this notion and proposed alternative microbes as the cause based on differences in the mortality, transmissibility and environmental conditions associated with the second and third pandemics. For many decades the discussions went on. But then, a little over a century after the discovery of Y. pestis, if became clear that this bacterium was indeed the agent behind the Black Death. The reason? The application of paleogenetics (the isolation, amplification, and sequencing of ancient DNA) to the studies of the history of plague pandemics; yet another demonstration of how the microbial sciences inform almost everything, in this case clearly guiding historians. Turns out that within the teeth of plague victims, pieces of Y. pestis DNA remain intact enough that they can be amplified with PCR and then sequenced. These techniques made it possible to obtain direct physical evidence that Y. pestis infections caused the death of individuals during the catastrophic events of the Black Death.
What followed the proof that Y. pestis was behind the Black Death was a literal explosion in the sequencing of remains from graves where plague victims had been buried at different times during the second pandemic. Consequently, a much more detailed view of the pandemic emerged. In addition, as the disease spread throughout Europe, the few changes in the Y. pestis genome permitted the construction of phylogenetic trees. After sequencing and aligning hundreds of genomes, from both human remains and present-day isolates, a four-branched tree emerged (a tree with a four-pronged polytomy at its base), where time and geographical location could be roughly overlapped with sequence divergence. Three branches contained only extant (modern) genomes, while all historical (reconstructed) genomes fell in a fourth branch. This meant that the even more tantalizing question of exactly when and where the second pandemic strain emerged might be answerable, i.e., it seemed possible to find a strain whose genome sequence was at the base of the four branches.
Regarding the initial arrival of the Black Death to Europe, the historical record pointed to the Genoese port city of Caffa, located in the Crimea. The Genoese had purchased the city from the Mongols in the late 1200s and established an important trading port. Tensions erupted between Genoese and Mongols who laid siege to the city in 1347. It's long been held that the Mongols carried the plague to Caffa and infected the Genoese who in turn carried it to Genoa from where is quickly spread throughout Europe. But where did the pandemic strain originate? Some of the early phylogenetic evidence suggested an origin in China, while other historical records pointed at location in Central Asia. In an enthralling historical essay from 2019, Philip Slavin presents mortality ratios in various regions from 1325 to 1357. The deaths recorded in tombstones in cemeteries in the region near lake Issyk-Kul (in present-day Kyrgyztan) spiked up to 16-fold in 1338-1339. Similar spikes in mortality were observed in Europe and the Middle East during the peak of the Black Death (1348-1350). That several of the tombstones included the words "died of pestilence" provided an additional clue. The stage was set to determine the sequence of the strains that had killed those people in the Issyk-Kul Lake region. That, however, was much easier said than done. But done it was, as a recent publication attests.
The problem was that those Issyk-Kul Lake region graves with tombstones from the peak mortality years had been excavated back in the 1880s! That introduced several problems in the search for Y. pestis strains. First, the human remains (hopefully teeth) would have to be found. Second, they would have to be matched with the corresponding tombstones. And third, the exposure to ambient conditions for over a century could have damaged whatever little remaining DNA might have been present. So, from the outset, this was clearly a high-risk endeavor. Fortunately for the investigators involved in the search for ancient pandemic strains, those in charge of the cemetery excavations had been meticulous in their annotations. Human remains were clearly marked and cataloged. And so were the tombstones. Unfortunately, they had been stored at separate locations in St. Petersburg, Russia: the tombstones at the Hermitage Museum and the human remains at the Kunstkamera, across the Neva River. Amazingly, through all the turmoil that St. Peterburg went through since the 1880 the investigators located both tombstones and human remains, and these could be matched reasonably accurately. Of course, that was just the beginning. Then came the extraction, amplification, and sequencing of the ancient DNA. Though it might seem impossible, they reconstructed two complete genomes representing one strain. And in comparing the sequence of that genome with all other sequenced Y. pestis genomes is where they struck gold. In the phylogenetic tree (Fig. 3) you can see the Issyk-Kul strain (in magenta) sitting right on top of the node that marks the polytomy where one branch contains all the historical genomes (in blue, light green and dark green). Thus, the Issyk-Kul strain represents the most recent common ancestor of the major diversification associated with the pandemic's emergence. In other words, they found the likely source of the strain that eventually spread throughout Europe and the Middle East during the Black Death. Truly spectacular forensic detective science!