Using a technique for extracting ancient DNA, researchers have found that the form of Yersinia pestis that caused the Black Death in medieval Europe may be extinct, according to a new study publishing today (August 29) in PNAS. The new approach could help researchers understand why that pandemic was so deadly.
“It’s a really interesting piece of work and really nicely done,” said Anne Stone, a biological anthropologist at Arizona State University. “Understanding the evolution of the bacterium is important for potentially predicting what future outbreaks might be like and why some outbreaks are worse than others.”
Between 1347 and 1350 the Black Death spread like wildfire from ports in Turkey to Italy, France, and England, killing around 30 to 50 million people, or a third to a half of Europe’s population. Researchers believe the plague bacterium, Yersinia pestis, was carried in ships by rats from its reservoir in Central Asia. Since then, there have been a series of less catastrophic outbreaks, and worldwide about 2,000 people still die of plague every year, said study co-author Hendrik Poinar, an evolutionary geneticist at McMaster University in Canada.
For years, Poinar and his colleagues have tried to characterize the bacteria responsible for the Black Death by amplifying DNA from the bones found in mass burial sites using PCR. “It was a nightmare,” he said, because only about 0.0001 percent of the DNA found in these bones is from the plague bacteria, with the vast majority coming from other environmental sources such as soil and plants, as well as the human hosts. In addition, after hundreds of years, environmental wear and tear has chopped up the bacterial DNA into tiny fragments no more than 50 base pairs long, Poinar added.
In the current study, the team used a strategy for extracting the DNA that had previously been used to extract mitochondrial DNA from Neanderthals. They used short sequences of DNA complementary to a portion of the modern Yersinia pestis genome to bind fragments in bone and teeth samples taken from plague victims buried in London. When they washed away all the extraneous DNA, they were left with short snippets of the bacterial DNA, which they then pieced together to recreate a plasmid of the plague-causing Yersinia pestis.
Comparing the plasmid to modern bacterial genomes, the researchers could find no exact match: the plasmid seemed to come from a strain that no longer exists. Modern plague victims are likely infected with different strains. In addition, the plasmid normally carries genes which affect how virulent the plague bacterium is, but the new sequence didn’t reveal any genes that would explain why the Black Death was so lethal, Stone said.
“It may be that other parts of the genome were important for making the pandemic particularly virulent,” she said. “But it is also a time when health care was basically nil,” so grim living conditions and sub-par medical treatment, rather than a particularly nasty strain of the disease, could have caused the higher mortality rate, she said.
The new method for extracting DNA could one day help answer why the Black Death was so deadly, Poinar said. “The million dollar question is, Can you use it to access whole genomes? Only when you have the entire genome will you be able to address that question,” he said.
V. Schuenemann, et al., “Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death,” PNAS, doi/10.1073/pnas.1105107108, 2011.