Oldest Strain of Plague Bacteria Found in 5,000-Year-Old Human Remains

Unlike the ‘Black Death’ in the 14th century, the ancient infection probably did not spread quickly between people

A photograph of human remains, a lower jawbone labeled RV 2039
Ancient DNA and proteins gathered from the specimen's bones and teeth revealed the presence of Yersinia pestis. Dominik Göldner, BGAEU, Berlin

The bacteria that causes the bubonic plague (Yersinia pestis) may be about 2,000 years older than previously thought, according to a new study published on Tuesday in the journal Cell Reports.

Scientists found a strain of the plague bacteria in 5,000-year-old human remains. Genetic analysis suggests the bacteria itself may have evolved about 7,000 years ago. Compared to the strain of bacteria that caused the infamous Black Death in the 14th century, the ancient microbe seems to lack the genes that would have enabled it to spread quickly from person to person.

“We think that these early forms of Y. pestis couldn’t really drive big outbreaks,” says lead author Ben Krause-Kyora, a biochemist and archaeologist at Christian-Albrecht University of Kiel, to Nicola Davis at the Guardian.

The first two hunter-gatherer graves were found in 1875 in a shell midden, an ancient pile of waste like mussel shells and fish bones, in Riņņukalns, Latvia. The specimens were lost during World War II and relocated in 2011, when researchers returned to the midden and found another two graves.

The researchers wanted to study the hunter-gatherers’ DNA, so they extracted samples from the specimens. They scanned the genetic data not only for human DNA, but also for signs of bacteria and viruses. Only one of the four specimens, from a man who was between 20 and 30 years old, had DNA from Y. pestis.

"It was kind of an accidental finding,” Krause-Kyora tells Gemma Conroy at ABC Science.

A second look revealed he was also carrying proteins from the bacteria, which means it had probably infected his blood.

"He most likely was bitten by a rodent, got the primary infection of Yersinia pestis and died a couple of days [later]—maybe a week later—from the septic shock," says Krause-Kyora to Helen Briggs at BBC News.

Because only one of the four burials carried Y. pestis and because the body was buried carefully, the researchers suspect the ancient infection appeared relatively mild. And it probably couldn’t spread very quickly from person to person.

About 5,000 years ago, Y. pestis would have had to transfer directly from the rodents to humans, like through a bite, because the bacteria lacked the genes that allowed later strains hide out in fleas. In the Middle Ages, the biting insects jumped from plague-infected rodents to people and carried the bacteria with them, accelerating the disease’s spread.

Instead, the 5,000-year-old plague would have affected people in small groups—only if they scuffled with a plague-infected rodents. The researchers say this finding challenges a theory that an epidemic of Y. pestis caused a huge decline in the European population at the time.

"We would need to have one discovery of many mass graves across a very large geographic area within a narrow time period to reach that kind of conclusion," says University of Adelaide evolutionary biologist Bastien Llamas, who was not involved in the study, to ABC Science. "There was probably a long period of adaptation needed for Y. pestis to reach that point at which it's going to become extremely contagious."

However, not everyone is convinced. University of Copenhagen biologist Simon Rasmussen, a co-author on a 2018 study that supported the theory of a Stone Age epidemic, tells the Guardian that he welcomes the new research.

“The individual does in fact overlap with the Neolithic decline and very likely died from the plague infection,” says Rasmussen to the Guardian. “We know that large settlements, trade and movement happened in this period and human interaction is therefore still a very plausible cause of the spread of plague in Europe at this time.”