Sequencing DNA to Profile the Perpetrators of Past Plagues
The ancient pathogens in old graves are as dead as the people they once infected. Still, they tell a vivid tale.
By Tim Vernimmen
From the Black Death to the Spanish flu, waves of infectious disease have repeatedly laid waste to human populations. Scientists from many disciplines have long been intrigued by the possibility of disclosing the exact identity of the responsible pathogens and figuring out what made them so deadly. Yet even after sequencing ancient DNA became possible, the omnipresence of microbes made it challenging to pinpoint the historical culprits.
New technology has now made it much easier and cheaper to sequence large amounts of DNA. And by tracking the damage that accumulates in genetic material as it ages, researchers have found ways to distinguish truly old DNA from that of modern contaminants, finally allowing them to identify the pathogens behind infamous scourges.
One of the pioneers of the field of microbial archaeology is geneticist Johannes Krause, founding director of the Max Planck Institute for the Science of Human History in Jena, Germany. Earlier this month, he published a paper in Nature Communications tracing the spread of the Black Death, which killed half the European population — 30 million to 50 million people — in less than five years, starting in 1347. Krause and coauthors examine the challenges and revelations to be had in exploring ancient pathogens in recent issues of the Annual Review of Microbiology and the Annual Review of Genomics and Human Genetics.
This interview has been edited for length and clarity.
The job of the average archaeologist, to uncover the ancient remains of humans and all of their artifacts, is hard enough. But how do you find microbes that infected people thousands of years ago?
We extract all the DNA we can get from those same human remains, often fossilized teeth or bone, and we sequence it. This allows us to distinguish human DNA from the DNA of the pathogens we’re looking for, and then to try and reconstruct their genomes. This way, we are building a molecular fossil record that can tell us how pathogens have changed through time. And that provides important information about the biology of the microbial villains that have caused major epidemics in the past.
Ancient DNA is often highly fragmented. How do you know which bits of the genome go where?
There are different ways of doing this. You can try to let the computer put the pieces together based on overlaps. But like a jigsaw puzzle, that can be challenging when pieces are missing. So that’s when we need to look at the puzzle box, so to speak, and try to fit the fragments to the DNA of a modern relative instead. Which means it is as good as impossible to discover a new species, or to recognize a species with genes that mutate very fast, as the sequences may have changed so much we have no idea what it is.
The first thing many people might think of when they hear the words “microbial” and “archaeology” in the same sentence is pathogens escaping from ancient graves, “curse of the pharaohs ”-style. Is this something you need to take precautions for?
It is certainly something we thought about early on. There have been some studies, in the 1980s, where people tried to grow ancient bacteria or viruses. But nobody has been able to revive a pathogen that is more than a hundred years old, so I think it is very unlikely that this will happen.
There also is not a single case in which anybody got infected from an old skeleton, and there are thousands of archaeologists and anthropologists in the world handling ancient human bones on a daily basis. These people often don’t use gloves, and some of them even touch tiny fragments with the tongue to find out whether the fragments are made of stone or bone — bone is a spongy material, so it will take up liquid from your tongue and stick to it.
The pathogens really appear to be as dead as the person is.
So the largest risk, in fact, may be the reverse: Ancient tissues of people who died from a disease you’re interested in could be contaminated by other microbes that interfere with the analysis?
Yes. Microbial DNA is everywhere — ancient tissue samples usually contain up to 99 percent microbial DNA, much of it modern. With the older approaches, almost everything used to show up as positive for the bacteria causing tuberculosis, for example — even stones or plants. That is in part because many pathogens have harmless relatives that are not in our databases yet.
So it is extremely important to make sure that DNA is indeed from the past. We have developed several approaches to do so, including one that looks at DNA damage. In 2011, we could show that the damage patterns in ancient bacterial DNA were identical to those we see in human DNA of the same age. That was the first time we could authenticate ancient bacterial DNA, and it changed the field. Now, if DNA does not have this damage, we don’t believe it is old.
When deciding on the first pathogen to target using the brand new ancient DNA toolbox you developed, how did you choose, as the saying goes, between plague and cholera?
Our main motivation to study plague was that when we started this research, it wasn’t really clear what had caused the Black Death. There was much discussion among historians on whether it was some sort of virus, or a disease that is unknown today. An important advantage was that we had access to 50 bodies from the famous East Smithfield cemetery in London, which was used only during the Black Death pandemic, leaving little doubt what the people buried there had died from. In about half of these people, we could identify the plague bacterium Yersinia pestis. So that likely caused it.
Does your research also reveal where the Black Death may have come from, originally?
The oldest historical records are from a city called Kaffa in Crimea, a region that was often disputed in the past, as it is today. In the first half of the 14th century, it was a Genoese colony, besieged from the east by the Golden Horde. According to historians, the assailants ended up bombarding Kaffa with dead bodies, which may have spread the disease within the city. This forced the Genoese to retreat to Italy, bringing the plague to Europe, where it spread very quickly, killing half the population in only five years.
Maria Spyrou, now a postdoc in my lab, collected ancient Yersinia pestis samples from different parts of Europe, and one of the genomes she looked at was a 14th century strain from the Samara region in Russia, about 1,500 kilometers northeast of Crimea. When she added that strain to the Yersinia family tree, it turned out to be ancestral to the Black Death, corroborating the idea that the disease may have come from the east.
All the other genomes she got from the Black Death period, from many different places in Europe, are 100 percent identical, showing how fast it must have spread. And though the bacteria did change later on, the strain from that time appears to be the common ancestor of most of the strains in the world today. So the Black Death was sort of the Big Bang for the plague.
Interestingly, the genomes from that period don’t have anything you don’t find in daughter strains today, which means the Black Death is still around.
Does that mean these bacteria could still cause a similar epidemic today?
Theoretically, I think they still could, certainly in a context similar to medieval Europe. Even today, there are about 2,500 human cases every year, and most of them are from related strains. The bacteria that infected a few hundred people in Madagascar in 2017 were very similar in their biology to those that caused the Black Death.
Fortunately, we now have good antibiotics, because without treatment, 60 percent of people die of plague within seven to 10 days, and plague occurs in rodent populations almost all over the world. In the Grand Canyon, for example, there are signs saying you shouldn’t touch the squirrels, because they carry Yersinia pestis. It really is a rodent disease — humans get infected only by accident. We don’t live with as many rodents as we used to, and the black rat, which was once very common and lived almost like a mouse, inside people’s houses, has since largely been replaced by the brown rat, which usually resides underground.
Last but not least, fleas have also nearly disappeared in many places thanks to improved hygiene. So I think these factors are probably more important than any genetic change in the bacteria — or in people.
In one of the reviews, you mention that a very close relative of Yersinia pestis, Yersinia pseudotuberculosis — which you initially used to piece together some of the early plague genomes — commonly occurs in the environment, including on “improperly washed” vegetables. Can your genetic analysis teach us why pestis is so dangerous and pseudotuberculosis is as good as harmless?
Yersinia pseudotuberculosis appears to be very bad at escaping the human immune system. There is no known case of it entering the blood, which is how pestis causes the tissue death that results in the black hands and feet that gave the Black Death its name.
Y. pseudotuberculosis also does not have the genes that are necessary for flea transmission. After a flea sucks blood from an individual infected with Y. pestis, the bacteria produce a biofilm that clogs the flea’s gut, preventing it from swallowing any more blood. So the flea is starving, and it starts biting hundreds of times a day, and every time it bites it brings the blood in contact with the biofilm, then spits it out again, transmitting the bacteria into the new bite mark. As Yersinia pseudotuberculosis does not have the genes to make this biofilm, it could not have been transmitted by flea bites.
Interestingly, we have recently found that Yersinia pestis bacteria from the Bronze Age and the Late Stone Age were missing some of those genes as well. They may instead have infected the lungs, and spread through the air, as some plague bacteria still do today. This is quite exciting: We are really starting to see how Yersinia pestis has emerged to become a dangerous human pathogen.
Originally published by Knowable Magazine, 10.30.2019, under the terms of a Creative Commons Attribution-NoDerivatives 4.0 International license.