Antibiotic resistance found in ancient bacteria

Modern soil bacteria make a variety of compounds,some of which generate the colours shown above and some of which have antibiotic activity. Gerard Wright/McMaster University

The same genes that make disease-causing bacteria resistant to today's antibiotics have been found in soil bacteria that have remained frozen since woolly mammoths roamed the Earth.

“We’ve shown for the first time that drug resistance is a really old phenomenon and it’s part of the natural ecology of the planet,” said Gerard Wright, a biochemist at McMaster University in Hamilton, Ont.

He led the study that was published online Wednesday in the journal Nature.

Wright said this evidence of ancient genes may explain how today's disease-causing bacteria have so quickly become resistant to modern antibiotics.

He also suggested that these findings, which involved the study of one type of bacteria that lived in one location, in the Yukon, 30,000 years ago, might just be the tip of the iceberg.

“Surely this history goes back millions of years,” he said. “We just don’t have those samples yet.”

Wright had conducted a study five years ago to see how prevalent antibiotic resistance was among common soil bacteria called Actinobacteria, which do not cause disease in humans.

“You know how dirt has that dirty dirt smell? That smell of earth? Well, that’s caused by [this type of] bacteria,” he said.

What he found in that study was that many of these bacteria were resistant to multiple antibiotics. That was true of both bacteria in urban and agricultural sites, as well as those in remote parts of northern Ontario. Still, to be certain the bacteria had never been exposed to human antibiotics, he needed to find bacteria from a pristine environment isolated from the modern world.

Duane Froese, a geologist at the University of Alberta, and Grant Zazula of the Yukon government’s paleontology program, had a solution. They gathered samples of permafrost in the Yukon that was buried under a layer of ash from a volcanic eruption 30,000 years ago.

“Samples taken immediately below that are essentially the same age,” Froese said.

The permafrost contained ice wedges, which form when the ground is so cold that it cracks open allowing water to freeze inside. The wedges can only form at the surface and their presence deep underground shows that the permafrost had never melted since it was buried.

The researchers tested the samples in the lab of Hendrik Poinar, a McMaster University anthropologist who specializes in DNA analysis. They found it contained DNA from ancient mammals, like the mammoths and horses that roamed the Yukon 30,000 years ago, but no modern mammals such as moose or elk. That confirmed that the bacteria was not contaminated with soils from above the ash layer.

The samples also contained DNA for at least a hundred species of bacteria, including Actinobacteria. And the Actinobacteria DNA contained genes that made it resistant to beta-lactam, tetracycline and glycopeptide antibiotics, including vancomycin.

Wright said that’s not surprising, since that type of bacteria is the source of many of those same antibiotics.

“They make probably 80 per cent of the drugs that are currently used today – they also make anti-cancer agents, they make immune suppressants, they are remarkable, remarkable little chemists.”

Permafrost sediments deposited 30,000 years ago in the Klondike area of the Yukon contained bison, horse and mammoth DNA as well as bacterial genes associated with antibiotic resistance. D.G. Froese/University of Alberta That antibiotic resistance likely jumped from the soil bacteria to disease-causing bacteria.

"These environmental bacteria are actually the wellspring of resistant genes that eventually make their way into disease-causing bacteria."

Wright said scientists don’t yet know why soil bacteria have a tendency to make antibiotics and be resistant to antibiotics, but they speculate it may help them compete with other bacteria in an environment crowded with millions of bacterial species.

He said most disease-causing bacteria evolved in the more isolated environments of animals' guts or skin, where they may not have had a need for antibiotic resistance.

The researchers don’t yet know how widespread antibiotic resistance is among other kinds of bacteria.

"We’re very keen to broaden our view of what the sources of resistance are," Wright said. "This is very probably the source of our problems – all the [antibiotic resistance] genes that have emerged in these disease-causing bacteria. So we really need to understand the diversity that exists out there so that we can be prepared for it if and when it emerges in pathogens."

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Black Death bacteria identified

A bacterial strain that is now extinct has been identified as the cause of the devastating Black Death plague in the 14th century.

The Black Death is estimated to have killed 30 to 50 million Europeans or about a third of Europe’s population between 1347 to 1351, after spreading there from China and the Middle East, making it one of the worst pandemics in human history.

Now, based on a DNA analysis study led by anthropologist Hendrik Poinar of McMaster University in Hamilton and archeologist Johannes Krause at the University of Tubingen in Germany has concluded the pandemic was caused by a now-extinct strain of Yersinia pestis, the bacterium that causes bubonic plague.

The results were published Monday in an article in the Proceedings of the National Academy of Sciences. The lead authors are Verena Schuenemann at the University of Tubingen in Germany and Kirsten Bos, a graduate student at McMaster University.

While some researchers have always thought Yersinia pestis could be responsible for the Black Death, others had argued it couldn't be.

"It’s been a big controversy in the literature for many, many years," said Poinar in an interview Tuesday. "The rate and speed and death, mortality that it caused just seemed contrary to what we know about modern bubonic plague.”

There are still 2,000 cases of bubonic plague worldwide each year, but it spreads slowly via flea bites. The quick spread of the Black Death suggested that disease was airborne.

To settle the question, the researchers analyzed DNA from 109 human skeletons at the East Smithfield mass grave site in London, England, where Black Death victims were known to be buried.

Co-authors Bos and Sharon DeWitte "were over there pulling teeth out of the jaws of these individuals, then drilling root pulp out of the teeth, and then replacing the teeth back into the jaws,” Poinar recalled.

The samples were initially taken back to McMaster University, where Bos painstakingly searched for Yersinia pestis DNA among the massive amount of other DNA in the sample from humans, plants, fungi and other bacteria. She consistently found it in the bones of teeth in some victims.

On other other hand, she did not find Yersinia pestis samples from a nearby mass grave site that did not contain Black Death victims, suggesting that it was in fact linked to the Black Death.

Rather than using polymerase chain reaction (PCR), the common genetic technique used for forensics and DNA testing, the researchers used very new techniques called targeted enrichment and high-throughput sequencing. Those allow researchers to reconstruct long sequences of ancient, damaged DNA that have degraded over time.

"The technology’s changed," Poinar said. "That’s the only reason we were able to do it.”

Using that technique, the researchers identified a strain of Yersinia pestis that contains the same loop of DNA called a plasmid, found outside the bacterium's main chromosome, that is responsible for virulence in the modern strain. Because of their similarities, the researchers don’t believe that that particular loop was responsible for the Black Death strain’s exceptional virulence.

However, a quick look at the bacterium's main chromosome showed the Black Death strain did contain several unusual genetic characteristics to the researchers' knowledge, “are not found in any previously reported modern or ancient sequence” for the bacterium.

Poinar acknowledged that the study doesn't rule out the possibility that the Black Death bacterium co-operated with another pathogen to create "the perfect storm."

It also doesn't indicate why the strain was so deadly compared to others. The researchers hope to figure that out in the next stage of research.

"If we sequence the entire bug, we can actually look very specifically at changes that have occurred on its lineage," Poinar said. "And that will hopefully help us understand, ‘Are there indeed added points of virulence that might explain why it was such a deadly outbreak?’”

the researchers analyzed DNA from 109 human skeletons at the East Smithfield mass grave site in London, England, where Black Death victims were known to be buried. British Museum of London Accessibility Links

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