Ancient bacteria found frozen in ice may help scientists in fight against superbugs

In the depths of Scarisoara cave in Romania sits one of the world’s biggest underground glaciers, a monumental slab of ice the size of roughly 40 Olympic swimming pools that began to form around 13,000 years ago.

Scientists studying ancient microbes once entombed in the cave’s ice say a bacterial strain they thawed and analyzed is resistant to 10 modern antibiotics used to treat diseases such as urinary tract infections and tuberculosis.

While there’s no evidence the bacteria are harmful to humans, awakening microbes that have lain dormant for thousands of years may sound like the plot of a sci-fi novel or movie. The new research, however, demonstrates how resistance has, in certain cases, evolved naturally in the environment, long before modern antibiotics were ever developed or prescribed by doctors.

“Ancient bacteria can resist modern antibiotics because antibiotic resistance is an ancient evolutionary characteristic that was shaped over millions of years by competition between microbes,” said Cristina Purcarea, a senior scientist at the department of microbiology at the Institute of Biology Bucharest of the Romanian Academy, and senior author of the study that published this week in the scientific journal Frontiers in Microbiology.

As they mix with one another over the course of millions of years, bacteria can share useful traits by exchanging small pieces of DNA, even between unrelated bacterial species, in an evolutionary arms race. This survival strategy has, coincidentally, resulted in some strains of bacteria being unaffected by certain antibiotics, drugs that trace their origins to natural compounds. This phenomenon is more common among microbial strains that live in extreme environments, the study noted.

“Modern antibiotics may speed up the spread of resistance, based on molecular mechanisms that existed in nature long before humans developed these drugs,” Purcarea added.

The scientists said the insights they have gained from the work may help in the fight against modern superbugs that can’t be treated by commonly used antibiotics

Core of ice

The newly identified strain of bacteria that Purcarea and her colleagues studied, known as Psychrobacter SC65A.3, thrives in cold environments and could not infect humans, she said.

“This strain is a psychrophile, meaning it’s a lover of the cold, not a lover of human bodies. Most Psychrobacter species are typically found in ice or refrigerated settings,” including foods, she said.

The sample in the study came from a 25-meter (82-foot) cylindrical core of ice the team drilled from an area of the cave known as the Great Hall. The core contained 13,000 years’ worth of frozen material, but the sample analyzed in the study was from 5,000-year-old ice.

In the lab, the researchers isolated various bacterial strains and sequenced their genomes to evaluate which genes allow the strain to survive in low temperatures and which are linked to antimicrobial resistance.

In the case of SC65A.3, when exposed to 28 antibiotics routinely used to treat bacterial infection, the researchers found the strain was resistant to 10, including trimethoprim, clindamycin and metronidazole, which treat bacterial infections.

As the planet warms and glaciers and ice caves melt, microbes trapped for thousands of years could be released, Purcarea said. “While most are harmless, some could carry antibiotic resistance or other unknown biomolecules that might affect current ecosystems,” she added via email.

Purcarea and her colleagues are not the only researchers assessing the risks of long-frozen microbes and the ancient nature of antimicrobial resistance as the world warms. Other researchers have revived 48,000-year-old viruses frozen in permafrost to examine the low but underappreciated risk of a disease outbreak unleashed by a long-dormant pathogen.

Risk and hope

The bacterial strain identified in the latest research also offers some hope in the fight against superbugs. Analysis of the Psychrobacter SC65A.3 genome revealed 11 genes that are potentially able to kill or stop the growth of other bacteria, fungi and viruses.

Most antibiotics are developed from bacteria and fungi and have been discovered by screening microorganisms that live in soil. But in recent decades, pathogens have become resistant to many of these drugs due to overuse.

The urgency to identify new antibiotic candidates has never been greater, with the world facing nearly 5 million deaths every year linked to antimicrobial resistance, according to the World Health Organization.

Matthew Holland, a postdoctoral researcher in medicinal chemistry at the UK’s University of Oxford, said that researchers were searching in new and extreme environments, such as ice caves and the seafloor, for biomolecules that could be developed into new antibiotic drugs. He was not involved in the new study.

“The team in Romania found this particular bug had resistance to 10 reasonably advanced synthetic antibiotics and that in itself is interesting,” he said. “But what they report as well is that it secreted molecules that were able to kill a variety of already resistant, harmful bacteria.

“So the hope is that can we look at the molecules it makes and see if there’s the possibility within those molecules to make new antibiotics.”

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