Although humans have been using antibiotics for only the past 60 years, antibiotic resistance genes have been around for thousands, maybe even millions, of years. In a new study published online in Nature today (August 31), researchers report finding genes encoding resistance to commonly used antibiotics such as penicillin, tetracycline, and vancomycin in 30,000 year-old bacterial samples from the Canadian permafrost.

Microbiologists have long suspected that antibiotic resistance genes have existed for much longer than antibiotics have been in use—perhaps even as long as microbes have been around—but “the data had not been there,” said Stuart Levy, a professor of microbiology at Tufts University School of Medicine who was not involved with the study. “This really is a solid piece of paper that shows that antibiotic resistance genes, which resemble those we have now, existed 30,000 years ago.”

The problem of antibiotic resistance...

In these pathogenic bacteria, the emergence of antibiotic resistance seemed to be tied to the widespread use of antibiotics in humans and in agriculture, said study author Gerry Wright, a biochemist who researches antibiotic resistance at McMaster University. But this is not the case with environmental bacteria, such as those living in the soils and in aquatic environments. When Wright carried out an extensive survey of antibiotic resistance in soil microbes in 2006, he found that for environmental bacteria, antibiotic resistance is the norm.

“These organisms are living in a pretty hostile place,” Wright explained. They are under a constant barrage of antimicrobial chemicals produced by fungi, plants, invertebrates, and other bacteria. “They pretty much had to develop resistance just to live where they live.”

In fact, pathogenic bacteria appear to get most of their antibiotic resistance genes through horizontal gene transfer from these organisms.

To see how far back he could find these resistance genes out in the environment, Wright and his team dug out cores of ice from the permafrost in Bear Creek in Yukon, Canada. Because the frozen soil has not thawed in tens of thousands of years, there has been no mixing of surface and subsurface bacteria.

With the help of ancient DNA expert at McMaster University in Canada, Hendrik Poinar, the team extracted the DNA from the icy samples dating back 30 millennia and probed them for known antibiotic resistance genes. They found traces of genes such as ß-lactamase (which confers resistance to penicillin), tetM (which protects cells against tetracycline antibiotics), and the three-gene combo necessary for resistance to the glycopeptide antibiotic vancomycin (vanH-vanA-vanX).

“They’re slightly different at the sequence level but they’re clearly part of the same family of genes,” Wright explained. Performing X-ray crystallography on a reassembled copy of the ancient vanA sequence revealed that its protein product had the same structure and function to that produced by the modern bacterium Enterococcus faecium.

The genes were “just as effective 30,000 years ago and they look just like the ones that exist now,” Wright said. “That tells us that resistance is old and pervasive in the environment.”

However, whether these genes were used to combat naturally occurring antibiotics still remains to be determined, Levy said. “We don’t know if they’re there because of resistance or if they’re doing something else.” It’s known, for example, that some antibiotic resistance compounds can act as signaling molecules. Alternatively, they may have been involved in the production of antibiotics themselves, if the ancient bacteria produced their own antibiotics.

"These genes are highly related to innate genes linked to pathways that create the antibiotic, which are part of the basic physiology of the antibiotic producing bacteria," said Marilyn Roberts who researches antibiotic resistance at the University of Washington and who was not involved in the study.

Nevertheless, studies such as this one should serve as a cautionary tale for the use of antibiotics, added Levy, who presides over the Alliance for the Prudent Use of Antibiotics. “We will not find an antibiotic which will not also have a resistance gene out there.”

V.M. D'Costa, et. al., “Antibiotic Resistance is Ancient,” Nature, doi:10.1038/nature10388, 2011.

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