The samples were collected from a part of Lechuguilla Cave in Carlsbad Cavern National Park in New Mexico that has been cut off from any input from the surface for four million to seven million years. (Max Wisshak/speleo-foto.de/McMaster University)

Bacteria that have never before come in contact with humans, their diseases or their antibiotics, but are nevertheless resistant to a variety of antibiotics, have been discovered in a U.S. cave.

"This supports a growing understanding that antibiotic resistance is natural, ancient," and an integral part of the genetic heritage of microbes, suggest researchers from McMaster University in Hamilton, Ont. and the University of Akron in Akron, Ohio, in a new study published this week in the journal PLoS ONE.

Scientists have long debated the relative roles of humans and nature in the evolution and spread of antibiotic-resistant bacteria, which can pose a serious problem in the treatment of diseases.

In order to figure out how ancient and naturally widespread antibiotic resistance is, some researchers have been trying to study bacteria in environments highly isolated from human activity, such as a part of Lechuguilla Cave in Carlsbad Cavern National Park in New Mexico. It has been cut off from any input from the surface for four million to seven million years. The area is so deep and difficult to access that researchers had to camp there while collecting samples, said a news release from McMaster University.

McMaster infectious disease researcher Gerry Wright and his colleagues isolated 93 strains of bacteria from the cave. They found that the majority of them were resistant to multiple antibiotics — and some were resistant to as many as 14 — suggesting that antibiotic resistance is "common and widespread" in "pristine" environments, the study said.

2 new kinds of antibiotic resistance

In fact, the bacteria used two methods to resist antibiotics that had never been seen before.

McMaster University research Gerry Wright said the diversity of antibiotic resistance among cave bacteria suggests there could also be undiscovered antibiotics among them. (McMaster University)

That serves as a warning that antibiotics should be used judiciously in order to avoid helping kinds of antibiotic resistance that exist in nature from moving into other kinds of bacteria, the study said.

"We can say to doctors, 'while this isn't a problem right now, it could be in the future so you need be aware of this pre-existing resistance and be prepared if it emerges in the clinic. Or you are going to have a problem,'" said Hazel Barton, a University of Akron biologist who co-authored the paper, in a statement.

The researchers think some bacteria in the cave may have evolved to produce antibiotic compounds to outcompete other bacteria in a harsh environment with limited resources. Other bacteria, in turn, evolved antibiotic resistance as a defence mechanism.

The diversity of antibiotic resistance among the cave bacteria means there could even be undiscovered antibiotics among them, Wright speculates: "It suggests that there are far more antibiotics in the environment that could be found and used to treat currently untreatable infections."

The project was funded by the Canada Research Chairs program, the Canadian Institutes of Health Research and the National Science Foundation.

Wright has previously found antibiotic resistance genes in other ancient bacteria. In 2011, he and his colleagues reported such genes in bacteria that had been frozen in permafrost for at least 30,000 years.