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A researcher is shown in Lechuguilla Cave in Carlsbad Cavern National Park, with calcite formations shown in the background.Max Wisshak/The Canadian Press

Deep inside a cave in New Mexico, researchers have made a startling discovery – bacteria that are resistant to antibiotics, yet have been pristinely isolated from human contact for more than four million years.

Bacterial resistance to antibiotics – the infection-killing wonder drugs that began with mass-produced penicillin in the early 1940s – was long thought to have arisen because of wholesale and indiscriminate use of the medications to treat disease in both people and animals.

Over time, more and more disease-causing bacteria, including the superbug MRSA, are becoming immune to most antibiotics now in use. And the growing number of bugs mutating to dodge the killing effects of the drugs has researchers and pharmaceutical companies scrambling to find new agents.

But the discovery of species of naturally resistant bacteria in the Lechuguilla Cave, in Carlsbad Caverns National Park, represents a major leap in the understanding of resistance threatening the treatment of infectious diseases around the world.

The conclusion: it isn't just man-made.

"Our study shows that antibiotic resistance is hard-wired into bacteria. It could be billions of years old, but we have only been trying to understand it for the last 70 years," said co-principal investigator Gerry Wright, scientific director of the Institute for Infectious Disease Research at McMaster University in Hamilton.

"This has important clinical implications," Dr. Wright said. "It suggests that there are far more antibiotics in the environment that could be found and used to treat currently untreatable infections."

That's because a particular bacterium creates its own antibiotic as a means of fighting off other bacteria, said co-author Hazel Barton, a cave microbiologist at the University of Akron who helped recover the micro-organisms within the New Mexico cave.

One way to think of it is the bacterial version of The Hunger Games – kill or be killed.

"They're carrying out germ warfare, so it's like an arms race," said Dr. Barton, explaining that the bacteria are competing for scarce food resources in their environment, whether in backyard soil or deep within a cavern.

"These chemical weapons that they make are antibiotics," she said.

"So these organisms have adapted by developing resistance to those chemical weapons. So even though somebody comes along and spits this weapon at them, they can defend themselves and that's where resistance comes from."

While most of us think of antibiotics as pills from a bottle, most in fact originated in nature, like the mould identified by Scottish biologist Alexander Fleming in 1928 that gave rise to penicillin.

"If you look at it in the soil, you've got one bacterium next to another bacterium," she said. "That bacterium is squirting out the same drug that you have in that pill."

In never-before-visited recesses far inside the Lechuguilla Cave, researchers collected strains of bacteria, scraping them off the surfaces of rock. An analysis showed none are capable of causing human disease and almost all were resistant to at least one antibiotic, with some able to fend off up to 14 of the drugs.

In all, resistance was found to virtually every antibiotic that doctors currently use to treat patients, according to the study published in the journal PLoS ONE.

The good news is that where there is resistance among bacteria in the environment, there must also be natural antibiotics other micro-organisms have created.

"What it means is that there's also a broad range of antibiotics we've yet to discover," said Dr. Barton, noting that the researchers have already isolated one and are working with a pharmaceutical company to develop it into a drug.

"So we're just hunting them down now."