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Cave Bacteria Finding Suggests Ancient Origins of Antibiotic-Resistant Superbugs

The views expressed are those of the author and are not necessarily those of Scientific American.


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Lechuquilla cave

Lechuquilla cave image courtesy of Max Wisshak

Our pill-popping culture and over-zealous livestock farmers typically take the blame for the widespread resistance of many harmful strains of bacteria to entire classes of antibiotics.

And the Food and Drug Administration took a bold move today with a new voluntary plan to help curtail the over-use of antibiotics in agriculture.

But the capacity to fend off antibiotics might actually be lodged deep in bacteria’s evolutionary history. A new study has uncovered dozens of species of bacteria in a 4 million-year-old cave that harbor resistance to both natural and synthetic antibiotics.

A team of researchers descended to 400 meters in distant, untrafficked reaches of Lechuguilla Cave in New Mexico to collect samples of bacteria. Few people have entered the cave’s deepest regions since its discovery in 1986, and surface water takes thousands of years to percolate through the nearby dense Yates Formation rock down to the cave. As a consequence, the area is a prime place to study naturally occurring antibiotic resistance, noted the researchers, whose results were published online April 11 in PLoS ONE.

“Our study shows that antibiotic resistance is hard-wired into bacteria,” Gerry Wright, director of McMaster University’s Michael G. DeGroote Institute for Infections Disease Research and co-author of the new study, said in a prepared statement. “It could be billions of years old.”

Members of this team had also recently shown that there was genetic evidence of antibiotic resistance in soil bacteria from 30,000 years ago. And other studies had found evidence of resistance in life found in the deep ocean and deep below the Earth’s surface. In both cases, as with the Lechuguilla Cave, it is unlikely that local bugs could be contaminated by modern-day antibiotics.

Lechuquilla cave

Lechuquilla cave image courtesy of Max Wisshak

Wright and his colleagues found that of the 93 bacterial strains tested from the cave, most were resistant to more than one of the 26 different antimicrobials. And some bacteria were resistant to more than a dozen antibiotics used by doctors, such as telithromycin, ampicillin and daptomycin, which is currently a treatment of last resort to combat resistant infections. The cave bacteria were not likely to cause infection in humans, but could provide the genetic traits that confer resistance to that are.

The finding hardly exonerates humans for our role in creating conditions that exert a strong selective pressure on bacteria to become tolerant and resistant to antibiotics. But it does mean that pathogenic drug-resistant bacteria might deploy genetic traits that were already circulating in the environment and put them to use against our pharmaceutical armamentarium. “Most practitioners believe that bacteria acquire antibiotic resistance in the clinic,” Wright said. “The actual source of much of this resistance are harmless bacteria that live in the environment,” responding to naturally occurring antibacterials.

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

In addition to familiar patterns of resistance, the researchers also discovered a new mechanism of resistance, suggesting that more drug-evading tricks might be waiting in nature’s wings. “This fact further underlines the importance of judicious use of antibiotics,” the researchers wrote in their paper.

Katherine Harmon Courage About the Author: Katherine Harmon Courage is a freelance writer and contributing editor for Scientific American. Her book Octopus! The Most Mysterious Creature In the Sea is out now from Penguin/Current. Follow on Twitter @KHCourage.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. JamesDavis 7:12 am 04/12/2012

    Antibiotics are less than a hundred years old and man made. Wouldn’t those bacteria have to be exposed to the antibiotic before they could become resistant to it? Maybe there were humans on this planet millions of years ago who developed that exact same antibiotic we did and that’s how the bacteria in that four million year-old cave acquired their resistance. Or maybe someone is secretly using that cave to dump medical waste. I wonder which one it could be?

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  2. 2. marclevesque 9:30 am 04/12/2012

    “Antibiotics are less than a hundred years old and man made.”

    The princible behind antibiotics is fairly recent, but humans have been making them for much longer without understanding how they worked. The article is just remarking the obvious in a round about way. Naturally occuring antibiotics prompt bacteria to evolve resistance just like man made antibiotics do.

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  3. 3. jgomez7061 1:00 pm 04/12/2012

    “Wouldn’t those bacteria have to be exposed to the antibiotic before they could become resistant to it? ”

    Good question! The answer is no. Think about this for a moment. If the antibiotic came first, it would kill the bacteria before it has a chance to mutate sufficiently to create resistance – This is the whole premise behind your M.D telling you to finish your antibiotic Treatment. Exposure to the antibiotic would only cause SELECTION for a particular allele – that is to say, all others would die except those that were “lucky” enough to have the resistance allele – implying then that he allele must have been already present in the organism prior to exposure, except the allele may have not had much use until that time. In fact, it has been shown that bacteria may share DNA, take in DNA from the environment and remove unwanted DNA from it’s genome.
    Of course, before other Molecular Biologist choke on there coffee after reading this, be warned that the genetics involved can get a bit more confusing than this, but hope this clears things up just a bit. Cheers!

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  4. 4. Don_Nanneman 5:12 pm 04/12/2012

    To get a better understanding of this ask yourself where did antibiotics come from – they were not man made they were discovered in nature. Many are produced by molds.
    Technically “antibiotic” means a chemical substance derivable from a mold or bacterium that can kill microorganisms and cure bacterial infections – the man-made antimicrobials are not true antibiotics.
    Many of the antibiotics in use today are molecules based on the naturally occurring antibiotics One of the reasons for altering these molecules is to get around the naturally occurring resistance in microbial populations. Use of antibiotics can selectively favor the survival of those microbial strains with resistance – It takes considerable mental gymnastic skill to posit that the microbes figure out how to become resistant..

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  5. 5. JamesDavis 11:40 am 04/14/2012

    I can see that your understanding and my understanding of antibiotics differ greatly. Goldenseal is natures best antibiotic and it has been around for million of years and still very effective against attacking bacterium and that is where its secret lies, and it is a smart antibiotic; man made antibiotics are not smart, they attack all bacterium. So to protect themselves, all the bacterium builds up a resistance against that antibiotic when they come in contact with it, like ant colonies do when attacked by a certain fungus. When a bacteria attacks a human, and it is always one kind – not all of them at once, there is something wrong with the bacteria, because bacteria is not programmed to attack humans, but protect them against invading viruses and live in harmony with us. When a bacteria attacks a human, goldenseal attacks just that bacteria and corrects it or eliminates it. This selective attack prevents the other bacteria from building up a resistance to the goldenseal, that is why it has been effective for millions of years. So again, who exposed those cave bacteria to the man made antibiotics and how?

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  6. 6. Torbjörn Larsson, OM 8:41 pm 04/14/2012

    You are confusing antibacterial with antibiotics:

    “An antibacterial is a compound or substance that kills or slows down the growth of bacteria.[1] The term is often used synonymously with the term antibiotic(s); today, however, with increased knowledge of the causative agents of various infectious diseases, antibiotic(s) has come to denote a broader range of antimicrobial compounds, including antifungal and other compounds.[2]

    The term antibiotic was coined by Selman Waksman in 1942 to describe any substance produced by a microorganism that is antagonistic to the growth of other microorganisms in high dilution.[3]”

    What made the antibiotics that the cave bacterial communities (often very complex ones) shield themselves against are other cave bacteria and fungus, naturally. The article describes how they can be sure that no humans have been involved, and how you can derive the age of the evolved traits.

    “When a bacteria attacks a human, and it is always one kind – not all of them at once, there is something wrong with the bacteria, because bacteria is not programmed to attack humans, but protect them against invading viruses and live in harmony with us.”

    Wow, I would love to have some of what you are smoking! Or better not, if you think goldenseal is a medicine – the wikipedia page mentions how it blocks actual medicines.

    Apparemtly you have no knowledge of biological evolution. It is the basic process of biology, that makes traits and species appear. If you look at how it works, it can’t “program” anything – it is a natural process.

    Yes, animals are often commensalist communities consisting of more bacterial cells and their DNA than anything else. But as bacteria exudes antivirals, viruses attacks viruses too and help us regulate the community. Pathological bacteria may or may not have evolved to infect us, for example of the latter flesh eating infections may be caused by soil bacteria, but most are of course. (Or they wouldn’t succeed as much.)

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  7. 7. checkmate4u 11:41 pm 04/18/2012

    Goldenseal is natures best antibiotic and it has been around for million of years and still very effective against attacking bacterium and that is where its secret lies, and it is a smart antibiotic; man made antibiotics are not smart, they attack all bacterium.

    Antibiotics function by inhibiting the ribosomal function of specific bacteria….specific meaning only the harmful one or sometimes similar ones that are not harmful. They don’t attack all bacteria in your body, otherwise you would be dead after the first time you took doxycycline….when you found out about your first chlamydial infection…

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