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Study finds widespread antibiotic resistance in nature

Resistance to commonly used antibiotics are in the genes of bacteria everywhere, researchers at the University of Lyon in…

Scientists have discovered that the natural environment is a major reservoir of antibiotic resistant genes. Flickr: bizjournal

Resistance to commonly used antibiotics are in the genes of bacteria everywhere, researchers at the University of Lyon in France have discovered.

A worldwide study of the gene sequences of bacteria, published in the journal Cell Biology today, has found resistance across 71 environments, including oceans, soil and human feces.

The researchers analysed gene samples from public repository websites.

Lead author of the study, Joseph Nesme, said while the finding that antibiotic resistance exists in the environment is not new, the results showed they were present in considerable abundance.

They found that 30 % of total known antibiotic drugs resistance genes could be found in a single soil sample.

“Such results reinforce models that consider the environment as a major reservoir of antibiotic resistance that can be transferred to pathogens,” he said.

Bacteria are known to borrow foreign DNA from their cell environment.

Professor of Infectious Diseases and Microbiology at Australian National University Peter Collingnon said it showed we have to be very careful about where we dispose of antibiotics and resistant bacteria.

“The proper way is making sure we have drugs that have shorter half lives so that they disintegrate and don’t persist in the environment for long periods of time,” he said.

But many of the antibiotic resistant genes found in the microbial communities during this study pre-date the industrial use of medicines.

According to Nesme, this is because most natural antibiotics are derived from soil microorganisms.

“There are still many antibiotic molecules to be found inside this overall environmental diversity,” he said.

Professor Collingnon said this is likely to mean there are new antibiotics that we haven’t found.

“That’s actually how we have found most antibiotics, by looking at natural products and seeing how they inhibited bacteria,” he said.

Allen Cheng, Associate Professor of Infectious Diseases Epidemiology at Monash University, said it’s not really a surprise that there are antibiotic resistant genes in nature because that’s how other organisms defend themselves.

“This [study] really is a survey of all the weapons that are out there. It’s sort of like an inventory of bacterial weaponry and all the defences they might have. It gives us an idea of what bacteria might use to combat antibiotics in the future,” he said.

“I think what this paper doesn’t really tell us is which of these mechanisms is important. Most of them we’ve seen before in some form, but if you use an antibiotic it doesn’t say which of these mechanisms are likely to become the next dominant problem,” Professor Cheng said.

Professor Collingnon said the real problem was that there aren’t really financial rewards, particularly for pharmaceutical companies, to go looking for new antibiotics.

“This is because antibiotics are the one drug that actually cures something. What pharmaceutical companies want is to develop drugs that you, and preferably 20% to 30 % of the population, have to take forever,” he said.

Professor Collingnon said from a research point of view, there were more opportunities to look for new antibiotics using molecular techniques.

“We can also do some of the more basic things we did 30, 40 or 50 years ago. This is where we look at a whole lot of things, either in insects, jungles or soil, and see what products are there that are maybe the antibiotics that we don’t know about yet,“ he said.

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13 Comments sorted by

  1. Trevor Kerr


    This unsurprising 'finding' from the natural environment is a good argument for a radical new compact, specifically for antimicrobials R & D, between Pharma and governments. Call an end to all the special interest pleading, headline grabbing & shroud waving behaviour that spoils the interface between public interest and pharmaceutical development. It's past time for honesty, collaboration and exposure of conflicts of interests. Who will go first?

    1. Trevor Kerr


      In reply to Trevor Kerr

      An excellent, long read by Matthew Herper @ Forbes shows some staggering numbers on Gleevec.
      "Patients stay on it for years, and it is so valuable that Novartis has quadrupled its annual price from $24,000 per year in 2001 to more than $90,000 today. Even the stingiest insurers pay, though some patients get it free. What the marketers thought was a $400 million drug, Jimenez notes, is now a $4.6 billion one, and Novartis’ top seller to boot."
      No wonder our Govt's beady eyes are glistening at buying into a piece of that pie. No wonder antibiotic R & D is running a sad last.

  2. David Stein


    Kind of disappointing - it takes humans millions of years to evolve, but bacteria can seemingly develop a resistance to antibiotics in the blink of an eye.
    Ah, but I see:
    "But many of the antibiotic resistant genes found in the microbial communities during this study pre-date the industrial use of medicines."
    "Professor Collingnon said this is likely to mean there are new antibiotics that we haven’t found."

  3. Peter Sommerville

    Scientist & Technologist

    Disappointed in the scarcity of comments on an excellent article. Perhaps it is an indication of the narrow audience that the Conversation appeals to.

    My personal opinion, as a scientist and an individual is that the resistance to anti-biotics is a far bigger problem than speculation about climate change. This is a very real threat that could decimate populations that have grown simply because. Antibiotics have been so effective.

    1. Bill Medley

      Senior Advisor

      In reply to Peter Sommerville

      I agree Peter. With the way things are going in this country it will get worse before it gets any better. We do not have a Minister for Science. Humans tend to ignore problems they cannot see and we have seen the results from this many times over. Reintroducing grammar into the school curriculum took how long? Despite calls for decades about graduates not being able to write properly. Our rankings in science and maths continue to fall and nothing changes. Mention sport, fashion and celebrities and the online comments multiply like a virulent bacteria!! We need politicians with vision not self interest.

    2. Allen Cheng

      Associate Professor in Infectious Diseases Epidemiology at Monash University

      In reply to Bill Medley

      When we try to encourage our medical staff to prescribe antibiotics appropriately, we often use the analogy to climate change in that antibiotics are a non-renewable resource.

      Of course, there is a fine line between raising this issue in the public consciousness to spur action and the risk of politicisation and denial. There have been murmurings along these lines, albeit buried in the medical literature

    3. Paul Prociv

      ex medical academic; botanical engineer at University of Queensland

      In reply to Peter Sommerville

      Peter, I'm not so sure that the article was meant to be read so pessimistically. I agree with you about scientific illiteracy in the public, and perhaps that politicians don't adequately support important research (if you did imply those), but all that the authors say here is that they found lots of antibiotic resistant organisms in soil. This might be the first time anyone has looked so specifically for this. As Peter Collingnon and Allen Cheng say, that is no great surprise, given that (by definition…

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    4. Peter Sommerville

      Scientist & Technologist

      In reply to Paul Prociv

      I agree Paul. My main point is that the problem is enormous and the contingent risks that follow our failure to react appropriately are far greater than those implied by the climate change scenarios.

    5. Michael Anderson

      logged in via Facebook

      In reply to Peter Sommerville

      "My personal opinion... speculation about climate change."

      Peter, the good thing about science is that it's true whether or not you believe in it.

  4. Phillip Chalmers

    Doctor at Private and Hospital medicine

    This is one of these papers which proves what all those experienced in the life sciences have been taking for granted all along. Millions of years of biological warfare between populations of micro-organisms must have resulted in countless different DNA strands coding for resistance to countless occurrences of other DNA stands managing to secrete a new lethal brew.
    It is good to have it documented.

    A huge number of these compounds which we call antibiotics have been identified. A large proportion…

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    1. Portia Westall

      PhD Candidate, Genetics and Bioinformatics at The University of Sydney

      In reply to Phillip Chalmers

      Where is a like button when you need it! *like*

  5. Glenn Baker


    It is a curious fact that every time we take a step to free ourselves from problems more step in to plague us. The constantly inventive scientific community revels in solutions ironically to many of the problems it has caused. And thus we go precariously along believing we are making progress walking through a minefield as the noose tightens.