Is organic agriculture leading to an increase in antibiotic resistance?

One of the mostly aggressively promoted attributes of organic agriculture–it uses ‘natural’ fertilizer, better known as manure–may be linked to animal health problems. It turns out that cows fed antibiotics to cure diseases can excrete them back into the environment and that could be one reason for increased antibiotic resistance in the soil.

We can’t be too hard on cows and chickens, people do the same thing and those traces of antibiotics have to be processed in sewage systems. We use a lot of antibiotics because people get sick–but a lot fewer die due to streptococcus and diphtheria than before man-made antibiotics entered the scene, and a lot fewer animals die also. Medical science has clearly saved hundreds of millions of human lives and tens of billions of animals, but how much difference is it making in modern antibacterial resistance?

Organic company marketing departments and their environmental corporation allies have capitalized on the use of antibiotics in livestock and, in many cases, misrepresented it when it comes to resistance. The National Resources Defense Council filed a lawsuit over antibiotic use for growth in 2011 but when California recently tried to pass a law mandating no antibiotics for growth and letting farmers revert to FDA guidelines for medical use, the NRDC lobbied against the bill and admitted that antibiotics for growth is actually a tiny percentage of outlier farmers.

Some claims about antibiotic resistance are even sillier. A blaring headline in Tuesday’s Daily Mail (UK) asked: “Can GM food cause immunity to antibiotics?”

A British study has revealed that volunteers who ate one meal containing genetically modified soya had traces of the modified DNA in bacteria in their small intestines. Scientists now fear that GM foods, which are often modified to be resistant to antibiotics, will leave Britons vulnerable to untreatable illnesses.

That’s the scare viewpoint promoted by many anti-GMO activists; there is just no support for in the empirical data. While a few scholars have tried to contend genetically modified foods can somehow be causing antibiotic resistance in humans, the speculation has been soundly debunked. In this outlier study, this gene transfer, a 1 in 1026 event, just happened to be found in a study of 7 people fed GM food to try and find that GM foods cause antibiotic resistance, is not being taken seriously by mainstream scientists.

Activists want magic buttons they can raise money to lobby for pushing, and they may be confused by science recently, but to microbiologists the origins of antibiotic resistance, and how much of it is man-made, has always been unclear.

It got less unclear in a recent paper in Proceedings of the National Academy of Sciences by microbiologist Professor Jo Handelsman and colleagues. Instead of implicating corporation farms and overuse of antibiotics, they found that organic manure was letting more resistant bacteria gain a foothold in the environment than synthetic fertilizers do. 

What gives? Science has long known that antibacterial resistance has never been as simple as ‘get rid of X and the environment is saved’ because bacteria in the environment have naturally developed antibiotic-resistance genes. Soil has always carried antibiotics, due to the influence of fungi, molds and bacteria in the ecosystem. Alexander Fleming discovered penicillin in 1928 because he found that mold inhibited bacterial growth naturally. So authoritatively blaming modern medicine for the antibiotic resistance being spread in soil was environmental marketing, but not science.

The authors of the new study wanted to find out if manure itself was really the problem. So they did a study treating soil samples with manure from cows that never had antibiotics and samples that had nitrogen-based fertilizer. Then they examined the soil samples for the enzymes produced by bacteria that are responsible for resistance to antibiotics like penicillin – called beta-lactamases.

After two weeks, the results were clear – the organic manure was causing more antibiotic resistance than synthetic fertilizer, by producing more β-lactamases in the soil and that was causing resistant bacteria to flourish more than in soil that would be present on a conventional farm. Environmentalists shouldn’t be too disheartened by the results. Even if organic manure causes more antibiotic resistance in the environment, there could still be other issues they could blame on humanity, like heavy metals.

What they cannot do is dismiss Handelsman as a shill for Big Ag – since 2013, she has been on leave of absence from Yale so she could serve as the Obama administration associate director for science at the White House Office of Science and Technology Policy, led by Obama Science Czar Dr. John Holdren.

Hank Campbell is founder of Science 2.0 and an award-winning science writer who has appeared in numerous publications, from Wired to the Wall Street Journal. In 2012 he was co-author of the bestselling book Science Left Behind. Follow him on Twitter @HankCampbell.

23 thoughts on “Is organic agriculture leading to an increase in antibiotic resistance?”

  1. What BS. Farmers practicing sustainable organic agriculture are not using bacteria laced manure produced by CAFOs. What utter nonsense you are purveying as you dole out your slanted critique of organic agriculture. [“Antibiotic use is prohibited in organic livestock practices.” from ]
    Organic agriculture is as much of a science, perhaps more, than so-called conventional agriculture. It may not be true in 100% of cases, but by and large farmers who want to follow organic guidelines care more about the soil and are overall better stewards of the land. That’s what farming should be about, not mono-cropping and CAFOs where antibiotic use is rampant; antibiotics leech into the soil and blow in the wind. It is in these unsustainable agricultural practices that antibiotic resistance is borne.

  2. As long as we’re quoting articles.

    But by dumping antibiotics into soil whose bacterial make-up has already
    been altered by manure, says Dantas, “you’re guaranteed 100% to
    exacerbate problems with resistance”. He adds that the latest work is the type of research that says “we really should be very, very careful about antibiotic use in agriculture”.

    Although farm owners do not always reveal the quantities or types of antibiotics they use, an analysis of FDA data by researchers at the Johns Hopkins Center for a Livable Future in Baltimore found that in 2009, some 13.1 million kilograms — 80% of the antibiotics sold in the United States that year — were used on farms.

    Antibiotic use on such a broad scale leads to resistant microbes. In a 1976 study, Stuart Levy, a microbiologist at Tufts University School of Medicine in Boston, Massachusetts, found that when farmers started using tetracycline, the numbers of tetracycline-resistant bacteria on the farms spiked. Within months, resistance had spread to microbes in farmworkers’ intestinal tracts. “You don’t have to look that far to see resistant bacteria moving to the environment,” Levy says.

  3. Hey Hank, Kevin, First Officer: try turning down the confirmation bias and turning up the rationality. Contrary to the claims made in this post, the study actually says practically nothing about the role of organic agriculture in increasing antibiotic resistance.
    The reasons are pretty apparent to the skeptical reader, so let’s play a game: I’ll give you 24 hours to offer a critique of this study that shows you can apply scientific scrutiny without bias.
    If you’re finding it difficult, try this thought experiment: replace the words “organic manure” with “GMO manure” (or “manure from cows fed GMOs” if you want more accuracy).
    …ready, set, go!

    • Well, one question is do we see this effect with conventional farming that also utilizes manure? I.e. they use both synthetic and manure, whatever the farmer deemed better to use at the time.

      I think, though, this does not negate the theory that overuse leads to resistance, in of itself.

      I, too, am curious, what was meant by organic manure and how it would differ from conventional (GM feed derived, or not) manure with respect to its enormous bacterial content. I’d suspect (but don’t know), you’d get similar results. I’d suspect it would have more to do with quality of the cows’ diet.

      Could it also be just a matter of the manure simply continuously innoculating the soil with bacteria?

  4. Have to agree with some other commenters that it is a stretch to claim the study is an indictment of organic practices, per se. It does seem reasonable that manure treated soil could provide more favorable habitat for bacteria, antibiotic resistant or otherwise. I’ve not read the study itself, but the account of it in this article says only that the manure was from animals not given antibiotics, the husbandry source is not clear — CAFO, manure scraped off pastures of grass fed animals, or was collected from a nearby research farm or an animal or two the researchers kept in a pen themselves. I’m not sure you can assume manure from animals not given anti-biotics did not originate from a CAFO as many livestock feeders participate in anti-biotic free certified feeding program s. Antibiotic free is not confined to organic certified. Also, manure application as a fertilizer or soil amendment is not confined to organic agriculture. I
    I can also believe it reasonable and well documented that non-therapeutic uses of antibiotics in livestock feeds as a routine husbandry practice promotes resistance. But the figure of 80% of antibiotic use is in agriculture another commenter quoted may be misleading in inferring livestock feeding as a major culprit in anti-biotic resistance in medically important antibiotics. It is my understanding few products used in feeds are the same or same types as important anti-biotics in human or veterinary medicine.

  5. It seems to me that the appropriate comparison would be 3 treatments – inorganic fertilizers, manures from antibiotic treated animals, and manures from antibiotic-free animals. The two way comparison is simplistic – manures ought to increase all types of biological activity (including the fungi that have endogenous antibiotics) in the soils, and the real question would be to see if there is a difference between the antibiotic and non-antibiotic treated manures with inorganic fertilizers as the effective control. I can’t gleefully re-post this article!

  6. I am putting one document here which can explain how superbugs are created? I agree that if you do organic farming then the soil becomes good I mean bacteria’s can grow much better. In simple way you can say that after doing organic farming your soil becomes live. And such soil is definitely good for plants and if you do not create superbugs then definitely organic farming is good for humans also.

    Super bugs.

    This is the abstract about the super bugs. I have referred many documents regarding the same. Every time,
    they are blaming someone else .Some time they say that you should not go to
    India for medical treatment as all the hospitals there, are full of super bugs
    and they are infecting the people who are admitted for treatment. Even the
    sewage in Delhi is over flooded with such bugs. In support they provide data and
    lab testing reports, so common man has to believe them.(At the same time they
    forget what has been already published. In some documents it is clearly
    mentioned that their sewages are nothing diff.) We blindly do that, as they are

    One such thing is regarding the Ozone layer. They had found out the
    depleted ozone layer over pole. In support they had given sufficient data also.
    They say that, the ultra violet rays coming from sun
    which were absorbed by the ozone are now reaching earth, and causing skin

    The gases used in refrigeration; cfcs were held responsible
    for that. So they requested authorities to ban them and get it done.

    We never thought that this may benefit someone
    rather this process might have been initiated by them.

    I had a doubt; as I was remembering one thing about the
    ozone, that it is unstable.

    So I searched and find out that,

    The ozone layer is at 4 to 5 kms from ground as
    ozone is generated over there by ultra violet rays .(specific band of ultraviolet.)

    Its half life time is just 35 minutes. (Means it
    reduces to half, to O2 in just 35 minutes. For this, it does not require any
    catalyst or something else.)

    So it is getting depleted itself.

    If the generation of it is stopped for a log
    time, then a hole in the layer is formed and the hazardous portion of ultra
    violet rays can reach the ground.( and cause you cancer as per their say.)

    But on the earth’s poles the night is for six months.
    Sun rays are absent. So thinning the ozone layer.

    The CFC’s are most inert, so can not harm ozone.(Now
    they are saying that cfc’s are acting as a catalyst in the depletion of ozone. So a single
    molecule can deplete huge volume of ozone. In support they have given so many
    chemical reactions and explained how cfcs are acting as catalyst.)

    The CFC’s are much heavier than the air, around
    10 times. So how can they reach to that height and deplete ozone?(In one
    document they have mentioned that it takes 7 years to reach to that height, when
    it is leaked from the refrigerator; as if they were just following that
    molecule for all the time.)

    Hole in ozone layer should move here and there, as
    it is not rigid, along with the wind flow. But it has never happened or they
    never mentioned about that in any of their reports.

    After ban of cfc’s, new gases were available (which
    can be used without any modification in the refrigerator or air conditioner)
    which were costly and exact replacement for the old one. Benefiting mostly one

    So who is causing skin cancer? Ultra
    violet rays? I remember that , Drs used to suggest sunbath (To people with white skin.) And that source
    of ultra violet were not having any filtering for that portion of ultra violet
    rays which causes skin cancer.( a particular band of wavelength)
    But now they prescribe the
    ointment which protects our skin from sun’s ultraviolet radiation.(this
    contains the chemicals such as titanium oxide which can cause more problems to
    dead portion of the skin.)

    I come back to the super bugs.
    They say,

    Bugs are
    getting resistant to antibiotics as we are using them on fields in Agriculture,
    feeding them to animals as a growth hormone or do not take them in appropriate
    dosage or take a complete treatment. So the bugs develop the resistance. Even
    mutation is one of the causes they mention.

    But these reasons are not true.

    I tried to find out whether the bacteria’s
    have any immune system to fight against pathogens like we have? Outcome was
    not. Nor they have adoptive immune like vertebrates.(One more thing we must
    remember, that bugs are not multi cellular so they do not have the diff organs
    like humans which help them to detect the foreign body and kill it by producing
    diff cells.) mostly cell membrane protects it, most of the time.

    But they are becoming resistant to antibiotics
    is a fact.

    Then who made them resistant? (To

    GMOS are responsible for this? How?

    When they transfer the foreign
    gene to the plant cell, they have to check whether it has been transferred or

    For this they had used antibiotic
    resistant gene.(This gene has been taken from the resistant bacteria) They had
    added it to recombinant DNA which they transferred to plant.

    So testing of gene transfer
    becomes simple. Otherwise they will have to use the costly methods.

    They patented the same.(The antibiotic
    resistant gin which they used.) So everyone has to use the different antibiotic
    resistant gene. (I could find out the list of such resistant genes which they
    used for this purpose.)

    When the
    gm plant grows, every cell of that contains this antibiotic resistant gene.
    When we eat gm food this gets transferred to gut
    bacteria making them resistant. The possibility of such transfer is low. But
    even a single transfer can change the situation, if the patient is under
    treatment. As only resistant bugs will survive, and multiply and after that,
    come out along the stools and reach the sewage. Process involved is horizontal
    gene transfer.(Horizontal gene transfer means the gene transfer without sexual contact.) So why, the sewage is
    flooded with super bugs. Even after treatment.

    When the leaves of the GM plant decay
    on the soil they can transfer this antibiotic resistant gene to soil bacteria
    making them resistant to antibiotic.( There are so many documents from the
    reliable institutes confirming this. One
    such is “Super bug with anthrax gene”.)

    Only those bugs which are coming
    in contact with gm material, are getting this resistant gene horizontally; for
    example e coli.

    Many of them know about this, but they want to
    shelter those who, are using this technology to produce products, like drugs,
    vaccines and many more, which bring them a big business.

    Again if the bugs are becoming
    superbugs then the doctors have to try so many antibiotics and have to do lot
    of testing. So increasing business as the patient has to stay more in hospital.
    So none of them, talks about the same. Even though they are the people who are
    working in the close proximity and at large risk of getting infected with such
    superbugs. But at what cost? Result is;
    we are losing usefulness of antibiotics, the wonder drug of modern science.

    Even though we are losing them one
    by one, nobody has invested funds since 1987 to find out the new antibiotic and
    now they want the governments should take the financial burden of such research.(Just
    see the annual budget of each of them)Do they not have any social obliquity?

    But at the same time, they have
    invested a lot, to find out new drugs for blood pressure, sugar. For these diseases,
    you have to take drugs for a long time,(till the death) creating a long term
    stable profit making business.(these drugs never cure the disease but only
    controls that.(With lot of side effects) And you can have a better control;
    only if you regularly check the levels, and consult the doctor.( So a very
    stable business for medical instrumentation +Doctors+ pathologist)

    No effort has been made to find
    out the reason why a big portion of the population is suffering from such
    disease. Every day % of the population, who is suffering, is going up. Similarly
    the budget allocation of every nation for the same purpose.

    Up till now diabetics, obesity,
    arthritis, cancer and very few were in the list. But the list is increasing
    every day. These all are related to us. How are animals? Plants? Fishes?

    Cancer is affecting at least one
    from every family.

    I can say that cancer is becoming

    In conformation just read the
    story of the Tasmanian devils. How they are dying of the facial cancer?

    A relation
    between viral attack and then cancer has already established. (All these
    strains of the viruses are absolutely new and somehow their origin is the viral
    promoter CAMV 35S used in most of the crops which were genetically modified.)

    They had given one more reason for this,( bugs
    converting to super bugs) is mutation. I checked about this possibility
    discussed with so many pathologist but none of them could explain me how
    mutation can create a new gene, which is exactly similar to antibiotic
    resistance gene? And why that never happened
    before the genetic engineering became commercial.

    Every one
    of them is using this technology. (Antibiotic resistant gene to detect the gene
    transfer in gmos) but never mentioned that it is hazardous. This is, one of the
    major side effects of GMO’S. But the
    other is more dangerous. That is the transfer of some genes from the CAMV promoter;
    they have used to trigger the added gene. (If you do not add the promoter along
    with the gene of interest, such as BT gene in cotton, it will not work in the new genome and produce the required protein.)

  7. Good lord, is this a stupid article. Do you think the manure would otherwise be shot into space? “Science 2.0” (or even real science) isn’t worth much without common sense, of which this author betrays none.

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