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Guest Column: Don Kelley on Dangers of Antibiotic Resistance from CAFOs

Two weeks ago, the Department of Environment and Natural Resources refused to hear testimony from physician Don Kelley on the role of confined animal feeding operations (CAFOs) in increasing the risk of antibiotic-resistant bacteria. Dr. Kelley has provided Dakota Free Press with what he would have told DENR had they deemed this public health threat relevant to their revision of the General Water Pollution Control Permit. Dr. Kelley, who chairs Dakota Rural Action, would have supported his comments with documents prefiled by DRA in teh permit hearing. I have added my own hyperlinks to relevant articles supporting Dr. Kelley’s statements.


Don Kelley, M.D., Dakota Rural Action chair. (Photo from DRA)
Don Kelley, M.D., Dakota Rural Action chair. (Photo from DRA)

Good morning, Mr. Secretary and Dept. members. My name is Don Kelley from the Deadwood, SD area, and I’d like to speak to you about an issue of great significance for all of us, which is the rapidly worsening antibiotic resistance of bacteria in our environment. There is good evidence from around the world (including the CDC here in the States) that confined animal feeding operations are contributing to this problem.

What I intend to show is:

  1. CAFO’s pose a risk to human health through environmental dissemination of antibiotics and antibiotic-resistant organisms
  2. Surface- and ground-water contamination is one of the documented routes of this dissemination from CAFO’s
  3. Further development of the animal-feeding industry in South Dakota should not be allowed until this risk is eliminated
  4. To continue permitting these current CAFO practices in South Dakota is contrary to the judgment of such authoritative groups as the CDC, the American Medical Association, the American Public Health Association, and the World Health Organization

To take the first point, just how serious is the human health risk from antibiotic-resistant bacteria? From the CDC, we get these typical annual numbers: 2 million antibiotic-resistant infections, 23,000 deaths, 8 million additional hospital days, and between $20 billion and $35 billion in excess direct health-care costs. Here in South Dakota, the state Dept. of Health has published antiobiograms from health facilities around the state, showing that we are experiencing the same problems with antibiotic resistance as are being seen elsewhere.

The problem is serious enough that some infectious disease experts have warned that we are nearing the end of the antibiotic era, when many infections will have become untreatable, and we will have to resort to quarantine and disinfectants alone. Right now it’s still rare to find an organism that’s completely untreatable, but some are being reported in the US. Much more commonly, there remain a few last-resort antibiotics that do work against partially-resistant organisms, but they are typically much more toxic and dangerous than the drugs which have become ineffective. For a variety of reasons, effective new classes of antibiotics are no longer emerging from the pharmaceutical industry.

Although the overuse of antibiotics in human medicine shares the blame for the development of antibiotic resistance, the CDC is clear in assigning part of the blame to industrial food-animal production. In the US, nearly 80% of the 32.6 million pounds of antibiotics sold annually are used in industrial livestock farming. [Sources indicate 32.6 million pounds may be the actual amount of anitbiotics used for livestock production. —CAH] In the US, we use more antibiotics per pound of meat produced than any other nation. The volume of antibiotic use in industrial ag increased 20% between 2009 and 2013. More than 60% of these antibiotics in agriculture are considered important for use in humans. Even among those drugs that aren’t used in humans, we’ve seen the development of antibiotic resistance which confers cross-resistance to some human antibiotics.

So, how does a bacterium become resistant to antibiotics? It’s initially by a selection process: all the susceptible bugs are killed, but a few mutants sometimes survive because they’ve developed a means of resisting the drug. With repeated exposure to the drug (especially at low doses), the resistant strain becomes the dominant form. Once this happens, bacteria have tricks by which they can actually transfer drug-resistance genes from one to another, and even from one bacterial species to another.

This process can happen within the body of an animal or human, but can also occur within a manure lagoon. Some of the antibiotic dose makes it through the animal’s system and ends up in manure along with the bacteria, so this selection and gene-transfer process can continue in the pooled manure, increasing the number of resistant organisms.

These problems have been recognized for years, but the industrial ag proponents have been generally successful in preventing any remedies from being enacted. They have seen that they can reduce problems resulting from dense crowding of animals who are exposed to one another’s manure, and who are being fed a diet for which their digestive systems weren’t designed, by putting antibiotics in their feed or water. Animals were also found to put on more weight when given routine antibiotics.

Recognizing how severe the antibiotic resistance problem has become, the FDA managed to enact some rules that took effect in 2015 which were intended to reduce this risk by designating certain antibiotics in feed which can only be administered under the supervision of a veterinarian. These rules would theoretically stop the routine use of antibiotics for growth promotion, but continued to allow their use for disease prevention among the animals. Since the crowding of stock presents a constant threat of disease spread, it’s easy to imagine that some CAFO operators could persuade some veterinarians that they need that extra insurance to prevent disease outbreaks, even when nobody is clearly sick. When you combine this with the nationwide shortage of veterinarians who have ample experience with food animal medicine, and vets who may be asked to authorize antibiotic feed without having examined an animal, you can see that this may not be very effective in curtailing antibiotic use. As we’ve mentioned, the trend in animal antibiotic sales is upward.

Much more effective legislation in Congress has been shot down by industrial ag interests every year since 2009. This legislation is the Preservation of Antibiotics for Medical Treatment Act (PAMTA), which has never made it out of committee due to extremely heavy lobbying pressure.

Our primary concern here today is how all this affects our water supply. There is now very good evidence that antibiotic resistance does get spread in the environment via the water route. Nowadays you can actually measure the concentration of bacterial antibiotic resistance genes in water, and people have done just that in the South Platte River, for example. Here, researchers measured the concentration of these genes upstream and downstream from CAFO’s, and did the same measurements upstream and downstream from municipal sewage-treatment plants along the river. They found a much greater increase in these resistance genes downstream from CAFO’s, as contrasted with the increase associated with municipal waste-water treatment plants.

Considering that humans and livestock share many of the same disease-causing microbes in our digestive tracts, and considering that the volume of waste produced in a large CAFO may be larger than that produced by many cities, a person could wonder why we wouldn’t insist that CAFO manure be dealt with as carefully as municipal sewage, particularly in light of the antibiotic resistance problem.

In conclusion, I think we can see that effective legislation to remove this threat to our water supply and to our future ability to rely on antibiotics has been thwarted so far, in spite of the fact that more than 400 health-related groups have endorsed the PAMTA legislation. In view of increasing public awareness of this issue, we could expect that present CAFO models for food production necessitating antibiotic use won’t be tolerated much longer. Meanwhile, it would be prudent of South Dakota to insist that anyone proposing CAFO development be required to show how they can avoid contributing to this problem.


  1. Darin Larson 2016-10-07

    “Further development of the animal-feeding industry in South Dakota should not be allowed until this risk is eliminated”

    This is the type of absolutist rhetoric that makes me skeptical of Dr. Kelly and frankly undermines progress on these issues. He raises an important issue and then proceeds to alienate the livestock industry by talking about stopping any expansion of the industry unless all risk is eliminated.

    Have we removed all risk in the use of automobiles? Have we removed all risk in any aspect of industry? Have we removed all risk in carrying a phone that might start on fire? No, we make judgments about what reasonably can be done to minimize risk in all aspects of life.

    Instead of immediately polarizing each side by using untenable absolutist language, I would prefer he had used more measured language. It also seems that the research on the issue needs to be developed more fully.

    This is not to say that I don’t think that measures shouldn’t be taken as initial steps to limit the spread of antibiotic resistant bugs. I believe the FDA is already moving on this issue and is the appropriate government agency to handle the science and regulations of antibiotics.

  2. Paul Seamans 2016-10-07

    Darin Larson, when automobiles are found to be unsafe the industry issues a recall. When lead in gasoline was finally found to be hazardous it was removed. Even these industries have tried to police themselves a little.

    I don’t see the same thing happening with the livestock industry regarding the overuse of antibiotics. They only give it a little lip service every now and then.

    Dr. Kelley was not calling for the elimination of the CAFO industry. The livestock industry needs to start policing themselves or the federal government will eventually do it for them.

  3. Darin Larson 2016-10-07

    Paul, an unsafe automobile is a subjective judgment and that is why I used it as an example.

    I believe the industry is well aware of the issue and progress is being made. More needs to be done, I’m sure. I also believe that the FDA is increasing regulation and has this issue squarely in their sights. Consumers and retailers are demanding less antibiotic use. It is clear we are moving to a smarter use of antibiotics. Doctors and patients have a role to play in limiting the use of antibiotics in humans when their use is of negligible efficacy and to save them for demonstrated needs.

    The problem I had was this sentence by Dr. Kelley: “Further development of the animal-feeding industry in South Dakota should not be allowed until this risk is eliminated.” In what area of our lives can we eliminate all risk? Certainly not in the use of automobiles. We will still need to use antibiotics for sick animals unless society is ready to say let the animals suffer and die to lessen the chance that antibiotic resistance occurs in humans.

  4. c carter 2016-10-07

    Water quality falls within the purview of DENR, which routinely reports on bacterial pollution in the rivers, streams and lakes of SD. DENR must also be well aware that manure applications contribute substantially to bacterial pollution of SD waterways, because the Central Big Sioux River Water Quality Master Plan (, which found that “cropland is the greatest overall bacteria load contributor” in the Big Sioux River watershed, is on DENR’s web page. There is substantial evidence (i will gladly provide multiple citations) that bacteria from manure applications enter surface and ground water, and antibiotic-resistant bacteria from manure contributes to human disease (just as one example, this study from Johns Hopkins found that “approximately 11 percent of community-acquired MRSA and soft tissue infections in the study population could be attributed to crop fields fertilized with swine manure.” However, SD agencies are often loathe to accept scientific results from elsewhere, and there appears to have been little research conducted in SD to identify and quantify specific sources of these bacteria and their antibiotic resistance genes. DENR needs to fund studies including bacterial assays on manure (which is routinely tested for N and P content), as well as downstream monitoring, including characterization of bacterial strains (and antibiotic resistance genes). Such studies would enable mapping and analysis of the relative contributions of field manure applications and possibly even of specific sites to bacterial pollution of waterways.

  5. Douglas Wiken 2016-10-07

    A moratorium on large feeding operations that pollute streams and air and contribute to antibiotic resistance is hardly absolutist thinking. Barging ahead and approving these operations come hell or high water is the absolutist thinking involved.

  6. Caleb 2016-10-08

    Darin, nowhere in the quote you provided did Dr. Kelly say “all” risk.

  7. Don Kelley 2016-10-14

    To Don Coyote, thanks for your comment. I am aware of current research involving novel strategies attacking antibiotic-resistant organisms, including the nanoparticles you mention. I think it’s fair to say that we’ve probably exhausted the least expensive or least technologically demanding options, which we’ve derived from nature’s store of interspecies molecular weapons. Using light-activated nanoparticles to attack a bacterial infection of a heart valve, for instance, sounds like a pretty expensive session in a heart catheterization lab. We have clearly gotten ourselves into a situation where the low-hanging fruit have been harvested, and we need to change some behaviors if we want to avoid depleting the remaining, readily usable and relatively safe options.

    One of the behaviors we might consider changing is to revise the concept of dense crowding of animals which we propose to use for food, and combatting the resulting disease risk among these animals by feeding them antibiotics. Any increased cost of food would be offset by savings in human healthcare.

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