Fate of antibiotic resistant bacteria and genes in manure storage

Manure storage and its application on cropland may contribute a form of environmental contamination: antimicrobial-resistant bacteria. These bacteria in manure are perceived to cause diseases in humans through environmental contamination. However, a recent study at the University of Nebraska-Lincoln feedlots near Mead, Nebraska concluded that long-term manure storage as static stockpiles has the advantage of inactivating antimicrobial-resistant bacteria, and it has the potential to reduce antimicrobial resistance genes.

What is antimicrobial resistance and why it is a problem?

Antimicrobial-resistant bacteria develop when bacteria cannot be killed by an antimicrobial designed to kill them, in other words, when bacteria uptake antimicrobial-resistant genes and continue to survive in the presence of the antimicrobial. Antimicrobial-resistant diseases occur when resistant bacteria cause disease that cannot be cured by effective antimicrobial treatment. Today, antimicrobials are losing their efficiency for an increasing number of diseases due to the rapid emergence of bacterial resistance, which has become a threat to human health. Resistance (bacteria or genes) is an ancient phenomenon, and bacteria have been resisting fatal effects of natural antimicrobials by using their genes for billions of years. However, overuse and misuse of antimicrobials have been shown to accelerate this process and increase resistant diseases in humans.

Can manure storage help?

Manure storage and its application on croplands are perceived to contribute to diseases of antimicrobial-resistant bacteria in humans through environmental contamination. A link is plausible, however, there is no scientific evidence showing the extent of the impact emerging from manure-born resistance. The assessment of health risks posed by manure related antimicrobial resistance is a complex and multifaceted problem. Nevertheless, long-term manure storage with high temperatures has the potential to reduce levels of antimicrobial resistance before land application, thus can limit risks of contamination in the environment and increase the value of manure as a fertilizer. Therefore, it is valuable to understand how manure management practices affect the emergence and spread of antimicrobial resistance. This knowledge is a major step toward fighting against resistance and reducing potential risks to human health.

What do we know about the survival of antimicrobial-resistant bacteria and genes in manure storage?


  • Thermophilic temperatures (between 106 and 252°F) are generally effective in decreasing antimicrobial-resistant bacteria and genes in manure.
  • Resistant bacteria concentrations in manure can be reduced through long-term storage at normal temperatures.

Survival of antimicrobial-resistant bacteria in manure storage is dependent on factors such as type of bacteria, initial bacterial concentration, soil type, nutrient availability, and climate. Unlike resistant bacteria, the association between gene degradation and these factors is not well understood.

Research indicates that thermophilic anaerobic digestion and composting may degrade antimicrobial-resistant bacteria in manure. For both treatment methods, the inactivation of antimicrobial-resistant bacteria occurs primarily by increased temperature and lowered pH. Depending on the temperature and treatment, antimicrobial-resistant bacteria can be decreased within days to months.

A recent study at the University of Nebraska-Lincoln feedlots near Mead, Nebraska revealed that beef cattle manure stored as static stockpiles had the advantage of inactivating antimicrobial-resistant bacteria over a three-month storage period. Results suggest manure management practices should include sufficient storage time before land application to kill resistant bacteria. However, antimicrobial resistance genes were not reduced over a three-month storage period. The persistence of resistance genes and even increase was observed by various manure storage practices. These results were likely due to lack of adequate temperature in manure storage for effective reduction of resistance genes since there is evidence that thermophilic temperatures (between 106 and 252°F) can reduce genes. In fact, the complete degradation of genes can be observed at temperatures greater than 158°F.

How does antimicrobial resistance occur in manure?

Antimicrobials are commonly introduced to livestock by feed and/or drinking water for disease treatment or prevention in the United States, however, they are not completely absorbed, and 30 to 90% is excreted in feces and in the urine. Once in manure, these antimicrobials can create a suitable condition for the emergence of antimicrobial-resistant bacteria in the environment. Furthermore, resistant bacteria and genes can be present in the gastrointestinal tract of animals naturally and can be excreted in feces. Thus, manure acts as a reservoir for the spread of resistance in the environment.

How does manure-born antimicrobial resistance spread?

Research indicates that manure-born resistance may have access to humans via multiple environmental pathways. For instance, resistant bacteria/genes can survive in abundance for a long time in manure after it is land applied, and they can be transferred to humans through wind or plants that are consumed raw. Surface water and groundwater near manure applied sites have been shown to be contaminated by manure, by which resistant bacteria can possibly have access to humans via ingestion of water.

Resistance tends to increase in the environment during manure storage and application. This is explained by the biology behind bacterial growth and gene transfer. One factor can be the exchange of resistance genes between manure and soil bacteria, which has been shown to occur naturally in the environment. Another factor can be the adaptation of native soil bacteria to resistance, which can be increased by higher nutrient input due to manure application.

What is manure’s role in the antimicrobial resistance problem?

Livestock feeding in the Unites States produces 335 million tons of manure dry weight per year. As an abundant source of macro and micronutrients for vegetation, most of the livestock manure is stored then recycled as the soil in forage and crop production. Although this practice contributes to sustainability in agriculture, the presence of antimicrobials and antimicrobial-resistant bacteria/genes in manure has become an increased concern as a human health risk.

Risks of manure-born resistance to human health may be exaggerated. Manure storage and application may contribute to the spread of resistance, however, the magnitude of the real threat to human health is uncertain for multiple reasons. One of the reasons is that the occurrence of a resistant disease requires a succession of rare events. For example, the exchange of resistance genes between bacteria to a pathogen (bacteria that can cause disease in humans), which happens rarely in the environment. In addition, it is unlikely that the exchanged genes in the pathogen cause failure of the antimicrobial treatment. Another reason is that the contamination pathways from manure to humans may include sufficient obstacles to minimize the risk of successful transfer of pathogens. An example of this may be airborne pathogens, as studies show that the risk of airborne contamination through land-applied manure is low.  Management options such as long-term storage and composting create additional obstacles for reducing human exposure to antimicrobial resistance in manure.


Ece Bulut – written while a student at University of Nebraska as a part of a course in animal manure management and originally published on water.unl.edu/manure

Reviewed by: Amy Schmidt, Mara Zelt, and Ben Samuelson, University of Nebraska

Further reading:

World Health Organization (WHO) – Antibiotic Resistance, http://www.who.int/news-room/fact-sheets/detail/antibiotic-resistance

Xu, S., Sura, S., Zaheer, R., Wang, G., Smith, A., Cook, S., Olson, A., Cessna, A.J., Larney, F.J., and McAllister, T. A. (2016). Dissipation of Antimicrobial Resistance Determinants in Composted and Stockpiled Beef Cattle Manure. Journal of Environment Quality. https://doi.org/10.2134/jeq2015.03.0146

Diehl, D. L., & Lapara, T. M. (2010). Effect of Temperature on the Fate of Genes Encoding Tetracycline Resistance and the Integrase of Class 1 Integrons within Anaerobic and Aerobic Digesters Treating Municipal Wastewater Solids. Environmental Science & Technology, 44(23), 9128–9133.

Communicating Science Using the Science of Communication

In the digital world in which we live today the public is presented with an overwhelming quantity of information, much of which is unscientific. In this webinar we will apply the lessons learned from antimicrobial resistance and health communications to more science communication challenges. This presentation was originally broadcast on August 14, 2020. More… Continue reading “Communicating Science Using the Science of Communication”

How do you like your steak?

People worry, and I am no exception. I spend more time than I would like to admit on social media, and I have seen some things, disturbing things, things that cannot be unseen. Turns out there is a lot out there to be worried about; so how do I know I am worried the right amount and not too much? For example, I know that antimicrobial resistance (AMR) is a serious and growing health problem, but what does that mean for me? I want to know which aspects of the AMR crisis are going to impact me, which I do not have to worry about, and what I or others can do about it. The first thing I want to know more about is meat safety. I have seen the labels about “antibiotic-free meat”, and I want to know – how safe is my burger? So, I got in contact with some folks who really know meat to find out.

I learned that researchers at the USDA’s Meat Animal Research Center have conducted a series of studies looking at how antibiotic use in beef cattle production could impact AMR present in processed beef. These studies addressed the following questions:

  • What is the difference in the levels of AMR present inside animals raised with or without antibiotics?
  • Does a short course of antibiotics fed to animals as a preventative treatment impact the level of AMR present in the animals at harvest?
  • How effective are conventional food safety measures at preventing AMR from animal environments from contaminating meat during the initial stages of processing?

The following summaries of study findings were written by the study authors and reproduced here with permission.

Beef “raised without antibiotics” contains a similar amount of antibiotic-resistant bacteria as conventional beef

Meat products, including ground beef, are thought to be routes of transmission for antibiotic resistance from animals to humans. Ground beef products produced from cattle “raised without antibiotics” (RWA) are perceived as harboring lower levels of antibiotic resistance than “conventional” (CONV) products, which may contain meat from animals that received antibiotics. This 2018 study looked at the bacteria and level of antibiotic resistance found in ground beef from animals raised with, or without antibiotics.

The study reports that the microbial flora and antibiotic resistance levels of CONV and RWA ground beef are similar, with negligible levels of resistant Salmonella, Staphylococcus aureus, and third-generation cephalosporin-resistant E.coli in either type of beef and similar levels of resistant Enterococcus spp. present in both types – roughly 90% contained tetracycline-resistant enterococci, and roughly 25% contained erythromycin-resistant enterococci. These results demonstrate that RWA ground beef does not deliver its major perceived benefit of having lower levels of antibiotic resistance than CONV ground beef when conventional production follows good production practices and correct withdrawal dates for antibiotic use.

These results are consistent with prior research demonstrating that the long-term antibiotic resistance impacts of antibiotic use during U.S. beef cattle production are minimal. They highlight the need for reevaluation of the claims of the detrimental impact of antibiotic use during U.S. beef cattle production on human health via ground beef.

Does preventative antibiotic use in livestock increase antibiotic resistance long-term?

Access to antibiotics has greatly increased the health of animals in livestock production. However, concerns have been raised that in-feed use of antimicrobials in livestock feed may increase AMR in bacteria associated with livestock and livestock environments. To test this, researchers considered the effect of a short-term course of antibiotics, given preventatively to calves, on the presence of resistant bacteria and AMR genes in the animals over their entire term in a feedlot environment.

Chlortetracycline (CTC) is an antimicrobial commonly fed to calves shortly after entry into feedlots. This treatment is given for the prevention of bovine respiratory disease. Researchers evaluated the impact of a 5-day in-feed CTC regimen on animal health, AMR in bacteria, and the presence of 10 antimicrobial resistance genes. A control group of cattle (n = 150) did not receive CTC, while a treated group (n = 150) received in-feed CTC from the 5th to the 9th day after feedlot arrival. Fecal swab and pen surface occurrences of antimicrobial-resistant E. coli and AMR genes were determined on five sample occasions: arrival at the feedlot, 5 days post-treatment (dpt) completion, 27 dpt, 75 dpt, and 117 dpt.

No differences in the levels of AMR genes between the CTC-treated and control groups at any time from 5 to 117 days after treatment were observed. On 5 dpt, there was an increase in antimicrobial-resistant E. coli for the treated group vs. the control group. For all other sample dates, there was no difference between the two groups. In addition, there was a significantly higher number of illnesses in the cattle that were not treated with CTC when compared to those animals that received CTC. In conclusion, it was shown that the in-feed CTC treatment reduces the number of illnesses in calves entering feedlot facilities with no long-term impact on the occurrence of antimicrobial-resistant E. coli or on the level of AMR genes.

What is being done to keep meat safe during processing?

Concerns have been raised that pathogenic E. coli and Salmonella strains present in beef cattle feeding operations can develop resistance to antimicrobials critically important to human medicine. These strains may survive food processing, end up in the foods eaten by consumers, and adversely affect human health. In response to these concerns, this study sought to assess standard beef production and processing practices for the persistence of AMR bacteria.

One hundred eighty-four beef cattle were sampled at seven points of processing route (feedlot fecal, processing fecal, feedlot hide, processing hide, preevisceration carcass, final carcass, and strip loin) to determine the occurrences and concentrations of AMR E. coli and Salmonella bacteria. Antimicrobial-resistant E. coli were present on 100% of hides both at feedlots and when cattle begin processing. Antimicrobial-resistant Salmonella were found on 11% of hides at feedlots and on 8% of hides when cattle begin processing.

However, over the course of processing, researchers observed less and less bacteria until finally antimicrobial-resistant E. coli were present on only 1% of final carcasses and were not found on final meat products. Antimicrobial-resistant Salmonella were not found on carcasses or final products. These results indicate that when conducted correctly, sanitizing interventions currently employed at beef processing plants are effective against antimicrobial-resistant bacteria, and that beef products are not a significant source of foodborne pathogens with AMR properties.

Worrying less

It was a load off my mind to read those studies and learn that there are strategies in place along the production chain to reduce the risks and help keep my food safe. Nothing is perfect of course; I know there are occasional food recalls when something goes wrong during production, processing, or transporting of foods. Which means I will have to continue to practice good food safety at home; making sure to clean, separate, cook (with a thermometer!), and chill all my food, including fresh beef, and frequently was my hands when preparing or prior to eating food. Still, I am happy to know that I can enjoy a good burger without worrying so much.


Commentary by Mara Zelt,  University of Nebraska, mzelt2@unl.edu with research summaries by:

Amit Vikram, Eric Miller, Terrance M. Arthur, Joseph M. Bosilevac, Tommy L. Wheeler, and John W. Schmidt of USDA-ARS to summarize their manuscript “Similar levels of antimicrobial resistance in U.S. food service ground beef products with and without a ‘‘raised without antibiotics’’ claim” published in Journal of Food Protection 81:2007-2018 (2018). doi: 10.4315/0362-028X.JFP-18-299.

Getahun E. Agga, John W. Schmidt, and Terrance M. Arthur of USDA-ARS to summarize their manuscript “Effects of In-Feed Chlortetracycline Prophylaxis in Beef Cattle on Animal Health and Antimicrobial-Resistant Escherichia coli published in Applied and Environmental Microbiology 82:598-608 (2016). doi: 10.1128/AEM.01928-16.

Eric Miller, Amit Vikram, Getahun E. Agga, Terrance M. Arthur, and John W. Schmidt of USDA-ARS to summarize their manuscript “Effects of in-feed chlortetracycline prophylaxis in beef cattle on antimicrobial resistance genes” published in Foodborne Pathogens and Disease 15:689-697 (2018). doi: 10.1089/fpd.2018.2475.

John W. Schmidt, Getahun E. Agga, Joseph M. Bosilevac, Dayna M. Brichta- Harhay, Steven D. Shackelford, Rong Wang, Tommy L. Wheeler, and Terrance M. Arthur of USDA-ARS to summarize their manuscript “Occurrence of antimicrobial-resistant Escherichia coli and Salmonella enterica in beef cattle production and processing continuum” publish in Applied and Environmental Microbiology 81:713-725 (2015). doi:10.1128/AEM.03079-14.

Reviewers: Lindsay Chichester, University of Nevada Extension and Jovana Kovacevich, Oregon State University.

Antimicrobial Resistance Resource Library

Antimicrobial-resistant (AMR) infections are a serious threat to global public health. Each year AMR accounts for roughly 700,000 deaths worldwide. While AMR-related research is ongoing, conveying research-based knowledge about AMR mechanisms, risks, and opportunities to improve outcomes to the general public, agricultural producers, food safety experts, educators, and consumers is imperative.

The iAMResponsible Project team, a nationwide extension effort for addressing AMR, has developed a shared resource library to curate and translate the latest news and research findings on AMR for a non-technical audience. This library is designed to provide educators and advisors with access to resources that will assist you in your discussion of antimicrobial resistance.  Please feel free to share and re-purpose educational products in this library with local audiences.

How to find materials

For those seeking specific resources, materials are organized type of media. However, the library can be sorted by any of the other fields included in each entry, including topics using the sort function, found in the top-left area of the library window. Additionally,  there is a search button in the top right corner of the insert that looks like a magnifying glass which will allow the user to search for specific keywords. Use the view larger version option in the lower right of the library window to expand to a full-screen view.

Is something missing from our library?

We welcome your suggestions for resources that you have found beneficial in your educational or advisory role.  Please email the project team at iamr.educate@gmail.com to let us know what additional topics or types of resources would be most valuable to you in discussing AMR.


The iAMResponsible project was started by Amy Schmidt at the University of Nebraska-Lincoln and Stephanie Lansing at the University of Maryland. Find out more about the project here. This product was funded by financial assistance from USDA-NIFA.

Are there alternatives to antibiotics?

A brief summary of the manuscript, Alternatives to Antibiotics: Why and How (Allen, 2017), a review of current and potential alternatives to antibiotics for use in human or veterinary medicine.

Key Takeaways:

  • Every time antibiotics are used, impacted bacteria adapt to survive. Bacteria that are not killed by the antibiotic pass on their new survival traits to later generations of bacteria, which limit the effect of the antibiotic the next time it is used.
  • Antibiotics are not the only way to treat bacterial diseases. Alternative treatment methods to consider include vaccines, immunotherapeutics, bacteriophage therapy, and probiotics.

In a 2017 discussion paper in the National Academy of Medicine, microbiologist Heather K. Allen explains how the antibiotic resistance crisis came about and describes some practical solutions that are available now to begin to address the issue in clinical settings. As a general principle, Allen explains, pathogens can evolve genetically, developing resistance to our medicines, simply through what amounts to natural selection (this is somewhat of an oversimplification of the process, but a helpful model for understanding it). Because antibiotics have been overused—particularly in their prophylactic use (meaning use to prevent a disease that doesn’t yet exist)—the already quick evolution of bacteria has ironically been lent a helping hand by humanity. The more quickly we kill off bacteria, the more rapidly the bacteria themselves must and do evolve to survive.

Allen recommends “antibiotic prudency,” or “the use of antibiotics only when they are expressly needed and at the most appropriate dose for disease treatment.” She admits that “this is a nebulous concept that is difficult to define,” but overall she emphasizes that changing cultural attitudes toward casual use of antibiotics as preventative measures is necessary, and she implies that physicians and veterinarians (as well as governmental bodies regulating food and drugs) can be one of the starting points for changing cultural attitudes toward when and how it is acceptable to use antibiotics.

Some of the alternatives she suggests include:

Vaccines –Because many resistant infectious occur secondarily to vaccine-preventable diseases (such as pneumonia after the flu), vaccines are a very effective way to prevent the necessity of antibiotics to begin with.

Immunotherapeutics – this involves augmenting the host’s immune system at specific times (such as postpartum) so that infection does not occur to begin with. They have to be very specifically targeted in regards to time, however, which is not always predictable.

Probiotics – maintaining the vitality of healthy body flora in many ways could curb overgrowths of pathogens (an example of this is a lack of healthy flora in the vagina resulting in yeast infections or fecal transplants to curb cDiff infections). The drawbacks to this option (called competitive exclusion) are that particularly in the gut, healthy flora are so diverse that we do not fully understand their functions, so harnessing their potential more accurately will take a great deal more research. One way we can boost probiotic growth is the inclusion of prebiotic foods in our diets. Prebiotics are types of fiber that humans are not able to digest so they serve as a food source for probiotic species in the gut. Many high-fiber foods including fruits, vegetables, and grain contain prebiotics.

Bacteriophage Therapy – this form of therapy involves reprogramming viruses to target certain harmful bacteria. It is one of the most hopeful newer alternatives to antibiotic resistance that exists. Drawbacks to this method include having to know the exact pathogenic strain at issue in an individual, which requires culturing, itself sometimes difficult to do successfully. Also, bacteria can evolve resistance to bacteriophages, but bacteriophage therapy could be updated occasionally to target the new bacteria.

In conclusion, Allen says that dealing with antibiotic resistance will come from not one, but all of these methods used discerningly and where appropriate.


Written by: Kari Nixon,  Scholar of Medical Humanities & Literature, Whitworth University; reviewed by Sid Thakur,  veterinary medicine, NC State & Jovana Kovacevic, food science and technology, Oregon State.

The scientific research summarized in this article was published as

Allen, H. K. (2017). Alternatives to Antibiotics: Why and How. NAM Perspectives, 7(7). https://doi.org/10.31478/201707g

This article presents the author’s interpretation of the published research for a general audience and should not be considered a reflection of the position or opinion of the researchers.

Antimicrobial Resistance in Developing Countries: Current State and Controlling Strategies

In most developing countries, access to antimicrobial drugs is as easy as a run to the grocery store or nearby pharmacy – with or without a prescription from a medical professional. Even with a prescription, patients may not complete their doses, or they may not fully recover from an infection that then continues after the duration of the medicine. How does this unregulated use of antibiotics and related medications relate to the development and spread of antimicrobial resistance in developing countries and what strategies may help mitigate this increasing health crisis?

Antimicrobial resistance herein referred to as AMR, is a complex issue that the World Health Organization (WHO) and the Centers for Disease Control (CDC) have designated a global threat. AMR occurs when bacteria, viruses, fungi, or other infectious organisms adapt and become able to survive in the presence of a medication previously used to kill them. Organisms like bacteria and viruses can even exchange their genetic materials with other susceptible pathogens, thereby enabling the receiving organisms to become resistant, as well. It is worth noting that many potentially deadly diseases – such as influenza, AIDs, and cancer, and COVID-19—become more deadly when secondary bacterial infections that co-occur with them (such as pneumonia) cannot be treated with antibiotics. In fact, a study of nearly 200 COVID-19 patients in a Wuhan, China hospital showed that 50% of patients who died tested positive for secondary infections compared to only one of the nearly 140 survivors. (Read the original article here.)

Bacteria – including AMR bacteria – are a natural part of our soil, water, and living bodies. Even in pristine environments (where humans have never been present), bacteria exist; even bacteria that are resistant to antibiotics. But that’s not to say that humans have not greatly impacted this issue. Any use of antibiotic drugs for the treatment of humans and animals can lead to the development of AMR. In many countries, including the U.S., people cannot access antibiotics without a prescription issued by a medical professional and a veterinarian must approve antibiotic use for animals. Across Asia and Africa, on-the-spot diagnosis and treatment by non-medical personnel are rampant. This may be the single greatest cause of AMR in these countries.

Mass production of generic antimicrobial drugs in industrialized countries also makes the accessibility to these drugs easier and less costly in developing countries. Amoxicillin, a first-line antimicrobial drug that could once treat multiple diseases, including bacterial pneumonia, chlamydia, and salmonella, is now often ineffective against these bacterial infections. In Kenya, renowned microbiology researcher Sam Kariuki reported to the New York Times that nearly 70% of salmonella infections had stopped responding to the most widely used antibiotic treatments.

The World Health Organization recognized AMR as a global public health threat requiring action across all government sectors and society. At their inaugural meeting during the World Antibiotic Awareness Week, the Ministry of Health in Kenya encouraged the collaboration between different stakeholders from agriculture and livestock production to public health. This effort is intended to identify and implement strategies that will institutionalize surveillance systems and encourage antimicrobial stewardship for both human and animal use of antibiotics. This “one-health” approach recognizes the interconnectedness and mutual dependency of human, animal, and environmental health.

Another driving factor to this crisis is poverty and the often accompanying lack of proper health amenities and basic sanitation practices. These factors lead to unregulated drug supply chains, improper diagnostics, and rampant spread of infectious diseases. Thus, the fight against AMR as a global public health threat must be combated by incorporating economic considerations into the disease mitigation model. Other notable organizations are working on strategies to bring awareness to AMR in the African continent and implementing such strategies through education, encouraging behavioral change, and conducting research.


This article was written by Noelle Atieno Mware,  PhD student at the University of Nebraska-Lincoln, as a part of a course on antimicrobial resistance and science communication. This article was reviewed by Drs. Amy Schmidt (aschmidt@unl.edu) and Kari Nixon, both members of the iAMResponsible extension team for antimicrobial resistance.

Antimicrobial Resistance is Native to the Environment

Germs are everywhere, some resistant to medical treatment

When I was a kid, I remember being called inside for lunch on a summer day and hearing, “Wash your hands! You’ve been playing in the dirt!” Of course, we all grew up knowing that dirty hands can spread germs. But, I didn’t know until I was much older that the same soil that made my hands dirty was also the source of some pretty amazing medicines.

Many widely used antibiotics were first discovered in soil. Penicillin, one of the first antibiotics used to treat infections in humans, was isolated from a mold called Penicillium notatum growing in soil. Vancomycin, discovered in a soil  sample from deep within the jungles of Borneo, is produced by a species of soil bacteria from the Actinobacteria phylum. And, chlortetracycline is an antibiotic produced by actinomycete, another type of bacteria found in soil. It may not be surprising that soil is home to such a vast array of microorganisms, but why do so many types of soil bacteria create antibiotic compounds?

The idea that all living things must adapt to their changing environment to preserve their species is often referred to as “survival of the fittest”. In a world of limited resources – including the soil environment – surviving means competing with other organisms for the necessary inputs, like nutrients, water, and oxygen, to stay alive. One way to ensure access to the resources needed is to eliminate the competition. For this reason, fungi and bacteria in soil may produce compounds that kill bacteria, a sort of “chemical warfare” at the microscopic level. Thankfully, scientists discovered many years ago that these antibiotic compounds made by organisms to fight off their competition in the soil environment can also fight off bacterial infections in the bodies of humans and animals.

Bacteria and other organisms, however, seldom go down without a fight. The bacterial targets of antibiotics fight back in an attempt to survive when they encounter these toxins, whether inside a human body, an animal, the soil, or any other environment. While an antibiotic may eliminate most of the target bacteria, some may survive because they have a trait that makes them less susceptible to the toxin or because the toxin is not delivered in a large enough quantity to kill all of its targets. “What doesn’t kill us makes us stronger” is certainly true for many of these bacteria. The surviving members of the bacterial population begin preparing for the next attack of that toxin by changing at a genetic level (altering their genes), transferring to their fellow bacterial neighbors the genetic material (genes) that enabled them to resist the initial attack and even receiving genetic material from viruses that infect them. The bacteria are developing “antibiotic resistance”. These processes are a natural part of a bacterium’s life cycle, and the new traits developed to resist the toxin are passed on to some of their offspring to help ensure the survival of their species.

What can we do about antibiotic resistance?

So, does this mean nature alone is to blame for the worldwide threat to human health by antimicrobial-resistant bacteria? Certainly not. But, it does mean that human development and the use of antibiotics for the treatment of bacterial infections did not create the phenomenon of antibiotic resistance. Antimicrobial-resistant traits among bacteria were present in nature long before the modern antibiotic era. Scientists studying the evolution of various antibiotics have discovered that some enzymes responsible for equipping bacteria to resist some antibiotics originated millions, or even billions, of years ago. Multi-drug-resistant bacterial isolates have been identified in environments unaffected by antibiotics, such as remote, undisturbed soils and pristine freshwater environments.

So, what does this all mean? I hate as much as the next person to hear the words, “it’s complicated”, when trying to make sense of something that is beyond my immediate understanding. But, the truth is, the historic and future evolution of antimicrobial resistance is complicated. As of yet, scientists have not established a simple “cause and effect” scenario for how and why drug-resistant strains of bacterial infections occur. We often hear people blame the “overuse and misuse” of antibiotics in humans and animals for the development of antibiotic resistance. Using the soil environment as an example, it is easy to see that any exposure to antibiotics can trigger bacterial species to begin developing resistance mechanisms. That is not to say that more prudent use of antibiotics in human and animal populations is not a critical component of the global battle against antimicrobial resistance health concerns. It simply means that human and animal health care practices are only one piece of a large and diverse puzzle for which we do not yet know how to fit all of the pieces together.

Unfortunately, antimicrobial resistance is complicated. But, while we have not yet “solved” the crisis of treatment failure for antimicrobial-resistant infections in the human clinical setting, we are learning more and more every day about how the environment, human medicine, livestock, and domestic animal health care, policy, and food production and handling practices influence the future of this health threat. And, we believe everyone has an obligation to develop an understanding of antimicrobial resistance – what it is, how it happens, and what risks may exist for us individually and collectively – and to adapt our individual practices based on scientific evidence to reduce AMR-related health risks. Simply put, we all have a role.

The problem of antibiotic resistance is real, and it is growing into one of the most significant health crises the world may ever see. However, responsibilities for creating and solving the crisis are quite broad, and some contribution comes from natural forces in the world totally unrelated to human activity. Understanding this will be important in identifying solutions to correctly address the problem.


Amy Schmidt, Livestock Bioenvironmental Engineer, University of Nebraska – Lincoln, aschmidt@unl.edu