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.