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Does composting reduce antibiotics or antibiotic resistance in animal manure?

August 10, 2015

Composting animal manure may be the best strategy to reduce antimicrobial resistance before the manure is released into the environment. There is evidence suggesting that although antibiotic resistant pathogenic organisms are rapidly killed in a composting environment, the antimicrobial resistance genes may persist for a longer period. There is also evidence that the concentrations of most antibiotic residues in manure are significantly reduced during the composting process, although the antibiotics degrade naturally in the soil or manure with time as well.

It is important to distinguish compost from rotted or stored manure. There are some jurisdictions where the term “composting” has no particular definition other than a period of decomposition. In other areas, the term “compost” is well defined to indicate a thorough decomposition process whereby all of the material has reached temperatures of > 55-60 C for a defined period of time.

Fate of Antibiotics During Composting

It appears that concentrations of many antibiotics are significantly reduced during the composting process. In a review on the fate of antibiotics in animal manure, Masse et al. (2014) concluded that composting was more effective than anaerobic digestion, and either process was more effective than application of the raw manure directly to the land.

Storteboom et al. (2007) found that intensively managed composting process slightly reduced the degradation period for three antibiotics present in horse and dairy cattle manure, including chlortetracycline, tylosin and monensin. Dolliver et al. (2008) reported that chlortetracycline concentrations were reduced by > 99%, monensin and tylosin concentrations were reduced by 54 to 76%, and sulfamethazine concentrations were not reduced after 35 days of composting. Sura et al. (2015) measured significant reduction of antibiotics in beef cattle manure during both composting and stockpiling of the manure, but noted that temperatures of the stockpiled manure also reached > 60 C.

In a study measuring antibiotics in fresh or composted manure used for vegetable production, Kang et al. (2012) concluded:

“a practical guideline for organic producers who use conventional manure for plant nutrient source will be to (1) apply composted manure rather than fresh manure, and/or (2) let the manure sit in the soil for as long as possible before planting vegetables in the spring. This extra time will help degrade antibiotics and thus lower the concentration available for plant uptake.”

Fate of Antibiotic Resistant Microbes During Composting

Most antibiotic resistant microbes that are potentially harmful to humans are destroyed by a consistent composting process, where the temperature is carefully controlled to exceed 55-60 C in all parts of the composting material.

Sharma et al (2009) measured substantial reduction of E. coli resistant to tetracycline and ampicillin during windrow composting of beef manure but observed that the resistance genes prevailed for a much longer period of time. Wang et al. (2015) reported measured a 4 to 7 log reduction in tetracycline and erythromcyin resistant bacteria during simulated composting of swine manure compared to a 1-2 log reduction during lagoon storage. Cook and Bolster (2015) observed that enterococci concentrations decreased to below detection within 21 days of composting swine slurry. Gao et al. (2015) measured significantly lower antibiotic resistant E. coli in composted manure than in raw pig manure in China.

Fate of Antibiotic Resistant Genes During Composting

Chen et al. (2010) found that composted manure contained up to seven orders of magnitude less AMR genes than manure treated by other technologies, including lagoon, aerobic treatment, and anaerobic treatments. Wang et al. (2012) reported that the six measured classes of erythromycin resistance gens and tetracycline resistance genes declined marginally during the first 17 days of composting, but dramatically afterward within 31 days of composting swine manure. In contrast, they measured no reduction in antimicrobial resistance genes during lagoon storage of manure.

Stoorteboom et al. (20o7) concluded that more than six months of composting may be required to reduce some of the AMR genes in horse and dairy manure. Keen (2009) measured rapid disappearance of potential pathogens during composting of poultry litter, but little reduction in the concentration of tetracycline resistance genes. Sharma et al (2009) measured reduction in abundance of AMR genes following windrow composting of beef manure. Marin et al. (2014) reported that E.coli was eliminated after one or two weeks of composting sheep manure, but the virulence and/or antibiotic resistance genes persisted even after 49 days of composting. Cook and Bolster (2015) measured a 36-97% reduction in bacteria with erythromycin AR genes, a 94-99% reduction in bacteria with tetracycline resistant genes, and a 53-84% reduction in bacteria with sulfonamide resistant genes following 112-142 days of composting swine manure.

In a review of manure treatment to reduce antimicrobial resistance, Wang and Yu (2012) concluded that anaerobic lagoons  were poorest at reducing risk and composting was the best treatment option.

“because animal manure is the largest reservoir of AMR, management and treatment of animal manure provide an opportunity to contain and destruct AMR arising from food animal production” (Wang and Yu 2012)


Short of reducing antibiotic use in agriculture, composting may be the best option for managing the large reservoir of antibiotic resistance contained in animal manures.  Pruden et al. (2013) recommended composting and digestion for reducing the risks associated with animal manure. Marin et al. (2014) concluded that “composting is a practical method that can effectively eliminate pathogens in manure, or at least promote a reduction in the number of pathogenic cells.” Wang et al. (2015) concluded that “composting can be an effective and practical approach to decrease dissemination of antibiotic resistance from swine farms to the environment”. Cook and Bolster (2015) concluded that; “As concerns over antibiotic resistance and pathogens increase, composting provides a valuable manure management tool for decreasing contaminants and improving the value of this material as a soil conditioner.”

We should do all that we can to reduce the risk of increased antibiotic resistance and its impact on human and environmental health. Finley et al. (2013) concluded that “reducing this risk must include improved management of waste containing antibiotic residues and antibiotic resistant organisms” 


Chen, J., F.C. Michel Jr., S. Sreevatsan, M. Morrison, and Z. Yu. 2010. Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine farms. Microbial Ecology 60:479-486.

Cook, K. and C. Bolster. 2015. Composting swine slurry to reduce indicators and antibiotic resistance genes. Animal Manure Management. http://www,

Dolliver, H., S. Gupta and S. Noll. 2008. Antibiotic degradation during manure composting. J. Environmental Quality 37: 1245-1253.

Finley, R.L., P. Collignon, D.G.J. Larsson, S.A. McEwen, X.-Z. Li, W.H. Gaze, R. Reid-Smith, M. Timinouni, E. Topp and D.W. Graham. 2013. The scourge of antibiotic resistance: the important role of the environment. Clinical Infectious Diseases, 57:  704-710.

Gao, L., J. Hu, X. Zhang, L. Wei, S. Li, Z. Miao and T. Chai. 2015.  Application of swine manure on agricultural fields contributes to extended-spectrum b-lactamase-producing Escherichia coli spread in Tai’an,China. Frontiers in Microbiology April 2015 Volume 6 Article 313.

Kang, D-H., S. Gupta, C. Rosen, V. Fritz, A. Singh, Y. Chander, and H. Murray. 2012. Antibiotic Uptake by Vegetable Crops from Manure-Applied Soils. A Report Submitted to North Central Region Sustainable Agricultural Research and Extension (SARE) Program

Keen, P.L. 2009. Seasonal dynamics of tetracycline resistance genes and antibiotics in a British Columbia agricultural watershed. PhD Thesis, University of British Columbia, Resource Management and Environmental Studies.

Marin, J.M., R.P. Maluta, C.A. Borges, L.G. Beraldo, S.A. Maesta, M.V.F. Lemos, U.S. Ruiz, F.A. Ávila and E.C. Rigobelo. 2014. Fate of non O157 Shigatoxigenic Escherichia coli in ovine manure composting. Arq. Bras. Med. Vet. Zootec., 66: 1771-1778.

Masse, D.I., N.M. Cata Saady and Y. Gilbert. 2014. Potential of Biological Processes to Eliminate Antibiotics in
Livestock Manure: An Overview. Animals 2014, 4, 146-163; doi:10.3390/ani4020146.

Pruden A, D.G.J. Larsson, A. Amézquita,  P. Collignon, K.K. Brandt, D.W. Graham, J.M. Lazorchak,  S. Suzuki, P. Silley, J.R. Snape, E. Topp, T. Zhang and Y-Guan Zhu. 2013. Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environmental Health Perspectives 121: 878-885

Sharma, R., F.J. Larney, J. Chen, L.J. Yanke, M. Morrison, E. Topp, T.A. McAllister, and Z. Yu. 2009. Selected antimicrobial resistance during composting of manure from cattle administered sub-therapeutic antimicrobials. J Environmental Quality, 38: 567-575.

Storteboom, H. N.,  S.C. Kim, K.C. Doesken,  K.H. Carlson J.G. Davis and A. Pruden. 2007. Response of antibiotics and resistance genes to high-intensity and low intensity manure management. J Environmental Quality 36: 1695-703.

Sura, S., T.A. McAllister, F.J. Larney, A.J. Cessna, I.D. Amarakoon, L.D. Tymensen, J. Charest, A.F. Olson, J.V. Headley, and F. Zvomuya. 2015. The Fate of Antimicrobial Residues during Composting and Stockpiling of Manure. Compost Matters. March 4-5, 2015, Red Deer, Alberta.

Wang, L., and Z. Yu. 2012. Antimicrobial resistance arising from food-animal productions and its mitigation, antibiotic resistant bacteria. – A continuous challenge in the New Millenium, Dr. Marina Pana (Ed.), ISBN 978-953-51-0472-8 InTech.

Wang, L., Y. Oda, S. Grewal, M. Morrison, F. C. Michel Jr. and Z. Wu. 2012. Persistence of resistance to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage.  Microbial Ecology 63: 32-40

Wang, L., A. Gutek, S. Grewal, F. C. Michel Jr. and Z. Wu. 2015. Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage.  Letters in Applied Microbiology. May 2015


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