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How antimicrobial resistance spreads in the environment

July 13, 2015

The safest place for untreated animal manure containing antibiotics, antibiotic resistant genes, or antibiotic resistant microbes is the soil, where the large reservoir of microorganisms is best likely able to manage them. Most microbes that are potentially pathogenic to humans do not survive long in soil because they require readily available carbohydrates and proteins and cannot compete well with other soil organisms. However, there is gene transfer from antibiotic resistant organisms in manure to non-pathogenic organisms in soil, resulting in the soil also being a large reservoir of antibiotic resistant genes.

Fate of Antibiotics, Antibiotic resistant organisms, and Antimicrobial resistant genes in Soil Following Manure Application

Concentrations of antibiotics, antibiotic resistant organisms and antimicrobial resistant genes in soil following manure application tend to increase, then decrease to background levels after some time.

Marti et al. (2014) measured an increase in antibiotic resistant genes in soil following a spring application of dairy or swine manure, and found that the gene levels decreased exponentially to background levels by the fall. Munir and Xagoraraki (2011) measured elevated antibiotic resistance genes for four months following application of manure from three farms in the U.S.  Despite reports of antimicrobial resistance genes following manure application returning to background levels, Popowska et al. (2012) measured consistently higher antibiotic resistant gene levels in agricultural soils with a history of manure application. You et al. (2012) measured tetracycline resistant genes in poultry manure amended soil for up to two years after manure application. They reported that the gene levels did decrease with time, but noted that horizontal gene transfer must have occurred into the large resident soil microbial population. You and Silbergeld (2014) provided an excellent review of the impact of low doses of antimicrobials used in agriculture on the development of the pool of antimicrobial resistance genes in the soil microbial community.

Antibiotics and antimicrobial resistant genes are taken up by plants

Leftover antibiotics in manure may be taken up by plants. Kumar et al. (2005) measured antibiotic concentrations ranging from trace levels to greater than 200 ppm in manure. Dolliver et al. (2007) found that sulfamethazine was taken up by lettuce, corn and potato plants, but that the total accumulation in plants was less than 0.1% of the amount applied to soil in manure. Seo et al. (2013) measured chlortetracycline, tylosin and sulfamethazine uptake in lettuce, tomato and hairy vetch following soil application of swine manure containing antibiotics. They noted that antibiotic uptake is dependent on antibiotic type and plant type. Kang et al. (2013) observed uptake of five antibiotics (chlortetracycline, monensin, sulfamethazine, tylosin and virginiamycin) by 11 vegetable crops in two different soils that were fertilized with raw turkey or hog manure. The uptake of the antibiotics was very low and there was no significant difference in uptake from the manured soil than from the control soil (amended with inorganic fertilizer). They concluded that antibiotic uptake by vegetable crops analyzed was not a major health concern to most adults unless one is allergic to that particular pharmaceutical.

It appears that antimicrobial resistant genes can also be taken up by plants from the soil. Marti et al. (2013) evaluated antibiotic resistant bacteria on vegetables such as tomato, cucumber, pepper, carrot, radish and lettuce. They did not find a corresponding increase in antibiotic resistant bacteria on plants following manure application, but they did report finding antibiotic resistant genes in the vegetables. They concluded that ingestion of antibiotic resistant bacteria naturally found in soil is inevitable through consumption of raw vegetables and fruits.

Antibiotics, antimicrobial resistant genes and antibiotic resistant microbes travel in the air

Recent reports have indicated that antibiotics, antibiotic resistant bacteria and antimicrobial resistance genes can be airborne on particulate matter. McEachran et al. (2015) reported measurable concentrations of monensin, tylosin, tetracycline, chlortetracycline and oxytetracycline in the airborne particulate matter measured up to 200 m downwind of ten beef feedlots in Texas. They also measured increased abundances of six tetracycline resistance genes downwind of the feedlots.

Graham et al. (2009) concluded that antimicrobial resistant organisms could be spread by flies around broiler poultry operations. Laube et al. (2014)  measured antibiotic resistant (ESBL) E. coli in the manure and surrounding air from seven poultry broiler farms in Germany, and concluded that antibiotic resistant organisms are dispersed in the exhaust air of the chicken barns.

Antimicrobial resistant genes and microbes are found in water

Holvoet et al. (2013) concluded that a significant source of antimicrobial resistant E. coli on eight vegetable farms was the irrigation water, and concluded the that antimicrobial genes in the water were of animal origin.

Krapac et al. (2004) reported increased presence of tetracycline resistance genes in groundwater near and downgradient from a swine manure storage lagoon than upgradient and further away.

Garder et al. (2012) found that 70% of the enterococci in manure samples were resistant to tylosin, but the concentrations of enterococci in the tile water were very low.

Manure must be applied at a time and in a manner that reduces the risk of runoff. Joy et al. (2013) reported runoff of both antibiotics and antibiotic resistant genes from soil amended with swine manure.

Luby (2014), following application of swine manure containing 65-100% tylosin resistant Enterococci, measured significantly increased frequency of resistance genes in the tile drains under soil receiving surface applications of swine manure. She also concluded that the increase in tylosin resistant bacteria and tylosin resistance genes in soil was short term, and reduced to background frequencies after one year.

Chow et al. (2015) reported that even low concentrations of antibiotics in aquatic environments can increase antibiotic resistance of the microbes in the water. They conclude:

“Given the huge quantities of antibiotics that are entering the environment, it is likely that this antibiotic pollution is generating antibiotic resistant organisms that may be a source of newly emerging threats to human and animal life.”


When we apply untreated manure to our agricultural soil, we are spreading antimicrobial resistance genes into the soil microbial pool, where transfer from one organism to another can take place. It is very important to manage manure in a sustainable manner, avoiding overapplication, respecting buffer zones to waterways, and applying the manure when the risk of runoff and potential pollution to ground and surface water is the lowest. Manure management to reduce greenhouse gas emissions also serves to limit the spread of antimicrobial resistance into the environment.

Denmark has been one of the first countries to limit non-therapeutic use of antimicrobials already 20 years ago. They found that if antimicrobial use was limited, there was less selective pressure for resistance, with a resulting decrease in the trait over time (Levy 2014).  This means that there is potentially good news if we reduce the amount of antimicrobials used in agriculture, particularly for non-therapeutic uses. Cogliani et al. (2011) reported that animal production continues to thrive in European countries where the ban on non-therapeutic use of antimicrobials actually led to a reduction in antimicrobial use.

We also can see a lesson from agriculture in the Netherlands. When the ban on non-therapeutic use of antimicrobials was implemented in 1999, there was no monitoring plan in place (Cogliani et al. 2011). This resulted in no change in antibiotic use, as the non-therapeutic use simply became therapeutic, until the Netherlands mandated a 50% reduction in antimicrobial use a few years ago.

“We may need to focus more resources on restricting the release of active compounds into the environment; for example, from pharmaceutical production plants, from farming activities, from hospitals and from water and sewage treatment plants, so as to restrict the selection of antibiotic resistance caused by low level exposure to drugs of the global bacterial population.” (Hughes 2015)

The soil remains a large reservoir of antimicrobial resistant genes. Although most potential pathogenic bacteria do not survive long in soil, there are a number of serious human pathogens that do. In the following posts, we will explore the effects of manure treatments, and their effect on antibiotic degradation, antimicrobial resistant organisms and antibiotic resistant genes.


Chow, L., L. Waldron and M.R. Gillings. 2015. Potential impacts of aquatic pollutants: sub-clinical antibiotic concentrations induce genome changes and promote antibiotic resistance. Frontiers in Microbiology August 5, 2015 doi: 10.3389/fmicb.2015.00803.

Cogliani, C., H. Goossens and C. Greko. 2011. Restricting Antimicrobial Use in Food Animals: Lessons from Europe. Microbe 6: 274-279.

Dolliver, H., K. Kumar and S. Gupta. 2007. Sulfamethazine uptake by plants from manure amended soil. Journal of Environmental Quality 36: 1224-1230.

Garder, J.L., M.L. Soupir adn T.B. Moorman. 2012. Occurrence and movement of antibiotic resistant bacteria, in tile drained agricultural fields receiving swine manure. ASABE Annual International Meeting, Dallas, Tx.

Graham, J.P., L.B. Price, S.L. Evans, T.K. Graczyk, and E.K. Silbergeld. 2009. Antibiotic resistant enterococci and staphylococci isolated from flies collected near confined poultry feeding operations. Science of the Total Environment 407: 2701-2710.

Holvoet, K., I. Sampers, B. Callens, J. Dewulf and M. Uyttendaele. 2013. Moderate prevalence of antimicrobial resistance in Escherichia coli isolates from lettuce, irrigation water and soil. Applied and Environmental Microbiology 79: 6677-6683.

Hughes D. Selection of resistance by very low levels of antibiotics. Presented at: AAAS Annual Meeting; Feb. 12-16, 2015; San Jose, California. Sourced at

Joy, S.R., S.L. Bartelt-Hunt, D.D. Snow, J.E. Gilley, B.L. Woodbury, D.B. Parker, D.B. Marx and X Li. 2013. Fate and transport of antimicrobials and antimicrobial resistance genes in soil and runoff following land application of swine manure. Environmental Science and Technology 47: 12081-12088.

Kang, D.H., S. Gupta, C. Rosen, V Fritz, A. Singh, Y. Chander, H. Murray and C. Rohwer. 2013. Antibiotic uptake by vegetable crops from manure-applied soils. Journal of Agriculture and Food Chemistry 61: 9992-10001.

Krapac, I.G., S. Koike, M.T. Meyer, D.D. Snow, S.F.J. Chou, R.I. Mackie, W.R. Roy and J.C. Chee-Sanford. 2004. Long term monitoring of the occurrence of antibiotics residues and antibiotic resistance genes in groundwater near swine containment facilities. in Proceedings of the 4rth International conference on pharmaceuticals and endocrine disrupting chemicals in water, Minneapolis, Minn., National Groundwater Association, October 13-15, 2004.

Kumar, K., S.C. Gupta, Y. Chander and A.K. Singh. 2005. Antibiotic use in agriculture and its impact on the terrestrial environment. Advances in Agronomy 87: 1-54.

Laube, H., A. Friese, C. von Salviati, B. Guerra and U. Rosler. 2014. Transmission of ESBL/Amp C-producing Escherichia coli from broiler chicken farms to surrounding areas. Veterinary Microbiology 172: 519-527.

Levy, S. 2014. Reduced antibiotic use in livestock: How Denmark tackled resistance. Environmental Health Perspectives Vol 122: A161-165.

Luby, E.M. 2014. Fate and transport of antibiotic resistant bacteria and resistance genes in artificially drained agricultural fields receiving swine manure application. MSc thesis. Iowa State University.

Marti, R., A. Scott, Y-C Tien, R. Murray, L. Sabourin, Y. Zhang and E. Topp. 2013. Impact of manure fertilization on the abundance of antibiotic resistant bacteria and frequency of detection of antibiotic resistance genes in soil and on vegetables at harvest. Applied and Environmental Microbiology 79: 5701-5709.

Marti, R., Y-C. Tien, R. Murray, A. Scott, L. Sabourin and E. Topp,  2014. Safely coupling livestock and crop production systems: how rapidly to antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure? Applied and Environmental Microbiology 80: 3258-3265.

McEachran, A.D., B.R. Blackwell, J.D. Hanson, K.J. Wooten, G.D. Mayor, S.B. Cox and P.N. Smith. 2015. Antibiotics, bacteria and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. Environmental Health Perspectives

Munir, M. and I. Xagoraraki. 2011. Levels of antibiotic resistance genes in manure, biosolids, and fertilized soil. Journal of Environmental Quality 40: 248-255.

Popowska, M., M. Rzeczycka, A. Miernik, A. Krawczyk-Balska, F. Walsh and B. Duffy. 2012. Influence of soil use on prevalence of tetracycline, streptomycin and erythromycin resistance and associated resistance genes. Antimicrob. Agents Chemother. 56: 1434-1443.

Seo., Y., B. Cho, A. Kang, B. Jeong and Y-S Jung. 2013. Antibiotic uptake by plants from soil applied with antibiotic treated manure. Korean J. Soil Sci. Fert. 43:

You, Y., M. Hilpert, and M.J. Ward. 2012. Detection of a common and persistent tet(L) – carrying plasmid in chicken-waste-impacted farm soil. Appl.Environ. Microb. 78: 3203–3213. doi:10.1128/AEM.07763-11

You, Y., and E.K. Silbergeld. 2014. Learning from agriculture: understanding low dose antimicrobials as drivers of resistome expansion. Frontiers in Microbiology Volume 5, Article 284.

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