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Managing Manure to Minimize Impacts of Antimicrobial Resistance

June 15, 2015

Although some may consider GHG emissions from animal agriculture, particularly nitrous oxide emission, a “laughing” matter, our global concern regarding manure management and antimicrobial resistance is not. The future of our planet in relation to antimicrobial resistance is quite literally in the dirt. We cannot undermine the power and adaptability of our microbes. This also includes the vast untapped resource of microbes that we have in our soil that are able to help us manage antimicrobial resistance. In 2015, the International Year of Soil, we can read about the importance of our soil for the health of our planet. Our soil is also critical in managing antimicrobial resistance.

“Soil is part of the solution to some of the greatest dilemmas of our time. It plays a critical role in mitigating the effects of climate change, increasing farm productivity and food security, and may hold the answers to eradicating antibiotic resistance. If we truly want to achieve the Sustainable Development Goals we’ve set for ourselves, we can’t afford to not focus on soil health” (Kainth, 2015)

What is the concern about antimicrobial resistance, what does manure have to do with antimicrobial resistance, and why is this important in Abbotsford, or in any other community for that matter? This is the first of a series that explains some of these questions, and addresses some potential manure management strategies to reduce the impact of antimicrobial resistance. Managing manure to reduce GHG emissions, particularly nitrous oxide emissions as outlined in previous posts, (Greenhouse Gas Emissions from Animal Agriculture in Abbotsford) is one excellent step in managing the risk of antimicrobial resistance from animal manures.

Antimicrobial resistance is one of our greatest health concerns

The Auditor General of Canada outlined the concern with antimicrobial resistance in a recent report (Office of the Auditor General 2015). This report provides an excellent introduction to the development of this concern from the time that antimicrobials were first discovered and developed, to the health impacts of antimicrobial resistance in the US and Europe. They stated:

“Antimicrobial resistance is a global public health challenge. It affects human and animal health, agriculture, the environment, and the economy. Organisms resistant to antimicrobial drugs can emerge in humans, animals, or the environment. These organisms can be transmitted from animals to humans through food or direct contact.”

A review in the UK acknowledges the 50,000 deaths per year in the US and Europe currently attributable to antibiotic resistance, and estimates that this number will increase to 10 million per year by 2050, with a cost of $ 100 trillion USD (O’Neill 2014). This report concludes that the extent of this crisis can be averted if we all act together soon.

In Canada, Grant et al. (2014) acknowledged the importance of working together as a global community and that past efforts in Canada to collect and report antimicrobial resistance in Canadian communities, as well as monitoring antimicrobial use in various human and animal settings has been lacking.  They stated that:

“the protection of public health from consequences of antimicrobial resistance in microorganisms is a shared responsibility including federal leadership for a strong national, public health based coordination of surveillance, with engagement and collaboration of provincial and territorial health agencies, professional associations, animal health, and food animal-industry stakeholders.”

In an excellent review of the origins and evolution of antibiotic resistance, Davies and Davies (2010) reported that:

Not withstanding all good intentions to control antibiotic usage (but limited action), there is little doubt that the situation with respect to antibiotic resistance is grim. Resistance mechanisms are pandemic and create an enormous clinical and financial burden on health care systems worldwide. There are no simple solutions to the problem. Decisive actions that require significant commitment  and enforcement are never popular, even if lives can be saved.”

“Fortunately, not all bacterial pathogens are resistant all of the time, and many respond to empirical treatment with antimicrobial agents administered in the community. Success is perhaps due to luck rather than good judgement.”

Antimicrobial use in agriculture is a contributor

The World Health Organization made recommendations on the use of antimicrobials in agriculture to protect human health in 2000. (WHO 2000). The contribution of animal agriculture to antimicrobial resistance in humans has been reported in Canada almost 20 years ago (Khachatourians 1998). This review provides an excellent explanation of some of mechanisms of antibiotic resistance. The review also noted that the impact of antibiotics used in animals have impacted human health already in 1963. Its interesting to note the public concern regarding this issue already then.

“Over the recent past the public has become increasingly alarmed by new scientific data that have made their way into the popular media about the connection between the overuse of antibiotics (or, more accurately, antimicrobial drugs) in both medicine and the agriculture–agrifood industry and the emergence and spread of antibiotic-resistant bacteria.”

A more recent review further explains the risks associated with antibiotic use in agriculture (You and Silbergeld 2014) Another recent review of the impact of antibiotic use in agriculture addresses attempts by some farm organizations to downplay the potential impact of antimicrobial use:

“Although resistance in human infections is mainly caused by human antibiotic use, for a range of bacteria, farm animal use contributes significantly, and for some infections, is the main source of resistance. This fact has been established by decades of research and is acknowledged by organizations like the WHO and the European Food Safety Authority” (Alliance to Save Antibiotics 2014).

The use of antibiotics in agriculture worldwide is expected to increase by up to 67% by 2030 (Van Boeckel et al. 2015), so the issue is not going to go away too quickly! In the US, the use of medically important antimicrobials increased 16% from 2009-2012 (FDA 2014), where an estimated 68% of medically important antimicrobials were used for food producing animals. In Canada, we don’t even know how much we are using! Prescott (2014) reported that Canada is not able to access information on the import, sale and use of antimicrobials not evaluated and registered by Health Canada. Prescott (2014) assigned Canada an “F” on this recommendation made many years earlier, where an “F” indicates that “Canadian practice is inadequate, displays an unsatisfactory understanding of the stewardship issues involved, and fails to address in any significant way international standards or Canadian recommendations.”

Antimicrobial Resistance in our British Columbia communities

There is a part of all of us that likes to think that the concerns with antimicrobial resistance may be out there somewhere, but not in our communities, or not on our farm. Unfortunately, this is not true. Antimicrobial resistant organisms or genes have been measured in our manure, our waterways, our vegetables and our meat.

The Government of Canada (2013) provides surveillance information on specific antibiotic resistance in humans, on retail meats, in the abattoir, and on farms. Some notable observations included Ciprofloxacin resistance in Campylobacter measured in British Columbia retail chicken increased from 8% in 2012 to 26% in 2013. Resistance to ceftiofur by E.coli in the chicken was 28%.

Antibiotic resistant coliform bacteria were found on vegetables at British Columbia farmers markets (Wood 2013). Wood et al. (2015) reported that 97% of the E.coli possessed resistance at least one or more of the antimicrobials tested for. During vegetable production on the farm, the coliform bacteria count was dramatically higher on vegetables irrigated with ditch water than on vegetables irrigated with city water (Wood 2013). Manure or compost used on the farm was also a proven source of coliform bacteria. The recommendation in this thesis was to utilize only compost from proven and trusted sources.

Poultry litter in BC was reported to be a source of antimicrobial residues and represents a reservoir
of multiple antibiotic-resistant E. coli (Furtula et al. 2010). They reported that bacitracin, chlortetracycline, monensin, narasin, nicarbazin, penicillin, salinomycin, and virginiamycin were commonly used in poultry production in British Columbia. They observed that antibiotics in the litter reflected the antibiotics in the feed on the nine commercial farms. They measured resistance to amoxicillin, spectinomycin, streptomycin, and sulfonamides in E. coli isolated from litter.

In our Sumas River watershed, Keen (2009) consistently measured tetracycline resistant genes in the water, and observed that they were higher in the fall than during the summer. It is interesting to note that tetracycline resistant genes were also present in the control stream (no agricultural activity), however, no increases in tetracycline resistant genes were measured during the winter. The conclusion was:

“A direct causal relationship between agricultural sources and the concentration of contaminants measured in stream water samples cannot be verified based on the data provided herein. It is, however, likely that such an interconnection exists.” 


We have antibiotic resistant microbes in our animals, in our soils, in our manure and in our water. We have to manage our resources carefully to limit the health risks in our communities. The soil organic matter plays an important role as a reservoir of antimicrobial genes, but also a huge resource of microbial biomass that also helps to purify our soil.  It is possible that our soil organic matter plays an important role in buffering the potential risks of antimicrobial risks in the environment, and is important in our future response to this concern. We will pursue this more in a following post.

In all fairness to agriculture, I am keenly aware that in our community, animals and animal manure is not the only threat to the spread of antimicrobial resistance in our environment. It is my hope that we all, including our key decision makers, can move from what appears to be a helpless disregard to an action plan that protects the short term and long term health of our community.

Our local communities could provide an excellent model for sustainable management of manure and other organic wastes that provide leadership and hope in a world that so desperately needs it. We have an urban – rural interface that provides a strong connection and awareness, we have an urban and rural population that is interested in local healthy sustainable food production, and we have the resources to make it happen.

Let’s dare to “make decisive actions that may require significant commitment and enforcement”, as suggested by Davies and Davies (2010), because “lives can be saved”.


Alliance to Save Our Antibiotics. 2014. Antimicrobial resistance – why the irresponsible use of antibiotics in agriculture must stop. An Alliance between the Soil Association, Compassion in World Farming, and Sustain.

Davies, J. and D. Davies. 2010. Origins and Evolution of Antibiotic Resistance. Microbiology and Molecular Biology Reviews, Sept 2010 pp 417-433.

Food and Drug Administration. 2014. 2012 Summary Report on Antimicrobials Sold or Distributed for Use in Food-Producing Animals. FDA Department of Health and Human Services September 2014.

Furtula, V., E.G. Farrell, F. Diarrassouba, H. Rempel, J. Pritchard and M.S. Diarra. 2010. Veterinary pharmaceuticals and antibiotic resistance of Escherichia coli isolates in poultry litter from commercial farms and controlled feeding trials. Poultry Science 89: 180-188.

Government of Canada. 2013. Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) Annual Report. Chapter 2. Antimicrobial Resistance. Public Health Agency of Canada, Guelph, Ontario.

Grant, J. Saxinger, L and Patrick, D. 2014. Surveillance of antimicrobial resistance and antimicrobial utilization in Canada. Winnipeg. Manitoba: National Collaborating Centre for Infectious Diseases.

Kainth, G.S. 2015. Healthy soil for healthy life – OpEd. 2015. Eurasia Review News and Analysis June 18, 2015.

Keen. P.L. 2009. Seasonal dynamics of tetracycline resistant genes and antibiotics in a British Columbia agricultural watershed. Ph.D. Thesis, University of British Columbia.

Khachatourians, G.G. 1998. Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria. Canadian Medical Association Journal 159:1129-36

Office of the Auditor General of Canada. 2015. Report 1. Antimicrobial resistance. Spring 2015. Minister of Public Works and Government Services.

O’Neill, J. 2014. Antimicrobial resistance: Tackling a crisis for the health and wealth of nations. A review on antimicrobial resistance. UK Prime Ministers Office

Prescott, J.F. 2014. Stewardship of antimicrobial drugs in animals in Canada: How are we doing? Canadian Veterinary Journal 55: 273-276.

Van Boeckel, T.P. C. Brower, M. Gilbert, B.T. Grenfell, S.A. Levin, T.P. Robinson, A. Teillant, and R. Laxminarayan. 2014. Global trends in antimicrobial use in farm animals.

Wood, J.L. 2013. Examination of Microbiological Quality of In-field Leafy Vegetables and Identification of On-farm Generic Escherichia coli Transmission Dynamics. MSc Thesis, University of British Columbia.

Wood, J.L., J.C. Chen, E. Friesen, P. Delaquis and K.J. Allen. 2015. Microbiological survey of locally grown lettuce sold at farmers’ markets in Vancouver, British Columbia. Journal of Food Protection 78: 203-208.

World Health Organization (WHO). 2000. WHO Global Principles for the Containment of Antimicrobial Resistance in Animals Intended for Food. Report of a WHO Consultation with the participation of the Food and Agriculture Organization of the United Nations and the Office International des Epizooties. Geneva, Switzerland June 2000.

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

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