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United States Department of Agriculture

Agricultural Research Service

Related Topics


Location: Meats Safety & Quality Research

2013 Annual Report

1a. Objectives (from AD-416):
Objective: 1. Identify the ecological and environmental factors, as well as critical points, that affect pathogen occurrence, survival, fate, and transport in cattle and swine production facilities, manure, and surrounding environments. Objective 2. Develop and evaluate intervention strategies that reduce or eliminate the occurrence, persistence, or movement of foodborne pathogens among food animals, their environment, and potential surrounding production environments.

1b. Approach (from AD-416):
The overall goal of this project is to reduce the risk of human foodborne illness, by providing scientific information that can be used to reduce or eliminate the transmission of zoonotic pathogens from animal manure to food, water, and the environment. Primary targets of the work include pathogenic strains of Escherichia coli (including non-O157 Shiga-toxigenic E. coli), Salmonella spp., and Campylobacter spp. in cattle and swine. Approaches for reducing these pathogens include the reduction of pathogen colonization and shedding by livestock, as well as the reduction of pathogens shed and present in the manure and production environment. Exploitable factors, including biological, environmental, and managerial factors, which affect the occurrence, survival, or transmission of pathogens in cattle and/or swine manure will be identified, then manipulated and evaluated to determine the impact on pathogens. Strategies and interventions to reduce the dissemination of foodborne pathogens in cattle and swine manure or production environments will be developed and evaluated. Approaches will include the use of dietary amendments, manure additives, and waste management systems, as well as other intervention strategies that may be suggested by information gathered in experiments. Approaches that are both effective at reducing foodborne pathogens and environmentally safe under animal production practices will be identified. Expected outcomes are scientific information and procedures that will be used to reduce or eliminate zoonotic foodborne pathogens both in livestock and their manure, thus contributing to a safer food and water supply and a lower risk of human foodborne illness.

3. Progress Report:
Reducing pathogen shedding by cattle will require identification of ecological and environmental factors that affect pathogen occurrence and persistence in the animal (Obj. 1). In 2013, we continued studies to determine if cattle shedding E. coli O157:H7 in high numbers, compared to animals that are consistently negative for the pathogen, are associated with specific differences in the gastrointestinal microflora, host genomic factors, immune response, and/or host behaviors, such as temperament, and eating or drinking habits. Also, we continued studies to identify specific bovine gastrointestinal tract locations that may have an important role in sustaining high levels of colonization and shedding of E. coli O157:H7 in feces. Our previous research indicated that feeding high levels of wet distillers grains to cattle can increase the levels of E. coli O157:H7 in their feces compared to corn diets. To discover the causes of this increase, we initiated studies to determine the effects of different components of distillers grains on pathogens in bovine feces. Understanding how these various factors impact E. coli O157:H7 is critical for developing intervention strategies to reduce this pathogen in cattle. Developing effective strategies to reduce pathogens in cattle requires understanding of factors that affect pathogen occurrence and transmission in the production environment (Obj. 1). There is increasing interest in the use of deep-bedded confinement facilities in the cattle feeding industry. In 2013, we completed studies to evaluate the effect of different wood-based bedding materials on the populations of E. coli in deep-bedded cattle waste, in order to identify materials that may limit the growth and persistence of these bacteria. The work is part of a larger collaborative effort that is seeking to quantify odor emissions from cattle deep-bedded barns, with the goal to develop recommendations for managing these facilities to reduce odor, gas emissions, and pathogens. We continued studies to confirm a role for environmental persistence of E. coli O157:H7 in feedlot surface manure in the persistence and transmission of this pathogen in cattle. Also, studies were initiated to determine if amendment with coal fly ash can reduce E. coli O157:H7 in feedlot surface material (Obj. 2). Airborne transport of E. coli O157:H7 is a potential mode of transmission of this pathogen among cattle in the production environment, as well as to the environments surrounding cattle production facilities. We continued studies to determine if E. coli O157:H7 can be transported in windborne bioaerosols from cattle feedlots. In 2013, we examined intervention strategies to reduce pathogens in swine (Obj. 2). Our previous research with nursery pigs demonstrated that lysozyme reduced Campylobacter coli and Shigatoxin genes in feces of the piglets. In 2013, we initiated a larger trial with young swine, with the objective to determine the impacts of diets containing lysozyme on performance and fecal shedding of the pathogens Salmonella, Campylobacter, and/or Shiga-toxin producing E. coli, compared to diets with and without dietary antibiotic growth promoters.

4. Accomplishments
1. Diet effects on the diversity of fecal microbial communities of feedlot cattle. The composition of diets that are fed to cattle can impact the types, concentrations, and relative proportions of different bacteria that live in the gastrointestinal tract and are shed in the feces (the “fecal bacterial microbiome”). ARS scientists in Clay Center, NE used cutting edge next-generation high-throughput sequencing technology to examine the differences in the fecal microbiome of over 400 cattle fed three different diets with varying amounts of forage and grain. The fecal microbiomes of the cattle were greatly affected by diet, particularly between high forage- and high grain-based diets. This research provides the most comprehensive data set developed to date that describes diet effects on the diversity of cattle fecal microbiome. These data provide important information that will be used to examine both diet effects and fecal microbiome effects on human bacterial pathogens that are shed by cattle. This research is anticipated to identify potential dietary approaches for reducing the occurrence and numbers of these pathogens in cattle, thereby reducing the risk of human foodborne illness associated with beef consumption.

2. Control of E. coli O157:H7 in deep-bedded cattle confinement facilities. There is growing interest in feeding beef cattle in enclosed deep-bedded confinement barns. Both E. coli O157:H7 prevalence and generic E. coli concentrations can occur at high levels in the manure/bedded packs of these facilities. ARS scientists in Clay Center, NE demonstrated that E. coli concentrations were lower in manure/bedded packs containing wood shavings, compared to manure/bedded packs with shredded paper and crop-based materials including corn stover, soybean stover, ground corn cobs, wheat straw, and switch grass. Reducing microbial survival in the manure/bedded packs is important because this waste can be a source of pathogens for contamination of additional cattle, or of water, food, and feed crops when the material is applied to cropland. This research provides important information that is needed to develop recommendations for the management of these facilities to reduce pathogens.

Review Publications
Wells, J., Kalchayanand, N., Berry, E.D., Oliver, W.T. 2013. Effects of antimicrobials fed as dietary growth promoters on faecal shedding of Campylobacter, Salmonella and shiga-toxin producing Escherichia coli in swine. Journal of Applied Microbiology. 114(2):318-328.

Oliver, W.T., Wells, J. 2013. Lysozyme as an alternative to antibiotics improves growth performance and small intestinal morphology in nursery pigs. Journal of Animal Science. 91(7):3129-3136.

Spiehs, M.J., Brown Brandl, T.M., Parker, D.B., Miller, D.N., Berry, E.D., Wells, J.E. 2013. Effect of bedding materials on concentration of odorous compounds and Escherichia coli in beef cattle bedded manure packs. Journal of Environmental Quality. 42(1):65-75.

Harris, L.J., Berry, E.D., Blessington, T., Erickson, M., Jay-Russell, M., Jiang, X., Killinger, K., Michel, F.C., Millner, P.D., Schneider, K., Sharma, M., Suslow, T.V., Wang, L., Worobo, R.W. 2013. A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the application of untreated soil amendments of animal origin on land used to grow produce that may be consumed raw. Journal of Food Protection. 76(6):1062-1084.

Durso, L.M., Wells, J., Kim, M.S. 2013. Diversity of microbiomes in beef cattle. In: Nelson, K., editor. Encyclopedia of Metagenomics. Springer Reference ( Berlin/Heidelberg, Germany: Springer-Verlag. Available:

Last Modified: 2/23/2016
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