Progress 01/19/11 to 01/18/16
Outputs
Progress Report 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. 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. This is the final report for Project 3040-32000-030-00D, which expired in 2016 and was replaced with new Project 3040-32000-032-00D. Additional information can be found in the Annual Report for Project 3040-32000-032- 00D. Substantial progress was made over the life of this project to identify factors that affect pathogen occurrence, survival, and transport in cattle and swine production environments (Objective 1) and to develop strategies to reduce the occurrences (Objective 2). The overall impact of these accomplishments is the development of information on which to make livestock management decisions and to reduce the risk of transmission of pathogens from manure to human food, water, and the environment. Our previous work demonstrated that cattle fed high levels of wet distillers grains with solubles (WDGS) had higher prevalence and enumerable levels of E. coli O157:H7 in feces and on hides, and that E. coli persisted longer in manure from cattle fed 40% WDGS than from cattle fed dry-rolled corn, which also suggested that environmental persistence is an important factor affecting the prevalence of E. coli O157:H7 in cattle production. In this project, we further demonstrated that reducing the amount of WDGS in the diet from 40% to 0 or 15% resulted in significantly less shedding of E. coli O157:H7, although the reduction took more than 28 days after the switch in diets. Diets also were shown to affect the diversity of fecal microbial communities of feedlot cattle. The abundance of bacterial populations in feces from cattle fed finishing diets high in WDGS were different compared to cattle fed mostly corn grain. There was diversity in fecal bacterial populations across cattle fed a similar diet, but the overall bacterial groups represented in the fecal microbiomes were more similar within diet than across different diets. In addition, cattle fed forage-based diets had significantly different fecal microbiomes compared to cattle fed concentrate-based diets. The fecal shedding of E. coli O157:H7 was not associated with specific community structures of the fecal microbiota. However, there do appear to be bacterial types that are associated with fecal shedding of E. coli O157:H7 that are strongly influenced by cattle diets. The colon and rectal-anal junction were demonstrated to have the highest concentrations of E. coli O157:H7 compared to other sites along the bovine gastrointestinal tract. These sites may have important roles in sustaining high levels of colonization and shedding of E. coli O157:H7 in cattle, thereby pinpointing regions that could be targeted for interventions to reduce the super shedding of this pathogen. Dietary antibiotics are used to improve animal performance and promote good health; however, concerns regarding transmission of antibiotic resistance have increased public pressure to reduce the use of antibiotics as growth promotants. Hence, alternatives to replace these antibiotics are needed. Dietary lysozyme improved performance and intestinal morphology in milk-fed piglets compared to antibiotic-free diets, and reduced the shedding of Campylobacter coli. In weaned piglets supplemented with lysozyme in the nursery diet, performance was similar to piglets fed traditional dietary antimicrobials, including chlortetracycline and tiamulin. In additional work, nursery piglets shed less Campylobacter in their feces when supplemented with lysozyme compared to piglets fed diets supplemented with or without antibiotics. The impact of proximity to a cattle feedlot on E. coli O157:H7 contamination of leafy green crops was evaluated. Results of this study indicated that the current setback distance guidelines of 400 feet from leafy greens may not be adequate to limit the occurrence of E. coli O157:H7 in crops planted near concentrated animal feeding operations. In addition, the risk for transport of E. coli O157:H7 from cattle production was increased in situations where feedlot pen surfaces are very dry, and this is combined with cattle management or movement activities that can generate substantial airborne dust. Deep-bedded confinement barns are increasing in popularity among beef cattle producers. However, there was little available information regarding the management of these barns to reduce manure nuisance problems like odor emissions or pathogens. Both E. coli O157:H7 prevalence and total E. coli concentrations were demonstrated to occur at high levels in the manure/bedded packs of these facilities, and varied with differences in ambient seasonal temperatures. E. coli concentrations were demonstrated to be lower in manure/bedded packs containing pine shavings, compared to packs with shredded paper and crop- based materials including corn stover, soybean stover, ground corn cobs, wheat straw, and switch grass. In addition, E. coli concentrations were shown to be similar in manure/bedded packs containing pine chips, dry cedar chips, or green cedar chips, thereby identifying additional wood- based materials for use as bedding materials in deep-bedded cattle facilities. Further work identified natural compounds for pen surface applications and manure treatments that can reduce pathogens in feedlot pen manure, thereby providing a preharvest intervention with the potential to break pathogen-host cycles that maintain pathogens in cattle production. Among a variety of low-cost natural antimicrobial compounds, pine oil (0.4%) was shown to be effective at reducing Listeria and Campylobacter in cattle manure when the compound was applied directly on the feedlot surface, but linalool was not effective for either pathogen and thymol did not reduce Listeria. Controlling microbial survival in the manure/bedded packs and on feedlot pen surfaces 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. Accomplishments 01 Bacterial diversity in the bovine colon. Bacteria are present throughout the mammalian gastrointestinal tract. Much research has described the bacteria in the bovine rumen, but until recently, little research has described the bacteria in the bovine colon. To better understand the composition of bacterial communities present in the bovine colon, ARS researchers at Clay Center, Nebraska, identified bacterial RNA gene sequences in different sequence databases and a statistical analysis of the sequences was performed. Colonic bacterial populations were significantly different than the ruminal bacterial populations. Although the rumen precedes the colon and ruminal bacteria continuously flow into the lower gastrointestinal tract and the colon, there were very few types of ruminal bacteria observed in the colon. The colonic microbiota is recognized to be important for animal health and well-being, and this work provides a foundation for understanding why the bacterial composition of this gastrointestinal location in cattle is unique, and how it changes with diet, antibiotic use, or pathogen carriage.
Impacts
(N/A)
Publications
- Wells, J., Kim, M. 2016. A meta-analysis of bacterial diversity in the feces of cattle. Current Microbiology. 72:145-15. doi:10.1007/s00284-015- 0931-6.
- Myer, P.R., Wells, J.E., Smith, T.P.L., Kuehn, L.A., Freetly, H.C. 2015. Cecum microbial communities from steers differing in feed efficiency. Journal of Animal Science. 93(11):5327-5340. doi: 10.2527/jas2015-9415
- Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2015. Microbial community profiles of the colon from steers differing in feed efficiency. SpringerPlus. 4:454.
- Foote, A.P., Hales, K.E., Tait Jr, R.G., Berry, E.D., Lents, C.A., Wells, J. E., Lindholm-Perry, A.K., Freetly, H.C. 2016. Relationship of glucocorticoids and hematological measures with feed intake, growth, and efficiency of finishing beef cattle. Journal of Animal Science. 94(1):275- 283. doi: 10.2527/jas2015-9407
- Myer, P.R., Wells, J., Smith, T.P., Kuehn, L.A., Freetly, H.C. 2016. Microbial community profiles of the jejunum from steers differing in feed efficiency. Journal of Animal Science. 94(1):327-338. doi: 10.2527/jas2015- 9839.
- Hales, K.E., Shackelford, S.D., Wells, J., King, D.A., Pyatt, N.A., Freetly, H.C., Wheeler, T.L. 2016. Effects of dietary protein concentration and ractopamine hydrochloride on performance and carcass characteristics of finishing beef steers. Journal of Animal Science. 94(5) :2097-2102. doi:10.2527/jas2015-0225
- Myer, P.R., Kim, M.S., Freetly, H.C., Smith, T.P. 2016. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers. Journal of Microbiological Methods. 127:132-140. doi: 10.1016/j.mimet.2016. 06.004.
- Spiehs, M.J., Brown-Brandl, T.M., Parker, D.B., Miller, D.N., Berry, E.D., Wells, J.E. 2016. Ammonia, total reduced sulfides, and greenhouse gases of pine chip and corn stover bedding packs. Journal of Environmental Quality. 45:630-637.
- Miller, D.N., Spiehs, M.J., Varel, V.H., Woodbury, B.L., Wells, J., Berry, E.D. 2016. Distillers by-product cattle diets enhance reduced sulfur gas fluxes from feedlot soils and manures. Journal of Environmental Quality. 45:1161-1168.
- Lindholm-Perry, A.K., Butler, A.R., Kern, R.J., Hill, R., Kuehn, L.A., Wells, J., Oliver, W.T., Hales, K.E., Foote, A.P., Freetly, H.C. 2016. Differential gene expression in the duodenum, jejunum and ileum among crossbred beef steers with divergent gain and feed intake phenotypes. Animal Genetics. 47(4):408-427. doi: 10.1111/age.12440.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report 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. 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. Reducing pathogen shedding by cattle will require identification of ecological and environmental factors that affect pathogen occurrence and persistence in the animal (Objective 1). In 2015, 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, fecal corticosterone, and/or host behaviors, such as temperament, and eating or drinking habits. Our previous research indicated that feeding high levels of wet distillers grains to cattle can increase the occurrence and levels of E. coli O157:H7 in their feces compared to corn diets. To discover the causes of this increase, we continued studies to determine the effects of different components of distillers grains such as tyramine on pathogens in bovine feces. Also in 2015, we completed studies to examine the effects of dietary beta-agonists fed to cattle on prevalence and shedding of E. coli O157:H7. Understanding how these various factors impact E. coli O157:H7 is critical for developing intervention strategies to reduce this pathogen in cattle. Reducing pathogen transmission from livestock and their manure will require the development of intervention strategies that reduce their prevalence and persistence in manure and the production environment, and/ or their dissemination into surrounding environments (Objective 2). In 2015, we continued studies to determine a role for environmental persistence of E. coli O157:H7 in feedlot surface manure in the persistence and transmission of this pathogen in cattle. Studies were completed to determine if feedlot pen surface amendment with thymol can reduce E. coli O157:H7 in feedlot manure, and in the feces and on the hides of cattle that are housed in the pens. In addition, we initiated studies to determine if the use of hydrated calcium hydroxide (lime) can be used to reduce the prevalence and levels of E. coli O157:H7 and antibiotic resistant bacteria on feedlot pen surfaces, and in the feces and on hides of cattle in these pens. Assessing intervention effects on antibiotic resistance genes will require the development of novel approaches to assay those genes that are of concern to both animal and public health. In 2015, we initiated the development of a high- throughput sequence-based assay for detecting and quantifying the broad spectrum of bacterial antibiotic resistance genes. Accomplishments 01 Fecal microbiome effects on E. coli O157:H7 shedding by cattle. Reducing E. coli O157:H7 colonization and shedding by cattle will require greater understanding of the many potential factors that may impact this complex trait. ARS scientists in Clay Center, Nebraska, evaluated the microbiome composition of feces from 368 cattle (the types, concentrations, and relative proportions of different types of bacteria in the feces). For each of the different cattle diets evaluated, numerous bacterial types had weak associations with the presence or absence of E. coli O157:H7 in feces. When the different bacterial types were analyzed collectively within a diet, strong associations with E. coli O157:H7 shedding prevalence and concentrations in feces were observed. The effect of the fecal microbiome on E. coli O157:H7 shedding appears to be limited to a small set of bacterial types, and these populations are strongly influenced by diet. This research identifies bacterial groups that can potentially be manipulated to reduce E. coli O157:H7 in cattle. 02 Identification of colonization sites of E. coli O157:H7. The bovine gastrointestinal tract is a source for E. coli O157:H7 and this pathogen can be found all along the tract, from the oral cavity to the anus. However, with the exception of bovine feces, no data has been reported for the concentrations of this pathogen in samples from different sites along the gastrointestinal tract. A small proportion of cattle shed high levels of E. coli O157:H7 (super shedders) and is the main source for the transmission of this pathogen among cattle. ARS scientists in Clay Center, Nebraska, evaluated super shedding feedlot cattle, and found that the colon and rectal-anal junction had the highest concentrations of E. coli O157:H7 (>10,000 cells per gram of sample). Samples collected from the oral cavity, rumen, abomasum, small intestine, cecum, and large intestine rarely had enumerable levels (<500 cells per gram of sample). This research identifies specific bovine gastrointestinal tract locations that may have important roles in sustaining high levels of colonization and shedding of E. coli O157:H7 in cattle, thereby pinpointing regions that could be targeted for interventions to reduce the number of super shedding animals for this pathogen.
Impacts
(N/A)
Publications
- Berry, E.D., Wells, J., Bono, J.L., Woodbury, B.L., Kalchayanand, N., Norman, K.N., Suslow, T.V., Lopez-Velasco, G., Millner, P.D. 2015. Effect of proximity to a cattle feedlot on Escherichia coli O157:H7 contamination of leafy greens and evaluation of the potential for airborne transmission. Applied and Environmental Microbiology. 81(3):1101-1110.
- Wells, J., Berry, E.D., Guerini, M., Varel, V.H. 2015. Evaluation of essential oils in beef cattle manure slurries and applications of select compounds to beef feedlot surfaces to control zoonotic pathogens. Journal of Applied Microbiology. 118;295-304.
- Wells, J., Berry, E.D., Kalchayanand, N., Rempel, L.A., Kim, M., Oliver, W. T. 2015. Effect of lysozyme or antibiotics on fecal zoonotic pathogens in nursery pigs. Journal of Applied Microbiology. 118:1489-1497.
- Spiehs, M.J., Brown-Brandl, T.M., Berry, E.D., Wells, J.E., Parker, D.B., Miller, D.N., Jaderborg, J.P., DiCostanzo, A. 2014. Use of wood-based materials in beef bedded manure packs: 2. Effect on odorous volatile organic compounds, odor activity value, Escherichia coli, and nutrient concentrations. Journal of Environmental Quality. Special Section. Livestock GraceNet. 43:1195-1206. DOI: 10.2134/JEQ2013.05.0165.
- Spiehs, M.J., Brown-Brandl, T.M., Parker, D.B., Miller, D.N., Jaderborg, J. P., DiCostanzo, A., Berry, E.D., Wells, J.E. 2014. Use of wood-based materials in beef bedded manure packs: 1. Effect on ammonia, total reduced sulfide, and greenhouse gas concentrations. Journal of Environmental Quality. Special Section. Livestock GraceNet. 43:1187-1194. DOI: 10.2134/ JEQ2013.05.0164.
- Oliver, W.T., Wells, J., Maxwell, C.W. 2014. Lysozyme as an alternative to antibiotics improves performance in nursery pigs during an indirect immune challenge. Journal of Animal Science. 92(11):4927-4934.
- Myer, P.R., Smith, T.P., Wells, J., Kuehn, L.A., Freetly, H.C. 2015. Rumen microbiome from steers differing in feed efficiency. PLoS One. 10(6) :e0129174.
- Freetly, H.C., Lindholm-Perry, A.K., Hales, K.E., Brown-Brandl, T.M., Kim, M.S., Myer, P.R., Wells, J. 2015. Methane production and methanogen levels in steers that differ in residual gain. Journal of Animal Science. 93(5) :2375-2381.
- Oliver, W.T., Wells, J. 2015. Lysozyme as an alternative to growth promoting antibiotics in swine production. Journal of Animal Science and Biotechnology. 6:35.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report 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. 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. Reducing pathogen shedding by cattle will require identification of ecological and environmental factors that affect pathogen occurrence and persistence in the animal (Obj. 1). 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 gut microflora, host genomic factors, immune response, and/or host behaviors, such as temperament, and eating or drinking habits. In addition, we completed studies to identify specific bovine gut 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 occurrence and levels of E. coli O157:H7 in their feces compared to corn diets. To discover the causes of this increase, we conducted studies to determine the effects of different components of distillers grains on pathogens in bovine feces. We initiated studies to examine the effects of dietary beta-agonists fed to cattle on prevalence and shedding of E. coli O157:H7. Understanding how these various factors impact E. coli O157:H7 is critical for developing intervention strategies to reduce this pathogen in cattle. Reducing pathogen transmission from livestock and their manure will require the development of intervention strategies that reduce their prevalence and persistence in manure and the production environment, and/ or their dissemination into surrounding environments (Obj. 2). There is increasing interest in the use of deep-bedded confinement facilities in the cattle feeding industry. Our previous research demonstrated that both E. coli O157:H7 and total E. coli can occur at high levels in the bedded pack material of these facilities. We initiated studies to evaluate the effect of aluminum sulfate amendment of bedding materials on the populations of E. coli in deep-bedded cattle waste, in order to identify compounds that may limit the growth and persistence of these bacteria. This 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. Studies were conducted to determine if amendment with thymol can reduce E. coli O157:H7 in feedlot surface material. In addition, studies were initiated to develop procedures to improve pathogen inactivation in minimally managed composting of feedlot pen surface manure. 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. We completed 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. Accomplishments 01 Natural antimicrobial compounds to replace antibiotics in swine diets. Antibiotics have been fed to farm animals at sub-therapeutic levels for nearly 60 years, and the young piglet appears to benefit from this dietary inclusion of antibiotics. Identification of alternative antimicrobial compounds to replace antibiotics is an urgent need if antibiotic use in food animal diets is no longer allowed. Lysozyme is a naturally occurring enzyme produced by animals that serves as a natural form of protection against microbial infection. ARS researchers at Clay Center, NE, fed diets containing lysozyme to nursery piglets and demonstrated reduced Campylobacter shedding in feces by these animals compared to control animals that were fed diets without and with antibiotics. Animals fed lysozyme performed as well or better than animals fed diets with antibiotics. Lysozyme appears to be a suitable natural compound that could be fed to piglets to improve performance in place of traditional antibiotics. 02 Set-back distances between feedlots and leafy greens to reduce pathogen contamination. Recent E. coli O157:H7 outbreaks linked to the consumption of spinach and lettuce have focused attention on cattle as sources of contamination, and demonstrated the need to determine appropriate set-back distances between cattle and produce crops that will effectively reduce the risk of E. coli O157:H7 transmission. Current guidelines for leafy green growers propose a provisional guidance distance of 400 feet between concentrated animal feeding operations and leafy green crops. ARS scientists in Clay Center, NE, evaluated the impact of proximity to a beef cattle feedlot on E. coli O157:H7 contamination of a leafy green produce crop. E. coli O157:H7 was recovered in leafy greens at low rates, but was found in leafy greens at all distances tested, including 600 feet. These results suggest that the current leafy green field distance guidelines of 400 feet may not be adequate to limit the occurrence of E. coli O157:H7 in crops planted near concentrated animal feeding operations. This information is critical for understanding the risks associated with growing leafy greens in close proximity to cattle production, and for determining safe distances between cattle feedlots and produce. 03 Reducing pathogens on cattle feedlot pen surfaces. Animal manures are rich in bacteria and can be a source of pathogens for the infection of additional animals in the production environment. Treatment of the manure to reduce pathogens can reduce this hazard, as well as reduce the risk for the contamination of human food and water when the manure is applied to farmland. ARS scientists at Clay Center, NE, evaluated a variety of low cost natural antimicrobial compounds for ability to reduce pathogens in animal manures, and pine oil, linalool, and thymol were selected for application in beef cattle feedlot pens. Pine oil (0. 4%) was effective at reducing Listeria and Campylobacter in cattle manure when the compound was applied directly on the feedlot surface, but linalool was not effective for either pathogen and thymol did not reduce Listeria. This research identifies natural compounds for pen surface applications that can reduce pathogens in feedlot pen manure, thereby reducing contamination risk and providing a preharvest intervention with the potential to break pathogen-host cycles that maintain pathogens in cattle production. 04 Control of E. coli O157:H7 in deep-bedded cattle confinement facilities. Deep-bedded confinement barns are increasing in popularity among beef cattle producers. Both E. coli O157:H7 prevalence and generic E. coli concentrations can occur at high levels in the manure/bedded packs of these facilities. Previous work showed that E. coli concentrations were lower in manure/bedded packs containing pine shavings, compared to manure/bedded packs constructed with other wood-based and crop-based materials. ARS scientists in Clay Center, NE, demonstrated that E. coli concentrations were similar in manure/bedded packs containing pine chips, dry cedar chips, or green cedar chips, thereby identifying additional wood-based materials for use as bedding materials in deep- bedded cattle facilities. Controlling 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 manage these facilities to reduce pathogens.
Impacts
(N/A)
Publications
- Jones, S., Salter, R.S., Goldsmith, T., Quintana, J., Rapnicki, P., Shuck, K., Wells, J., Schneider, M.J., Griffin, D. 2014. Development and model testing of anti-mortem screening methodology to predict prescribed drug withholds in heifers. Journal of Food Protection. 77(2):292-298.
- Kim, M.S., Kim, J., Kuehn, L.A., Bono, J.L., Berry, E.D., Kalchayanand, N., Freetly, H.C., Benson, A.K., Wells, J. 2014. Investigation of bacterial diversity in the feces of cattle fed different diets. Journal of Animal Science. 92:683-694.
- Berry, E.D., Millner, P.D., Wells, J., Kalchayanand, N., Guerini, M.N. 2013. Fate of naturally occurring Escherichia coli O157:H7 and other zoonotic pathogens during minimally managed bovine feedlot manure composting processes. Journal of Food Protection. 76(8):1308-1321.
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Progress 10/01/12 to 09/30/13
Outputs
Progress Report 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. 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. 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. Accomplishments 01 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. 02 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.
Impacts
(N/A)
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 (www.springerreference.com). Berlin/Heidelberg, Germany: Springer-Verlag. Available:
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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. Reducing pathogen shedding by cattle will require identification of the ecological and environmental factors that affect pathogen occurrence and persistence in the animal. In 2012, we completed studies to determine if switching diets to predominantly corn can reduce the load of E. coli O157:H7 in cattle that were fed high levels of wet distillers grains. We continued studies to determine if cattle shedding E. coli O157:H7 in feces at high numbers, compared to animals that are consistently negative for the pathogen, are associated with specific differences in the gastrointestinal microflora, specific host genomic factors, immune response, and/or host behaviors, such as temperament, and eating or drinking habits. In addition, 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. Understanding how these various factors impact E. coli O157:H7 in cattle is critical for developing intervention strategies to reduce this pathogen in cattle. Developing effective strategies to reduce pathogens in cattle also will require the understanding of factors that affect pathogen occurrence and transmission in the production environment. There is increasing interest in the use of deep-bedded confinement facilities in the cattle feeding industry for a variety of reasons, including ease of manure management and improved cattle performance compared to open lot feedlots. In FY 2012, we completed studies to evaluate the influence of different bedding materials on the populations of E. coli in deep-bedded cattle waste, in order to identify bedding materials that may limit the growth and persistence of these bacteria. The work is part of a larger collaborative effort that is also seeking to quantify and characterize odor emissions from cattle deep-bedded barns, with the goal to develop recommendations for managing these facilities to reduce odor, gas emissions, and pathogens. In addition, we initiated 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. 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 2012, we examined production factors impacting pathogens in swine, as well as intervention strategies to reduce pathogens in swine. Studies were completed to determine if age of piglets at weaning affects pathogen shedding in swine fed antibiotic-free diets. In addition, studies with 21-day-old nursery piglets were completed, to determine the impacts of diets containing the natural antimicrobial lysozyme on production 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. Accomplishments 01 Natural antimicrobials to replace antibiotics in swine diets. Young swi often are fed dietary antibiotics to improve health, reduce pathogen loa and enhance performance. However, few natural alternatives have been identified to replace these compounds in the diet if swine producers are required to eliminate antibiotic use. Lysozyme is a naturally occurring enzyme produced by animals to combat microbial colonization. ARS scientists at Clay Center, NE, determined that a commercial product containing lysozyme could replace dietary antibiotics in 10-day old earl weaned piglets. Dietary lysozyme reduced Campylobacter coli and Shigatoxin genes in feces of piglets, compared to diets without supplemented antibiotics. Lysozyme and antibiotic treatments had simila effects on pathogen load. Use of lysozyme in diets of young piglets cou maintain a safe food supply and reduce the use of prophylactic antibioti that are typically used for swine production.
Impacts
(N/A)
Publications
- Puchala, R., Animut, G., Patra, A.K., Detweiler, G.D., Wells, J., Varel, V. H., Sahlu, T., Goetsch, A.L. 2012. Methane emissions by goats consuming Sericea lespedeza at different feeding frequencies. Animal Feed Science And Technology. 175:76-84.
- Wells, J., Shackelford, S.D., Berry, E.D., Kalchayanand, N., Bosilevac, J. M., Wheeler, T.L. 2011. Impact of reducing the level of wet distillers grains fed to cattle prior to harvest on prevalence and levels of Escherichia coli O157:H7 in feces and on hides. Journal of Food Protection. 74(10):1611-1617.
- Berry, E.D., Wells, J. 2012. Soil solarization reduces Escherichia coli O157:H7 and total Escherichia coli on cattle feedlot pen surfaces. Journal of Food Protection. 75(1):7-13.
- Vogel, J.R., Gilley, J.E., Woodbury, B.L., Berry, E.D., Eigenberg, R.A. 2011. Transport of trace elements in runoff from unamended and pond-ash amended feedlot surfaces. Transactions of the ASABE. 54(4):1269-1279.
- Casas, E., Garcia, M.D., Wells, J., Smith, T.P.L. 2011. Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis. Animal Genetics. 42:571-577.
- May, K.D., Wells, J., Maxwell, C.V., Oliver, W.T. 2012. Granulated lysozyme as an alternative to antibiotics improves growth performance and small intestinal morphology of 10-day-old pigs. Journal of Animal Science. 90(4):1118-1125.
- Varel, V.H., Wells, J., Shelver, W.L., Rice, C., Armstrong, D.L., Parker, D.B. 2012. Effect of anaerobic digestion temperature on odour, coliforms and chlortetracycline in swine manure or monensin in cattle manure. Journal of Applied Microbiology. 112:705-715.
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report 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. 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. Feedlot diets with high levels of distillers grains can increase the prevalence of E. coli O157:H7 shedding by cattle. In 2011, we completed and analyzed studies to determine if high levels of wet distillers grains in cattle diets result in increased pathogen load on cattle in summer months when E. coli O157:H7 prevalence is typically high, and to determine if switching diets to predominantly corn can reduce the pathogen load. We also conducted studies to determine if cattle shedding E. coli O157:H7 in feces at high numbers, compared to animals that are consistently negative for the pathogen, are associated with specific differences in the gastrointestinal microflora, specific host genomic factors, immune response, and/or host behaviors, such as temperament, and eating or drinking habits. In addition, we initiated 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. Understanding how these various factors impact E. coli O157:H7 in cattle and the production environment is critical for developing approaches for reducing this pathogen in cattle. Studies were initiated to determine if age of piglet at weaning affects pathogen shedding in swine fed antibiotic-free diets. In addition, studies with 10-day-old early-weaned piglets were completed and studies with 21-day-old nursery piglets were initiated, to determine the impacts of diets containing the natural antimicrobial lysozyme on production 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. There is increasing interest in the construction of deep-bedded confinement facilities in the cattle feeding industry for a variety of reasons, including ease of manure management and improved cattle performance compared to open lot feedlots. In FY2011, we continued studies to evaluate the influence of a variety of different bedding materials on the populations of E. coli in deep-bedded cattle waste, in order to identify bedding materials that may limit the growth and persistence of these bacteria. The work is part of a larger collaborative effort that is also seeking to quantify and characterize odor emissions from cattle deep-bedded barns, with the goal to develop recommendations for managing these facilities to reduce odor, gas emissions, and pathogens. Accomplishments 01 Reducing the foodborne pathogen E. coli O157:H7 in cattle fed wet distillers grains. Wet distillers grains with solubles are a by-product ethanol production commonly fed to cattle and previous data indicate tha feeding high levels of wet distillers grains to feedlot cattle can increase the levels of E. coli O157:H7 in their feces compared to corn diets. ARS scientists at Clay Center, NE, investigated if shifting from higher to lower levels of wet distillers grains in the feedlot finishing diet would reduce the levels and frequency of E. coli O157:H7. In anima fed 40 or 70% wet distillers grains and switched to 0 or 15% wet distillers grains, E. coli O157:H7 frequency and levels in feces were lower compared to those in animals continuously fed 40% wet distillers grains. By day 56 after the switch, E. coli O157:H7 frequency and level in feces were similar to that of animals fed 0% corn. Because feeding we distillers grains is more economical than corn for beef producers, switching finishing cattle from high levels of wet distillers grains in the diet to 15% or less at least 56 days prior to harvest may be a viabl option for minimizing consumer food safety risks attributable to E. coli O157:H7 while retaining the advantages of feeding wet distiller grains.
Impacts
(N/A)
Publications
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