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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Research Project #439046

Research Project: Prevention and Mitigation of Pathogen Transmission from Cattle and Swine to Food, Water, and Environment

Location: Meat Safety and Quality

2022 Annual Report

Objective 1: Determine ecological and environmental factors associated with the levels and persistence of pathogens and antibiotic resistance in the host animal and transmission in the livestock production environment. Sub-objective 1.A: Determining sources and transmission of pathogens and antibiotic resistance in preharvest beef production environments. Sub-objective 1.B: Determining the development of AMR in commensal and pathogenic bacteria and their transmission in feedlot cattle and production systems. Sub-objective 1.C: Determining the impact of intestinal microbiome development on the longitudinal colonization and shedding of foodborne pathogens and antibiotic resistance in swine. Objective 2: Develop and evaluate intervention strategies that reduce or eliminate the occurrence, transmission, or persistence of foodborne pathogens in cattle, swine, their production systems, and the environment. Sub-objective 2.A: Evaluating the potential for dietary supplements to reduce pathogen and antibiotic resistance shedding in beef cattle feces and into the environment. Sub-objective 2.B: Identification of alternatives to antibiotics for use in nursery swine to reduce pathogens and AMR bacteria.

The overall goal of this project is to reduce the risk of foodborne illness, by providing information that can be used to reduce transmission of zoonotic pathogens and antibiotic resistance from cattle and swine production to food, water, and the environment. Cattle and swine remain important reservoirs for foodborne pathogen and antibiotic resistance, increasing the potential for transmission of foodborne pathogens to humans. Primary targets of the work include Escherichia coli O157:H7 and other Shiga-toxigenic E. coli, Salmonella, Campylobacter, and antibiotic resistant bacteria. Specific objectives are to (1) Determine ecological and environmental factors associated with the levels and persistence of pathogens and antibiotic resistance in the host animal and transmission in livestock production environments; and (2) Develop and evaluate intervention strategies that reduce or eliminate the occurrence, transmission, or persistence of foodborne pathogens in cattle, swine, their production systems, and the environment. Understanding the potential sources and transmission dynamics of pathogens in production environments is critical for identifying strategies to reduce their introduction and dissemination. Systems approaches examining multiple pathways and sample types will be used to identify the most important sources and transmission routes of pathogens and antibiotic resistance, using the U.S. Meat Animal Research Center (USMARC) preharvest beef and swine production environments. Moreover, research will determine how antibiotic use in cattle and swine affects pathogens and the development of antibiotic resistance in animals and their production environment. Research will also be conducted to identify alternatives to antibiotic use in cattle and swine. Expected outcomes are scientific information and management strategies that can be used to reduce foodborne pathogens and antibiotic resistance in livestock production, thus contributing to a safer food and water supply and a lower risk of human foodborne illness. These outcomes will benefit U.S. agriculture and numerous stakeholders, including livestock producers, animal harvest and meat processing industries, regulatory agencies, and consumers.

Progress Report
Under Objective 1 and 2. Understanding the impact of antibiotic use in swine and cattle production will be important to determining the potential for the development of antibiotic resistance in commensal and pathogenic bacteria. Under Sub-objective 1A, sampling and analysis in a long-term study was continued, to identify factors that affect the occurrence and transmission dynamics of multiple pathogens and antibiotic resistance in cattle and waterways in pasture-based cattle production. Factors under study include wildlife, migratory waterfowl, and other environmental and seasonal effectors. Water, sediment, and feces were collected and analyzed, and weather and camera data were recorded. Feedlot cattle are treated with antibiotics at arrival to the feedlot to reduce the incidence of bovine respiratory illnesses, particularly with high-risk cattle that have been directly weaned and sold at sale barns. Under Sub-objective 1B, research with high-risk cattle was continued with collaborators at Texas Tech University (TTU) and University of Nebraska-Lincoln to study how metaphylactic use of antibiotics might impact pathogens and antimicrobial-resistant (AMR) bacteria. A study with sale barn sourced cattle was completed at the TTU Burnett Center. The cattle were treated with saline, or one of three antibiotics commonly used for metaphylactic treatment in feedlot cattle, and fecal samples were collected over time and analyzed for pathogenic and AMR bacteria. Bacterial isolates were tested for antimicrobial susceptibilities according to National Antimicrobial Resistance Monitoring System (NARMS) protocols. The use of antibiotics on cattle at feedlot arrival had significant impact on the levels of some antimicrobial resistant bacteria in the feces early in the production phase but these levels transiently decreased after the first month. Many of the antimicrobial resistant bacteria increased after the second month in the feedlot and were at the highest levels at harvest. Salmonella in feces was also monitored over time and antibiotic treatment at arrival had a significant impact on levels and prevalence in the feces up to harvest. However, antibiotic use in feedlot cattle did not appear to increase antibiotic resistant Salmonella. For Sub-objective 2A, the environment was evaluated using samples of feed and of the feedlot surface material collected prior to and for 56 days after animals were placed into the pens. Antibiotic treatment appeared to impact the onset of bovine respiratory disease and the shedding of Salmonella and AMR Escherichia coli (E. coli) in the feces. Follow-up work will also determine if horizontal gene transfer occurs between multidrug resistant E. coli and Salmonella within these cattle and the feedlot environment. Reducing pathogen and AMR bacteria persistence and transmission from cattle and swine will require the development of intervention strategies that reduce their prevalence in the animal, the manure, and the production environment (Objective 2). Under Sub-objective 2A, one study was continued from fiscal year (FY) 2021 and a second study was initiated with feedlot cattle to determine the impact of dietary antimicrobials on fecal shedding of AMR E. coli and Enterococcus spp. Fecal and environmental samples were collected prior to and after the supplementation of dietary antimicrobials. Under Sub-objective 2B, research with a potential fungal probiotic was conducted at Clay Center, Nebraska, in collaboration with scientists from Beltsville, Maryland. Piglets were orally treated with saline or the probiotic fungi on days 10 and 24 of age. Fecal samples were collected at weaning and at the end of the nursery phase to determine pathogen and AMR presence. Samples were obtained end of the nursery phase to determine the distribution of pathogens and AMR bacteria throughout the gastrointestinal tract. Interestingly, AMR bacteria were observed at high levels in piglets regardless of age and the cecum appears to be a reservoir for AMR in the young piglet. Additional research was conducted to determine transcriptomics of milk in nursing sows, and numerous genes associated with pathogen recognition and immune response were observed to be differentially expressed in sows of different age and milk type. Efforts are continuing to identify milk oligosaccharides and determine relationships with pathogen colonization and shedding in piglets.

1. Management intensive grazing protects water quality. Riparian areas are the zones that occur along streams and other water bodies, and these areas are characterized by unique vegetation and soil that is influenced by the presence of the water. Riparian vegetation can provide nutritious forage for cattle and other livestock, and benefits of grazing include the control of palatable weeds, woody species, other undesirable vegetation that may increase fire risk or lead to excessive biomass in the stream flow. However, unmanaged grazing can negatively impact water quality by degrading this vegetation, which serves to protect streams by stopping the erosion of sediment, excessive nutrients, and other contaminants that can be carried by runoff from the adjacent land. ARS scientists at Clay Center, Nebraska, determined that short-term management-intensive grazing of riparian areas limits the negative effects of cattle grazing on water quality. The ability to use this forage resource without negatively affecting water quality is advantageous to livestock producers, through access to high quality forages while protecting the riparian environment.

2. Assessing antimicrobial resistance across U.S. waterways. Pathogenic and antimicrobial resistant bacteria are a concern in agriculture and for human health. A better understanding of the distribution of these bacteria in the environment, especially with surface water, has been deemed important relative to the One Health approach to achieve optimal health outcomes. ARS researchers from Clay Center, Nebraska, worked in collaboration with colleagues at other ARS locations and other Federal agencies to design a study to evaluate the presence and distribution of antimicrobial resistance (AMR) in United States surface waters, and identify potential environmental factors that might impact AMR in water. This team of scientists determined that a single study was not adequate to answer these questions and that a combination of a national probabilistic survey and targeted in-depth studies of individual streams would better accomplish the project goals. As a result of ARS input, a robust scientific approach to better understand the contributions and persistence of bacterial antimicrobial resistance in U.S. surface water was developed and is currently being implemented and coordinated across the U.S. by these Federal agencies.

3. Methodologies for detecting pathogens in water. Methodologies for the detection of pathogenic and antimicrobial resistant bacteria have been developed predominantly for clinical samples, and few methods have been validated for water where the contaminating bacteria are typically present at very low levels. ARS scientists at Clay Center, Nebraska, and ARS colleagues at other locations evaluated various methodologies for the detection and isolation of Escherichia coli and Salmonella from water and developed tailored protocols for use with National Antimicrobial Resistance Monitoring System surface water samples. As a result of these efforts, a robust set of protocols was developed to better understand the contributions and persistence of pathogens and bacterial antimicrobial resistance in U.S. surface water which will ensure robust, accurate data will be collected on antimicrobial resistance for use in addressing public health concerns for consumers and the livestock industries.

Review Publications
Rubeck, L.M., Wells, J.E., Hanford, K.J., Durso, L.M., Schacht, W.H., Berry, E.D. 2022. Management-intensive grazing impacts on total Escherichia coli, E. coli O157:H7, and antibiotic resistance genes in a riparian stream. Science of the Total Environment. 817. Article 152611.
Rempel, L.A., Keel, B.N., Oliver, W.T., Wells, J.E., Lents, C.A., Nonneman, D.J., Rohrer, G.A. 2022. Dam parity structure and body condition during lactation influence piglet growth and gilt sexual maturation through pre-finishing. Journal of Animal Science. 100(4):1-9. Article skac031.
Weinroth, M.D., Belk, A.D., Dean, C.J., Noyes, N.R., Dittoe, D.K., Rothrock Jr, M.J., Ricke, S.C., Myer, P.R., Henniger, M.T., Ramirez, G.A., Oakley, B.B., Summers, K.L., Miles, A.M., Ault-Seay, T.B., Yu, Z., Metcalf, J., Wells, J. 2022. Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. Journal of Animal Science. 100:1018.
Keel, B.N., Lindholm-Perry, A.K., Oliver, W.T., Wells, J.E., Jones, S.A., Rempel, L.A. 2021. Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities. BMC Genomic Data. 22. Article 25.
Lindholm-Perry, A.K., Kuehn, L.A., Wells, J., Rempel, L.A., Chitko-McKown, C.G., Keel, B.N., Oliver, W.T. 2021. Hematology parameters as potential indicators of feed efficiency in pigs. Translational Animal Science. 5(4). Article txab219.
Henniger, M.T., Wells, J.E., Hales, K.E., Lindholm-Perry, A.K., Freetly, H.C., Kuehn, L.A., Schneider, L.G., McLean, K.J., Campagna, S.R., Christopher, C.J., Myer, P.R. 2022. Effects of a moderate or aggressive implant strategy on the rumen microbiome and metabolome in steers. Frontiers in Animal Science. 3. Article 889817.
Long, N.S., Wells, J.E., Berry, E.D., Legako, J.F., Woerner, D.R., Loneragan, G.H., Broadway, P.R., Carroll, J.A., Sanchez, N.C.B., Fernando, S.C., Bacon, C.M., Helmuth, C.L., Smock, T.M., Manahan, J.L., Hoffman, A.A., Hales, K.E. 2022. Metaphylactic antimicrobial effects on occurrences of antimicrobial resistance in Salmonella enterica, Escherichia coli, and Enterococcus spp. measured longitudinally from feedlot arrival to harvest in high-risk beef cattle. Journal of Applied Microbiology. Article 15691.