Location: Meat Safety and Quality
2025 Annual Report
Objectives
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.
Approach
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 Objectives 1 and 2. Understanding the impact of antibiotic use in swine and cattle production is 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. Final analyses are underway of initial studies. To better understand the spatial and temporal fluctuations of pathogens in the waterway samples, weekly sampling of the surface water was implemented.
ARS scientists in Clay Center, Nebraska, have been participating in a multi-agency effort to determine bacterial antibiotic resistance and pathogen load in samples of surface water. Surface water was determined to be a suitable proxy for environmental loads of antibiotic resistance and pathogens. Different methods for detecting and isolating Salmonella were evaluated and have been reported. Additional studies are being completed to evaluate different methods for the enumeration and isolation of total E. coli and antibiotic-resistant E. coli in surface waters. Results from these later studies will provide guidance for future research efforts studying E. coli in surface water.
Feedlot cattle, in particular high-risk cattle that have been directly weaned and sold at sale barns, are a concern for pathogens and antibiotic resistance. 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, and to identify interventions to reduce this risk. A study with sale barn sourced cattle was completed at the TTU Burnett Center. The use of antibiotics on cattle at feedlot arrival had a 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 multidrug-resistant Salmonella. Additional studies have been conducted in collaboration with scientists at West Texas A&M University, Texas Tech University (TTU), and USDA/ARS Lubbock, Texas, to characterize Salmonella isolates from the beef food chain continuum. Preliminary results indicated that Salmonella isolates from internal tissues, such as lymph nodes, and fecal samples were genetically similar.
For Sub-objective 2A, the pathogens and AMR bacteria in animal feces and the environment were evaluated. Multidrug resistant Salmonella were routinely recovered from feedlot surface samples but were not recovered from bovine feces. Follow-up work will also determine if horizontal gene transfer occurs between multidrug resistant E. coli and Salmonella within the feedlot environment. Additional research in collaboration with scientists at Texas Tech University, South Dakota State University, and USDA/ARS Lubbock, Texas, has been completed that indicated that geographic location in the high plains impacted shedding of pathogens and antimicrobial resistant bacteria.
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 completed, and a second study was continued with feedlot cattle to determine the impact of dietary antimicrobials on fecal shedding of AMR E. coli and Enterococcus spp. Under Sub-objective 2B, research with a potential fungal probiotic was completed at Clay Center, Nebraska, in collaboration with ARS scientists from Beltsville, Maryland. Weaning of the piglet was found to result in significant changes in the fecal microbiome and could result in susceptibility to pathogen colonization. Additional research with scientists at University of Nebraska-Lincoln was conducted to determine how dietary antimicrobial treatment after weaning could impact pathogens and antimicrobial resistant bacteria in the feces. Additional research was completed 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 host genetic determinants that are impacting pathogen colonization and shedding in the piglet.
Salmonella serotype Reading was responsible for a significant outbreak in ground turkey products in 2018 and 2019. Research efforts have been initiated to conduct a retrospective analysis of the Salmonella Reading outbreak in turkey products to understand factors that enable a switch between endemic and epidemic states. A new clonal group of Reading with increased pathogenicity and transmission was the causative agent, but the mechanisms through which this group became the dominant type remain unknown. Our aim is to investigate all possible factors which may have contributed to the Reading outbreak to better understand how Salmonella outbreaks occur in general. We will use a variety of computational approaches to understanding the factors which contributed to this outbreak. We are currently in the data collection and assumption checking phase of this project.
Additional efforts are directed towards conducting a historical analysis of Salmonella using pre-existing data. The goals of this project are to 1) develop a framework for understanding where, why, and how certain Salmonella strains emerge to cause outbreaks, and 2) to produce for industry a short-list of early warning signs and monitoring recommendations to predict the next outbreak before it happens. Following methods developed previously, we identified Serotypes of greater Concern for human health (SoCs) over a variety of time periods to identify the period which allows us to detect meaningful changes in SoC classifications. Now, we are developing case studies to test hypotheses about why, how, and where these SoCs emerged using ancestral state reconstruction and phylogeographic analyses. This will aid in our understanding of how dominant serotypes and SoCs gain the genetic elements needed to emerge and identify trends and patterns that may warn us about the next emergence.
Efforts have also been directed to developing a bioinformatic pipeline to enhance characterization of sequence differences among Salmonella isolates within single nucleotide polymorphisms (SNP) clusters identified by the National Center for Biotechnology Information (NCBI) Pathogen Detection System. We have analyzed multiple Salmonella SNP clusters across meat commodities and serotypes using the NCBI PDIB methods as well as more detailed bioinformatic methods (which incorporate bacteriophages, genomic islands, etc.) to understand the true diversity of isolates in SNP clusters. We have also developed a software pipeline to automate this workflow for non-bioinformaticians (stakeholders) and have created a point-and-click user interface to allow ease of access to use of the pipeline.
Accomplishments
1. Identification and characterization of an agriculturally sourced multidrug resistant Escherichia coli control strain for laboratory analyses. Bacteriological control strains with known characteristics ensure consistency and reproducibility of assay performance across different laboratories and are an important cornerstone of quality control in the microbiology laboratory. However, for work involving antibiotic resistance, most controls come from human and veterinary clinical sources and are not optimized for work in agriculturally impacted environments or not widely available. ARS scientists from Clay Center, Nebraska; Lincoln, Nebraska; Beltsville, Maryland; Riverside, California; and Athens, Georgia, identified two agriculturally sourced, fully characterized, and genetically sequenced control strains for use as laboratory controls in research involving antibiotic resistant Escherichia coli isolated from the environment. These strains are readily available for research and will lead to greater consistency in experimental design and more impactful solutions to antibiotic resistance in agriculture environments.
Review Publications
Hoffman, A.A., Fernando, S.C., Wells, J., Woerner, D.R., Manahan, J.L., Long, N.S., McDaniel, Z.S., Smock, T.M., Line, D.J., Broadway, P.R., Carroll, J.A., Sanchez, N.C., Hales, K.E. 2024. Use of a novel direct-fed microbial as an alternative for tylosin phosphate to control liver abscesses and decrease antimicrobial use in finishing beef steers. Applied Animal Science. 40(3):307-316. https://doi.org/10.15232/aas.2023-02483.
Hoffman, A.A., Dornbach, C.W., Fernando, S.C., Broadway, P.R., Sanchez, N.C., Long, N.S., McDaniel, Z.S., Smock, T.M., Wells, J., Hales, K.E. 2025. Effects of a novel direct-fed microbial on occurrences of antimicrobial resistance in Salmonella enterica, Escherichia coli, and Enterococcus spp. measured longitudinally from feedlot arrival to harvest in finishing beef steers. Journal of Food Protection. 88(5). Article 100484. https://doi.org/10.1016/j.jfp.2025.100484.
Rivera-Colon, I., Harkow, K., Cole, R., O'Meally, R., Garrett, W.M., Xiong, W., Oliver, W.T., Wells, J., Summers, K.L., Chhetri, N., Postnikova, O.A., Rempel, L.A., Crouse, M.S., Neville, B.W., Davies, C.L. 2025. A metaproteomic analysis of the piglet fecal microbiome during the weaning transition. Frontiers in Microbiology. 16. Article e1504433. https://doi.org/10.3389/fmicb.2025.1504433.
Wells, J., Durso, L.M., Ibekwe, A.M., Frye, J.G., Sharma, M., Williams, C.F., Shamimuzzaman, M. 2025. Agriculturally sourced multidrug-resistant Escherichia coli for use as control strains. Pathogens. 14. Article 14050417. https://doi.org/10.3390/pathogens14050417.