Location: Meat Safety and Quality
2023 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 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. Preliminary analyses indicate that pathogen presence in the waterway might be impacted by season. Arcobacter and Campylobacter were rarely detected in summer months and Salmonella were rarely detected in the winter months. Salmonella were regularly detected in feces from wildlife. Escherichia coli were always present but enumerations are highest in the summer. Although pastured cattle were in close proximity to the waterway throughout the year, E. coli O157:H7 were rarely detected.
ARS scientists in Clay Center, Nebraska, also participated 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 and Escherichia (E. coli) were evaluated. A modified filter-based method followed by selective enrichment was determined to provide the best recovery for Salmonella in 1-liter of surface water, and the method Is currently being used to collect preliminary data for Salmonella distribution in the surface water of a mixed-use watershed. Additional studies are being conducted 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 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 sourced from sale barns was completed 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. 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. Antibiotic use in feedlot cattle did result in changes to susceptibility for individual antibiotics but overall 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 E. coli in the feces. Multidrug resistant Salmonella were routinely recovered from feedlot surface samples but were never recovered from bovine feces. Follow-up work will determine if horizontal gene transfer occurs between multidrug resistant E. coli and Salmonella within the feedlot environment. An additional study related to this objective was conducted in collaboration with scientists at Texas Tech University, South Dakota State University, and USDA/ARS Lubbock, Texas, to determine the impact of location in the high plains on antimicrobial resistance and pathogen shedding in feces. Preliminary evidence suggests that location can impact the fecal shedding of antimicrobial resistant and pathogenic bacterial populations, and relocation of animals to regions of low incidence can significantly reduce fecal shedding of antimicrobial resistant and pathogenic 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, a 2-year study was completed 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. The targeted bacterial species were enumerated, and bacterial isolates have been tested for antimicrobial susceptibilities according to NARMS protocols. 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. The distribution of pathogens and AMR bacteria throughout the gastrointestinal tract was determined in piglets at weaning and at the end of the nursery phase. 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. Supplementation of the probiotic fungi did not impact animal performance or shedding of AMR. 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. Relationships between the transcriptome and pathogen shedding are being determined currently. Efforts are continuing to identify milk oligosaccharides and determine relationships with pathogen colonization and shedding in piglets.
Accomplishments
1. Antimicrobial resistance in metaphylactic antimicrobial treated cattle. Feedlot cattle at high risk to develop bovine respiratory disease are commonly treated with antimicrobials at arrival to reduce respiratory illnesses. Little is known about the impact of antimicrobial use on feedlot cattle at arrival on the development and persistence of antimicrobial resistance in treated cattle. In collaboration with scientists at Texas Tech University and ARS scientists in Lubbock, Texas, ARS scientists in Clay Center, Nebraska, treated high risk cattle at arrival with saline or one of three antimicrobials. Type of antimicrobial impacted the initial resistant E. coli populations over the course of the study. However, by the end of the study, antimicrobial resistant E. coli populations were similar across all treatments. The use of antimicrobials at arrival also had no impact on the development or persistence of resistant Salmonella. Antimicrobial resistance in this study was not associated with use of a metaphylactic antimicrobial in cattle on arrival at the feedlot.
2. Impact of antimicrobial use on Salmonella in feedlot cattle. Feedlot cattle can be a significant source of Salmonella in the food chain. In collaboration with scientists at Texas Tech University and ARS scientists in Lubbock, Texas, ARS scientists in Clay Center, Nebraska, monitored Salmonella in feces from arrival to harvest of cattle treated at arrival with saline or one of three antimicrobials (tulathromycin, ceftiofur or florfenicol). Cattle treated with tulathromycin had significantly higher fecal and hide prevalence of Salmonella throughout the 8-month study compared to cattle treated with ceftiofur or florfenicol. However, Salmonella presence in the lymph nodes was not affected by antimicrobial treatment. The use of tulathromycin as a treatment for cattle at arrival to the feedlot may increase the amount of Salmonella detected in the feces and pen environments, thus feedlot cattle producers, beef processors, and consumers would benefit from using alternative antimicrobials when possible.
