Project : USDA ARS

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Research Project: Ecological Reservoirs and Intervention Strategies to Reduce Foodborne Pathogens in Cattle and Swine

Location: Food and Feed Safety Research

2019 Annual Report

Objectives
Objective 1: Identify the ecological niches or reservoirs for pathogenic and antimicrobial resistant foodborne bacteria and determine nutritional, immunological, biological and environmental factors impacting their ability to colonize, survive, and persist in the gut and environment of food producing animals using metagenomic and molecular characterization of competitiveness, resistance and virulence. 1.A: Determine the effect of dietary components, feedstuffs, phytochemical extracts, and organic acids on the intestinal microbiome and functional genomics of the gut, and the impact of these changes on enterohemorrhagic E. coli and Salmonella. 1.B: Characterize the effects of short chain nitrocompounds on hydrogen ecology, pathogen competitiveness and gene expression in E. coli, Salmonella, and Campylobacter. Objective 2: Characterize the biological factors affecting infection and maintenance of Salmonella in lymphatics of food producing animals and elucidate management practices to mitigate infection. 2.A: Determine the duration of Salmonella infection in the peripheral lymph nodes of cattle. 2.B: Determine the role of mucous membranes in uptake and distribution of Salmonella to the peripheral lymph nodes of cattle. 2.C: Determine the prevalence, antimicrobial susceptibilities, genetic relatedness, serotypes, and molecular characteristics of Salmonella isolated from head meat and trim intended for ground pork. Objective 3: Identify, develop, and test interventions, including exploring possible synergies of multiple interventions and alternatives to antibiotics that can kill pathogenic or antibiotic resistant foodborne pathogens or mitigate their virulence and resistance in the animal production environment. 3.A: Enhance the effectiveness of naturally occurring phytochemicals and organic acids in reducing E. coli and Salmonella in the animal gut. 3.B: Reduce-to-practice ß-D-thymol as a feed additive prebiotic pathogen control technology for swine. 3.C: Determine if feeding sodium chlorate will reduce populations of Salmonella within the peripheral lymph nodes. 3.D: Determine if application of a bacteriophage cocktail will reduce or eliminate Salmonella from the peripheral lymph nodes of experimentally-infected cattle. 3.E: Determine if killed, irradiated, or spent chemostatic effluent of a recombined porcine-derived competitive exclusion culture can stimulate in vitro and in vivo immune responses and characterize the production and efficacy of biofilms and bacteriocins associated with the culture. Objective 4: Investigate the ecology of antimicrobial and disinfectant resistance within the gut of food producing animals and their production environment and elucidate factors contributing to the acquisition, exchange, dissemination and maintenance of resistant elements in foodborne pathogens and commensal bacteria. 4.A: Determine association between multidrug resistance (MDR) and virulence traits in Escherichia coli and non-typhoidal Salmonella enterica serovars isolated from food producing animals that might provide a dissemination advantage.

Approach
Basic and applied research will be conducted to achieve project objectives. Studies employing metagenomic analysis will elucidate ecological niches or reservoirs where pathogens may exist, and when combined with traditional epidemiological and microbiological cultural methods, these studies will help reveal environmental, nutritional, and biological factors affecting fitness characteristics contributing to persistent colonization, survival, and growth of these pathogens in food animals and their production environment. Research involving both in vitro and in vivo methods will be used to assess and characterize adaptive responses microbes may exhibit to intrinsic and extrinsic stressors, such as those exerted by disinfectants and antimicrobials, as well as to learn how these stressors may influence pathogenicity, virulence, and resistance of the microbes. Animal studies conducted under clinical and field situations will be used to develop and evaluate interventions, thereby revealing specific metabolic endpoints, cellular mechanisms, and sites of action of cellular processes that may ultimately be exploited to decrease carriage and shedding of pathogens during production and at slaughter. When applicable, Cooperative Research and Development Agreements will be implemented with industry partners to aid in technology transfer.

Progress Report
Work under the project during FY 2019 resulted in significant progress in identifying critical control points for the application of new and improved intervention needs by providing new knowledge on routes of pathogen infection (Objective 3) and mechanisms of antimicrobial resistance dissemination (Objective 4). Project work continued ongoing efforts aimed at the development of practical, cost-effective interventions and management practices to reduce the carriage and environmental dissemination of pathogenic and antimicrobial-resistant microbes by food-producing animals (Objectives 1 and 2). Where practical, these interventions are being designed to contribute to the efficiency and profitability of animal production; industry partners are collaborating to facilitate implementation of these technologies. New technologies and protocols developed from this work will help U.S. farmers and ranchers produce safer, more wholesome meat products at less cost to the consumer.

Accomplishments
1. New antibiotic alternatives to treat methicillin resistant staphylococci. Certain staphylococci are recognized as important pathogens of humans, livestock, and other animals. The recent emergence of staphylococcal strains expressing antibiotic resistance in food-producing livestock has raised concerns of greater health risks to livestock workers and consumers of potentially contaminated foods. ARS scientists at College Station, Texas, in collaboration with scientists from the University of Novi Sad, Serbia, and the Universidad Autónoma de Chihuahua, México, investigated six different chemicals with potential antimicrobial activity against representative antibiotic-resistant staphylococci. The work established that Staphylococcus aureus and staphylococci that express multiple antibiotic resistance were highly sensitive to chemicals called 2-nitropropanol and chlorate, each alone decreasing growth rates and total amounts of growth by these bacteria by 58 to 99%, albeit via different biological mechanisms that were complementary when added together. These results provide important information on potential new non-antibiotic interventions that, when combined, may yield persistently effective anti-staphylococcal treatments that will help livestock producers meet the goal of providing high quality, wholesome, and safe foods at less cost to the American consumer.

2. Increased resistance of Campylobacter to commonly used disinfectants. Disinfectants are often used on the farm, in veterinary medicine, by the food processing industry, in restaurants, and in consumers' homes to control pathogenic microorganisms such as Campylobacter coli. Limited information is available on how these pathogens may become more resistant to the disinfectants during years of use. ARS scientists at College Station, Texas, in collaboration with scientists from the U.S. Food and Drug Administration investigated disinfectant profiles for 111 Campylobacter coli strains obtained in 1998, 1999, and 2015. Results revealed that there was a shift in susceptibility profiles of the tested Campylobacter strains, with higher amounts of several commercial disinfectants being needed to inhibit growth of strains sampled in 2015 versus strains sampled in 1998 and 1999. Based on calculations of minimum inhibiting concentrations of active components present in the disinfectants, it was determined which ingredients retained antimicrobial potency and which did not. These results provide important information on how to best manufacture and use disinfectants to control Campylobacter on the farm, during processing, and in the household so that American consumers can continue to have access to high quality, wholesome food at an affordable cost.

U.S. DEPARTMENT OF AGRICULTURE

Food and Feed Safety Research: College Station, TX