Location: Food and Feed Safety Research2017 Annual Report
1a. Objectives (from AD-416):
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.
1b. Approach (from AD-416):
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.
3. Progress Report:
Work under the project during FY 2017 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 Salmonella infection (Objective 3) and mechanisms of antimicrobial resistance dissemination (Objective 4). Project work has 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. 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.
1. Incidence of Salmonella enterica in swine. Salmonella enterica (SE) is an important cause of foodborne illness globally every year. ARS researchers at College Station, Texas, in collaboration with scientists from Texas Tech University and Texas A&M University, hypothesized that SE in cattle lymph nodes could pose a risk for human infection if these lymph nodes were included in edible meat products reaching the consumer. The work analyzed data from 1200 cheek meat and head trim tissues from pork carcasses collected bi-monthly over a 12 month period from a pork processing plant. The analysis showed high carriage rates of diverse SE serotypes from these pork samples. The majority of isolations occurred during colder months compared to warmer months and approximately 60% of isolates were multi-drug resistant (resistant to 3 or more antimicrobials). These data are important because they point out the potential risk of human exposure to SE if these by-product tissues are incorporated into edible meats, and they suggest that intervention methods, both pre- and post-harvest, should be explored.
2. Antimicrobial resistance dissemination in bovine gut bacteria. Antibiotics have traditionally been used in animal agriculture to prevent disease and promote growth, although concerns have arisen that their continued use may result in the emergence of resistant bacteria potentially capable of further disseminating their resistance via genetic transfer to other microbes. To gain a better understanding of how resistance genes can be spread between bacteria, ARS researchers at College Station, Texas, studied rates and mechanisms of resistance transfer between multidrug-resistant Escherichia coli strains isolated from cattle, with other E. coli and Salmonella strains having no prior resistance genes. Results showed near equal rates of transfer between the multi-drug resistant strains and the non-resistant E. coli and Salmonella strains. The incidence of transfer approached 30% which was achieved mainly by specific plasmid-mediated exchange mechanisms; plasmids are relatively small genetic fragments. This accomplishment will aid in the design and implementation of successful pre-harvest intervention strategies to reduce the carriage of resistant bacteria in food-producing animals.
Edwards, H.D., Shelver, W.L., Choi, S., Nisbet, D.J., Krueger, N.A., Anderson, R.C., Smith, S.B. 2017. Immunogenic inhibition of prominent ruminal bacteria as a means to reduce lipolysis and biohydrogenation activity in vitro. Journal of Food Chemistry. 218:372-377.
Anderson, R.C., Ripley, L.H., Bowman, J.G., Callaway, T.R., Genovese, K.J., Beier, R.C., Harvey, R.B., Nisbet, D.J. 2016. Ruminal fermentation of anti-methanogenic nitrate- and nitro-containing forages in vitro. Frontiers in Veterinary Science. 3:62. doi: 10.3389/fvets.2016.00062.
Ruiz-Barrera, O., Anderson, R.C., Hume, M.E., Corrales-Millan, J., Castillo-Castillo, Y., Corral-Luna, A., Guevara-Valdez, J.L., Salinas-Chavira, J., Rodriguez-Muela, C., Arzola-Alvarez, C. 2016. Short chain nitrocompounds as a treatment of layer hen manure and litter; effects on in vitro survivability of Salmonella, generic E. coli, and nitrogen metabolism. Journal of Environmental Science and Health. 52(1):23-29. doi: 10.1080/03601234.2016.1224698.
Zhang, Y., Long, R.J., Anderson, R.C., Hume, M.E., Coverdale, J.A., Latham, E.A., Nisbet, D.J. 2016. Characterization of nitrate-reducing and amino acid-using bacteria prominent in nitrotoxin-enriched equine cecal populations. Journal of Equine Veterinary Science. 46:47-53.
Beier, R.C., Franz, E., Bono, J.L., Mandrell, R.E., Fratamico, P.M., Callaway, T.R., Andrews, K., Poole, T.L., Crippen, T.L., Sheffield, C.L., Anderson, R.C., Nisbet, D.J. 2016. Disinfectant and antimicrobial susceptibility profiles of the big six non-O157 Shiga toxin-producing Escherichia coli strains from food animals and humans. Journal of Food Protection. 79(8):1355-1370.
Edrington, T.S., Loneragan, G.H., Genovese, K.J., Hanson, D.L., Nisbet, D.J. 2016. Salmonella persistence within the peripheral lymph nodes of cattle following experimental inoculation. Journal of Food Protection. 79(6):1032-1035.
Maki, C.R., Monteiro, A.P., Elmore, S.E., Tao, S., Bernard, J.K., Harvey, R.B., Romoser, A.A., Phillips, T.D. 2016. Calcium montmorillonite clay in dairy feed reduces aflatoxin concentrations in milk without interfering with milk quality, composition or yield. Animal Feed Science And Technology. 214:130-135.
Cernicchiaro, N., Ives, S.E., Nagaraja, T.G., Edrington, T.S., Renter, D.G. 2016. Efficacy of a Salmonella siderophore receptor protein vaccine on fecal shedding and lymph node carriage of Salmonella in commercial feedlot cattle. Foodborne Pathogens and Disease. 13(9):517-525.