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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Food and Feed Safety Research » Research » Research Project #430283

Research Project: Identification of the Ecological Niches and Development of Intervention Strategies to Reduce Pathogenic Foodborne Pathogens in Poultry

Location: Food and Feed Safety Research

2021 Annual Report

Objective 1: Define the differential host-pathogen interactions between Salmonella and chicken and poultry mucosal immune systems using genomic technologies. Determine the relationship between foodborne pathogens and the mucosal innate immune response, focusing on epigenetic reprogramming of host immune genes in persistent infections. Objective 2: Identify and develop key strategies including waste, vaccination (using innate immunity), and lighting management strategies for use at animal production facilities that mitigate and reduce the bacterial load of Salmonella and other foodborne pathogens without the use of antibiotics during pre-harvest production in broiler chickens and turkeys. Objective 3: Analyze and characterize both host and Salmonella proteins that are modulated in expression during infection using quantitative proteomic. Develop strategies to reduce foodborne pathogens by targeting host immune-metabolic signaling pathways affected by Salmonella and Campylobacter virulence factors. Objective 4: Investigate potential alternatives to antibiotics, such as chitosan preparations and other commercially available products, on the cecal levels of Salmonella and Campylobacter using an experimental model and metagenomics. Investigate the potential for use and the mechanism used by specific nutritional supplements to inhibit the transfer of genetic resistance elements, such as plasmids, by conjugation between commensal and foodborne bacteria. Objective 5: Investigate the interaction between yeast and fungi and foodborne bacteria to determine their role as commensals and inhibitors or their use as alternatives to antibiotics as pre-and probiotics. Objective 6: Identify ecological reservoirs of pathogens and the potential role of dispersal of animal waste that enable the retention of foodborne pathogens within animal production facilities and the surrounding environments.

The Centers for Disease Control and Prevention continues to monitor multistate foodborne outbreaks that impact health of the nation over the last 10 years. One area of concern is the reduction of Salmonella as a foodborne pathogen. Despite control efforts that cost over a half a billion dollars annually, foodborne illnesses due to Salmonella continues to impact the consumer. Poultry are commonly identified as a major source of Salmonella. To develop urgently needed new control strategies against Salmonella, we will take a multi-faceted, but integrated approach to identify and evaluate factors at the pre-harvest level that can be used. Based on previous research and collaborations with industry, we will identify and modify management practices that may decrease foodborne pathogen load, as well as environmental conditions associated with higher risk that would be conducive to pathogen survival and growth. Cost effective alternatives will be suggested throughout the poultry production phase. Environmental areas of concern, such as poultry waste and insect vectors will be included. At a more micro-level, interactions among fungi, protozoa, and other microbes will be evaluated under commercial production practices with the outcome of proposed new strategies for pathogen reduction. Campylobacter, a foodborne pathogen in poultry, has become an increasing concern due to the development of antibiotic resistance, especially to fluoroquinolones. The proposed research will investigate strategies to reduce pre-harvest Campylobacter, which will enhance the microbiological safety of poultry. This is important for food safety, but also for the reduction of potential antimicrobial resistance in animal agriculture and public health. Immune modulation is one approach for new anti-infective therapies, whereby natural mechanisms in the host can be exploited to strengthen therapeutic benefits. The stimulation of innate immunity has considerable potential to induce a profound and rapid cross-protection against multiple serovars of bacteria. Using "omic" techniques, including functional genomics, epigenetics, proteomics, and metabolomics, we will identify effective modulators of innate immunity to control infections, especially in situations where vaccination is not appropriate. Furthermore, metabolism and host immunity are essential requirements for survival. Mounting an immune response requires major changes to metabolic processes. Thus, the integration of central metabolic pathways and nutrient sensing with antibacterial immunity alters cellular energy homeostasis and contributes to the prevention or resolution of infectious diseases. Hence, immune and metabolic response processes govern infectious diseases. Research taken will focus on obtaining a greater understanding of the critical nodes of immunometabolism during Salmonella and Campylobacter infection.

Progress Report
This project expired on March 16, 2021, and was replaced by the new project 3091-32000-037-00D. Project work in Fiscal Year 2021 finalized research that described new mechanisms on modulating the immune system of poultry to enhance the microbiological safety of poultry meat products reaching the consumer. Work under Objective 3 identified novel biomarkers formed during the development of a nutritionally-based gut inflammation model which can be used by industry to assess overall flock health and performance, and accurately assess and predict the effects of food poisoning microorganisms on gut tissues. The identification of these biomarkers will facilitate the commitment by industry to produce poultry with a healthier gut, that are less susceptible to colonization by foodborne pathogens including Salmonella and Campylobacter, and that will provide microbiologically safer poultry products for the consumer. Objective 4 work focused on alternative approaches to the use of in-feed antibiotics in poultry production. Natural plant products, called tannins, when added to poultry diets or incorporated into drinking water, enhanced both immune and metabolic responsiveness of young chickens. This resulted in increased resistance to infection/colonization by pathogenic microorganisms and increased performance in the tannin-fed birds. Work under Objective 4 showed that the addition of a microencapsulated blend of organic acids and botanicals to poultry feed enhanced the innate immune responsiveness of young chicks. Collectively, these results gave clear evidence that such non-conventional approaches to maintenance of chick health, in the absence of conventional antibiotics, will result in growing birds that are significantly more resistant to pathogen colonization. Overall, during the life of the project, major accomplishments were achieved that provide a much clearer perspective on how the innate poultry immune system functions to protect the birds from infection by pathogenic bacteria, and by bacteria that can contaminate poultry products reaching the consumer level. Highly productive relationships with industry partners were established and will lead to products and protocols that will be implemented in commercial production facilities. Project accomplishments will result in microbiologically safer poultry products, and enhanced consumer health.

1. New alternatives to antibiotics in poultry production. The colonization of commercial poultry by food poisoning microorganisms including, Clostridium, Salmonella, Campylobacter, and others, remains a serious problem. Historically, such pathogens were controlled by traditional antibiotics, which are at present greatly restricted given both microbial resistance, and consumer and regulatory pressure. New approaches are needed to assure ongoing poultry health, performance, and consumer safety. ARS researchers at College Station, Texas, working with university and industry collaborators, established that feeding chicks a diet supplemented with a blend of organic acids and botanicals resulted in significantly less pathological tissue damage in birds experimentally infected with Clostridium. In addition, the treated birds had improved performance over the control, untreated birds, and suffered significantly less adverse health issues. This accomplishment has identified a viable alternative to traditional antibiotics in assuring bird health, and in protecting them from harmful bacteria which can also result in human food poisoning.

Review Publications
Kogut, M.H. 2019. Understanding gut function in poultry: the role of commensals, metabolites, inflammation and dysbiosis in intestinal immune function and dysfunction. In: Ricke S. editor. Improving Gut Health in Poultry. Cambridge, United Kingdom: Burleigh Dodds Science Publishing Limited. p. 143-153.
Redweik, G.A., Kogut, M.H., Arsenault, R.J., Mellata, M. 2020. Oral treatment with ileal spores triggers immunometabolic shifts in chicken gut. Frontiers in Veterinary Science. 7: Article 629.
Zhao, D., Kogut, M.H., Genovese, K.J., Hsu, C., Lee, J., Farnell, Y.Z. 2020. Altered expression of lactate dehydrogenase and monocarboxylate transporter involved in lactate metabolism in broiler wooden breast. Poultry Science. 99(1):11-20.
Feye, K.M., Swaggerty, C.L., Kogut, M.H., Ricke, S.C., Piva, A., Grilli, E. 2020. The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota. BMC Microbiology. 20. Article 332.
Ogunrinu, O.J., Norman, K.N., Vinasco, J., Levent, G., Lawhon, S.D., Fajt, V.R., Volkova, V.V., Gaire , T., Poole, T.L., Genovese, K.J., Wittum, T.E., Scott, H.M. 2020. Can the use of older-generation beta-lactam antibiotics in livestock production over-select for beta-lactamases of greatest consequence for human medicine? An in vitro experimental model. PLoS ONE. 15(11). Article e0242195.
Johnson, C.N., Hashim, M.M., Bailey, C.A., Byrd II, J.A., Kogut, M.H., Arsenault, R.J. 2020. Feeding of yeast cell wall extracts during a necrotic enteritis challenge enhances cell growth/survival and immune signaling in the jejunum of broiler chickens. Poultry Science. 99(6):2655-2966.
Dal Pont, G.C., Farnell, M., Farnell, Y., Kogut, M.H. 2020. Dietary factors as triggers of low-grade chronic intestinal inflammation in poultry. Microorganisms. 8(1). Article 139.
Lee, A., Dal Pont, G., Farnell, M.B., Jarvis, S., Battaglia, M., Arsenault, R.J., Kogut, M.H. 2021. Supplementing chestnut tannins in the broiler diet mediate a metabolic phenotype of the ceca. Poultry Science. 100(1):47-54.
Beier, R.C., Byrd II, J.A., Andrews, K., Caldwell, D.Y., Crippen, T.L., Anderson, R.C., Nisbet, D.J. 2021. Disinfectant and antimicrobial susceptibility studies of the foodborne pathogen Campylobacter jejuni isolated from the litter of broiler chicken houses. Poultry Science. 100(2):1024-1033.