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

2020 Annual Report

Objectives
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.

Approach
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
Work under this project in fiscal year (FY) 2020 developed important new information on how the immune system of poultry can be exploited/manipulated to enhance the microbiological safety of poultry meat products reaching the consumer. Work under Objective 1 focused on the key innate immune pathways associated with the mucosal lining of the gut of poultry and on defining factors associated with resistance to colonization by Salmonella. Under Objective 3, biological indicators known as biomarkers were used in work focused on development of a gut inflammation model that 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. Work thus far has identified specific immune biomarkers that are associated with gut inflammation. The work will ultimately facilitate the commitment by industry to produce poultry that have a more healthy gut, that are less susceptible to colonization by foodborne pathogens including Salmonella and Campylobacter, and that therefore will result in microbiologically safer poultry products. Under Objective 4, work focused on evaluation of alternative approaches to the use of in-feed antibiotics in poultry production. The work established that tannins, natural plant products, when added to poultry diets or incorporated into drinking water, enhanced both immune and metabolic responsiveness of young chickens, which is predicted to result in increased resistance to infection/colonization by pathogenic microorganisms. Work under Objective 4 also 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. Work by this project in FY2020, overall, developed important new information and approaches that will be adapted by industry to produce poultry products that are wholesome and less likely to contain harmful microorganisms.

Accomplishments
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 currently greatly restricted given microbial resistance, and consumer pressure. New approaches are needed to assure ongoing poultry health and performance. 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 that can also result in human food poisoning.

2. Prevention of wooden breast syndrome in poultry. The syndrome known as wooden breast is a relatively new problem affecting poultry production. It is evidenced by highly fibrous breast muscle that greatly impacts carcass quality. The cause of the syndrome is not fully known, but is likely multifactorial, and is generally considered to result from poor gut health. New approaches are needed to minimize or prevent the problem. ARS researchers at College Station, Texas, working closely with interested industry partners, established that nutrient rich diets contributed to the development of gut inflammation and resulting woody breast. Sodium butyrate, a naturally occurring short chain fatty acid, when consumed by poultry, resulted in a significant improvement in the gut health of birds, which is projected to significantly lessen woody breast. This research is important in directing future research efforts to find practical protocols for solution of the woody breast problem in commercial poultry.

3. Tungsten for Salmonella control in poultry. Salmonella remains the leading bacterial cause of foodborne illness and is a significant contributor to food poisoning associated with consumption of poultry meat products. It has been established that gastrointestinal tract inflammation contributes significantly to Salmonella colonization in birds. ARS researchers at College Station, Texas, established that metallic tungsten, administered in the diet to commercial poultry, significantly reduced gut inflammation in an experimental chicken model, and also reduced the Salmonella load carried by the birds. This accomplishment has identified a new approach for management of Salmonella in poultry. It will guide future research aimed at developing novel approaches and protocols to both assure poultry health and performance in commercial production, and lessen the occurrence of Salmonella colonization and the resulting risk to consumers.

Review Publications
Feye, K.M., Dittoe, D.K., Shi, Z., Woitte, J.L., Owens, C.M., Kogut, M.H., Ricke, S.C. 2019. The reduction of pathogen load on Ross 708 broilers when using different sources of commercial peracetic acid sanitizers in a pilot processing plant. Microorganisms. 7(11):503. https://doi.org/10.3390/microorganisms7110503.
Beier, R.C., Byrd II, J.A., Caldwell, D.Y., Andrews, K., Crippen, T.L., Anderson, R.C., Nisbet, D.J. 2019. Inhibition and interactions of Campylobacter jejuni from broiler chicken houses with organic acids. Microorganisms. 7(8):1-18. https://doi.org/10.3390/microorganisms7080223.
Crippen, T.L., Sheffield, C.L., Singh, B., Byrd, J.A., Beier, R.C. 2019. How management practices within a poultry house during successive flock rotations change the structure of the soil microbiome. Frontiers in Microbiology. 10:2100. https://doi.org/10.3389/fmicb.2019.02100.
Yang, Y., Feye, K.M., Shi, Z., Pavlidis, H.O., Kogut, M.H., Ashworth, A.J., Ricke, S. 2019. A historical review on antibiotic resistance of foodborne Campylobacter. Frontiers in Microbiology. 10:1-8. https://doi.org/10.3389/fmicb.2019.01509.
Shi, Z., Dittoe, D.K., Feye, K.M., Kogut, M.H., Ricke, S.C. 2019. Short communication: Preliminary differences identified in genes responsible for biofilm formation in poultry isolates of Salmonella enterica Heidelberg, Enteritidis, and Kentucky. Microorganisms. 7(7):1-11. https://doi.org/10.3390/microorganisms7070196.
Johnson, C.N., Kogut, M.H., Genovese, K.J., He, L.H., Kazemi, S., Arsenault, R.J. 2019. Administration of a postbiotic causes immunomodulatory responses in broiler gut and reduces disease pathogenesis following challenge. Microorganisms. 7(8):1-19. https://doi.org/10.3390/microorganisms7080268.
Sanchez-Zamora, N., Silva-Vázquez, R., Rangel-Nava, Z.E., Hernandez-Martinez, C.A., Kawas-Garza, J.R., Hume, M.E., Herrera-Balandrano, D.D., Mendez-Zamora, G. 2019. Agave inulin and oregano oil improve the broiler performance. Ecosistemas y Recursos Agropecuarios. 6(18):523-534. https://doi.org/10.19136/era.a6n18.2197.
Cázares-Gallegos, R., Silva-Vazquez, R., Hernandez-Martinez, C.A., Gutierrez-Soto, J.G., Kawas-Garza, J.R., Hume, M.E., Mendez-Zamora, G. 2019. Performance, carcass variables, and meat quality of broilers supplemented with dietary Mexican oregano oil. Brazilian Journal of Poultry Science. 21(1):1-10. https://doi.org/10.1590/1806-9061-2018-0801.
Kogut, M.H., Santin, E. 2019. Advances in vaccines for controlling foodborne Salmonella spp. in poultry. In: Venkitanarayanan K., Thakur S., Ricke S., editors. Food Safety in Poultry Meat Production. Cham, Switzerland: Springer Nature Switzerland. p. 161-189.
Lu, Y., Wen, Y., Hu, G., Liu, Y., Beier, R.C., Hou, X. 2019. Genomic sequence analysis of the multidrug-resistance region of avian Salmonella enterica serovar Indiana strain MHYL. Microorganisms. 7(8):1-10. https://doi.org/10.3390/microorganisms7080248.
Swaggerty, C.L., He, L.H., Genovese, K.J., Callaway, T.R., Kogut, M.H., Piva, A., Grilli, E. 2020. A microencapsulated feed additive containing organic acids, thymol, and vanillin increases in vitro functional activity of peripheral blood leukocytes from broiler chicks. Poultry Science. 99(7):3428-3436. https://doi.org/10.1016/j.psj.2020.03.031.
Swaggerty, C.L., Arsenault, R.J., Johnson, C., Piva, A., Grilli, E. 2020. Dietary supplementation with a microencapsulated blend of organic acids and botanicals alters the kinome in the ileum and jejunum of Gallus gallus. PLoS One. 15(7):e0236950. https://doi.org/10.1371/journal.pone.0236950.