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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

2019 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
Work under the project during FY 2019 concentrated on establishing the effects of gut microbial metabolites (postbiotics) on reducing foodborne bacterial colonization. Following the restriction of in-feed antibiotics, the search for antibiotic alternatives has become critically important. Postbiotics are non-viable bacterial products or metabolic byproducts from probiotic microorganisms that have positive effects on the host or microbiota. These are a promising alternative to antibiotics. Work by project scientists described a mechanism of action of a postbiotic in the context of a Clostridium perfringens challenge model (Objective 4). The postbiotic improved weight gain, lesion scores, Clostridium perfringens counts, and mortality compared to challenge groups. The postbiotic was shown to predominantly affect the innate immune response and appears to be immunomodulatory (Objective 1). In the context of infection, it reduces the proinflammatory responses and generates a homeostatic-like response. This postbiotic is a viable alternative to antibiotics to improve poultry health in the context of Clostridium perfringens pathogen challenge.

1. Differential host peptide response to Salmonella infection. In a different approach evaluating Salmonella persistence, ARS scientists at College Station, Texas, in collaboration with scientists at the University of Delaware, used an immune peptide array to show that the host kinome profile (protein phosphorylation patterns) in broilers with a high burden of S. Enteritidis is distinct from that of broilers with lower levels of colonization. As expected, the birds with lower loads of S. Enteritidis, meaning the host's immune response had minimized bacterial colonization, showed increased activity in key signaling pathways associated with a number of immune cell types (chemokine, Jak-Stat, MAPK, and T-cell) receptor signaling. These findings provide the groundwork for more in-depth studies into specific biomarkers to select individual birds that are more resistant to S. Enteritidis colonization. Collectively, these studies have laid a solid foundation for future experiments to determine practical approaches to reduce the incidence of foodborne illnesses associated with poultry-acquired Salmonella.

2. Correlations between microbiotic bacterial and immune cell (cytokine) gene expression. To better understand the ecology of the poultry gastrointestinal (GI) environment (microbiome) and its interactions with the host, ARS scientists at College Station, Texas, in collaboration with scientists at the College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, compared GI bacterial communities over time and measured the expression of key immune cells (cytokines IL18, IL1ß, and IL6, IL10, and TGF-ß4). At a young age (1-week) versus older (6-weeks), chickens showed significant differences in concentrations of varius bacteria, and where they were mainly detected in the GI tract. Cytokine expression was correlated in different ways (positive or negative) with the changes in bacterial presence. These are the first studies done in poultry which demonstrate that specific bacteria within the poultry gut are directly associated with immune regulation and will form the basis for future studies on developing immune-specific probiotics.

Review Publications
Broom, L.J., Kogut, M.H. 2018. The role of the gut microbiome in shaping the immune system of chickens. Veterinary Immunology and Immunopathology. 204:44-51.
Swaggerty, C.L., Genovese, K.J., He, L.H., Byrd II, J.A., Kogut, M.H. 2018. Mechanisms of persistence, survival, and transmission of bacterial foodborne pathogens in production animals. Lausanne: Frontiers Media. 130 p.
He, L.H., Genovese, K.J., Swaggerty, C.L., Nisbet, D.J., Kogut, M.H. 2018. Mitogen-activated protein kinase p38, not ERK1/2 and JNK, regulates nitric oxide response to Salmonella Heidelberg infection in chicken macrophage HD11 cells. International Journal of Bacteriology & Parasitology. 2018(2):1-5. doi: 10.29011/IJBP-107.000007.
Bearson, S.M., Bearson, B.L., Sylte, M.J., Looft, T.P., Kogut, M.H., Cai, G. 2019. Cross-protective Salmonella vaccine reduces cecal and splenic colonization of multidrug-resistant Salmonella enterica serovar Heidelberg. Vaccine. 37(10):1255-1259.
Swaggerty, C.L., Callaway, T.R., Kogut, M.H., Piva, A., Grilli, E. 2019. Modulation of the immune response to improve health and reduce foodborne pathogens in poultry. Microorganisms. 7(3):65.
Sohail, M.U., Hume, M.E. 2019. Evaluation of antimicrobial action of chitosan and acetic acid on broiler cecal bacterial profiles in anaerobic cultures inoculated with Salmonella Typhimurium. Journal of Applied Poultry Research. 28(1):176-183.
He, L.H., Arsenault, R.J., Genovese, K.J., Swaggerty, C.L., Johnson, C., Nisbet, D.J., Kogut, M.H. 2019. Inhibition of calmodulin increases intracellular survival of Salmonella in chicken macrophage cells. Veterinary Microbiology. 232:156-161.
Kogut, M.H. 2019. The effect of microbiome modulation on the intestinal health of poultry. Animal Feed Science And Technology. 250:32-40.
Betancourt, L., Hume, M.E., Rodríguez, F., Nisbet, D.J., Sohail, M.U., Afanador-Tellez, G. 2019. Effects of Colombian oregano essential oil (Lippia origanoides Kunth) and Eimeria species on broiler production and cecal microbiota. Poultry Science.
Hernández-Coronado, A.C., Silva-Vázquez, R., Rangel Nava, Z.E., Hernández-Martínez, C.A., Kawas-Garza, J.R., Hume, M.E., Méndez-Zamora, G. 2019. Mexican oregano essential oils given in drinking water on performance, carcass traits, and meat quality of broilers. Poultry Science. 98(7):3050-3058.