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United States Department of Agriculture

Agricultural Research Service

Research Project: Animal Intestinal Microbiomes, Foodborne Pathogens, and Antimicrobials Project Number: 5030-31320-003-00
Project Type: Appropriated

Start Date: Dec 16, 2010
End Date: Dec 15, 2015

Objective:
1) Identify and characterize intestinal ecological niches and their impact on foodborne pathogen survival, persistence, colonization, or virulence. In a broader systematic approach, evaluate the interactions among environmental influences (e.g., management, production) and ecological niches on phenotypic and genotypic characteristics and food safety. 2) Evaluate the effects of antimicrobials on intestinal microbiomes, and on the expression and transmission of virulence, fitness, and antimicrobial resistance genes in culture and the host. Evaluate the effects of antimicrobial alternatives (dietary fermentation products) on swine intestinal health, enteric microbiomes, and foodborne pathogens such as Salmonella, under normal and heat stress conditions. 3) Develop a functional metagenomic approach to identify gene products that inhibit foodborne pathogen growth, interfere with virulence gene expressions, or reduce antimicrobial resistance (and enhance food safety). Develop and evaluate alternatives to antibiotics, emphasizing immunological /vaccine strategies, for impacting the host immunome and reducing the risk of Salmonella transmission to humans. 4) Assess role of commensal intestinal bacteria in evolution, persistence, or transmission of resistance genes. Evaluate novel strategies for reducing antimicrobial resistant organisms and resistance genes. 5) Evaluate the effects of environmental influences (e.g., management, production), ecological niches and vaccine strategies on phenotypic and genotypic characteristics of Campylobacter (specifically in turkeys).

Approach:
Research to control Campylobacter in turkeys will be pursued by subfractionating, identifying and characterizing microbial species in turkey ceca which are potential Campylobacter antagonists. Cecal populations will be subfractionated in vivo by antibiotic applications and dexamethasone induced stress. Potentially useful species will initially be associated with Campylobacter reductions in vivo and confirmed in vitro by using co-cultures. Two other approaches for controlling Campylobacter will be tested: dietary additives (prebiotics and probiotics) and a prime-boost vaccination strategy using Campylobacter. jejuni surface membrane protein CjaA expressed in a recombinant strain of attenuated Salmonella. The commensal anaerobe Megasphaera elsdenii (M. elsdenii) will be used as an archetype intestinal bacterium to identify common antibiotic resistance genes and transfer mechanisms in the intestinal tract and to test M. elsdenii as a site for tetracycline resistance gene evolution in that ecosystem. In a probiotic type attempt, a mix of five antibiotic sensitive M. elsdenii strains will be used to block the transmission of antibiotic resistant strains from mother sow to offspring pigs. Various technologies will be used to assess the effects of alternatives to antibiotics (e.g. fermentation products) on swine performance and intestinal health. Technologies include intestinal microbiome analyses by QPCR-, phylotype census-, culture-based methods; metagenomic analyses of animal host gene expression (esp. immunome); and traditional immunological techniques. A variable heat stress model for swine will be developed and used to test diurnal heat cycle impacts on animal health and on colonization/shedding of foodborne pathogens such as Salmonella, as well as amelioration of the impacts by antibiotic alternatives. Immunotherapeutic measures (vaccine) will be examined for their impact on the swine immunome and Salmonella shedding. Other areas of research will include the influence of subinhibitory antibiotics on the production of Salmonella bacteriophages carrying fitness or virulence genes and on phage mediated gene transfer between Salmonella strains (transduction). These studies will be carried out with Salmonella Typhimurium strains in culture and in a mouse model. Functional metagenomics assays involving recombinant Escherichia coli and Salmonella strains containing reporter plasmids will be used to identify gene products which either affect Salmonella virulence or are inhibitory for Salmonella growth.

Last Modified: 11/24/2014
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