Genomic and Proteomic Approaches for the Characterization of Foodborne Pathogens in Poultry

Objective 1: Employ molecular methods to characterize and scientifically guide the development of intervention and mitigation strategies for Campylobacter (C.) spp. during poultry production and processing. Sub-Objective 1a: Continue Whole Genome Sequence (WGS) comparisons of 50 genetically distinct C. jejuni isolates that vary in their ability to colonize broiler chickens. Sub-Objective 1b: Evaluate and refine an atmospheric cold plasma based antimicrobial packaging system (ACP) using genetically diverse C. jejuni isolates, and subsequently perform proteomic analyses to determine the mechanisms associated with die-off. Objective 2: Survey local, pastured-raised, multi-commodity, antimicrobial growth promoter (AGP)-free poultry farms for the presence and variability of common food-borne pathogens as well as to establish changes in the microbial ecology along the “local” farm to fork continuum. Sub-Objective 2a: Employ microbiological methods for the recovery of Campylobacter spp. from broiler feces during production, environmental samples, and processing samples. Sub-Objective 2b: Perform microbiome analyses on samples to establish changes in the microbial ecology along the “local” farm to fork continuum. Objective 3: Develop, refine and implement improved methods for the detection and recovery of Campylobacter spp. and other potentially emerging foodborne pathogens, so that the methods meet the needs of associated regulatory agencies. Sub-Objective 3a: Continue collaboration with Pathsensors Inc. for the development of a rapid and specific antibody biosensor for the detection of Campylobacter spp. from environmental samples. Sub-Objective 3b: Compare traditional selective media/recovery technologies and a non-selective/filtration (Campycheck) methodology, with various molecular methods (PCR, real-time PCR, and high throughput sequencing), for the detection of Campylobacter spp. from poultry samples (embryonic broiler GI tracts, yolk, broilers raised without antibiotics, processed broilers, retail product) and poultry-associated environmental samples (soil, poultry litter, processing water, retention pond water, stream water, standing water, other agricultural animals, wild birds) on small, multi-commodity, antimicrobial growth promoter (AGP)-free farms.