Limits of detection and feasibility of DNA-based detection of Salmonella in poultry production

1. Establish limits of detection (LoD) for key pathogens in chicken feed and caeca using different metagenomics approaches and polymerase chain reaction (PCR)-based culture-independent diagnostic tests (CIDTs). 2. Provide proof-of-principle for DNA-based detection of pathogens in chicken feed and caeca. 3. Evaluate the use of microbial community diversity and composition as an indicator of flock health, and to identify potential microbial hazards. 4. Develop guidance for the appropriate use of metagenomics and CIDTs in hazard monitoring in primary food production.