GENOMIC AND EPIDEMIOLOGICAL PARAMETERS TO INFORM INTERVENTIONS STRATEGIES FOR ENTERIC DISEASES OF POULTRY

1. Determine the molecular mechanisms of virulence within and across Eimeria strains affecting poultry and investigate the genetic and phenotypic responses by the bird. 1A. Isolate, sequence and propagate strains of E. acervulina, E. maxima, and E. tenella to identify genotypes/virulence genes associated with infection. 1B. Investigate the molecular mechanisms of virulence associated with co-infection of Eimeria species. 1C. Investigate the effect(s) of host genotypes and environmental interaction that predispose birds to infection with different Eimeria species. 2. Determine the molecular mechanisms of virulence to Clostridium perfringens-based enteritis to inform the development of a safe and effective vaccine. 2A. Sequencing virulent field strains of C. perfringens and identify genotypes/virulent genes associated with gut damage, mortality, and poor performance. 2B. Investigate host genotype and environmental interaction that predispose young birds to C. perfringens-induced enteritis. 2C. Identify and develop vaccine targets and resulting immunological responses to C. perfringens-induced enteritis. 3. Develop alternatives to antibiotics for preventing or treating Eimeria- and C. perfringens-based enteritis. 3A. Investigate the longitudinal impact of site of digestion on microbiota, and host physiological response to Eimeria- and C. perfringens-induced enteritis in commercial birds. 3B. Investigate the mechanistic actions of probiotics and prebiotics as antibiotic alternatives for Eimeria- and C. perfringens-induced enteritis in commercial birds. 3C. Investigate the modes of action of dietary amino acids and nutrients on gut development/integrity, and host physiological response to Eimeria- and C. perfringens-induced enteritis.