Location: Endemic Poultry Viral Diseases Research
Project Number: 6040-32000-080-003-A
Project Type: Cooperative Agreement
Start Date: Sep 22, 2025
End Date: Sep 21, 2028
Objective:
1. Investigate the mechanisms of pathogenicity of Eimeria field isolates that cause poultry coccidiosis and assess the bird responses to infections.
1A. Reproduce strains of major Eimeria species, sequence their genomes, and identify unique virulence genes associated with coccidiosis.
1B. Investigate the host responses to individual and mixed infections with Eimeria isolates.
1C. Determine the differential responses of the hosts as influenced by their genetic background and environmental conditions and its subsequent association with predisposition to secondary infections.
2. Identify and characterize the molecular mechanisms of Clostridium perfringens infections resulting in necrotic enteritis and develop effective vaccines.
2A. Isolate and propagate field strains of C. perfringens and sequence their genomes to identify genetic markers associated with clinical and subclinical necrotic enteritis.
2B. Interrogate the potential effects of the host genetic background on its responses to C. perfringens-induced enteritis.
2C. Identify molecular targets to be employed in vaccine development to mitigate necrotic enteritis.
3. Test and determine effective non-drug alternatives to antibiotics for the prevention and treatment of coccidiosis and necrotic enteritis.
3A. Determine the specific effects of probiotics, prebiotics, and postbiotics on the host microbiome and other associated immunological and physiological responses to infections by Eimeria sp. and C. perfringens.
3B. Identify the mechanistic actions of effective antibiotic alternatives in response to Eimeria- and C. perfringens induced enteritis in commercial birds.
Approach:
In Objective 1, the team will (1) propagate and harvest pure cultures of Eimeria isolates to obtain high quality DNA for generating full genome sequences of Eimeria parasites; (2) test the ability of divergent isolates to induce coccidiosis in commercial birds and measure the differential responses to individual and mixed infections; and (3) study the influence of host genetics on resistance, susceptibility, and tolerance to field Eimeria isolates, in combination with defined environmental conditions that influence the birds’ microbiome and intestinal integrity leading to pathological status and pre-disposition to secondary infections.
In Objective 2, the team will (1) employ next-generation sequencing to fully characterize the genomes of C. perfringens isolates (collected from field cases in the Southeast and mid-Atlantic regions) causing necrotic enteritis and comparatively analyze those sequences to identify virulence factors that contribute to the development of clinical and subclinical enteritis; this will allow a better understanding of the incidence of necrotic enteritis in the context of coccidiosis in commercial poultry; (2) test the effects of those isolates on the pathological and immunological responses of chickens with divergent genetic backgrounds, which could further delineate the differential responses in commercial chicken breeds to aid in identifying and using species genetics in commercial operations; (3) use the identified virulence factors as targets for designing and developing vaccines (based on already established nanoparticle platforms) as alternative measures to antibiotics for controlling enteritis.
For Objective 3, there is an impetus to find effective non-drug alternatives and the team will employ an integrated approach involving applied studies to better understand the mechanistic actions of several alternative candidates on performance, physiological, microbial, immunological, and metabolic responses of the host. In vivo (birds) and in ovo (late-stage embryos) trials will investigate the applications of well-defined probiotics, prebiotics, postbiotics, and phytogenics during coccidiosis and necrotic enteritis to characterize these critical physiological changes that directly impact bird health and performance. Specific measurable variables at the enteric and systemic levels will collectively provide strong host response correlates that can be utilized in translational studies to refine the applications of such effective alternatives in commercial settings.