GENOMIC ANALYSIS OF EIMERIA POPULTATIONS IN RELATION TO PERFORMANCE LEVELS OF BROILDER CHICKEN FARMS IN ARKANSAS AND NORTH CAROLINA, U.S.A.

Authors: Schwarz, Ryan; KLOPP, S - TOWNSEND POULTRY, DE; Miska, Kate; Jenkins, Mark

Submitted to: Journal of Parasitology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2009
Publication Date: 8/1/2009
Citation: Schwarz, R.S., Klopp, S., Miska, K.B., Jenkins, M.C. 2009. Genomic analysis of Eimeria spp. populations in relation to performance levels of broiler chicken farms in Arkansas and North Carolina. U.S.A. Journal of Parasitology. 95:871-880.

Interpretive Summary: Avian coccidiosis is a common disease of chickens that can be caused by at least seven species of parasites within the genus Eimeria (Apicomplexa: Eimeriidae). Eimeria are single-celled parasites that infect cells lining the digestive tract. During their development these parasites destroy the cells along the gut wall, resulting in disease that causes the chickens to have diarrhea and malnourishment resulting in minor to severe weight loss. It is thought that the severity of this disease depends upon the species of Eimeria that infect the chicken. Recent reports suggest severity of disease may also be associated with the particular combination of species that infect the chicken. Strains of certain Eimeria species have also been documented and may affect severity of disease, although these strains remain to be genetically characterized and their impact on disease severity remains to be tested. To collect data on the species and strains of chicken Eimeria in correlation with their impact on severity of disease we used a large scale sampling approach from chicken farms in Arkansas (AR) and North Carolina (NC). Since coccidiosis disease causes weight loss, a common measure of disease severity, and thus performance level, is to weigh the birds at poultry facilities. In this way, we identified multiple facilities that were categorized as high vs. low performance. Eimeria were collected from these facilities and DNA was extracted and pooled according to each performance category and state. We used primers to amplify a specific region of their DNA that is unique to each species, thus determining the composition of Eimeria species present at each facility. All but one of the seven species was identified and each facility was infected by a diffent combination of species. To assess genetic diversity, we used primers to amplify 3 additional regions of the Eimeria genome, which we then cloned and sequenced to identify each nucleotide within these regions. Analyses of these data identified distinct genetic variants from several species of Eimeria. Two of these genetic variants were uniquely associated with low performance farms. In addition, we identified distinct groups of sequences that were not part of any of the seven recognized species and are thought to be from a putative 8th species, whose validity has remained elusive over the past several decades.

Technical Abstract: The impact of coccidiosis outbreaks on the productivity of broiler chicken farms can be substantial, depending on the severity of disease caused by the particular species and strain of Eimeria. Polymorphism in the strains of Eimeria species infecting chickens may confer variation in the pathogenicity of coccidiosis. Four groups of broiler chicken farms in Arkansas and North Carolina, U.S.A. classified as having either high (AR = 7, NC = 8) or low (AR = 7, NC = 8) performance levels were sampled for Eimeria oocysts. gDNA from oocysts was amplified using genus-specific DNA primers targeting 2 nuclear genome regions (18s ribosomal DNA and the first and second internal transcribed spacer regions) and 1 mitochondrial genome region (cytochrome c oxidase subunit I) along with established species-specific primers. The Eimeria species identified revealed a different composition at each of the 4 facility groups. Phylogenetic analyses of sequences from the 3 genomic loci revealed multiple E. maxima and E. mitis genetic variants. Two E. maxima sequence variants were unique to low performance farms. In addition, distinct populations of both 18S and COI sequences amplified from oocysts at the NC high performance facilites were identitifed as E. mivati based on homology searches of GenBank. These findings report multiple genetic variants of Eimeria in association with the performance of poultry facilities from which they were isolated and demonstrate the utility of analyzing multiple genomic loci to assess composition and polymorphisms in Eimeria populations.