Detection and molecular characterization of the species and genetic variants of Eimeria spp. in extensive, semi-intensive and intensive broiler and layer chicken farms from the west of the state of Santa Catarina and northwest of the state of São Paulo

Abstract

Coccidiosis, a disease caused by protozoa of the genus Eimeria, is one of the most economically important diseases for the poultry industry. Seven species of Eimeria infect the domestic fowl (E. acervulina, E. praecox, E. mitis, E. maxima, E. necatrix, E. brunetti, and E. tenella). In addition, three genetic variants, named operational taxonomic units (OTUs x, y and z) were recently detected in several countries. These variants may represent new species of Eimeria and are antigenically distinct from the seven already classified species. Eimeria infection has a high prevalence in industrial poultry farming, and it is unlikely that a flock of intensively reared birds will not show infection by at least one species of Eimeria. There are few studies related to the epidemiology of eimeriosis in industrially produced birds in Brazil, and no study carried out in the national territory has investigated the presence of genetic variants. Therefore, this study aims to determine the prevalence of infection by Eimeria spp., operational taxonomic OTUs x, y, and z, and new genetic variants of Eimeria in broiler and laying birds from extensive, semi-intensive and extensive farms in the western region of the state of Santa Catarina and northwest region of the state of São Paulo, and to perform genotypic diversity analyses of Eimeria spp. Two studies will be performed: in the first study, genera-specific PCR (gene ITS-1) will be accomplished to detect Eimeria spp. positive samples, which will be further examined by a genera-specific nested-PCR followed by next generation genetic sequencing for identification of Eimeria species and genetic variants in samples originated from broiler and laying birds from extensive, intensive, and semi-intensive farms in the state of São Paulo. In the second experiment, fecal samples will be collected from commercial broiler farms in the western region of the state of Santa Catarina and in the northwest region of the state of São Paulo. The samples will be subjected to purification and concentration of oocysts by centrifugal flotation in Sheather solution. The sediments resulting from the purification will be submitted to screening for Eimeria spp. oocysts by microscopy. All sediments will be submitted to genomic DNA extraction and samples negative by microscopy will be submitted to genus-specific PCR (ITS1 gene). All samples positive by microscopy or by genus-specific PCR will be submitted to a genera-specific nested-PCR followed by next generation genetic sequencing for identification of Eimeria species and genetic variants. Data will be tabulated and analyzed to determine the prevalence considering the 95% confidence interval and the genotypic diversity of Eimeria species. (AU)