Molecular Investigation of Eimeria spp. Infection in Weaned Dairy Calves in Thessaly, Greece, and Associated Risk Factors

This study presents the first molecular investigation into the prevalence and risk factors of <i>Eimeria</i> spp. infection among weaned dairy calves in Thessaly, Greece. Utilizing a cross-sectional design, 665 fecal samples were collected from 35 intensive dairy cattle farms and analyzed via genus-specific PCR and species-specific multiplex PCR targeting the internal transcribed spacer 1 (ITS-1) region. The overall molecular prevalence was found to be 46.3%, with <i>Eimeria bovis</i> (24.7%) and <i>Eimeria zuernii</i> (14.0%) emerging as the most prevalent species. Mixed infections were common, occurring in 51.0% of the positive cases. Multivariable analysis revealed that dairy calves aged less than 60 days had 2.15 times higher odds of infection compared to older calves. Environmental factors also significantly influenced infection rates, specifically ground flooring, the use of immovable/concrete water troughs and infrequent cleaning of floors, feeders and water troughs. These results highlight the high burden of pathogenic <i>Eimeria</i> in dairy cattle herds of Thessaly, Greece, and underscore the importance of integrating rigorous hygiene protocols with age-targeted management to control bovine coccidiosis.