Prevalence and molecular characterization of Eimeria species infecting broiler and layer chickens in Morogoro Municipality, Tanzania

Abstract Coccidiosis destroys intestinal tract epithelial cells, leading to anorexia and reduced feed intake, maldigestion, malabsorption, dehydration, blood loss, and anaemia, causing great economic losses in the poultry industry. In chickens, seven species of protozoan parasite Eimeria are known to cause coccidiosis: E. tenella, E. acervulina, E. maxima, E. necatrix, E. brunetti, E. praecox , and E. mitis. The disease remains understudied in Tanzania, with limited epidemiological data hindering effective prevention and control strategies. This study investigated the prevalence of coccidial infection in broiler and layer chickens from Morogoro Municipality, Tanzania using molecular methods. Pooled faecal samples collected from 50 broiler farms and 50 layer farms were screened for unsporulated oocysts using the flotation technique. For species determination, deoxyribonucleic acid (DNA) was extracted from fresh faecal samples and amplified by polymerase chain reaction targeting the internal transcribed spacer 1 (ITS-1) region, followed by sequencing and GenBank homology analysis. Among the collected samples, 31% tested positive for unsporulated Eimeria oocysts, representing all seven Eimeria species. E. tenella and E. acervulina were the most prevalent, detected in 74% and 64% of positive samples, respectively. These species yielded amplifiable ITS-1 sequences, showing 94%–98% homology with reference sequences from other countries. We conclude that coccidiosis is highly prevalent in both broiler (35.5%) and layer (64.5%) chickens in Morogoro, Tanzania, and that mixed infections are common. Our findings support further studies on chicken coccidiosis to facilitate strategic planning and implementation of effective disease prevention and control measures.