Coccidiosis, caused by Eimeria(E.) tenella, poses a significant threat to poultry farming. This study aimed to determine the prevalence, molecular characterization and to assess the epidemiological factors associated with E. tenella infection in backyard chickens in District Bannu, Khyber Pakhtunkhwa, Pakistan. Over six months (April to September 2022), faecal samples from 160 chickens of various breeds were microscopically screened for E. tenella oocysts, followed by DNA extraction and ITS-1 marker-based molecular analysis. Phylogenetic analysis compared the obtained sequences with global Eimeria isolates. The overall prevalence of E. tenella infection was 34.37%, varying across tehsils, with the highest in Bannu tehsil (40%), which was statistically non-significant (P>0.05). Age-related susceptibility was evident, with grower chickens exhibiting the highest prevalence (41.17%), which was statistically significant (P<0.05). Females showed a higher prevalence (36.57%) than males (23.08%), with non-significant association (P>0.05). Housing types revealed varying prevalence: cages (21.05%), night shelters (29.87%), and free-range chickens (43.75%), with no statistically significant difference (P>0.05). Feed types also influenced prevalence, with commercial (11.11%), natural/household (40.54%), and mixed feeds (22.50%) with a statistically significant difference (P<0.05). The highest prevalence at 44 and 42.86%, respectively, was observed in August and September, aligning with increased humidity, with no significant association (P>0.05). Single nucleotide polymorphisms (SNPs) in the ITS-1 region of E. tenella showed significant variations across samples, with distinct nucleotide substitutions at positions 108, 111, 123, 134, and 313. Phylogenetic analysis of 27 isolates, including 15 from this study, revealed a distinct cluster closely related to E. tenella from multiple countries. The tree also identified four separate clusters for E. mitis, E. maxima, E. acervulina, and E. brunetti, each grouping isolates from diverse geographic regions. This study provides novel insights into the prevalence of E. tenella in backyard chickens which may be helpful to have targeted control strategies for poultry farming.

To Cite This Article: Khan FU, Badshah F, Belkahia H, Hussain M, Akbar N, Zigo F, Lacková Z, Khan MS, Naz W, Ben Said M and Khan SN 2025. Molecular prevalence and genetic characterization of Eimeria tenella in backyard chickens. Pak Vet J. http://dx.doi.org/10.29261/pakvetj/2025.225