Phylogenetic Analysis of the Most Common Chicken Coccidia, Eimeria acervulina , Isolated From Commercial Poultry Farms in Bangladesh

Achoimre

ABSTRACT Background Eimeria acervulina is the predominant species of coccidia infecting chickens worldwide, leading to significant production losses. The study explores molecular detection and phylogenetic relationships of E. acervulina in poultry farms of Bangladesh. Methods A total of 206 microscopically positive faecal samples were processed for PCR amplification. Oocysts were isolated using flotation techniques following microscopic examination. After recovering the genomic DNA, PCR amplification was performed using species‐specific primers focusing on the internal transcribed spacer‐1 (ITS‐1) region. A subset of 36 E. acervulina ‐positive samples was randomly sequenced and analysed for genetic diversity and phylogenetic relationships. Results A total of 198 (96.11%) E. acervulina samples with a specific 321‐bp amplicon were detected. Sequence analysis identified 15 distinct genotypes and seven single‐nucleotide substitutions, indicating intra‐species genetic variation. Nucleotide diversity (0.00717) and genotype diversity (0.911) suggested a genetically diverse population with closely related variants. The studied genotypes of E. acervulina formed a cluster with the previously identified reference sequence retrieved from GenBank with strong bootstrap support (98%). Similarly, other Eimeria species formed distinct clades independent of geographic origin. Among the studied sequences, two major clusters were observed, with no clear regional structuring. Conclusion This study provides the first molecular characterization of E. acervulina from commercial poultry farms in Bangladesh. The findings reveal measurable genetic diversity of E. acervulina circulating in Bangladesh, providing baseline data for epidemiological understanding and control strategies for avian coccidiosis.