Prevalence and phylogenetic analysis of avian pathogenic Escherichia coli strains from cases of colibacillosis infection in broiler chickens in different regions of Nineveh Governorate, Iraq

Background: The primary causative agent of colibacillosis in broiler chickens is avian pathogenic Escherichia coli (APEC), leading to serious health problems and substantial economic losses in broiler production. Aim: This study aimed to investigate the prevalence and genetic diversity of APEC in broiler farms in the Nineveh Governorate, Iraq. Methods: From June 2024 to December 2024, 391 swab samples were collected from 76 broiler chicken farms and subjected to bacteriological and molecular analyses. Four tissue swabs (heart, air sacs, liver, and peritoneum) werepooled into a single sample for each bird. Escherichia coli was isolated using CHROMagar™ E. coli and confirmed through biochemical tests and polymerase chain reaction amplification of the 16S rRNA gene. A phylogenetic tree was constructed using the 16S rRNA-F and 16S rRNA-R primers for 10 local strains, each selected from a different region of Nineveh Governorate to ensure geographic representation. These strains were compared with reference strains from various countries. Results: The results revealed a high overall APEC prevalence of 78.26%, with regional rates ranging from 70.0% to 85.52%, with the highest prevalence observed in Rabia and Al-Hamdaniya. The phylogenetic analysis revealed marked genetic heterogeneity among the local strains, indicating that they are not all derived from a single source. Interestingly, some isolates clustered closely with strains previously reported from Turkey and Iran. This genetic relatedness indicates that E. coli could be introduced or exchanged through cross-border trade, bird migration, or other regional interactions in broiler chickens, thereby influencing the local epidemiology of the disease. Other strains formed distinct clades, indicating local evolution. Conclusion: These findings highlight the endemic presence and diverse genetic background of avian pathogenic E. coli in broiler chicken farms in Nineveh, underscoring the urgent need for enhanced biosecurity, surveillance, and control strategies.