Genotypic Characterization of Fungal Species Isolated From Broiler Breeder Chickens, Dead-In-Shell and Hatched Chicks

To investigate the prevalence of fungal agents in local Egyptian broiler breeder chicken’s premises, tracheal and cloacal swabs from chickens, feed, and water samples were collected. The targeted breed's dead-in-shell eggs and newly hatched chick’s samples were also tested. All fungal isolates were morphologically typed and the predominant fungal species were further subjected to molecular typing using PCR-RFLP and gene sequence analysis of the β-tubulin gene. Results revealed a high prevalence of fungal isolates in tracheal and cloacal swabs (39.3 - 48.1%) and feed and water samples (37.5% and 28.6%, respectively). Fungal isolation rates in dead-in-shell eggs of all breeds were high except in Dahaby breed. Aspergillus species including A. niger, A. flavus, and A. terreus were the predominantly isolated fungi from all collected samples. The ß-Tubulin genes PCR-RFLP of selected Aspergillus isolates showed a characteristic restriction pattern for each species; however, the method was unable to distinguish between strains. The β-tubulin gene phylogenetic and sequence analysis of selected A. flavus, and A. terreus from breeder chickens and their hatching chicks indicated their relatedness to isolates from bronchopulmonary Aspergillosis in humans in the Middle East. In conclusion, the Aspergillus species remains the most prevalent fungi in breeder chickens, their incubated eggs and hatched chicks indicating their widespread in hatcheries. The PCR-RFLP is an easy tool to discriminate between Aspergilli species, however, the β-tubulin sequence analysis more descriptive of potential sources of fungal contamination. Further epidemiological studies are needed to monitor avian and human Aspergilli in poultry houses with a special focus on antifungal drug-resistant strains.