Regarding high morbidity, mortality, and production losses, fungi infections have their importance among infectious illnesses and seem to be one of the main challenges facing poultry producers. This study aims to identify the genotypic characteristics of some fungi isolated from poultry. To reach this end, in El-Gharbia Governorate, Egypt, a total of 210 birds with a history of respiratory distress were randomly selected from a variety of private farms and hatcheries. The birds were sacrificed; tissue pieces were collected. In addition, a total of 87 samples of the poultry surroundings including 40 samples of poultry ration, 14 bedding materials, 4 air samples, and 29 water samples were collected. Using traditional fungal isolation, four fungal species were recovered, namely, Aspergillus niger, Aspergillus flavus, Cladosporium perangustum, and Penicillium chrysogenum. PCR was performed by fungus-specific universal primer pairs (ITS1 and ITS4) to identify and describe the genotype of isolated fungi. All examined isolates' ITS1-5.8SrDNA regions could be amplified. A purified PCR product was sequenced according to the Emerald Amp GT PCR master mix. This was initially performed to establish sequence identity to GenBank accession numbers. The rRNA gene for 5.8 sRNA divides the two ITS sections, which are situated between the 18S and 28S rRNA genes. ITS-1 gene sequence of the isolated Cladosporium perangustum (GeneBank accession number was OM 407392). The Sequence of the ITS-1 of isolated Penicillium chrysogenum (GeneBank accession numbers for studied nucleotide sequences were OM407401; OM407402; OM403685, and OM403686). For the examined nucleotide sequences, the GeneBank accession number for the ITS-1 internal transcribed spacer region of single Aspergillus niger was OM407391. GeneBank accession numbers for the isolated Aspergillus flavus ITS-1 sequence examined nucleotide sequences were OM403676, OM403677, and OM403678. In conclusion, genotypic characterization confirmed the phenotypic traditional fungal identification in the present study.  Aspergillus species are the major fungi associated with birds in Egypt farms. The predominantly identified species were Aspergillus flavus and Penicillium chrysogenum.

Poultry production is affected by several fungal diseases. Such fungal infection occurs in poultry farms via using a moldy litter, or ingestion of contaminated drinking water or moldy ration. In this study, a total of 210 birds with a history of respiratory distress of different breeds were collected randomly from sporadic different private farms and hatcheries in El–Gharbia Governorate, Egypt. The birds were sacrificed, then a total of 1050 tissue specimens from lung, air sacs, liver, crop and trachea were collected. In addition, 40 samples of poultry ration, 14 bedding materials, 4 air samples and 29 water samples were also collected. The collected samples were cultured on Sabouraud’s agar plates. Macromorphological and micromorphological fungal examinations were performed for phenotypic characterization. Histopathological examinations were also performed using with hematoxylin and eosin stains. Antifungal sensitivity testing was screened using Mueller’s Hinton Agar for studying the susceptibility of the recovered fungal isolates to the most commonly used antifungal drugs in Egypt, namely amphotericin B, clotrimazole, fluconazole, itraconazole, ketoconazole, and nystatin. The obtained results demonstrated that mold isolation was the highest in the collected samples from birds at 36.84%, followed by drinking water (31.57%). The highest incidence of mold isolation was recorded at the lungs of broilers and baladi birds followed by the air sacs. While in saso birds, the highest incidence was at the air sac. Collectively, 97 mold strains were identified from the lung, 74 from the air sacs, 30 from the liver, 61 from the trachea, and 44 from the crop. In addition, 19 mold isolates were recovered from the bird surroundings. Aspergillus niger as well as Penicillium chrysogenum were recovered and showed resistance to ketoconazole, while Cladosporium perangustum was resistant to fluconazole. All of the isolated molds were sensitive to itraconazole and nystatin except A. flavus that was resistant to nystatin. All Aspergillus spp. were resistant to fluconazole except A. niger. In conclusion, Aspergillus spp. was the most associated mold with poultry species and their surroundings in Egypt farms. Itraconazole and nystatin could be applied as proper antifungal drugs the control of for Aspergillus infection in birds.