الفهرس 
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Abstract
Poultry accounts for nearly one-third of global meat production. Therefore, a main objective of the existing poultry industry applications is to minimize the incidence of infectious diseases. Despite the potential severity of poultry diseases, including fungi, few studies have investigated the effects of exposure to fungi on poultry.
On the other hand, an increase in the incidence of mycotic diseases is to be expected as a result of the widespread use of antibiotic preparations in the treatment of many diseases, as well as the widespread use of antibiotics as feed additives, which increase mycotic complications. Malnutrition, vitamin D deficiency, poor hygiene, prolonged use of antibiotics that suppress normal bacterial flora, and stress from an immunosuppressive disease are all risk factors for fungal infection and disease progression. Resistance to many of the currently used antifungal agents has emerged and appears to be a problem. However, the emergence of chemical drug resistance among various pathogenic strains, as well as their high toxicity, prompted research into new antifungal agents.
Many plants’ essential oils are known to have antibacterial and antifungal activity against a variety of organisms. Because of the presence of a variety of volatile molecules such as terpenes and terpenoids, phenol-derived aromatic components, and aliphatic components, the anti-fungal activity of some E. Os has been recognized as an excellent alternative for chemical medication in recent years.
Several studies illustrated the limitations for phenotypic, morphological and microscopical identification techniques of Aspergillus spp. which are usually labor intensive and need expert mycologist to differentiate between fungal species and do not enable us to fully track the potential source of isolated fungi so, it had led to the development of nucleic acid-based identification systems enabled us to characterize the different isolated Aspergilli. They added that newer molecular biological tests had generated interest; but not yet standardized or readily available in most clinical laboratory settings nor had they been validated in large clinical trials. these techniques are beneficial for understanding the fungal pathogens distribution and epidemiology in avian farms. Several molecular techniques approaches have been used for the identification of Aspergillus spp. including PCR amplification of targets and fragment length analysis, DNA probe hybridization and sequence analysis.
The purpose of this study was to investigate the prevalence of fungal pathogens by mycological and molecular characterization of fungi in local breeds and broiler chickens, and the effect of different oils on the growth of recovered fungal isolates.
In the current study out of 218 samples were collected. 124 from broiler chickens, 60 local breed samples, 22 local dead-in-shell embryos and 12 local egg yolk sacs. Resulted in 133 positive isolates with 155 fungal isolates were recovered due to mixed infection which identified as 94 (60.6%) mould isolates and 61 (39.4%) yeast isolates.
One-hundred four (124) isolates were isolated from broiler chicken organs as 31 air sacs, 31 heart, 31 kidney and 31 liver samples. A total of 111 fungal isolates were recovered (89.5%); of which 68 mould (54.8%) and 43 yeasts (34.7%).
Thirty fungal isolates (96.8%) were recovered from 31 air sacs samples; 20 mould (64.5%) and 10 yeasts (32.3%). Also, 29 isolates (93.5%) were recovered from 31 heart samples; 13 mould (41.9%) and 16 yeasts (51.6%). from kidney samples (n=31), 29 isolates (93.5%) were recovered; 19 mould (61.3%) and 10 yeasts (32.3%). Meanwhile, from 31 liver samples, 23 isolates (74.2%) were recovered; 16 mould (51.6%) and 7 yeasts (22.6%).
Sixty (60) isolates were isolated from local breeds organs as 15 air sacs, 15 heart, 15 kidney and 15 liver samples. A total of 23 fungal isolates were recovered (38.3%); of which 6 moulds (10%) and 17 yeasts (28.3%).
Three fungal isolates (20%) were recovered from 15 air sacs samples; 1 mould (6.7%) and 2 yeasts (13.3%). Also, 4 isolates (26.6%) were recovered from 15 heart samples; 2 moulds (13.3%) and 2 yeast (13.3%). from kidney samples (n=15), 7 isolates (46.7%) were recovered; 1 mould (6.7%) and 6 yeast (40%). Meanwhile, from 15 liver samples, 9 isolates (60%) were recovered; 2 moulds (13.3%) and 7 yeast (46.7%).
Thirty-four (34) isolates were isolated from local breeds eggs as 22 sample taken from dead-in-shell embryos organs premises as air sacs, heart, kidney and liver, and 12 samples taken from egg yolk. A total of 21 fungal isolates were recovered (61.8%); of which 20 mould (58.8%) and 1 yeast (2.9%).
Regarding dead-in shell embryos samples collected from internal organs; air sacs, heart, kidney and liver (n=22), 12 fungal isolates (54.5%) were recovered; of which 11 mould (50%) and 1 yeast (4.5%).
Concerning egg yolk samples (n=12), 9 fungal isolates (75%) were recovered all of them were moulds meanwhile no yeast isolate was recorded.
Ninty three (93) mycelial isolates: (42.7%) recovered from a total 218 samples. Six mycelial species were recovered, A. fumigatus (n=9), A. flavus (n=16), A. niger (n=25), Rhizopus spp. (n=21) Cladosporium spp. (n=5) and Penicillium spp. (n=17) at a rate of 4.1, 7.3, 11.5, 9.6, 2.3 and 7.8%, respectively.
A total of 62 yeast isolates were recovered from 218 samples broiler chickens. These isolates were identified morphologically and biochemically as 60 Candida spp. and 2 Cryptococcus spp. The recovered Candida spp. (n= 60) were identified as 25 C. albicans (11.5%), 5 C. stellatoidea (2.3%), 11 C. pseudotropicalis (5%), 10 C. krusei (4.6%) and 9 C. rugosa (4.1%). The two recovered Cryptococcus spp. were identified as C. neoformans (0.9%).
All yeasts isolate tested to chlamydospore and germ tube production (60 Candida species and 2 Cryptococcus species). C. albicans isolates were the only which produced chlamydospores and formed germ tube while the rest of Candida species as well as Cryptococcus species did not.
Moreover, the antifungal activities of eucalyptus, ginger oils and bacteriocins against the recovered Fungai were tested using agar dilution method.
Results revealed that antifungal activity of eucalyptus oil at concentrations of 0.5, 1 and 2% using agar dilution method. The results revealed that eucalyptus oil completely inhibited the growth of all the tested fungal isolates at concentrations 1 and 2% until 8 days after cultivation. Meanwhile concentration of 0.5% showed retardation of the growth of C. albicans, A. niger, A. flavus, A. fumigatus and penicillium spp. with losing the pigmentation of the fungal colony of all tested isolates and gave whitish color of conidia.
Also, antifungal activity of ginger oil at concentrations of 2 and 3% using agar dilution method. The results revealed that ginger oil has no antifungal activities and not affected the growth of all the tested fungal isolates at concentrations 2%. Meanwhile concentration of 3% showed retardation of the growth of C. albicans, A. niger, A. flavus, A. fumigatus and penicillium spp. with losing the pigmentation of the fungal colony of all Aspergillus tested isolates and gave whitish color of conidia.
As well as antifungal activity of bacteriocins at concentrations of 2 and 3% using agar dilution method. The results revealed that bacteriocin have no antifungal activities and not affected the growth of all the tested fungal isolates at concentrations 2%. Meanwhile concentration of 3% showed retardation of the growth of C. albicans, A. niger, A. flavus, A. fumigatus and penicillium spp. with losing the pigmentation of the fungal colony of all Aspergillus tested isolates and gave whitish color of conidia.
In current study, 12 selected isolates as 8 pure (not treated) fungal isolates and 4 fungal isolates treated by eucalyptus oil 0.5% that allowed fungal growth, but the fungal colony lost its pigmentation with restricted growth have been identified morphologically, microscopically and biochemically, were further characterized using PCR and oligonucleotide primers targeting ITS region. Isolates were, 3 yeast, (1) C. albicans from air sac broiler chicken, (2) C. neoformans from kidney local breed before and after treated with eucalyptus oil. 3 A. niger, (2) from air sac local breed before and after treated with eucalyptus oil and (1) from air sac broiler chicken. 3 A. flavus, (2) from liver broiler chicken before and after treated with eucalyptus oil and (1) from baby chick yolk local breed. 3 A. fumigatus (2) from heart broiler chicken before and after treated with eucalyptus oil and (1) from dead-in shell embryo local breed. The selection aimed to evaluate molecular detection for the changes in DNA genes density and structure before and after treatments.
As the Candida spp., cryptococcus spp. and Aspergillus spp. isolates showed positive results respectively of PCR test with amplification of the (400-500bp) of candida spp. and cryptococcus spp., (570-600bp) fragment of ITS region of Aspergillus spp. respectively.
Moreover, sequence analysis test was applied; as a confirmation to PCR.
The results showed that The PCR products of 12 samples which were identified as A. fumigatus, A. flavus, A. niger, C. albicans and Cryptococcus were subjected for sequencing. The result of sequencing showed that 2 A. flavus, 2 A. niger, 2 A. fumigatus, 1 C. catinulata were gave alignment with their resembles in gene bank, while one sample of A. fumigatus was sequency errored and sample of C. albicans was broken through shipping.