Mycological examinations on the fungal flora of the chicken comb

Characterization of the eukaryotic microbial communities in the chicken ileum in cage-free and conventional commercial housing systems

The current shift from conventional cage (CC) hen housing facilities towards cage-free (CF) hen housing in the egg industry has left many questions regarding how level of fecal exposure and exposure to other hens may influence the hen intestinal microbiota. In a previous publication we reported differences in the bacterial ileal communities and ileal morphology between hens in CC and CF production environments at a single commercial site. Here, we present the first 18S rRNA gene amplicon sequencing-based characterization of the eukaryotic ileal microbiota of adult layer hens, and their associations with intestinal health parameters and the bacterial microbiota. DNA was extracted from the ileal digesta of hens (n = 32 CC, n = 48 CF) using the Qiagen Powerlyzer Powersoil kit, followed by amplification of the V9 region of the 18S rRNA gene. Paired end sequencing was performed with the Illumina MiSeq platform, and the resulting reads were processed according to the Mothur MiSeq protocol in Mothur v1.43.0. De novo operational taxonomic unit (OTU) clustering was performed in mothur with a 99% similarity threshold, and OTUs were taxonomically classified with the SILVA SSU v138 reference database. OTUs classified as vertebrate, plant, or arthropod were removed, resulting in 3,136,400 high quality reads and 1,370 OTUs. Associations between OTUs and intestinal parameters were calculated using PROC GLIMMIX. PERMANOVA over Bray-Curtis distances revealed differences between CC and CF eukaryotic ileal microbiota at the whole community level, but no OTUs were differentially abundant after correcting for false discovery (P > 0.05; q > 0.1). Kazachstania and Saccharomyces, closely related genera of yeast, represented 77.1% and 9.7% of sequences respectively. Two Kazachstania OTUs and 1 Saccharomycetaceae OTU were positively correlated with intestinal permeability (r² ≥ 0.35). Eimeria accounted for 7.6% of sequences across all samples. Intriguingly, 15 OTUs classified as Eimeria were inversely associated with intestinal permeability (r² ≤ -0.35), suggesting Eimeria may play a more complex role in the microbiota of healthy birds than has been observed in disease challenges.

Malassezia: Zoonotic Implications, Parallels and Differences in Colonization and Disease in Humans and Animals

Malassezia spp. are commensals of the skin, oral/sinonasal cavity, lower respiratory and gastrointestinal tract. Eighteen species have been recovered from humans, other mammals and birds. They can also be isolated from diverse environments, suggesting an evolutionary trajectory of adaption from an ecological niche in plants and soil to the mucocutaneous ecosystem of warm-blooded vertebrates. In humans, dogs and cats, Malassezia-associated dermatological conditions share some commonalities. Otomycosis is common in companion animals but is rare in humans. Systemic infections, which are increasingly reported in humans, have yet to be recognized in animals. Malassezia species have also been identified as pathogenetic contributors to some chronic human diseases. While Malassezia species are host-adapted, some species are zoophilic and can cause fungemia, with outbreaks in neonatal intensive care wards associated with temporary colonization of healthcare worker’s hands from contact with their pets. Although standardization is lacking, susceptibility testing is usually performed using a modified broth microdilution method. Antifungal susceptibility can vary depending on Malassezia species, body location, infection type, disease duration, presence of co-morbidities and immunosuppression. Antifungal resistance mechanisms include biofilm formation, mutations or overexpression of ERG11, overexpression of efflux pumps and gene rearrangements or overexpression in chromosome 4.

Survey of Keratinophilic Fungi from Feathers of Birds in Tuscany

Although keratinophilic fungi on avian feathers have been widely described, data from European literature are quite lacking regarding Mediterranean countries. The aim of the present study was therefore to evaluate the occurrence of fungal species on feathers of different avian species in Italy. A total of 378 feather samples from both aquatic (n = 254) and terrestrial birds (n = 124), for a total of 30 bird species, were cultured for keratinophilic fungi. Fungal isolates were recognized by their macro- and micro-scopical morphology, and results were corroborated by PCR and sequencing. Keratinophilic fungi belonging to 11 different species (Scopulariopsis brevicaulis, Chrysosporium keratinophilum, Trichophyton terrestre, Microsporum gypseum, Sepedonium sp., Chrysosporium pannorum, Myriodontium sp., Chrysosporium tropicum, Chrysosporium pruinosum, Chrysosporium luteum and Aphanoascus fulvescens) were isolated from 71 animals (18.8%). The frequency of isolation of keratinophilic species from terrestrial birds was significantly higher in waterfowl. Migratory birds in Italy have been proven to carry pathogenic fungi such as dermatophytes, (A. platyrhyncos, A. crecca, E. rubecula), besides saprophytic species.

In Vivo Efficacy of Clove Essential Oil Ointment for Microsporum gallinae Avian Dermatophytosis-A Randomized Controlled Trial

Avian favus (dermatophytosis) is a superficial mycosis caused by Microsporum gallinae in poultry. This disease is an important problem in poultry husbandry, but the standard antifungal treatment can leave drug residues in farm products. The aim of this study was to compare the efficacy of a clove essential oil ointment (3%, w/w) with commercially available ketoconazole cream (2%, w/w) for the treatment of M. gallinae infection in chickens. An in vitro time-kill assay showed that clove essential oil ointment reduced the number of viable M. gallinae ATCC 90749 by 99.99% within 1 hr. A randomized controlled trial showed that the therapeutic efficacy of clove essential oil ointment (3%, w/w) was noninferior to ketoconazole cream (2%, w/w) in M. gallinae-infected chickens. The percentage of completely recovered (culture-negative) animals in both treatment groups was 90% in day 35 after initial treatment. This study indicates that clove essential oil is suitable for preparation as an alternative topical treatment for avian dermatophytosis.

Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus

The yeast Magnusiomyces capitatus is an opportunistic human pathogen causing rare yet severe infections, especially in patients with hematological malignancies. Here, we report the 20.2 megabase genome sequence of an environmental strain of this species as well as the genome sequences of eight additional isolates from human and animal sources providing an insight into intraspecies variation. The distribution of single-nucleotide variants is indicative of genetic recombination events, supporting evidence for sexual reproduction in this heterothallic yeast. Using RNAseq-aided annotation, we identified genes for 6518 proteins including several expanded families such as kexin proteases and Hsp70 molecular chaperones. Several of these families are potentially associated with the ability of M. capitatus to infect and colonize humans. For the purpose of comparative analysis, we also determined the genome sequence of a closely related yeast, Magnusiomyces ingens. The genome sequences of M. capitatus and M. ingens exhibit many distinct features and represent a basis for further comparative and functional studies.

The identification of fungi collected from the ceca of commercial poultry

Under normal conditions, fungi are ignored unless a disease/syndrome clinical signs are reported. The scientific communities are largely unaware of the roles fungi play in normal production parameters. Numerous preharvest interventions have demonstrated that beneficial bacteria can play a role in improving productions parameters; however, most researchers have ignored the impact that fungi may have on production. The goal of the present study was to record fungi recovered from commercial broiler and layer houses during production. Over 3,000 cecal samples were isolated using conventional culture methodology and over 890 samples were further characterized using an automated repetitive sequence-based PCR (rep-PCR) methodology. Eighty-eight different fungal and yeast species were identified, including Aspergillus spp., Penicillium spp., and Sporidiobolus spp, and 18 unknown genera were separated using rep-PCR. The results from the present study will provide a normal fungi background genera under commercial conditions and will be a stepping stone for investigating the impact of fungi on the gastrointestinal tract and on the health of poultry.

An epidemiological study of animals dermatomycoses in Iran

OBJECTIVE

To determine the fungal species isolated from skin lesions of different animals suspected of having dermatomycoses and their prevalence in different regions of Iran.

MATERIALS AND METHODS

A total of 1011 animals (292 dogs, 229 cats, 168 horses, 100 camels, 98 cows, 60 squirrels, 37 birds, 15 sheep, 6 goats, 5 rabbits and 1 fox) suspected of having dermatomycoses were examined. The samples were obtained by plucking the hairs and feathers with forceps around the affected area and scraping the epidermal scales with a sterile scalpel blade. All collected samples were analyzed by direct microscopy and culture. Laboratory identification of the fungal isolates was based on their colonial, microscopic and biochemical characteristics.

RESULTS

Fungal agents were recovered from 553 (54.7%) animals suspected of having dermatomycoses. Of 553 confirmed cases, 255 (49.7%) were positive for dermatophytosis, 251 (45.4%) for Malassezia dermatitis, 14 (2.5%) for candidiasis, 12 (2.2%) for aspergillosis and 1 (0.2%) for zygomycosis. Cats (36.3%) were the most prevalent infected animals, followed by camels (13.4%), dogs (12.8%), horses (12.5%), cows (12.3%), squirrels (5.4%), birds (3.6%), sheep (2%), goats (1.1%), rabbits (0.4%) and fox (0.2%). Microsporum canis (M. canis) was the most frequent fungus isolated from dogs and fox, Malassezia pachydermatis (M. pachydermatis) from cats, horses and squirrels, Trichophyton verrucosum (T. verrucosum) from cows and camels, T. mentagrophytes var. mentagrophytes from sheep, goats and rabbits, and Aspergillus fumigatus (A. fumigatus) from birds.

CONCLUSION

The results suggested that periodic screening of animals suspected of having dermatomycoses and necessary treatments could help in the management of their public health problem.

Fungal/mycotic diseases of poultry-diagnosis, treatment and control: a review

Fungal/mycotic diseases cause significant economic losses to the poultry industry either due to their direct infectious nature or due to production of mycotoxins, the secondary fungal metabolites produced in grains or poultry feed. Several fungi have created havoc in the poultry industry and some of them cause direct harm to human health due to their zoonotic implications. They are responsible for high morbidity and mortality, especially in young birds and cause stunted growth and diarrhea; and fatal encephalitis. Mycotic dermatitis is a possible health hazard associated with poultry houses. Mycotoxins are the leading cause of producing immunosuppression in birds, which makes them prone to several bacterial and viral infections leading to huge economic losses to the poultry industry. In comparison to bacterial and viral diseases, advances in diagnosis, treatment, prevention and control of fungal diseases in poultry has not taken much attention. Recently, molecular biological tools have been explored for rapid and accurate diagnosis of important fungal infections. Effective prevention and control measures include: appropriate hygiene, sanitation and disinfection, strict biosecurity programme and regular surveillance/monitoring of fungal infections as well as following judicious use of anti-fungal drugs. Precautionary measures during crop production, harvesting and storing and in feed mixing plants can help to check the fungal infections including health hazards of mycotoxins/mycotoxicosis. The present review describes the fungal pathogens causing diseases in poultry/birds, especially focusing to their diagnosis, prevention and control measures, which would help in formulating appropriate strategies to have a check and control on these unwanted troubles to the poultry producers/farmers.

The biology of the Cryptococcus neoformans species complex

Cryptococcus neoformans is a major cause of fungal meningoencephalitis in immunocompromised patients. Despite recent advances in the genetics and molecular biology of C. neoformans, and improved techniques for molecular epidemiology, aspects of the ecology, population structure, and mode of reproduction of this environmental pathogen remain to be established. Application of recent insights into the life cycle of C. neoformans and its different ways of engaging in sexual reproduction under laboratory conditions has just begun to affect research on the ecology and epidemiology of this human pathogenic fungus. The melding of these disparate disciplines should yield rich dividends in our understanding of the evolution of microbial pathogens, providing insights relevant to diagnosis, treatment, and prevention.