Fungal species concepts in the genomics era.

The 140 000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and (or) molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals.

Ecology of cultivable yeasts in pristine forests in northern Patagonia (Argentina) influenced by different environmental factors.

Environmental factors influencing the occurrence and community structure of soil yeasts in forests are not well studied. There are few studies dedicated to Southern Hemisphere soil yeasts populations and even fewer focused on temperate forests influenced by volcanic activity. The present work aimed to study the ecology of soil yeast communities from pristine forests influenced by different environmental factors (precipitation, physicochemical properties of soil, tree species, soil region, and season). The survey was performed in 4 northern Patagonian forests: 2 dominated by Nothofagus pumilio and 2 by Nothofagus antarctica. Yeast communities were described with ecological indices and species accumulation curves, and their association with environmental characteristics was assessed using multivariate analysis. Each forest site showed a particular arrangement of species as a result of environmental characteristics, such as dominant plant species, nutrient availability, and climatic characteristics. Cryptococcus podzolicus was most frequently isolated in nutrient-rich soils, Trichosporon porosum dominated cold mountain forests with low nutrient and water availability in soil, and capsulated yeasts such as Cryptococcus phenolicus dominated forest sites with low precipitation. The present work suggests that environmental factors affecting yeast communities may not be the current soil characteristics but the result of complex interactions of factors including natural disturbances like volcanic activity.

[Identification of yeasts from commercial attiéké in Abidjan (Côte d'Ivoire): Preliminary study]. / Identification des espèces de levures isolées de l'attiéké commercialisé sur les marchés à Abidjan (Côte d'Ivoire) : étude préliminaire.

OBJECTIVE: This study aims to identify yeasts from commercial attiéké. PATIENTS AND METHODS: This descriptive cross-sectional survey involving 103 samples of attiéké sold on the market from August to September 2017. It was conducted from the mycology laboratory of the Institut Pasteur of Côte d'Ivoire. The samples were seeded on YGC medium. The colonies of positive culture were counted and seeded again on chromogen medium. Identification of yeasts species was carried out by MALDI-TOF mass spectrometry (Vitek MS bioMérieux). RESULTS: As a whole, 63 samples were contaminated with fungi i.e. an overall prevalence of 61.1 %. Fifty-nine of yeasts were identified i.e. 57.2 %. Candida rugosa was most frequently isolated (62.7 %), followed by Ccandida albicans (8.5 %), Candida krusei (8.5 %) et Candida tropicalis (8.5 %). Geotrichum candidum represented 6.8 % isolated yeasts. The yeast average load is 10,124×102 CFU/g with high contamination of commercial attiéké in the commune of Abobo. CONCLUSION: The contamination of attiéké by yeasts is a reality. C. rugosa was most frequently isolated. It would be necessary to investigate the food chain to determine the source of contamination.

Incidence and biodiversity of yeasts, dermatophytes and non-dermatophytes in superficial skin infections in Assiut, Egypt.

OBJECTIVE: The aim was to identify the incidence of the causal agents from dermatophytes, non-dermatophytes and yeasts in Assiut Governorate employing, beside the morphological and physiological techniques, the genotypic ones. PATIENTS: Samples from infected nails, skin and hair were taken from 125 patients. MATERIALS AND METHODS: Patients who presented with onychomycosis, tinea capitis, tinea corporis, tinea cruris and tinea pedis during the period from February 2012 to October 2015 were clinically examined and diagnosed by dermatologists and were guided to Assiut University Mycological Centre for direct microscopic examination, culturing and identification. RESULTS: Onychomycosis was the most common infecting (64.8% of the cases) followed by tinea capitis (17.6%). Direct microscopic preparations showed only 45 positive cases, while 96 cases showed positive cultures. Infections were more frequent in females than males. Fifty-one fungal species and 1 variety were obtained. Yeasts were the main agents being cultured from 46.02% of total cases. Non-dermatophytes were the second etiologic agents. Aspergillus was responsible for infecting 19.47% of total cases and dermatophytes appeared in only 15.93% of the cases. CONCLUSIONS: Yeasts were the main causal agents followed by non-dermatophytic fungi (mainly species of Aspergillus, then Alternaria, Scopulariopsis and Fusarium). Both direct microscopic preparations and culturing are recommended for mycological evaluation of clinical specimens. Sequence analysis of ITS region is recommended for yeast identification.

[Fungal aetiologies and contributing factors of interdigital tinea pedis among policemen in Abidjan (Ivory Coast)]. / Étiologies fongiques et facteurs favorisant les intertrigos inter-orteils chez les gendarmes à Abidjan (Côte d'Ivoire).

AIM OF THE STUDY: Fungal interdigital tinea pedis are poorly documented in Ivory Coast. This study aimed to determine the distribution of fungal species and contributing factors of the disease among policemen in Abidjan. PATIENTS AND METHODS: Our cross-sectional study was carried out at the police school in Abidjan. Our patients consisted of symptomatic or non-symptomatic police students. Samples of scales or serosities taken from inter-toes spaces were examinated with KOH mount and cultured on Sabouraud-chloramphenicol and Sabouraud-chloramphenicol-actidione media. The method of identification depended on the observed fungus. RESULTS: Among the 303 police students with clinical lesions of the inter-toe folds, 233 (76.9%; IC 95%=71.9-81.4) had a positive diagnosis after mycological examination. Lesions were predominantly located in the 3rd and 4th interdigital plantar spaces, with desquamation (100%) followed by maceration (82.5%) as the predominant functional sign. Dermatophytes accounted for 86.3% of the strains isolated with as majority species : Trichophyton interdigitale (40.3%), Microsporum langeronii (30.0%) and Trichophyton rubrum (15.5%). Yeasts accounted for 13.7% of the strains with Candida albicans (7.7%) as the most found species. The duration at the police school (P=0.004) and the practice of sports activities (P=0.0001) were statistically associated with the occurrence of the disease. CONCLUSION: A good hygiene of feet would reduce the incidence of the disease among the defense and security forces. Also, investigations for the influence of the seasons in the occurrence of interdigital tinea pedis will allow a better understand of epidemiology of this dermatomycosis.

[Causative agents of superficial mycoses isolated in Dakar, Senegal: Retrospective study from 2011 to 2015]. / Champignons agents de mycoses superficielles isolés à Dakar (Sénégal) : une étude rétrospective de 2011 à 2015.

INTRODUCTION: Superficial fungal infections, particularly of the skin, scalp and nails are very common and have been reported worldwide. The most common causative agents of these mycoses are dermatophytes, yeasts and molds. However, these agents vary with time and depend on many factors including the geography. The objective of this study was to identify the causative agents of superficial mycoses diagnosed at the Le Dantec University Hospital in Dakar (Senegal). MATERIAL AND METHODS: The study concerned 1851 outpatients received in the parasitological and mycological laboratory of Le Dantec hospital during the period from January 2011 to December 2015. Every patient benefited from direct examination and mycological culture. RESULTS: Among the 1851 patients, 633 were confirmed with superficial mycoses and the prevalence was 34.2 %. The age of patients ranged from two months to 81 years with a mean age of 31 years. Superficial mycoses were found more in women (70.3 %) than men (29.7 %) and a little more than thirty-nine percent (39.3 %) were adults. The causative agents identified were: dermatophytes (58 %), yeast (36.7 %) and non-dermatophytic filamentous fungi (NDFF, 5.3 %). The most isolated species were: Candida albicans (26.9 %), Trichophyton soudanense (24.9 %) and T. rubrum (13.7 %). These fungi were responsible for different clinical aspects, isolated and other associated. Among the isolated clinical aspects, those affecting hair (tinea capitis) were by far the largest with 44.8 %, followed by tinea unguium (34.5 %). Associations were especially type of tinea capitis and tinea manuum (2.4 %) and toenails onychomycosis associated with interdigital tinea pedis (2.7 %). Tinea capitis agents were exclusively dermatophytes and the predominant agent was T. soudanense with 47,8 %. Tinea unguium agents were yeast (79 %), dermatophytes (18 %) or NDFF (3 %) and the most found species was C. albicans (63.9 %). Dermatophytes, yeasts and molds were respectively found more in children and young adults, older adults and young adults and older adults and the elderly. CONCLUSION: In definitive, these epidemiological data should enable better diagnostic and therapeutic management of superficial mycoses.

Fungal interdigital tinea pedis in Dakar (Senegal).

Fungal interdigital tinea pedis (FITP) is the most frequent dermatomycosis in industrial countries. In African tropics, it's a rare motive of consultation and is discovered while complicated. The aims of this article were: to determine the frequency of interdigital tinea pedis among overall mycological analysis in our laboratory; to study epidemiological, clinical and mycological aspects of FITP in outpatients attending the Le Dantec mycology laboratory in Dakar. A total of 62 males (60%) and 42 females (40%), mean age: 43.15 years (range: 11-81 years), were received from January 2011 to December 2015 for suspicion of FITP. Skin specimens were taken from all patients for microscopy and fungal culture. The frequency of ITP represents 5.6% (104/1851) among our overall mycological analysis. FITP was confirmed in 68 patients (SPI=65.38%), mainly located between the 4th and 5th toes and 71 fungal species were isolated (CPI=68.27%). Among patients with confirmed FITP, there were 38 males (56%) and 30 females (44%). The prevalence was highest in patients between 44 and 54 years (26%). Candida albicans, Fusarium solani and Trichophyton interdigitale were shown to be the most common pathogens respectively for yeasts (39%), non-dermatophytic filamentous fungi (NDFF; 21%) and dermatophytes (11%). So FITP isn't a common reason for consultation in Dakar but its simple parasitic index (SPI) is still very high and dermatophytes formerly the main causative agents are being relegated to third place behind yeasts and NDFF.

Digestive tract mycobiota: a source of infection.

The human mycobiome includes 390 fungal species detected on the skin, in the vagina, in the oral cavity, and in the digestive tract that includes 335 species and 158 genera. Among these, 221 species are found only in the digestive tract, 88 only in the oral cavity, and 26 in both. These species belong to 126 genera of yeast and filamentous fungi, of the Ascomycota, Basidiomycota, and Zygomycota phyla. Forty species were identified only by culture, 188 species by molecular techniques, and 19 species with both techniques. Fungal diversity does not differ significantly according to sex but Basidiobolus ranarum is significantly more prevalent in male individuals and Paecilomyces fumosoroseus in female individuals. Fungal diversity is significantly higher in adults than in infants. Only 42 species are identified in the course of inflammatory bowel disease, with 27 species specific to IBD. Twenty-nine are identified in HBV infected patients including 17 specific species, and 11 in HIV-infected patients with the specific Histoplasma capsulatum. Genotyping proved that the gut mycobiome was a source of fungal infection caused by Candida albicans and Candida glabrata. The authors suggest updating the repertoire of the human digestive tract in healthy individuals and patients. Fungal culturomics must be intensified to complete this repertoire.

In vitro anti-yeast activity of chloramphenicol: A preliminary report.

Chloramphenicol is a bacteriostatic antimicrobial agent but its antifungal activity is not known. The present study aimed to investigate the activity of chloramphenicol against 30 representative yeasts. The antimicrobial assay of chloramphenicol (50mg/mL; 100mg/mL and 200mg/mL) was determined by the disc diffusion method using Mueller-Hinton agar against 30 representative yeast strains. Zone of inhibition was read after 48-72h incubation at 37°C and results were compared with some standard antifungal agents. Most of the tested yeasts (73.3%) showed inhibition zones (5 up to 35mm) to chloramphenicol impregnated discs (200mg/mL). Three out of the four tested Candida albicans as well as Candida famata, Candida glabrata, Candida haemolonei and Cryptococcus neoformans showed no inhibition zones to chloramphenicol (200mg/mL). Caspofungin acetate (50mg/mL) inhibited 83.3% of the strains; ketoconazole (200mg/mL) 70% and metronidazole 10%. Chloramphenicol discs: 50 and 100mg/mL showed less activity (6.7% and 36.7%, respectively) compared to the 200mg discs; whereas chloramphenicol (BBL; 3µg/mL) inhibited 13.3% of the strains. The anti-yeast activities of chloramphenicol were comparable to other known antifungal compounds. Moreover, it is cheap, has fewer side effects and its inclusions in selective fungal media such as Mycosel have to be questioned.

[Mycological diagnosis of onychomycosis]. / Méthodes de diagnostic d'une onychomycose.

Onychomycosis represents about 50% of ungueal pathology. Dermatophytes (especially Trichophyton rubrum and Trichophyton interdigitale) are the main species involved in tinea pedis. Yeasts of the Candida (Candida albicans, Candida parapsilosis,...) genus are predominant on hands and very often associated with ungueal disease and perionyxis. Fungi other than the classic dermatophytes and yeasts can be rarely isolated from nail diseases. Among them, species belonging to Scopulariopsis, Aspergillus and Fusarium genus are mainly found, but their involvement in the disease must be proved. Other fungi, presenting a special affinity to keratin (pseudodermatophytes), such as Neoscytalidium dimidiatum (ex Scytalidium dimidiatum) from tropical and subtropical areas and Onychocola canadensis from Northern America and Europe, are considered as real pathogens in nail diseases. A multidisciplinary approach, including clinicians and biologists, is required to confirm the mycosis. This comparative review emphasizes the importance of histological examination, as well as molecular approaches, which are very contributive to the diagnosis of onychomycosis. The role of the laboratory is to identify at the species level the fungus isolated from nail scrapings and to show its involvement in the ungueal lesions.

[Biological diagnosis of onychomycoses. Direct examination after simplified technique of PAS staining]. / Diagnostic biologique des onychomycoses. Examen direct après coloration PAS simplifiée.

Confirmation of fungal origin of onychopathy by mycological examination is essential. For that purpose, in parallel to the cultivation of biological samples, achieving a sensitive and informative direct examination of nail fragments and subungual material is primordial. Among the direct examination techniques, and inspired from a technique of reference in histo-pathology (the "periodic acid-Schiff reagent" reaction), the simplified technique of PAS staining according to Hotchkiss and MacManus is the technique of choice. Easy to implement and very sensitive, it can immediately and formally confirm the diagnosis of onychomycosis, mention the type of fungus (yeast, dermatophyte, Hyphomycete opportunistic) and suspect a possible multiple involvement.