Evaluation of the API 20C yeast identification system for the differentiation of some dematiaceous fungi

Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family

Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.

A comparative study of extracellular enzymes from chromoblastomycosis agents reveals the potential association of phospholipase with the severity of the lesions

Chromoblastomycosis is a chronic, progressive subcutaneous mycosis that is endemic in tropical and subtropical countries. Cladophialophora carrionii and Fonsecaea pedrosoi are prevalent etiological agents. The potential role of the proteolytic activity of extracellular enzymes in these fungi and its relationship with the pathogenesis of the disease has not been proven. Some phenotypic traits have been associated with the virulence of other fungi; i.e., their different rate of protease, phospholipase, and esterase excretion, melanin, and thermotolerance. The aim of this study was the identification of extracellular enzymes that could be considered virulence markers of chromoblastomycosis agents. Therefore, we tested 29 C. carrionii and 11 F. pedrosoi clinical isolates to determine their hydrolytic and physiologic characteristics. All the tested isolates grew at a range of 30°-37 °C; except 2 strains of F. pedrosoi that grew slowly at 40 °C. We noticed that the hydrolytic capabilities of the tested isolates were positive for urea hydrolysis in almost all, while both strains were negative for DNase, hemolysin, and gelatin. C. carrionii and F. pedrosoi had phospholipase and esterase activity. These findings were similar for most isolates. All strains showed an association between phospholipase activity and moderate to severe lesions. However, only in F. pedrosoi isolates, the association remains significant. We conclude that the different enzymatic production reported here may be linked to the clinical manifestations of these pathologies. Notwithstanding, the influence of other virulence factors is not excluded.

Molecular Identification, Antifungal Susceptibility, and Geographic Origin of Clinical Strains of Sporothrix schenckii Complex in Mexico

Sporotrichosis is a subcutaneous mycosis caused by Sporothrix schenckii complex. The disease has been reported worldwide. However, the incidence of the etiological agent varies in its geographic distribution. We studied 39 clinical isolates of Sporothrix schenckii from diverse regions in Mexico, collected from 1998 to 2016. Molecular identification was performed by sequence analysis of the partial calmodulin gene. In vitro antifungal susceptibility to amphotericin B (AMB), itraconazole (ITC), voriconazole (VRC), posaconazole (PSC), fluconazole (FLC), terbinafine (TRB), caspofungin (CSF), anidulafungin (ANF), and micafungin (MCF) was evaluated. Thirty-eight isolates of S. schenckii complex were divided into five supported clades in a phylogenetic tree. The predominant clinical form was lymphocutaneous (92.3%), fixed cutaneous (5.1%), and disseminated (2.5%). Terbinafine exhibited the best in vitro antifungal activity, while fluconazole was ineffective against Sporothrix schenckii complex. Our results showed diverse geographic distribution of clinical isolates in eight states; definitive identification was done by CAL gen PCR-sequencing. In Mexico, S. schenckii is considered to be an etiological agent of human sporotrichosis cases, and lymphocutaneous is the most prevalent form of the disease. This study revealed four clades of S. schenckiisensu stricto by phylogenetic analysis. Furthermore, we report one case of S. globosa isolated from human origin from the North of Mexico.

Virulence markers of opportunistic black yeast in Exophiala

The black yeast genus Exophiala is known to cause a wide variety of diseases in severely ill individuals but can also affect immunocompetent individuals. Virulence markers and other physiological parameters were tested in eight clinical and 218 environmental strains, with a specific focus on human-dominated habitats for the latter. Urease and catalase were consistently present in all samples; four strains expressed proteinase and three strains expressed DNase, whereas none of the strains showed phospholipase, haemolysis, or co-haemolysis activities. Biofilm formation was identified in 30 (13.8%) of the environmental isolates, particularly in strains from dishwashers, and was noted in only two (25%) of the clinical strains. These results indicate that virulence factors are inconsistently present in the investigated Exophiala species, suggesting opportunism rather than pathogenicity.

Chromoblastomycosis caused by Rhinocladiella aquaspersa

A case of chromoblastomycosis of the hand caused by Rhinocladiella aquaspersa is described. The case was acquired locally in tropical Venezuela and was successfully treated with oral itraconazole.

Molecular diversity of Cladophialophora carrionii in patients with chromoblastomycosis in Venezuela

We identified 29 Cladophialophora carrionii isolates recovered from Venezuelan patients with chromoblastomycosis using phenotypic and molecular characteristics. The genetic diversity of isolates was assessed by enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) fingerprinting. We detected four electrophoretic patterns divided into two main clusters (I and II) comprising 10 and 17 isolates, respectively, and two minor clusters (III and IV) with one isolate each. An interesting cluster-age-lesion type association was detected. The median age of patients in cluster I was 37.5 years and in cluster II, 55 years of age (P = 0.04). The C. carrionii isolates found in cluster I were generally obtained from crusty lesions (60%) and isolates in cluster II were usually recovered from plaque type lesions (53%) even though the P values were only slightly less than significant (P = 0.08). No associations were found among the genetic features strains in the two clusters and gender, occupation, geographic origin, lesion size, severity, and duration of the disease. There was also no correlation between antifungal susceptibilities and strain clustering. In conclusion, molecular typing using ERIC-PCR revealed a genomic heterogeneity in the C. carrionii clinical isolates studied.

Phenotypic and molecular characterization of Madurella pseudomycetomatis sp. nov., a novel opportunistic fungus possibly causing black-grain mycetoma

A case of black-grain mycetoma occurring on the lower jaw with an odontogenic origin, which to our knowledge is the first case reported in China, is presented here. The clinical manifestation, histopathological morphology, and microbiological features are described. The new species, Madurella pseudomycetomatis, isolated from the black grains discharged by this patient, was analyzed using sequence data of the multiloci of ribosomal DNA (rDNA) and its ability to ferment carbohydrate as well as morphology. The analyses of the internal transcribed spacer (ITS) region and the D1/D2 hypervariable region of the 28S ribosomal gene sequences support a new species designation. Antifungal susceptibility testing was conducted, indicating that Madurella pseudomycetomatis was highly susceptible to itraconazole, voriconazole, and amphotericin B; moderately susceptible to terbinafine; and resistant to fluconazole and flucytosine.

Exophiala spinifera and its allies: diagnostics from morphology to DNA barcoding

Diagnostic features of morphology, physiology, serology and genetics of species belonging to the Exophiala spinifera clade (including 11 species: Exophiala oligosperma, E. spinifera, E. xenobiotica, E. jeanselmei, E. exophialae, E. nishimurae, E. bergeri, E. nigra, Rhinocladiella similis, Ramichloridium basitonum and Phaeoannellomyces elegans), comprising a large number of human-associated Exophiala species, are summarized. Several species have closely similar morphological characters and physiological profiles. Taxonomy is therefore primarily based on sequence diversity of the Internal Transcribed Spacer (ITS) region of ribosomal DNA (rDNA). Multilocus sequencing has shown that ITS is reliable for identification of the species in this clade, and is a therefore a good candidate for barcoding species of Exophiala. Species-specific fragments were searched in the ITS region of species in the Exophiala spinifera clade and can be used to design probes for diagnosis by hybridization.

Specific oligonucleotide primers for identification of Cladophialophora carrionii, a causative agent of chromoblastomycosis

Cladophialophora carrionii is one of the relatively common causative agents of chromoblastomycosis. We have developed the specific oligonucleotide primer set based on the internal transcribed spacer regions of ribosomal DNA for the rapid identification of this pathogen. PCR with this primer set amplified a 362-bp amplicon from C. carrionii strains. From other relevant dematiaceous species, including medically important dematiaceous fungi, such as Fonsecaea pedrosoi, Phialophora verrucosa, and Exophiala dermatitidis, and eight species of medically important yeasts, such as Candida albicans and Cryptococcus neoformans var. neoformans, the primer set did not produce any amplicon. PCR with this primer set may be a useful tool for the identification of C. carrionii.

Identification of pathogenic dematiaceous fungi and related taxa based on large subunit ribosomal DNA D1/D2 domain sequence analysis

The nucleotide sequences of the D1/D2 domains of large subunit (26S) ribosomal DNA for 76 strains of 46 species of pathogenic dematiaceous fungi and related taxa were determined. Intra-species sequence diversity of medically important dematiaceous fungi including Phialophora verrucosa, Fonsecaea pedrosoi, Fonsecaea compacta, Cladophialophora carrionii, Cladophialophora bantiana, Exophiala dermatitidis, Exophiala jeanselmei, Exophiala spinifera, Exophiala moniliae, and Hortaea werneckii were extremely small; as few as 0 changes were detected in C. bantiana, Fonsecaea and Exophiala species, 1 bp in C. carrionii and H. werneckii, and 2 bp in P. verrucosa. Inter-species nucleotide diversity between most species was higher. These data suggested that the D1/D2 domain is sufficiently variable for identification of pathogenic dematiaceous fungi and relevant species. The phylogenetic trees constructed from the sequence data revealed that most human pathogenic species formed a single cluster and that Cladosporium and Phialophora species were distributed polyphyletically into several clusters.

Identification of Exophiala mesophila isolated from treated dental unit waterlines

Members of the genus Exophiala are often difficult to identify to the species level because of their variable morphological appearances. This paper describes the methods used to identify Exophiala mesophila and provides salient differential features for distinguishing other mesophilic members of the genus.

Specific oligonucleotide primers for identification of Hortaea werneckii, a causative agent of tinea nigra

Hortaea werneckii, a black yeast-like hyphomycete that is widely distributed in tropical and subtropical environments, can cause superficial mycotic infection in humans. This fungus was recently isolated from superficial infectious lesions of a guinea pig in Japan. An oligonucleotide primer set specific for Hortaea werneckii was designed on the basis of the internal transcribed spacer regions of the ribosomal DNA (rDNA). Polymerase chain reaction (PCR) with this primer set yielded a 306 bp PCR amplicon from only H. werneckii. This primer set did not amplify DNAs of 42 other related dematiaceous species, including the medically important dematiaceous fungi Cladophialophora carrionii, Fonsecaea pedrosoi, Phialophora verrucosa, and Exophiala dermatitidis, and eight species of medically important yeasts, including Candida (C.) albicans, C. dublinensis, C. glabrata, C. parapsilosis, C. tropicalis, Cryptococcus neoformans var. neoformans, Malassezia furfur, and Trichosporon asahii var. asahii. PCR with this primer set may be a useful technique for rapid identification of H. werneckii.

Developments in fungal taxonomy

Fungal infections, especially those caused by opportunistic species, have become substantially more common in recent decades. Numerous species cause human infections, and several new human pathogens are discovered yearly. This situation has created an increasing interest in fungal taxonomy and has led to the development of new methods and approaches to fungal biosystematics which have promoted important practical advances in identification procedures. However, the significance of some data provided by the new approaches is still unclear, and results drawn from such studies may even increase nomenclatural confusion. Analyses of rRNA and rDNA sequences constitute an important complement of the morphological criteria needed to allow clinical fungi to be more easily identified and placed on a single phylogenetic tree. Most of the pathogenic fungi so far described belong to the kingdom Fungi; two belong to the kingdom Chromista. Within the Fungi, they are distributed in three phyla and in 15 orders (Pneumocystidales, Saccharomycetales, Dothideales, Sordariales, Onygenales, Eurotiales, Hypocreales, Ophiostomatales, Microascales, Tremellales, Poriales, Stereales, Agaricales, Schizophyllales, and Ustilaginales).

Ability of RapID Yeast Plus System to identify 304 clinically significant yeasts within 5 hours

The RapID Yeast Plus System (Innovative Diagnostic Systems, Norcross, Ga.) is a qualitative micromethod that uses conventional and chromogenic substrates for the identification of medically important yeasts. The ability of the RapID Yeast Plus system to accurately identify 304 clinical yeast isolates within 5 h was evaluated. The RapID Yeast Plus method correctly identified 286 (94.1%) of strains to the species level without the need for additional tests. A further 12 strains (3.9%) were classified as correct to the genus level or to a low-probability identification with two or more possibilities. In these latter cases, additional tests were required to delineate the correct identification. Organisms in the latter group comprised Candida parapsilosis (n = 1), Candida tropicalis (n = 1), Candida ciferrii (n = 1), Candida guilliermondii (n = 2), Candida humicola (n = 1), Candida kefyr (n = 1), Cryptococcus neoformans (n = 1), and Rhodotorula rubra (n = 4). Six strains (2.0%) were misidentified or did not yield codes in the manufacturer's database. These included one Candida utilis (identified as Candida famata/Candida guilliermondii), one Trichosporon beigelii (identified as Cryptococcus neoformans), one Candida diddensiae (identified as Candida albicans), one Candida membranaefaciens (identified as Candida parapsilosis), one Candida norvegensis (identified as Candida zeylanoides), and one Candida catenulata (no code) isolate; the last four strains are not included in the firm's current database. The RapID Yeast Plus system yielded excellent results and may be recommended for use in the routine laboratory for accurate same-day identification of clinically significant yeasts.

Nutritional physiology of type isolates of currently accepted species of Exophiala and Phaeococcomyces

Nutritional physiological and tolerance tests were performed for all type strains of species currently classified in the black yeast genera Exophiala and Phaeococcomyces, including some additional type strains of taxa recently reidentified as Exophiala species. Most described Exophiala species can be distinguished by physiological characters. Exophiala jeanselmei with its varieties, and E. castellanii should all be retained as separate taxa. The pairs of strains Mycotorula schawii/Exophiala dermatitidis, Hormodendrum negronii/Exophiala jeanselmei var. lecaniicorni and Sporotrichum gougerotii/Torulabergeri were found to be conspecific. Phenetic analyses of physiological data support the identity of Phaeococcomyces exophialae as a yeast-like synanamorph of Exophiala spinifera. The taxonomic positions of the genera Nadsoniella, Phaeoannellomyces and Wangiella are discussed. The genera Exophiala and Phaeococcomyces are unrelated.

Clinical and mycological spectra of Wangiella dermatitidis infections

The article reviews 37 cases of phaeohyphomycosis from the world literature up to 1992 accepted as being caused by Wangiella dermatitidis. The various clinical aspects of these infections are characterized, and the nomenclatural implications in the history of this emerging pathogen are discussed.

Nutritional physiology and selective isolation of Exophiala dermatitidis

The nutritional physiology of ten strains of Exophiala dermatitidis was investigated. The growth reactions to lactose, citrate, nitrate, nitrite, lysine, creatine and creatinine differ from those found in closely related black yeasts. In addition, it is the only Exophiala species which is able to grow at 40 degrees C. A selective medium containing meso-erythritol as sole carbon source was evaluated. This medium is particularly useful for the isolation of black yeasts from lungs of patients with cystic fibrosis as well as from the environment.

Nutritional pattern and eco-physiology of Hortaea werneckii, agent of human tinea nigra

The life cycle of Hortaea werneckii includes yeast-like, hyphal and meristematic growth. The preponderance of each form of propagation can be influenced by environmental conditions. The clinical entity 'tinea nigra' is explained by ecological similarities between supposed natural niches and human hyperhydrotic skin. The species is recognizable by assimilation of lactose, nitrate and nitrite, no or little growth with L-lysine, cadaverine, creatine and creatinine, and tolerance of 10% NaCl. It generally does not grow at 36 degrees C.

The medically important dematiaceous fungi and their identification

Dematiaceous fungi include a large group of organisms that are darkly pigmented (dark brown, olivaceous, or black). In most cases the pigment is melanin, and specifically, dihydroxynaphthalene melanin. The diseases produced include chromoblastomycosis, eumycotic mycetoma, and phaeohyphomycosis. Phaeohyphomycosis is a new classification for a diverse group of previously known entities grouped together on the basis of finding dematiaceous hyphal and/or yeast-like forms in tissue; tissue involvement may be superficial, cutaneous and corneal, subcutaneous, or systemic. Identification of these fungi is based mostly upon morphology. Important structures include annellides (Phaeoannellomyces, Exophiala), phialides (Phialophora, Wangiella), adelophialides (Phialemonium without collarettes, Lecythophora with collarettes), differentiation of conidiophores (Xylohypha versus Cladosporium) and conidial hilum, septation and germination (Bipolaris, Drechslera, Exserohilum). Useful laboratory tests include the 12% gelatin test (controversial), nitrate assimilation (W. dermatitidis is negative, most other species are positive), and determination of temperature maxima (especially 37 degrees C for E. jeanselmei, 40 degrees C for W. dermatitidis and B. spicifera, 42 degrees C for X. bantiana, and 45 degrees C for Dactylaria constricta var. gallopava and Scedosporium inflatum).

Differentiation between Trichophyton mentagrophytes and T. rubrum by sorbitol assimilation

Trichophyton rubrum was easily differentiated from T. mentagrophytes by its ability to assimilate sorbitol with an API 20C AUX strip. One hundred percent of 36 T. rubrum strains and none of 147 T. mentagrophytes strains assimilated sorbitol.