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Augustin J.O.,Federal University of Viçosa | Groenewald J.Z.,Centraalbureau Voor Schimmelcultures Fungal Biodiversity Center | Nascimento R.J.,Federal University of Viçosa | Mizubuti E.S.G.,Federal University of Viçosa | And 4 more authors.
PLoS ONE | Year: 2013

Background: Symbiotic relationships modulate the evolution of living organisms in all levels of biological organization. A notable example of symbiosis is that of attine ants (Attini; Formicidae: Hymenoptera) and their fungal cultivars (Lepiotaceae and Pterulaceae; Agaricales: Basidiomycota ). In recent years, this mutualism has emerged as a model system for studying coevolution, speciation, and multitrophic interactions. Ubiquitous in this ant-fungal symbiosis is the "weedy" fungus Escovopsis (Hypocreales: Ascomycota), known only as a mycoparasite of attine fungal gardens. Despite interest in its biology, ecology and molecular phylogeny - noting, especially, the high genetic diversity encountered - which has led to a steady flow of publications over the past decade, only two species of Escovopsis have formally been described. Methods and Results: We sampled from fungal gardens and garden waste (middens) of nests of the leaf-cutting ant genus Acromyrmex in a remnant of subtropical Atlantic rainforest in Minas Gerais, Brazil. In culture, distinct morphotypes of Escovopsis sensu lato were recognized. Using both morphological and molecular analyses, three new species of Escovopsis were identified. These are described and illustrated herein - E. lentecrescens , E. microspora, and E. moelleri - together with a re-description of the genus and the type species, E. weberi . The new genus Escovopsioides is erected for a fourth morphotype. We identify, for the first time, a mechanism for horizontal transmission via middens. Conclusions: The present study makes a start at assigning names and formal descriptions to these specific fungal parasites of attine nests. Based on the results of this exploratory and geographically-restricted survey, we expect there to be many more species of the genus Escovopsis and its relatives associated with nests of both the lower and higher Attini throughout their neotropical range, as suggested in previous studies. © 2013 Augustin et al.

Ge Y.P.,Peking Union Medical College | Lv G.X.,Peking Union Medical College | Shen Y.N.,Peking Union Medical College | Li M.,Peking Union Medical College | And 4 more authors.
Medical Mycology | Year: 2012

We report the first case and clinical course of a case of human subcutaneous phaeohyphomycosis caused by Ochroconis tshawytschae, a rare fish pathogen. The diagnosis was based upon histopathological and mycological examinations of clinical samples. Identification of the etiologic agent was assessed on its phenotypic characteristics and subsequently, confirmed by molecular data. In vitro antifungal susceptibility of the isolate was investigated and a comparison was prepared of all of its features to those of its two most relevant related species, O. gallopava and O. humicola. © 2012 ISHAM.

Ge Y.P.,Peking Union Medical College | Boekhout T.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | Zhan P.,Dermatology Hospital of Jiangxi Province | Lu G.X.,Peking Union Medical College | And 4 more authors.
Medical Mycology | Year: 2012

Candida parapsilosis, which was previously considered to be a complex of three genetically distinct groups, has emerged as a significant agent of nosocomial infections. Recently, this complex was separated into three species: C. parapsilosis sensu stricto, C. orthopsilosis and C. metapsilosis. In China, data pertaining to these fungi are limited. In this study, we examined 57 isolates of members of the C. parapsilosis complex collected from four cities in East China, i.e., Nanjing (n = 22), Nanchang (n = 20), Shanghai (n = 12) and Jinan (n = 3). C. parapsilosis sensu stricto represented 71.9% of all isolates, while C. metapsilosis accounted for the remaining 28.1%. C. orthopsilosis could not be identified. A significantly high prevalence of C. metapsilosis was observed in strains recovered from Nanchang, 60% (12/20) of the isolates were C. metapsilosis. Sequence analysis of internal transcribed spacer region revealed two unevenly distributed genotypes among the C. metapsilosis strains. A PCR-restriction fragment length polymorphism assay was described for rapid identification. The strains were susceptible to fluconazole, voriconazole, amphoterincin B and micafungin. Six (15%) isolates of C. parapsilosis sensu stricto and three (18.8%) of C. metapsilosis were found to be dose-dependent susceptible to itraconazole. C. parapsilosis sensu stricto strains were less susceptible to micafungin than C. metapsilosis. © 2012 ISHAM.

Heinrichs G.,RWTH Aachen | Hubner I.,RheinEnergie AG | Schmidt C.K.,RheinEnergie AG | de Hoog G.S.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | And 2 more authors.
Mycopathologia | Year: 2013

Formation of tenacious and massive black biofilms was occasionally observed at the water-air interphase of water taps and in associated habitats at several locations in Germany. Exophiala lecanii-corni was proven to be the dominant component of these biofilms. Water utility companies were interested to understand by which route fungi building these black biofilms enter their habitat at affected sites in domestic sanitary. A wide variety of fungi is known to be common in wet indoor environments, as well as in the drinking water resources. Two possible routes of entry are therefore considered as follows: (a) distribution by the drinking water system or (b) a retrograde route of colonisation. Previous compositional analysis revealed that the black constituents of biofilms primarily belong to the herpotrichiellaceous black yeast and relatives. Therefore, a systematic search for black fungi in the drinking water system was performed using Sabouraud's glucose agar medium with chloramphenicol and erythritol-chloramphenicol agar as isolation media. Cadophora malorum was the dominant fungus in the investigated drinking water systems, and samples taken from the house connections (n = 50; 74 %, <200 cfu/L), followed by a so far undescribed Alternaria sp. (28 %; <10 cfu/L) and E. castellanii (26 %; <10 cfu/L). Of note, C. malorum was not present in any previously analysed biofilm. Since E. lecanii-corni was not found in any water sample from the distribution system tested, but represented the most abundant species in dark biofilms previously analysed, a retrograde route of contamination in case of E. lecanii-corni can be assumed. © 2013 Springer Science+Business Media Dordrecht.

Saunte D.M.,Statens Serum Institute | Saunte D.M.,Copenhagen University | Tarazooie B.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | Arendrup M.C.,Statens Serum Institute | And 3 more authors.
Mycoses | Year: 2012

Black yeast-like fungi are rarely reported from superficial infections. We noticed a consistent prevalence of these organisms as single isolations from mycological routine specimens. To investigate the prevalence of black yeast-like fungi in skin, hair and nail specimens and to discuss the probability of these species to be involved in disease. Slow-growing black yeast-like fungi in routine specimens were prospectively collected and identified. A questionnaire regarding patient information was sent to physicians regarding black yeast-like fungus positive patients. A total of 20746 dermatological specimens were examined by culture. Black yeast-like fungi accounted for 2.2% (n=108) of the positive cultures. Only 31.0% of the samples, culture positive for black yeast-like fungi were direct microscopy positive when compared with overall 68.8% of the culture positive specimens. The most prevalent species were Phialophora europaea (n=29), Coniosporium epidermidis (n=12), Ochroconis cf. humicola (n=6) and Cladophialophora boppii (n=4). These are not common saprobes and thus less likely to be coincidental colonizers. In 10/30 cases, discolouration of nail/skin had been noticed. A limited number of black yeast-like fungi were repeatedly isolated from routine specimens suggesting that they may play a role in superficial infections or as colonizers. © 2011 Blackwell Verlag GmbH.

Zalar P.,University of Ljubljana | Novak M.,University of Ljubljana | De Hoog G.S.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | De Hoog G.S.,University of Amsterdam | And 3 more authors.
Fungal Biology | Year: 2011

Habitats in human households may accommodate microorganisms outside the common spectrum of ubiquitous saprobes. Enrichment of fungi that may require specific environmental conditions was observed in dishwashers, 189 of which were sampled in private homes of 101 towns or communities. One-hundred-two were sampled from various localities in Slovenia; 42 from other European countries; 13 and 3 from North and South America, respectively; 5 from Israel; 10 from South Africa; 7 from Far East Asia; and 7 from Australia. Isolation was performed on samples incubated at 37°C. Species belonging to genera Aspergillus, Candida, Magnusiomyces, Fusarium, Penicillium and Rhodotorula were found occasionally, while the black yeasts Exophiala dermatitidis and Exophiala phaeomuriformis (Chaetothyriales) were persistently and most frequently isolated. Sixty-two percent of the dishwashers were positive for fungi, and 56. % of these accommodated Exophiala. Both Exophiala species are known to be able to cause systemic disease in humans and frequently colonize the lungs of patients with cystic fibrosis. We conclude that high temperature, high moisture and alkaline pH values typically occurring in dishwashers can provide an alternative habitat for species also known to be pathogenic to humans. © 2011 British Mycological Society.

Zhou X.,Chongqing Medical University | Zhou X.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | Rodrigues A.M.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | Rodrigues A.M.,Federal University of São Paulo | And 6 more authors.
Fungal Diversity | Year: 2014

Molecular phylogeny has revealed that sporotrichosis is caused by several Sporothrix species which differ in clinical behavior. The complex is embedded within Ophiostoma, a genus mainly comprising fungi that live in association with bark beetles, but differs by a high virulence towards humans and other mammals. The different ecology is corroborated by phylogenetic separation. The aim of the present study was to determine the validity of the rDNA internal transcribed spacer (ITS) region as a marker for diagnostics of species in the clinical group, using beta-tubulin sequences to calibrate species delimitations. The topology of the two gene trees was concordant, and all clinically relevant Sporothrix species could easily be recognized by means of the ITS region. An increased geographic sampling did not affected delimitation success in the clinical clade of the S. schenckii complex. © 2013 Mushroom Research Foundation.

De Hoog G.S.,Centraalbureau Voor Schimmelcultures Fungal Biodiversity Center | De Hoog G.S.,University of Amsterdam | De Hoog G.S.,Peking University | De Hoog G.S.,Sun Yat Sen University | And 3 more authors.
Journal of Clinical Microbiology | Year: 2012

A new species of nonsporulating fungus, isolated in a case of black-grain mycetoma in Sudan, is described as Madurella fahalii. The species is characterized by phenotypic and molecular criteria. Multigene phylogenies based on the ribosomal DNA (rDNA) internal transcribed spacer (ITS), the partial β-tubulin gene (BT2), and the RNA polymerase II subunit 2 gene (RPB2) indicate that M. fahalii is closely related to Madurella mycetomatis and M. pseudomycetomatis; the latter name is validated according to the rules of botanical nomenclature. Madurella ikedae was found to be synonymous with M. mycetomatis. An isolate from Indonesia was found to be different from all known species based on multilocus analysis and is described as Madurella tropicana. Madurella is nested within the order Sordariales, with Chaetomium as its nearest neighbor. Madurella fahalii has a relatively low optimum growth temperature (30°C) and is less susceptible to the azoles than other Madurella species, with voriconazole and posaconazole MICs of 1 μg/ml, a ketoconazole MIC of 2 μg/ml, and an itraconazole MIC of > 16 μg/ml. Since eumycetoma is still treated only with azoles, correct species identification is important for the optimal choice of antifungal therapy. Copyright © 2012, American Society for Microbiology. All Rights Reserved.

Staats M.,Wageningen University | Erkens R.H.J.,Maastricht University | Erkens R.H.J.,University Utrecht | van de Vossenberg B.,National Reference Center | And 7 more authors.
PLoS ONE | Year: 2013

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well. © 2013 Staats et al.

Heinrichs G.,RWTH Aachen | De Hoog G.S.,Centraalbureau Voor Schimmelcultures Fungal Biodiversity Center | De Hoog G.S.,Institute of Biodiversity and Ecosystem Dynamics | Haase G.,RWTH Aachen
Journal of Clinical Microbiology | Year: 2012

Herpotrichiellaceous black yeasts and relatives comprise severe pathogens flanked by nonpathogenic environmental siblings. Reliable identification by conventional methods is notoriously difficult. Molecular identification is hampered by the sequence variability in the internal transcribed spacer (ITS) domain caused by difficult-to-sequence homopolymeric regions and by poor taxonomic attribution of sequences deposited in GenBank. Here, we present a potential solution using short barcode identifiers (27 to 50 bp) based on ITS2 ribosomal DNA (rDNA), which allows unambiguous definition of species-specific fragments. Starting from proven sequences of ex-type and authentic strains, we were able to describe 103 identifiers. Multiple BLAST searches of these proposed barcode identifiers in GenBank revealed uniqueness for 100 taxonomic entities, whereas the three remaining identifiers each matched with two entities, but the species of these identifiers could easily be discriminated by differences in the remaining ITS regions. Using the proposed barcode identifiers, a 4.1-fold increase of 100% matches in GenBank was achieved in comparison to the classical approach using the complete ITS sequences. The proposed barcode identifiers will be made accessible for the diagnostic laboratory in a permanently updated online database, thereby providing a highly practical, reliable, and cost-effective tool for identification of clinically important black yeasts and relatives. Copyright © 2012, American Society for Microbiology. All Rights Reserved.

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