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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.

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.

Augustin J.O.,Federal University of Vicosa | Groenewald J.Z.,Centraalbureau voor Schimmelcultures Fungal Biodiversity Center | Nascimento R.J.,Federal University of Vicosa | Mizubuti E.S.G.,Federal University of Vicosa | 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.

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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