Comparative analysis of whole genomes and transcriptomes of Microsporum canis from invasive dermatophytosis and tinea capitis.

ABSTRACTGenomes of strains of the zoophilic dermatophyte Microsporum canis from invasive (disseminated and subcutaneous) and noninvasive (tinea capitis) infections were compared. Especially the disseminated strain showed significant syntenic rearrangements, including multiple translocations and inversions, and numerous SNPs and Indels in comparison to the noninvasive strain. In transcriptome analysis, both invasive strains were enriched for GO pathways related to components of the membrane, iron binding and heme binding, which possibly enables them to invade deeper into dermis and blood vessels. At 37 °C, invasive strains showed gene expression enriched for DNA replication, mismatch repair, N-glycan biosynthesis and ribosome biogenesis. The invasive strains were slightly less susceptible to multiple antifungal agents suggesting that acquired elevated drug resistance might be involved in the refractory disease courses. Patient with disseminated infection failed to respond to a combined antifungal treatment with itraconazole, terbinafine, fluconazole and posaconazole.

Novel black yeast-like species in chaetothyriales with ant-associated life styles.

Among ancestral fungi in Chaetothyriales, several groups have a life style in association with tropical ants, either in domatia or in carton-nests. In the present study, two strains collected from ant carton in Thailand and Malaysia were found to represent hitherto undescribed species. Morphological, physiological, phylogenetic data and basic genome information are provided for their classification. Because of the relatively large phylogenetic distances with known species confirmed by overall genome data, large subunit (LSU) and Internal Transcribed Spacer (ITS) ribosomal DNA sequences were sufficient for taxonomic circumscription of the species. The analyzed strains clustered with high statistical support as a clade in the family Trichomeriaceae. Morphologically they were rather similar, lacking sporulation in vitro. In conclusion, Incumbomyces delicatus and Incumbomyces lentus were described as new species based on morphological, physiological and phylogenetic analysis.

Comparative Analysis of Clinical and Environmental Strains of Exophiala spinifera by Long-Reads Sequencing and RNAseq Reveal Adaptive Strategies.

Exophiala spinifera, a capsule-producing black yeast, is overrepresented as agent of disseminated infection in humans with inherited dysfunction of the CARD9 gene. In a review of published caspase recruitment domain-containing protein 9 (CARD9) deficiency cases, black fungi were linked to mutations other than those prevalent in yeast and dermatophyte cases, and were found to respond to a larger panel of cytokines. Here, we sequenced and annotated the genomes of BMU 08022 from a patient with CARD9 deficiency and two environmental strains, BMU 00051 and BMU 00047. We performed genomic and transcriptomic analysis for these isolates including published black yeasts genomes, using a combination of long-read (PACBIO) and short-read (Illumina) sequencing technologies with a hybrid assembly strategy. We identified the virulence factors, fitness, and the major genetic and gene expression differences between the strains with RNAseq technology. Genome assembly reached sub-chromosome level with between 12,043 and 12,130 predicted genes. The number of indels identified in the clinical strain was higher than observed in environmental strains. We identify a relatively large core genome of 9,887 genes. Moreover, substantial syntenic rearrangements of scaffolds I and III in the CARD9-related isolate were detected. Seventeen gene clusters were involved in the production of secondary metabolites. PKS-cluster 17 was consistently found to be absent in the clinical strain. Comparative transcriptome analysis demonstrated that 16 single-copy genes were significantly differentially expressed upon incubation in brain-heart infusion broth vs. Sabouraud glucose broth. Most of the single-copy genes upregulated with Brain Heart Infusion (BHI) were transporters. There were 48 unique genes differentially expressed exclusively to the clinical strain in two different media, including genes from various metabolic processes and transcriptional regulation. Up-regulated genes in the clinical strain with Gene Ontology (GO) enrichment are mainly involved in transmembrane transport, biosynthetic process and metabolic process. This study has provided novel insights into understanding of strain-differences in intrinsic virulence of the species and indicated that intraspecific variability may be related to habitat choice. This indicates that strains of E. spinifera are differentially prone to cause infection in susceptible patient populations, and provides clues for future studies exploring the mechanisms of pathogenic and adaptive strategies of black yeasts in immunodeficient patients.

Fixed cutaneous sporotrichosis in a patient with numerous fungal elements.

Sporotrichosis generally shows no or a small number of fungal cells in tissue. Numerous fungal elements are usually associated with suppression of cellular immunity, either acquired or innate. The present case demonstrates that also topical immunosuppression can lead to increased fungal load at the affected site.

Possible rabbit breeders' Trichophyton mentagrophytes infection characterized by Majocchi's granuloma in immunocompetent host: Case report.

We report on a family of three in a rabbit farm, especially children with Majocchi granuloma as the main clinical feature of cross-infection of Trichophyton mentagrophytes, provides experience in reducing the rate of clinical misdiagnosis. Based on the pathological features of Majocchi's granuloma, taking into account that severe inflammatory reactions are also responsible for the damage of the body. In Majocchi's granuloma treatment strategy, we recommend the use of anti-inflammatory Chinese medicines that have a hormonal effect and have no side effects.

Onychomycosis with greenish-black discolorations and recurrent onycholysis caused by Candida parapsilosis.

Candida parapsilosis (C. parapsilosis) has become a common pathogen, especially in immunocompromised hosts. Here, we present an immunocompetent adult with greenish-black discoloration of the right first finger nail in combination with recurrent onycholysis. C. parapsilosis was isolated from the right first finger nail and was confirmed by morphological characteristics as well as by DNA molecular analysis. Patient was successfully treated with oral itraconazole in a regimen of 5 cycles of 200 mg twice daily for one week, followed by an interruption of treatment for 3 weeks. To our knowledge, this is the first report of C. parapsilosis-induced onychomycosis with recurrent onycholysis.

Peritonitis by Exophiala dermatitidis in a pediatric patient.

Fungal peritonitis is frequent on peritoneal dialysis, with rare cases by Exophiala dermatitidis. A 25-month-old female admitted to the pediatric ICU with acute renal failure was submitted to peritoneal dialysis. After 10 days patient presented fever. Peritoneal fluid culture showed yeast colonies molecularly identified as E. dermatitidis. Patient was treated with voriconazole and hemodialysis. The literature was reviewed. Disseminated infections are frequently fatal, but appropriate diagnose and therapeutic led to cure in this case.

Current antifungal treatment of fusariosis.

Fungi of the genus Fusarium are well known as major plant pathogens and soil inhabitants, but also cause a broad spectrum of human infections. Fusariosis is the second most common mould infection after aspergillosis, and keratitis is the most encountered implantation infection in immunocompetent individuals. Natamycin is active against Fusarium species both in vitro and in vivo, and is used along with voriconazole as the mainstay of treatment for Fusarium keratitis. Onychomycosis is treated with terbinafine, voriconazole and sometimes itraconazole. Cure is possible despite high in vitro minimum inhibitory concentrations (MICs). Recently, disseminated infections have increased dramatically, mainly affecting severely immunocompromised patients. The remarkable intrinsic resistance of Fusarium species to most antifungal agents results in high mortality rates in this patient population. Recovery of neutropenia is essential for patient survival and treatment should include voriconazole or amphotericin B as first-line and posaconazole as salvage therapy.

Fungi growing on aromatic hydrocarbons: biotechnology's unexpected encounter with biohazard?

The biodegradation of aromatic hydrocarbons by fungi has traditionally been considered to be of a cometabolic nature. Recently, however, an increasing number of fungi isolated from air biofilters exposed to hydrocarbon-polluted gas streams have been shown to assimilate volatile aromatic hydrocarbons as the sole source of carbon and energy. The biosystematics, ecology, and metabolism of such fungi are reviewed here, based in part on re-evaluation of a collection of published hydrocarbon-degrading isolates obtained from authors around the world. Incorrect or outdated identifications in original publications are corrected by ribosomal DNA sequence analysis. The data show that many volatile-hydrocarbon-degrading strains are closely related to, or in some cases clearly conspecific with, the very restricted number of human-pathogenic fungal species causing severe mycoses, especially neurological infections, in immunocompetent individuals. Neurochemistry features a distinctive array of phenolic and aliphatic compounds that are related to molecules involved in the metabolism of aromatic hydrocarbons. Hence, there may be physiological connections between hydrocarbon assimilation and certain patterns of mammalian infection.

Taxonomy and phylogeny of the xerophilic genus Wallemia (Wallemiomycetes and Wallemiales, cl. et ord. nov.).

The genus Wallemia comprises xerophilic species. Based on parenthesome ultrastructure it has been linked to the Filobasidiales (basidiomycetes). Species show a unique type of conidiogenesis, including basauxic development of fertile hyphae, segregation of conidial units more or less basipetally, and disarticulation of conidial units into mostly four arthrospore-like conidia. Wallemia is known from air, soil, dried food (causing spoilage), and salt. It can be isolated from hypersaline water of man-made salterns on different continents. Based on analyses of the nuclear small subunit ribosomal DNA (SSU rDNA) Wallemia has been placed into a highly supported clade together with Ustilaginomycetes and Hymenomycetes (Basidiomycota). Within this clade, it possesses an isolated position distantly related to the Filobasidiales and was characterized by numerous nucleotide substitutions not shared by any other fungus. Tests on xerotolerance indicated that Wallemia presents one of the most xerophilic fungal taxa. Xerotolerance is otherwise rare in the Basidiomycota. To acknowledge its unique morphology, evolution, and xerotolerance, a new basidiomycetous class Wallemiomycetes covering an order Wallemiales, is proposed. Based on differences in conidial size, xerotolerance, and sequence data of the rDNA internal transcribed spacer regions (ITS rDNA), at least three Wallemia species are segregated, identified as Wallemia ichthyophaga, Wallemia sebi, and Torula epizoa var. muriae, for which the combination Wallemia muriae is proposed. The three species are neotypified. Wallemia ichthyophaga differs from W. sebi and W. muriae in numerous nucleotides of the SSU and ITS rDNA. This high variation within Wallemia indicates existence of at least two cryptic genera not distinguishable by morphological characters.