Evolutionary trends in antifungal resistance: a meta-analysis.

The present paper includes a meta-analysis of literature data on 318 species of fungi belonging to 34 orders in their response to 8 antifungal agents (amphotericin B, caspofungin, fluconazole, itraconazole, ketoconazole, posaconazole, terbinafine, and voriconazole). Main trends of MIC results at the ordinal level were visualized. European Committee on Antimicrobial Susceptibility Testing and Clinical & Laboratory Standards Institute (CLSI) clinical breakpoints were used as the staff gauge to evaluate MIC values ranging from resistance to susceptibility, which were subsequently compared with a phylogenetic tree of the fungal kingdom. Several orders (Hypocreales, Microascales, and Mucorales) invariably showed resistance. Also the basidiomycetous orders Agaricales, Polyporales, Sporidiales, Tremellales, and Trichosporonales showed relatively high degrees of azole multi-resistance, while elsewhere in the fungal kingdom, including orders with numerous pathogenic and opportunistic species, that is, Onygenales, Chaetothyiales, Sordariales, and Malasseziales, in general were susceptible to azoles. In most cases, resistance vs susceptibility was consistently associated with phylogenetic distance, members of the same order showing similar behavior. IMPORTANCE: A kingdom-wide the largest set of published wild-type antifungal data comparison were analyzed. Trends in resistance in taxonomic groups (monophyletic clades) can be compared with the phylogeny of the fungal kingdom, eventual relationships between fungus-drug interaction and evolution can be described.

A taxonomic review of the genus Paracoccidioides, with focus on the uncultivable species.

Paracoccidioides species have always been surrounded by taxonomic uncertainties. The continuing nomenclatoral muddle was caused in part by the failure of Adolfo Lutz and Jorge Lôbo to name the etiologic agents of human paracoccidioidomycosis and Jorge Lôbo's diseases, respectively. Early in their history, it was postulated that the cultivable species causing systemic infections belonged in the genus Paracoccidioides, whereas the uncultivable species, causing skin disease, were not part of the genus. The taxonomy of these pathogens was further complicated when a similar skin disease with numerous yeast-like cells in infected dolphins was also reported. Due to its phenotypic similarities with that described by Jorge Lôbo in human and its uncultivable nature, it was assumed that the disease in dolphins was caused by the same fungus. Recent molecular and population genetic analysis, however, found the DNA extracted from the uncultivable yeast-like cells affecting dolphins shared common phylogenetic traits with cultivable Paracoccidioides species. The study revealed that the uncultivable pathogens comprised 2 different Paracoccidioides species, now known as P. ceti and P. loboi, correspondingly. To validate P. loboi binomial, a comprehensive historical critical review of Jorge Lôbo etiology was performed. This review showed the proposed binomial P. loboi was previously used, and, thus, a replacement name is introduced, Paracoccidioides lobogeorgii nom. nov. In addition, in this review, several cultivable human Paracoccidioides species are validated, and the generic type species, P. brasiliensis, is neotypified as the original material could not be traced.

Actinomortierella wolfii: Identity and pathology.

Actinomortierella wolfii (Mortierellales), formerly Mortierella wolfii, is a causative agent of bovine systemic infection and abortion. Human infections caused by this species are extremely rare. Here, we present a case of a patient with B-Cell Acute Lymphoblastic Leukemia (B-ALL) who was diagnosed with a rhinocerebral infection caused by this fungus. Amphotericin treatment of the patient proved unsuccessful. This type of disease is otherwise nearly exclusively limited to members of the order Mucorales. The taxonomy of the causative agent is discussed.

Majocchi's granuloma: Autoinoculation and adaption of Trichophyton rubrum with molecular evidence.

BACKGROUND: Trichophyton rubrum, an important aetiological agent of superficial dermatophytosis, occasionally penetrates into deeper tissues, causing inflammation and a granulomatous response. Only few case reports of T. rubrum granuloma with molecular evidence for autoinoculation have been published. OBJECTIVES: To find the genetic basis of adaptation to a different microhabitat following autoinoculation of Trichophyton rubrum. METHODS: A case of Majocchi's granuloma is reported, with isolation of T. rubrum strains from foot and chin, respectively. Whole-genome sequencing of the two strains has been performed. Phylogenetic reconstruction and SIFT analysis were conducted. RESULTS: A phenotypic difference has been observed between the two isolates. 20 and 19 indels, 8 and 15 SNVs were found in foot and chin strains, respectively. Foot and chin strains formed a monophyletic group. Two non-synonymous mutations of chin strains were observed in the TERG_06754 gene encoding cytochrome c peroxidase (CCP). The G293C amino acid change in TERG_03373 was predicted to affect protein function significantly. The mutated amino acid (cysteine) was only found in the chin strain in all dermatophyte non-redundant sequences. CONCLUSIONS: Non-synonymous mutations located in TERG_06754 and TERG_03373 were predicted to affect protein functions, which may facilitate the adaption for invasion of the superficial cutaneous strain. As the different living environments of these two strains (oxygenous, lower-temperature for the pedal strain; hypoxia, higher-temperature for the chin strain), a stratum corneum-to-dermal adaption hypothesis of T. rubrum was proposed.

Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.

The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the "Shed light in The daRk lineagES of the fungal tree of life" (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments.

Gloeostereum cimri, a novel shelf fungus isolated from a human pulmonary cyst.

Filamentous basidiomycetes are uncommon agents of human diseases, despite their ubiquitous presence in the environment. We present a case of symptomatic pulmonary infection in a 38-year-old male with cough and fever; a thin-walled cyst in the posterior left upper pulmonary lobe was revealed by radiography. A non-sporulating fungus was isolated from sputum and biopsy material from the cyst. ITS and LSU sequences placed the fungus phylogenetically in Agaricales, family Cyphellaceae, and identified it as a member of shelf fungi in Gloeostereum, but without identity to any known species. The new species is described as Gloeostereum cimri. The clinical strain showed high MIC to voriconazole (>8 µg/ml) but had low MIC to amphotericin B (0.5 µg/ml).

Lineages Within the Trichophyton rubrum Complex.

The most important species of the Trichophyton rubrum group are T. rubrum, causing mainly skin and nail infections, and T. violaceum which is mostly scalp-associated. The status of a third species, T. soudanense, has been under debate. With a polyphasic approach, using molecular phylogenetic techniques, MALDI-TOF mass spectrometry and physiological and morphological analysis, we re-evaluated the T. rubrum complex. Our results support four genetic lineages within the complex each with a distinct morphology and identifiable via MALDI-TOF MS: T. rubrum, T. violaceum, T. soudanense and the T. yaoundei clade. However, ITS and Bt2 sequencing data could not confirm these taxa as four monophyletic species. Our results also suggest that strains formerly identified as T. kuryangei and T. megninii should be considered in future taxonomic studies.

Virulence and antifungal susceptibility of microsatellite genotypes of Candida albicans from superficial and deep locations.

A set of 185 strains of Candida albicans from patients with vulvovaginal candidiasis (VVC) and from non-VVC clinical sources in southwest China was analysed. Strains were subjected to genotyping using CAI microsatellite typing and amplification of an intron-containing region of the 25S rRNA gene. Microsatellite genotypes of strains from non-VVC sources showed high polymorphism, whereas those of VVC were dominated by few, closely similar genotypes. However, among non-VVC strains, two genotypes were particularly prevalent in patients with lung cancer. 25S rDNA genotype A was dominant in VVC sources (86.7%), whereas genotypes A, B, and C were rather evenly distributed among non-VVC sources; known genotypes D and E were not found. In an experimental mouse model, isolates from lung cancer and AIDS patients proved to have higher virulence than VVC strains. Among 156 mice infected with C. albicans, 19 developed non-invasive urothelial carcinoma. No correlation could be established between parameters of virulence, source of infection, and incidence of carcinoma. C. albicans strains from VVC were less susceptible to itraconazole than the strains from non-VVC sources, whereas there was small difference in antifungal susceptibility between different 25S rDNA genotypes of C. albicans tested against amphotericin B, itraconazole, fluconazole, and flucytosine.

Disseminated Mycosis by Arthrocladium fulminans Jeopardizing a Patient with GATA2 Deficiency.

GATA2 deficiency is characterized by monocytopenia, deficiency of dendritic cells, and a variable degree of lymphocytopenia affecting B cells and NK cells, leading to an enhanced risk of mycobacterial, viral, and fungal infections. Here we present a patient with a heterozygous intronic GATA2 mutation who acquired a fatal disseminated mycosis due to the black yeast-like fungus Arthrocladium fulminans following an infection with Mycobacterium sherrisii. This case illustrates that in patients with severe uncommon infections, immunodeficiency syndromes must be ruled out.

Scedosporium and Lomentospora: an updated overview of underrated opportunists.

Species of Scedosporium and Lomentospora are considered as emerging opportunists, affecting immunosuppressed and otherwise debilitated patients, although classically they are known from causing trauma-associated infections in healthy individuals. Clinical manifestations range from local infection to pulmonary colonization and severe invasive disease, in which mortality rates may be over 80%. These unacceptably high rates are due to the clinical status of patients, diagnostic difficulties, and to intrinsic antifungal resistance of these fungi. In consequence, several consortia have been founded to increase research efforts on these orphan fungi. The current review presents recent findings and summarizes the most relevant points, including the Scedosporium/Lomentospora taxonomy, environmental distribution, epidemiology, pathology, virulence factors, immunology, diagnostic methods, and therapeutic strategies.

Ecology of the Human Opportunistic Black Yeast Exophiala dermatitidis Indicates Preference for Human-Made Habitats.

Exophiala dermatitidis is an ascomycetous black yeast from the order Chaetothyriales. Its growth characteristics include the polymorphic life cycle, ability to grow at high and low temperatures, at a wide pH range, survival at high concentrations of NaCl, and survival at high UV and radioactive radiation. Exophiala dermatitidis causes deep or localized phaeohyphomycosis in immuno-compromised people worldwide and is regularly encountered in the lungs of cystic fibrosis patients. Regardless of numerous ecological studies worldwide, little is known about its natural habitat or the possible infection routes. The present review summarizes the published data on its frequency of occurrence in nature and in man-made habitats. We additionally confirmed its presence with culture-depending methods from a variety of habitats, such as glacial meltwater, mineral water, mineral-rich salt-pan mud, dishwashers, kitchens and different environments polluted with aromatic hydrocarbons. In conclusion, the frequency of its recovery was the highest in man-made indoor habitats, connected to water sources, and exposed to occasional high temperatures and oxidative stress.

Chromoblastomycosis.

Chromoblastomycosis (CBM), also known as chromomycosis, is one of the most prevalent implantation fungal infections, being the most common of the gamut of mycoses caused by melanized or brown-pigmented fungi. CBM is mainly a tropical or subtropical disease that may affect individuals with certain risk factors around the world. The following characteristics are associated with this disease: (i) traumatic inoculation by implantation from an environmental source, leading to an initial cutaneous lesion at the inoculation site; (ii) chronic and progressive cutaneous and subcutaneous tissular involvement associated with fibrotic and granulomatous reactions associated with microabscesses and often with tissue proliferation; (iii) a nonprotective T helper type 2 (Th2) immune response with ineffective humoral involvement; and (iv) the presence of muriform (sclerotic) cells embedded in the affected tissue. CBM lesions are clinically polymorphic and are commonly misdiagnosed as various other infectious and noninfectious diseases. In its more severe clinical forms, CBM may cause an incapacity for labor due to fibrotic sequelae and also due to a series of clinical complications, and if not recognized at an early stage, this disease can be refractory to antifungal therapy.

An updated comprehensive systematic review of Cladophialophora bantiana and analysis of epidemiology, clinical characteristics, and outcome of cerebral cases.

Cladophialophora bantiana is a phaeoid fungus that only rarely has been isolated from sources other than the human brain. It has a particular tropism for the central nervous system (CNS). We have integrated and updated large-scale data related to several aspects of C. Bantiana and reviewed all the available reports on its cerebral infections, focusing on their geographical distribution, infection routes, immune status of infected individuals, type and location of infections, clinical manifestations and treatment and outcome, briefly looking over the spectrum of other disease entities associated with C. bantiana, that is, extra-cerebral and animal infections and on the environmental sources of this fungus. Among the agents of phaeohyphomycosis, a term used to describe an infection caused by a dark pigmented fungus, C. bantiana has some significant specific features. A total of 120 case reports were identified with a significantly higher percentage of healthy subjects than immune-debilitated patients (58.3% vs. 41.7%). Infections due to C. bantiana occur worldwide. The main clinical manifestations are brain abscess (97.5%), coinfection of brain tissue and meninges (14.2%) and meningitis alone (2.5%). Among immunocompetent patients, cerebral infection occurred in the absence of pulmonary lesions. The mortality rate is 65.0% regardless of the patient's immune status. The therapeutic options used include surgery or antifungals alone, and the combination of both, in most cases the fatal outcome being rapid after admission. Since the fungus is a true pathogen, laboratory workers should be made aware that BioSafety Level-3 precautions might be necessary.

Mucormycosis in Iran: a systematic review.

Fungi in the order Mucorales cause acute, invasive and frequently fatal infections in susceptible patients. This study aimed to perform a systematic review of all reported mucormycosis cases during the last 25 years in Iran. After a comprehensive literature search, we identified 98 cases in Iran from 1990-2015. The mean patient age was 39.8 ± 19.2 years. Diabetes was the most common underlying condition (47.9%), and 22.4% of the patients underwent solid organ or bone marrow transplantation. The most common clinical forms of mucormycosis were rhinocerebral (48.9%), pulmonary (9.2%) and cutaneous (9.2%). Eight cases of disseminated disease were identified. Overall mortality in the identified cases was 40.8%, with the highest mortality rate in patients diagnosed with disseminated infection (75%). The mortality rate in rhinocerebral infection patients was significantly lower (45.8%). Rhinocerebral infection was the most common clinical manifestation in diabetes patients (72.9%). Patients were diagnosed using various methods including histopathology (85.7%), microscopy (12.3%) and culture (2.0%). Rhizopus species were the most prevalent (51.7%), followed by Mucor species (17.2%). Sixty-nine patients were treated with a combination of surgery and antifungal therapy (resulting survival rate, 66.7%). Owing to the high mortality rate of advanced mucormycosis, early diagnosis and treatment may significantly improve survival rates. Therefore, increased monitoring and awareness of this life-threatening disease is critical.

Development of a new MLST scheme for differentiation of Fusarium solani Species Complex (FSSC) isolates.

Fungi belonging to the Fusarium solani Species Complex (FSSC) are well known plant pathogens. In addition to being the causative agent of some superficial infections, FSSC has recently emerged as a group of common opportunistic moulds, mainly in patients with haematological malignancies. Molecular typing methods are essential in order to better understand the epidemiology of such opportunistic agents with the final goal of preventing contamination. A three-locus typing scheme has thus been developed for FSSC; based on polymorphisms in the domains of the ITS, EF-1 alpha, and RPB2 genes. This method is now considered to be a useful reference for phylogenetic and taxonomic studies. In other significant clinical fungi (e.g., Candida sp., Cryptococcus neoformans, and Aspergillus fumigatus), genes coding for metabolic enzymes have been widely used and proven to be very informative for diagnosis and epidemiology. The contribution of these genes has never been evaluated for Fusarium sp. and more specifically for F. solani Species Complex. Here, we have evaluated the contribution of 25 genes for diagnosis and epidemiological purposes. We then report a new five-locus MLST scheme useful for diagnosis and typing of clinical FSSC isolates. The method has been validated on 51 epidemiologically unrelated strains of FSSC and presents a high power of discrimination calculated at 0.991.

A polyphasic approach to the taxonomy of the Alternaria infectoria species-group.

Different taxa in the species-group of Alternaria infectoria (teleomorph Lewia spp.) are often isolated from various cereals including barley, maize and wheat grain, ornamental plants and skin lesions from animals and humans. In the present study we made a polyphasic characterization of 39 strains morphologically identifiable as belonging to the A. infectoria species-group together with 12 strains belonging to closely related species: Alternaria malorum (syn. Cladosporium malorum), Chalastospora cetera (syn. Alternaria cetera) and Embellisia abundans. Morphological examination separated the 51 strains in three groups based on conidial appearance and arrangement: the A. infectoria species-group, E. abundans and a group containing C. cetera and A. malorum. The metabolite analyses on three different media showed two clusters, one containing all 39 A. infectoria species-group strains and one containing 10 strains of E. abundans, C. cetera and A. malorum. One E. abundans strain and one A. malorum strain were not included due to insufficient metabolite production. The separation of the A. infectoria species-group from E. abundans, C. cetera and A. malorum resulted mainly from the ability to produce altertoxins and novae-zelandins. The metabolite analyses also showed that all 51 strains were able to produce infectopyrones. The metabolite profiles of C. cetera and A. malorum were very similar with several metabolites of unknown structure in common. This is the first time that E. abundans, C. cetera and A. malorum have been reported as producers of infectopyrones. Sequence analyses of the internal transcribed spacer region (ITS), glyceraldehyde-3-phosphate dehydrogenase (gpd) and translocation elongation factor 1alpha (tef-1alpha) showed two clades: one with the 39 strains from the A. infectoria species-group and one with the 12 strains of E. abundans, C. cetera and A. malorum. The polyphasic approach in this study suggests that A. malorum var. polymorpha and the eight A. malorum strains do not belong in Alternaria, but in Chalastospora, however, as several distinct species. Splits Tree alignment of gpd sequences of 38 strains belonging to the A. infectoria species-group indicates that only three strains showed signs of recombination, while the remaining strains appeared to be clonal. Long term incubation at 7 degrees C in the dark showed that 12 out of 33 tested strains from the A. infectoria species-group were able to produce proascomata in axenic culture, but with no mature ascospores after 6 months. These findings suggest that Lewia/A. infectoria species-group must, at least in part, be homothallic. The results presented in this study show that ITS, tef-1alpha and gpd do not reflect ecology, secondary metabolism or morphology of the A. infectoria species-group and that molecular cladification and phylogeny cannot predict pathogenicity, host specificity or mycotoxin production.

Disseminated phaeohyphomycosis in weedy seadragons (Phyllopteryx taeniolatus) and leafy seadragons (Phycodurus eques) caused by species of Exophiala, including a novel species.

During the period from January 2002 to March 2007, infections by melanized fungi were identified with greater frequency in aquarium-maintained leafy seadragons (Phycodurus eques) and weedy seadragons (Phyllopteryx taeniolatus), pivotal species to the educational and environmental concerns of the aquarium industry and conservation groups. The objective of this study was to characterize the pathology and identify fungi associated with phaeohyphomycotic lesions in these species. Samples from 14 weedy and 6 leafy seadragons were received from 2 institutions and included fresh, frozen, and formalin-fixed tissues from necropsy and biopsy specimens. Fresh and frozen tissues were cultured for fungi on Sabouraud dextrose agar only or both Sabouraud dextrose agar and inhibitory mold agar with gentamicin and chloramphenicol at 30 degrees C. Isolates were processed for morphologic identification and molecular sequence analysis of the internal transcribed spacer region and D1/D2 domains of the large subunit ribosomal RNA gene. Lesions were extensive and consisted of parenchymal and vascular necrosis with fungal invasion of gill (11/20), kidney (14/20), and other coelomic viscera with or without cutaneous ulceration (13/20). Exophiala sp. isolates were obtained from 4 weedy and 3 leafy seadragons and were identified to species level in 6 of 7 instances, namely Exophiala angulospora (1) and a novel species of Exophiala (5), based on nucleotide sequence comparisons and phylogenetic analyses. Disseminated phaeohyphomycosis represents an important pathologic condition of both weedy and leafy seadragons for which 2 species of Exophiala, 1 a novel species, have been isolated.

Eumycetoma caused by Cladophialophora bantiana successfully treated with itraconazole.

A 57-year-old male presented with dermatosis of the dorsum of the foot consisting of tumefaction, deformity and sinus tract formation. The direct examination of exudates as well as the biopsy tissue, demonstrated the presence of black granules. A dematiaceous fungus was isolated from the lesions and was identified by ribosomal DNA sequencing as Cladophialophora bantiana. This is the second report of this fungus as an etiologic agent of eumycetoma in humans. Clinical and mycologic cure was achieved after 20 months of treatment with itraconazole at a starting dose of 300 mg/day that was tapered during the course of therapy. The patient's isolate had an itraconazole MIC of 0.012 microg/ml.