Rare Fungus Research Articles

Azole Resistance in Moulds—Approach to Detection in a Clinical Laboratory

The multitude of factors has contributed to the increasing number of fungal infections caused by species of difficult-to-treat opportunistic moulds, such as Fusarium, Scedosporium, and cryptic Aspergilli. Also, rare fungi sporadically encountered, such as Rasamsonia argillacea, Penicillium oxalicum, and melanized fungi, are now well recognized. The high mortality associated with these rare and uncommon fungi is primarily linked to the difficulty in diagnosis and limited therapeutic options, as many of them exhibit resistance to antifungals including azoles. Azole resistance in Aspergillus fumigatus has been increasingly reported because standardized methods for susceptibility testing and associated clinical breakpoints and epidemiological cutoff values became available. However, such advances in antifungal susceptibility testing (AFST) in non-Aspergillus moulds barring mucorales have been lacking. Notwithstanding the fact that the true incidence of these non-Aspergillus filamentous moulds in clinical settings is hitherto unknown, also data on AFST by standardized methods is largely lacking. Determination of minimum inhibitory concentration (MIC) by reference techniques is the gold standard to detect azole resistance in filamentous fungi. In recent years, some progress has been made toward the description of resistance mechanisms at molecular level especially in Aspergillus. This paper reviews the present state of azole resistance in Aspergillus and other filamentous mould species and discusses their relevance to clinical practice.

Fungal Keratitis in North India: Spectrum of Agents, Risk Factors and Treatment.

To assess the prevalence of fungal keratitis, we conducted a retrospective study over 7years (2005 through 2011) at a tertiary care center in North India. Effort has been made to analyze the disease burden, spectrum of agents and treatment history. The findings were compared with an earlier study at the same center for any change in the epidemiology of the disease. Microbiology records were screened at the Postgraduate Institute of Medical Education and Research, Chandigarh, India, to identify fungal keratitis cases, and available clinical records of those cases were analyzed. Of 2459 clinically suspected fungal keratitis cases, 765 (31%) cases were direct microscopy confirmed. Of these microscopy-confirmed cases, fungi were isolated in 393 (51.4%), with Aspergillus spp. ranked top (n=187, 47.6%), followed by melanized fungi (n=86, 21.9%) and Fusarium spp. (n=64, 16%). A male predominance of 78.7% was noted with a peak in the incidence of fungal keratitis during post-monsoon season (September to November). A delay in diagnosis was significantly associated (p<0.001) with keratitis cases due to melanized fungi. In comparison with an earlier study, higher isolation of melanized fungi was noted with a widening of the spectrum of agents identified. Thus, fungal keratitis due to Aspergillus spp. remains a serious ocular illness among the active male population in North India with relative rise of keratitis due to melanized fungi. The spectrum of agents causing fungal keratitis has broadened with many rare fungi that are implicated.

Cystoderma carpaticum (Basidiomycota, Agaricales), a rare fungus newly recorded from Croatia

Cystoderma carpaticum was collected and originally described from the Carpathians in Poland. Later, it was recombined in the genera Lepiota and Echinoderma. Two recent collections from Croatia allowed for reliable phylogenetic and morphological comparative analyses of this rare fungus, including the holotype specimen. Our results confirmed that this taxon is a distinct species, and a member of the genus Cystoderma, not Lepiota nor Echinoderma (= Lepiota sect. Echinatae). C. carpaticum is re-described in detail, and data on its ecology and distribution are newly presented. Additional two studied collections of C. carpaticum (Austria, Czech Republic) were misidentified and they belong to C. subvinaceum. Synonymization of C. carpaticum with Leucopholiota decorosa is rejected.

Progressive multifocal leukoencephalopathy and black fungus in a patient with rheumatoid arthritis without severe lymphocytopenia

Introduction:Progressive multifocal leukoencephalopathy (PML) is a rare demyelinating brain infection caused by JC polyomavirus (JCV), primarily seen in patients with severely compromised cellular immunity. Clinical presentation varies depending on the affected white matter. PML prognosis is variable and effective treatments are lacking.Case presentation:A 75-year-old Chinese woman with type 2 diabetes mellitus, chronic kidney disease and rheumatoid arthritis, treated with low-dose methotrexate and prednisolone for 2.5 years, developed a Pleurostomophora richardsiae infection of her left arm. After 6 months of treating this rare black fungus infection with voriconazole, surgery and immunosuppression discontinuation, she presented with progressive afebrile encephalopathy with right-sided hemiparesis. There were no signs of inflammation or metabolic abnormalities. Brain magnetic resonance imaging revealed diffuse frontal white matter lesions and a cerebrospinal fluid PCR confirmed PML due to JC virus. Severe lymphopenia was never present, and at PML diagnosis, CD4 and CD8 T-cell counts were 454 mm−3 and 277 mm−3. CD8 T-cells were able to respond to JCV VP1 peptide stimulation with TNFα secretion. Peripheral B-cell count was only 8 mm−3. Mirtazapine and Maraviroc were started, but unfortunately, she rapidly deteriorated and died 5 weeks after PML diagnosis.Conclusion:Although peripheral lymphocyte counts were never low and CD4 T-cell count was close to normal, the persistent black fungus infection was a hallmark of severely compromised cellular immunity. The unexpected extremely low absolute B-cell count might suggest a protective role for B-cells. The paradoxical, clinical PML onset months after immunosuppressive discontinuation suggests that it was only discovered in the context of an immune reconstitution inflammatory syndrome.

Squamanita odorata (Agaricales, Basidiomycota), new mycoparasitic fungus for Poland

Abstract The rare and interesting fungus Squamanita odorata (Cool) Imbach, a parasite on Hebeloma species, is reported for the first time from Poland, briefly described and illustrated based on Polish specimens. Its taxonomy, ecology and distribution are discussed.

Kodamaea ohmeri Fungemia in a Patient with Carcinoma of the Ampulla of Vater

Kodamaea ohmeri, previously known as Pichia ohmeri or Yamadazyma ohmeri, is an ascosporogenous yeast that belong to the Saccharomycetaceae family, and it is a rare yeast-form fungus recently identified as an etiological agent of fungemia, endocarditis, urinary tract infection and peritonitis in immunocompromised patients. This paper presents a case of K. ohmeri fungemia in a 70-year-old man with carcinoma of the ampulla of Vater. After receiving endoscopic retrograde cholangiopancreatography (ERCP) for releasing obstruction of ampulla of Vater by insertion of the biliary stent, he was pyrexial with a temperature of 38.5°C. Two set of blood samples were obtained from a peripheral vein for culture. The pathogen was identified as K. ohmeri using the Vitek YST card (bioMérieux, France) and was confirmed by the sequencing of the D1/D2 domains of the 26S rRNA gene and the internally transcribed spacer region. The minimal inhibitory concentrations of the antifungal agents were as follows: amphotericin B 0.5 μg/mL; fluconazole 2 μg/mL; voriconazole ≤ 0.12 μg/mL; fluocytosine ≤ 1 μg/mL. According to the Clinical and Laboratory Standard Institute recommended breakpoint for Candida spp, the isolate was susceptible to fluconazole, amphotericin B, voriconazole, and flucytosine. This is the first report of the isolation of K. ohmeri in the patient with a gastrointestinal neoplasm following ERCP.

The Fungal Mycobiota: Small Numbers, Large Impacts.

Fungi are an underappreciated component of the human gut microbiota. In this issue of Cell Host & Microbe, Wheeler etal. (2016) demonstrate that fungal dysbiosis induced by antifungal treatment or inoculation with typically rare fungi results in exaggerated immune responses, suggesting that fungal colonizers play key roles in immune homeostasis.

MICROBIAL COMPOSITION OF VARIOUS SURFACES OF SKIN DURING DEVELOPMENT OF ATOPIC DERMATITIS BASED ON DATA FROM MALDI-TOF MASS-SPECTROMETRY IDENTIFICATION METHOD

Study transformation of skin microflora during development of atopic dermatitis. 45 patients with various forms of atopic dermatitis (AtD) were examined. Control group consisted of 26 healthy individuals. The strains were cultivated on elective nutrient media. Identification ofthe isolated strains was carried out by MALDI-TOF mass-spectrometry method. A low frequency of occurrence of taxon Staphylococcus epidermidis on face skin and high frequency of occurrence of Staphylococcus aureus on upper and lower limb skin was established for AtD patients compared with healthy individuals. The frequency of occurrence of proteolyti-cally active isolates of S. aureus in AtD patients was 3 times higher than in healthy carriers of this taxon. Taxons of microorganisms not inherent to healthy individuals such as Bacillus mycoides, Pseudomonas putida, Pseudomonas radiobacter were isolated on lower limb and neck skin of AtD patients. A high frequency of occurrence of Cryptococcus satoi, Candida albicans, Malassezia globosa fungi was noted. A decrease of barrier functions of skin during AtD facilitates contamination of patients' skin with rare bacterial taxons and fungi. One of the possible mechanisms of suppression of immune competent cell functions could be proteolytic enzymes of S. aureus.

The environmental source of emerging Apophysomyces variabilis infection in India.

The rare mucoraceous fungus, Apophysomyces species complex ranks second after Rhizopus arrhizus causing mucormycosis in India. The source of this agent in the environment is not clearly known. We conducted an environmental study to find its presence in Indian soil. The soil samples from different geographical locations were analyzed for isolation of Mucorales. Rhizopus arrhizus (24.6%) was most commonly isolated from soil, followed by Lichtheimia spp. (23.2%), Cunninghamella spp. (21.7%), Rhizopus microsporus (14%) and Apophysomyces spp. (4.5%). The isolation of Apophysomyces species complex was significantly associated with low nitrogen content of the soil. Based on sequencing of internal transcribed spacer (ITS) and 28S (D1/D2) regions of ribosomal DNA, the Apophysomyces isolates were identified as Apophysomyces variabilis with 98 to 100% similarity to type strain A. variabilis (CBS658.93). The analysis of amplified fragment length polymorphism (AFLP) fingerprinting data demonstrated genomic diversity of A. variabilis isolates with multiple clades (similarity 40-90%). The minimum inhibitory concentrations (MIC), MIC50 and MIC90 for A. variabilis isolates were 1 and 4 μg/ml for amphotericin B, 0.25 and 0.5 μg/ml for itraconazole, 0.125 and 0.25 μg/ml for posaconazole, 0.06 and 0.12 μg/ml for terbinafine, respectively. The present study revealed abundant presence of A. variabilis in Indian soil with low nitrogen content, its genetic heterogeneity and relatively high MICs for amphotericin B.

Isavuconazole treatment for mucormycosis: a single-arm open-label trial and case-control analysis

Mucormycosis is an uncommon invasive fungal disease with high mortality and few treatment options. Isavuconazole is a triazole active in vitro and in animal models against moulds of the order Mucorales. We assessed the efficacy and safety of isavuconazole for treatment of mucormycosis and compared its efficacy with amphotericin B in a matched case-control analysis. In a single-arm open-label trial (VITAL study), adult patients (≥18 years) with invasive fungal disease caused by rare fungi, including mucormycosis, were recruited from 34 centres worldwide. Patients were given isavuconazole 200 mg (as its intravenous or oral water-soluble prodrug, isavuconazonium sulfate) three times daily for six doses, followed by 200 mg/day until invasive fungal disease resolution, failure, or for 180 days or more. The primary endpoint was independent data review committee-determined overall response-ie, complete or partial response (treatment success) or stable or progressive disease (treatment failure)-according to prespecified criteria. Mucormycosis cases treated with isavuconazole as primary treatment were matched with controls from the FungiScope Registry, recruited from 17 centres worldwide, who received primary amphotericin B-based treatment, and were analysed for day-42 all-cause mortality. VITAL is registered with ClinicalTrials.gov, number NCT00634049. FungiScope is registered with ClinicalTrials.gov, number NCT01731353. Within the VITAL study, from April 22, 2008, to June 21, 2013, 37 patients with mucormycosis received isavuconazole for a median of 84 days (IQR 19-179, range 2-882). By day 42, four patients (11%) had a partial response, 16 (43%) had stable invasive fungal disease, one (3%) had invasive fungal disease progression, three (8%) had missing assessments, and 13 (35%) had died. 35 patients (95%) had adverse events (28 [76%] serious). Day-42 crude all-cause mortality in seven (33%) of 21 primary-treatment isavuconazole cases was similar to 13 (39%) of 33 amphotericin B-treated matched controls (weighted all-cause mortality: 33% vs 41%; p=0·595). Isavuconazole showed activity against mucormycosis with efficacy similar to amphotericin B. Isavuconazole can be used for treatment of mucormycosis and is well tolerated. Astellas Pharma Global Development, Basilea Pharmaceutica International.

Diversity of conidial fungi and some abiotic variables of the water after the reopening of the Pirarungaua stream in the Jardim Botânico, São Paulo, São Paulo State, Brazil

ABSTRACT To evaluate the fungal diversity in the Pirarungaua stream reopened after remaining channeled about 40 years in the Botanical Garden of São Paulo, Brazil, two experiments in the cold and dry season and two in the hot and rainy season were performed. Leaves of Tibouchina pulchra Cogn and mixed leaf litter were confined in nylon litter bags, submerged and collected monthly, together with free leaf litter samples. Some abiotic factors were measured in the water. The leaves were fragmented, incubated in sterile water at 22 ºC and microscopically analyzed. We identified 33 conidial fungal taxa, among which, 23 are new to this area. Comparing seasons, the similarity of the mycota of confined T. pulchra leaves corresponded to 39% and to 56% regarding the confined mixed leaf litter. Similarities of 48-50% occurred between the mycota of confined and free leaf litter samples. Confined leaves showed a tendency to support higher numbers of species, whereas some rare fungi like Ulocoryphus mastigophorus Michaelides L. Hunter &amp; W.B Kendr were more frequent in free leaf litter. Based on the results, it is recommended to monitor the limnological conditions of the stream and to promote awareness among the local population and visitors about the importance of a water body, even artificial, for the establishment of microclimatic features, and for the biodiversity of fungi.

Transcriptome analysis of Ophiocordyceps sinensis before and after infection of Thitarodes larvae

Ophiocordyceps sinensis, also referred to as the Chinese caterpillar fungus, is a rare entomopathogenic fungus found in the Qinghai–Tibetan Plateau that is used as a traditional Chinese medicine. O. sinensis parasitizes the larvae of the ghost moth Thitarodes. Characterization of the transcriptome of O. sinensis before and after host infection may provide novel insight into the process by which the fungus interacts with Thitarodes and may help researchers understand how to sustain this valuable resource. In this study, we performed RNA-sequencing (RNA-seq) using Illumina HiSeqTM 2000 technology to generate gene expression profiles of two developmental stages of O. sinensis. Thread-like hyphae before infection and yeast-like hyphal bodies after infection of host larvae were collected for transcriptome analysis. We found that 1640 genes were differentially expressed (q-value < 0.05), of which 818 were upregulated (49.878 %) and 822 were downregulated (50.122 %). Gene ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were especially enriched in terms associated with Biological Process and Molecular Function. Several genes encoding transporter and permease proteins, three glycoside hydrolases, two mycotoxin-related proteins, an antigen protein, and an allergen were identified as being significantly up- or downregulated. Collectively, our findings provide a novel resource for understanding O. sinensis during two critical developmental stages, and offer the opportunity to further investigate the functional mechanisms underlying these stage-specific molecular differences.

New records of rare and threatened larger fungi from middle Danube plain, Bulgaria

New data about the distribution of eleven rare larger fungi for Bulgaria from the Middle Danube Plain (Pleven District) are presented in the paper. Nine species are of a high conservation value, included in the Red List of fungi in Bulgaria. Three of them are enlisted also in the Red Data Book of the Republic of Bulgaria. Seven taxa are new records from Middle Danube Plain.

Glomus segmentatum, rediscovery of a rare epigeous sporocarpic fungus to Cuba

Glomus segmentatum, rediscovery of a rare epigeous sporocarpic fungus to Cuba

Identification and Characterization of a Rare Fungus, Quambalaria cyanescens, Isolated from the Peritoneal Fluid of a Patient after Nocturnal Intermittent Peritoneal Dialysis

Peritonitis is the leading complication of peritoneal dialysis, which is primarily caused by bacteria rather than fungi. Peritonitis is responsible for approximately 18% of the infection-related mortality in peritoneal dialysis patients. In this paper, we report the isolation of a rare fungus, Quambalaria cyanescens, from the peritoneal fluid of a man after he switched from continuous ambulatory peritoneal dialysis to nocturnal intermittent peritoneal dialysis. Based on the morphological examination and multigene phylogeny, the clinical isolate was confirmed as Q. cyanescens. This pathogen exhibited low sensitivity to all tested echinocandins and 5-flucytosine. Interestingly, morphological characterization revealed that Q. cyanescens UM 1095 produced different pigments at low temperatures (25°C and 30°C) on various culture media. It is important to monitor the emergence of this rare fungus as a potential human pathogen in the tropics. This study provides insight into Q. cyanescens UM 1095 phenotype profiles using a Biolog phenotypic microarray (PM). Of the 760 nutrient sources tested, Q. cyanescens UM 1095 utilized 42 compounds, and the fungus can adapt to a broad range of osmotic and acidic environments. To our knowledge, this is the first report of the isolation of Q. cyanescens from peritoneal fluid, revealing this rare fungus as a potential human pathogen that may be misidentified using conventional methods. The detailed morphological, molecular and phenotypic characterization of Q. cyanescens UM 1095 provides the basis for future studies on its biology, lifestyle, and potential pathogenicity.

Deciphering the salinity adaptation mechanism in Penicilliopsis clavariiformis AP, a rare salt tolerant fungus from mangrove.

Penicilliopsis clavariiformis AP, a rare salt tolerant fungus reported for the first time from India was identified through polyphasic taxonomy. Scanning electron microscopy showed that the fungus has unique features such as biverticillate penicilli bearing masses of oval to ellipsoidal conidia. The fungus has been characterized for salt tolerance and to understand the relevance of central carbon metabolism in salt stress adaptation. It showed optimal growth at 24 °C and able to tolerate up to 10% (w/v) NaCl. To understand the mechanism of adaptation to high salinity, activities of the key enzymes regulating glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle were investigated under normal (0% NaCl) and saline stress environment (10% NaCl). The results revealed a re-routing of carbon metabolism away from glycolysis to the pentose phosphate pathway (PPP), served as a cellular stress-resistance mechanism in fungi under saline environment. The detection and significant expression of fungus genes (Hsp98, Hsp60, HTB, and RHO) under saline stress suggest that these halotolerance conferring genes from the fungus could have a role in fungus protection and adaptation under saline environment. Overall, the present findings indicate that the rearrangement of the metabolic fluxes distribution and stress related genes play an important role in cell survival and adaptation under saline environment.

Epidemiology of Fungemia in Hematological Malignancies: Preliminary Report of Seifem-2015 Survey

Introduction: Incidence of fungal infections is reducing in the last years due to wider use of effective antifungal prophylaxis. On this basis, we evaluated clinical characteristics and outcome of patients (pts) with hematological malignancies (HMs) and fungal bloodstream infections (FBSI).Patient and Methods: This retrospective/prospective study gathered consecutive documented FBSI observed among HMs diagnosed between January 2011 and June 2015 in 19 Italian Hematology Departments that refer to SEIFEM (Sorveglianza Epidemiologica Infezioni Fungine Emopatie Maligne) group.Results: We collected overall 100 patients including retrospective pts and those observed in the first six months of the prospective study with FBSI among 16 centers; further 3 centers reported no cases of FBSI. Regarding patients' characteristics male/female ratio was 1, median age was 55 yeras. (IQR 18-88). Two-third of FBSI were detected in AML (43 - 43%) and NHL (27 - 27%); the remaining pts were affected by ALL (9 - 9%), MM (6 - 6%), MDS (5 - 5%), MDS/MPN (5 - 5%), CLL (3 - 3%) and HL (2 - 2%). Thirty-five pts had FBSI at the onset of HM or after the first induction, 47 after treatment for refractory/relapsed disease, 13 when in remission, 28 pts during transplant procedures (17 from allogeneic donor, 11 from autologous cells). Fifty-nine pts were receiving antifungal prophylaxis at FBSI breakthrough: 26 posaconazole, 16 fluconazole, 6 itraconazole, 3 amphotericin B, 3 caspofungin, 1 voriconazole, and 4 combination of amphotericin B/azoles; 4 pts were treated with secondary prophylaxis after previous fungal infection. Eighty-nine pts had a central venous catheter. Eighty-four pts presented a neutrophils count < 500/mmc for a median time of 7 days before FBI onset (0-70 d); 50 pts received steroids and other 17 immunosuppressive treatment for allo-HSCT.Yeasts were the most common agent detected. Candida spp. represent the most represented yeast, counting for 77% of all infections; (21 albicans and 56 non albicans); 8% of FBI were due to 8% Geotrichum, 3% Trichosporon and 2% Rhodotorula, Molds were rare but not infrequent: 8% were caused by Fusarium and 1% by Scedosporium.Three patients died before starting any antifungal. Fifty-two received echinocandins (49 caspofungin and 3 anidulafungin), 22 liposomal amphotericin B (L-AmB), 15 azoles (7 fluconazole, 3 posaconazole, 3 voriconazole and 2 itraconazole) and 8 pts combo therapy (5 posa+L-AmB, 2 Caspo+L-AmB, 1 vori+caspo).Thirty-eight pts died within 30 days from FBSI diagnosis, 28 (74%) of whom due to infection. Among these 12 (43%) suffered from AML (1 in induction, 1 in CR, 10 had refractory/relapsed disease), 2 (7.2%) from ALL (all with refractory/relapsed disease), 7 (25%) from NHL (2 in induction, 2 in CR, 3 with refractory/relapsed disease), 4 (14%) from refractory/relapsed MM, 1 (3.6%) from MDS in remission, 2 (7.2%) from newly diagnosed MDS/MPN. In 8 pts (21%) for whom we cannot discriminate if death was subsequent to FBSI only or to uncontrolled HMs, fungal isolates were all rare yeast or molds except 2. Mortality was related only with advanced phase of underlying HM (p<0.0001), molds fungemia (p<0.06) and rare fungi isolation (p<0.06). There is no difference in overall mortality rate among pts treated with echinocandins or azole or amphotericin B compounds or combo.Conclusions: Nowadays FBSI represents a rare complication of HMs, as a consequence of wider availability of effective antifungal prophylaxis. Candidemia still represents the most important cause of FBSI, although about 25% of FBSI are due to rare yeast or molds. Regardless a lowering incidence, the observed mortality remains high even with target treatment. DisclosuresNo relevant conflicts of interest to declare.

Two rare ophiocordycipitaceous fungi newly recorded in Taiwan.

BackgroundOphiocordycipitaceae is a highly diverse fungal family parasitizing a wide range of arthropods and hypogeous fungi. We collected two ophiocordycipitaceous species previously unknown in Taiwan: one emerged from hypogeous fruiting bodies of an Elaphomyces fungus and the other was associated with dragonflies.ResultsBased on gross morphology, microscopic features, ITS sequences, and hosts, the two ophiocordycipitaceous fungi were identified as Tolypocladium japonicum and Ophiocordyceps odonatae. We isolated axenic cultures of these two fungi, and their anamorphs were obtained. The simplicillium-like anamorph of T. japonicum is described herein for the first time. The anamorph of O. odonatae produce conidia holoblastically in sympodial sequence and is assignable to Hymenostilbe. A dichotomous key to the species of Ophiocordycipitaceae reported in Taiwan is provided.ConclusionA thorough literature study indicates that the two fungi reported herein have rarely been collected. Our identifications of T. japonicum and O. odonatae agree well with descriptions in the literature and are highly supported by DNA sequence analysis.

First report of Chamonixia caespitosa (Boletaceae, Boletales) from Japan and its phylogeographic significance

The rare sequestrate fungus, Chamonixia caespitosa, is known to occur in Europe and North America. The species has also been reported once from China, but the precise information on its occurrence in Asia is unknown. We collected fruiting bodies of C. caespitosa in a subalpine coniferous forest in central Japan. The internal transcribed spacer phylogeny shows that the Japanese collections are more closely related to one of the North American infraspecific lineages than to the European lineage. Thus, these Japanese collections could be a missing link in the phylogeography of the genus Chamonixia.

Scedosporium apiospermum: A Rare Case of Cavitary Lung Disease

Scedosporium apiospermum: A Rare Case of Cavitary Lung Disease