The Canadian Fungal Research Network: current challenges and future opportunities.

Fungi critically impact the health and function of global ecosystems and economies. In Canada, fungal researchers often work within silos defined by subdiscipline and institutional type, complicating the collaborations necessary to understand the impacts fungi have on the environment, economy, and plant and animal health. Here, we announce the establishment of the Canadian Fungal Research Network (CanFunNet, https://fungalresearch.ca), whose mission is to strengthen and promote fungal research in Canada by facilitating dialogue among scientists. We summarize the challenges and opportunities for Canadian fungal research that were discussed at CanFunNet's inaugural meeting in 2019, and identify 4 priorities for our community: (i) increasing collaboration among scientists, (ii) studying diversity in the context of ecological disturbance, (iii) preserving culture collections in the absence of sustained funding, and (iv) leveraging diverse expertise to attract trainees. We have gathered additional information to support our recommendations, including a survey identifying underrepresentation of fungal-related courses at Canadian universities, a list of Canadian fungaria and culture collections, and a case study of a human fungal pathogen outbreak. We anticipate that these discussions will help prioritize fungal research in Canada, and we welcome all researchers to join this nationwide effort to enhance knowledge dissemination and funding advocacy.

Ethnomycological knowledge among Kaqchikel, indigenous Maya people of Guatemalan Highlands.

BACKGROUND: The Guatemalan Highlands is a region of great but so far poorly known mycological diversity. People living in this area have long used wild fungi as a source of food and income. However, our knowledge of the ethnomycological practices of the Mayan peoples of Guatemala is still rudimental, especially if compared with information reported for the neighboring region of Mexico. Among the main indigenous groups of the Maya people inhabiting the highlands of Central Guatemala, stand the Kaqchikel, accounting for nearly 8% of the entire Guatemalan population. The main aim of this study was to record the traditional knowledge and use of edible wild mushrooms by inhabitants of the municipality of San Juan Sacatepéquez that lies at the heart of the Kaqchikel area in the central highlands of Guatemala, also describing the relevant selling practices and dynamics. A secondary aim was to compare the diversity and composition of the mushroom assemblage offered at the market with the macrofungal diversity of woods in the area. METHODOLOGY: This study is the result of 4 years of ethnomycological research, conducted through continuous visits to the municipal market and focused interviews with collectors and vendors. Field sampling in pine-oak forested areas surrounding San Juan Sacatepéquez, from where the mushrooms sold at the market are foraged, were also conducted, in the presence of local collectors. RESULTS: The results show a significant richness of species sold in the market, a network of commerce of purchase, sale, and resale of several species, with relatively stable prices, and knowledge about edible and inedible species that is transmitted mainly within the family nucleus. The business of selling mushrooms in the market is an exclusive activity of women, who are supplied by collectors or by other vendors. Fungi are sold and bought only as food, while no consumption of hallucinogenic mushrooms or medicinal mushrooms was recorded. Several species of Amanita, Cantharellus, Boletus, Lactarius, and Russula were those most commercialized in the 4 years of the study, but we also spotted fungi never reported before as consumed in the country, including Gastropila aff. fumosa (= Calvatia fumosa) and several species of Cortinarius. Field sampling in nearby pine-oak forests confirmed an elevated local macrofungal diversity. CONCLUSION: Our study unveiled the contemporary wealth of Kaqchikel culture for what concerns mushrooms, demonstrating that mushrooms continue to be culturally and economically important for these communities despite the erosion of traditional knowledge. Our results also confirmed the need to investigate in greater detail the Guatemalan mycodiversity that is vast and poorly known.

Effect of different lignocellulosic wastes on Hericium americanum yield and nutritional characteristics.

BACKGROUND: The aim of this study was to investigate the possibility of using cottonseed hulls (CSH) and olive press cake (OPC) as new supplement materials for substrate preparation in Hericium americanum cultivation. Some chemical properties of the substrates prepared by mixtures of oak sawdust (OS) with wheat bran (WB), CSH and OPC in different ratios were determined. In addition, the effect of mixtures of OS:CSH and OS:OPC on spawn run time, yield and biological efficiency (BE), average mushroom weight and nutrition content of the fruiting body were compared with the control substrate (8OS:2WB). RESULTS: The yield, BE and average mushroom weight of substrates containing CSH and OPC were higher than the control substrate and increased with an increase in the rate of CSH and OPC in the mixtures. Hericium americanum showed (on a dry weight basis) 8.5-23.7% protein, 9.9-21.2 g kg-1 P, 26.6-35.8 g kg-1 K, 0.63 - 1.33 g kg-1 Mg, 0.19 - 0.23 g kg-1 Ca, 1.34-1.78 g kg-1 Na, 49.5-72.2 mg kg-1 Fe, 6.22-10.11 mg kg-1 Mn, 32.8-82.8 mg kg-1 Zn and 8.6-11.2 mg kg-1 Cu on different growing substrates. The nutritional value of mushrooms was greatly affected by the growing media. CONCLUSION: The results revealed that CSH and OPC could be used as new supplement materials for substrate preparation in H. americanum cultivation. © 2016 Society of Chemical Industry.

Feasibility and Acceptability of Cryptococcal Antigen Screening and Prevalence of Cryptocococcemia in Patients Attending a Resource-Limited HIV/AIDS Clinic in Malawi.

BACKGROUND: The World Health Organization (WHO) recommends screening patients living with AIDS to detect and treat early cryptococcal infection. METHODS: The authors evaluated a cryptococcal antigen (CrAg) screening and treatment program at an HIV/AIDS clinic in Malawi. Eligible patients were of age >18 years, had a CD4 count <100 cells/µL or WHO clinical HIV/AIDS stage III or IV. RESULTS: Of 552 patients who presented for care, 113 were eligible, and all (100%) agreed to CrAg screening. Of them, 2 (1.8%; 95% confidence interval [CI]: 0-4.2%) patients were CrAg positive. Among those with CD4 count <100 cells/µL or WHO stage IV, the CrAg prevalence was 3.5% (95% CI: 0-8.4%) and 5.0% (95% CI: 0-15%), respectively. CONCLUSION: A CrAg screening program was acceptable to new patients in a Malawian HIV/AIDS clinic. The CrAg prevalence for patients with CD4 count < 100 cells/µL and WHO stage IV was consistent with cost-effectiveness estimates. CrAg screening and treatment programs for patients living with AIDS should be expanded.

Systematic analysis of funding awarded for mycology research to institutions in the UK, 1997-2010.

OBJECTIVES: Fungal infections cause significant global morbidity and mortality. We have previously described the UK investments in global infectious disease research, and here our objective is to describe the investments awarded to UK institutions for mycology research and outline potential funding gaps in the UK portfolio. DESIGN: Systematic analysis. SETTING: UK institutions carrying out infectious disease research. PRIMARY AND SECONDARY OUTCOME MEASURES: Primary outcome is the amount of funding and number of studies related to mycology research. Secondary outcomes are describing the investments made to specific fungal pathogens and diseases, and also the type of science along the R&D value chain. METHODS: We systematically searched databases and websites for information on research studies from public and philanthropic funding institutions awarded between 1997 and 2010, and highlighted the mycology-related projects. RESULTS: Of 6165 funded studies, we identified 171 studies related to mycology (total investment £48.4 million, 1.9% of all infection research, with mean annual funding £3.5 million). Studies related to global health represented 5.1% of this funding (£2.4 million, compared with 35.6% of all infectious diseases). Leading funders were the Biotechnology and Biological Sciences Research Council (£14.8 million, 30.5%) and Wellcome Trust (£12.0 million, 24.7%). Preclinical studies received £42.2 million (87.3%), with clinical trials, intervention studies and implementation research in total receiving £6.2 million (12.7%). By institution, University of Aberdeen received most funding (£16.9 million, 35%). Studies investigating antifungal resistance received £1.5 million (3.2%). CONCLUSIONS: There is little translation of preclinical research into clinical trials or implementation research in spite of substantial disease burden globally, and there are few UK institutions that carry out significant quantities of mycology research of any type. In the context of global health and the burden of disease in low-income countries, more investment is required for mycology research.

Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA).

Rapid identification of clinically important yeasts can facilitate the initiation of anti-fungal therapy, since susceptibility is largely species-dependent. We evaluated melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA) as an identification tool for distinguishing between 16 Candida spp., i.e. Candida albicans, Candida bracarensis, Candida dubliniensis, Candida famata, Candida glabrata, Candida guilliermondii, Candida inconspicua, Candida kefyr, Candida krusei, Candida lipolytica, Candida lusitaniae, Candida nivariensis, Candida norvegensis, Candida parapsilosis, Candida tropicalis and Candida sojae, and Saccharomyces cerevisiae and one species pair, i.e. Candida metapsilosis/Candida orthopsilosis. Starting from a cultured isolate, ITS2-MCA led to differentiation of these species within 6 h. According to our findings, ITS2-MCA offers a simple, rapid and cost-effective method for identification of cultured isolates of the clinically most relevant and prevalent Candida species. Further studies will be necessary to evaluate how it performs on mixed samples and clinical samples.

Rapid strain classification and taxa delimitation within the edible mushroom genus Pleurotus through the use of diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy.

Fourier transform infrared (FT-IR) spectroscopy has been successfully applied for the identification of bacteria and yeasts, but only to a limited extent for discriminating specific groups of filamentous fungi. In the frame of this study, 73 strains - from different associated hosts/substrates and geographic regions - representing 16 taxa of the edible mushroom genus Pleurotus (Basidiomycota, Agaricales) were examined through the use of diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. A binary matrix, elaborated on the basis of presence/absence of specific absorbance peaks combined with cluster analysis, demonstrated that the spectral region 1800-600 cm(-1) permitted clear delimitation of individual strains into Pleurotus species. In addition, closely related species (e.g., Pleurotus ostreatus and Pleurotus pulmonarius) or taxa of the subgenus Coremiopleurotus demonstrated high similarity in their absorbance patterns, whereas genetically distinct entities such as Pleurotus dryinus, Pleurotus djamor, and Pleurotus eryngii provided spectra with noteworthy differences. When specific regions (1800-1700, 1360-1285, 1125-1068, and 950-650 cm(-1)) were evaluated in respect to the absorbance values demonstrated by individual strains, it was evidenced that this methodology could be eventually exploited for the identification of unknown Pleurotus specimens with a stepwise process and with the aid of a dichotomous key developed for this purpose. Moreover, it was shown that the nature of original fungal material examined (mycelium, basidiomata, and basidiospores) had an effect on the outcome of such analyses, and so did the use of different mycelium growth substrates. In conclusion, application of FT-IR spectroscopy provided a fast, reliable, and cost-efficient solution for the classification of pure cultures from closely related mushroom species.

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast.

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.

Cost-effectiveness of serum cryptococcal antigen screening to prevent deaths among HIV-infected persons with a CD4+ cell count < or = 100 cells/microL who start HIV therapy in resource-limited settings.

BACKGROUND: Cryptococcal meningitis (CM) remains a common AIDS-defining illness in Africa and Asia. Subclinical cryptococcal antigenemia is frequently unmasked with antiretroviral therapy (ART). We sought to define the cost-effectiveness of serum cryptococcal antigen (CRAG) screening to identify persons with subclinical cryptococcosis and the efficacy of preemptive fluconazole therapy. METHODS: There were 609 ART-naive adults with AIDS who started ART in Kampala, Uganda, and who had a serum CRAG prospectively measured during 2004-2006. The number needed to test and treat with a positive CRAG was assessed for > or = 30-month outcomes. RESULTS: In the overall cohort, 50 persons (8.2%) were serum CRAG positive when starting ART. Of 295 people with a CD4(+) cell count < or = 100 cells/microL and without prior CM, 26 (8.8%; 95% confidence interval [CI], 5.8%-12.6%) were CRAG positive, of whom 21 were promptly treated with fluconazole (200-400 mg) for 2-4 weeks. Clinical CM developed in 3 fluconazole-treated persons, and 30-month survival was 71% (95% CI, 48%-89%). In the 5 CRAG-positive persons with a CD4(+) cell count < or = 100 cells/microL treated with ART but not fluconazole, all died within 2 months of ART initiation. The number needed to test and treat with CRAG screening and fluconazole to prevent 1 CM case is 11.3 (95% CI, 7.9-17.1) at costs of $190 (95% CI, $132-$287). The number needed to test and treat to save 1 life is 15.9 (95% CI, 11.1-24.0) at costs of $266 (95% CI, $185-$402). The cost per disability-adjusted life year saved is $21 (95% CI, $15-$32). CONCLUSIONS: Integrating CRAG screening into HIV care, specifically targeting people with severe immunosuppression (CD4(+) cell count < or = 100 cells/microL) should be implemented in treatment programs in resource-limited settings. ART alone is insufficient treatment for CRAG-positive persons.

Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei.

BACKGROUND: Chemostat cultures are commonly used in production of cellular material for systems-wide biological studies. We have used the novel TRAC (transcript analysis with aid of affinity capture) method to study expression stability of approximately 30 process relevant marker genes in chemostat cultures of the filamentous fungus Trichoderma reesei and its transformant expressing laccase from Melanocarpus albomyces. Transcriptional responses caused by transient oxygen deprivations and production of foreign protein were also studied in T. reesei by TRAC. RESULTS: In cultures with good steady states, the expression of the marker genes varied less than 20% on average between sequential samples for at least 5 or 6 residence times. However, in a number of T. reesei cultures continuous flow did not result in a good steady state. Perturbations to the steady state were always evident at the transcriptional level, even when they were not measurable as changes in biomass or product concentrations. Both unintentional and intentional perturbations of the steady state demonstrated that a number of genes involved in growth, protein production and secretion are sensitive markers for culture disturbances. Exposure to anaerobic conditions caused strong responses at the level of gene expression, but surprisingly the cultures could regain their previous steady state quickly, even after 3 h O2 depletion. The main effect of producing M. albomyces laccase was down-regulation of the native cellulases compared with the host strain. CONCLUSION: This study demonstrates the usefulness of transcriptional analysis by TRAC in ensuring the quality of chemostat cultures prior to costly and laborious genome-wide analysis. In addition TRAC was shown to be an efficient tool in studying gene expression dynamics in transient conditions.

An evaluation of the cost-effectiveness of using CHROMagar for yeast identification in a routine microbiology laboratory.

CHROMagar, a chromogenic differential culture medium, is claimed to facilitate the isolation and presumptive identification of certain clinically important yeast species, e.g., Candida albicans. This study evaluated the cost-effectiveness and time advantage of using it in comparison with Sabouraud dextrose agar (SDA). Three possible pathways, each of which included the use of one or both media, were compared in a routine laboratory. A total of 21 yeast isolates was cultured from 298 clinical samples from neutropenic and AIDS patients. An overall sensitivity of 95.2% was observed for each medium and primary isolation on CHROMagar was found to be 100% sensitive and 100% specific for C. albicans. For identification purposes, after initial culture the use of CHROMagar provided the most economical and least time-consuming method. Direct inoculation on to CHROMagar is recommended for blood cultures when yeast cells are seen on microscopy and where early appropriate therapy is imperative.

Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers.

Performance of fungal blood cultures by using the Isolator collection system: is it cost-effective?

Enhanced recovery of fungal isolates from blood by using the Isolator system has been reported previously. We examined bacterial and fungal blood cultures during a 14-month period to determine if this enhanced recovery required a separate fungal culture and to determine the differential utility between a fungal blood culture and a routine bacterial culture. During this period, 84 of 5,196 (1.6%) fungal blood cultures and 170 of 25,702 (0.6%) bacterial blood cultures were positive for yeast or filamentous fungi. Thirty-seven positive fungal cultures, simultaneously collected, had correspondingly positive bacterial cultures. An additional 15 positive fungal cultures yielded isolates that had either been previously recovered from a bacterial culture or were recovered from a bacterial culture collected within 48 h. Of the 32 unpaired fungal cultures remaining, 5 were Candida albicans whose unique isolation was believed to be the result of specimen sampling variance rather than any enhanced recovery characteristics of fungal culture methods. Examination of patient data relating to the 27 remaining isolates (24 patients episodes) showed that only five fungal blood cultures (0.096% of all collected) had any impact on patient therapy decisions, and one of these was judged to be the cause of unnecessary therapy. Our data suggest that separate fungal cultures of blood are not cost-effective for those laboratories using the Isolator for routine blood cultures and furthermore may not be cost-effective for laboratories using automated broth systems that are comparable to the Isolator in recovery of fungi.

Rapid methods for nucleic acids extraction from Petri dish-grown mycelia.

We have developed rapid and economic methods for the isolation of nucleic acids from filamentous fungi. The main advantages of these methods are: (1) the mycelium is directly recovered from a Petri-dish culture, (2) the complete experiment takes place in microfuge tubes, (3) it is very fast and allows for the processing of 24 samples in the same day, and (4) up to 100 micrograms of total DNA or RNA are recovered, both of which are sufficiently pure for most purposes. Of particular interest is the recovery of large amounts of mitochondrial DNA as visualised by electrophoresis in ethidium bromide-stained gels.