Journal of Fungi

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Open AccessReview

Omics for Investigating Chitosan as an Antifungal and Gene Modulator

by Federico Lopez-Moya and Luis V. Lopez-Llorca

J. Fungi 2016, 2(1), 11; https://doi.org/10.3390/jof2010011 - 03 Mar 2016

Cited by 26 | Viewed by 5288

Chitosan is a biopolymer with a wide range of applications. The use of chitosan in clinical medicine to control infections by fungal pathogens such as Candida spp. is one of its most promising applications in view of the reduced number of antifungals available. [...] Read more.

Chitosan is a biopolymer with a wide range of applications. The use of chitosan in clinical medicine to control infections by fungal pathogens such as Candida spp. is one of its most promising applications in view of the reduced number of antifungals available. Chitosan increases intracellular oxidative stress, then permeabilizes the plasma membrane of sensitive filamentous fungus Neurospora crassa and yeast. Transcriptomics reveals plasma membrane homeostasis and oxidative metabolism genes as key players in the response of fungi to chitosan. A lipase and a monosaccharide transporter, both inner plasma membrane proteins, and a glutathione transferase are main chitosan targets in N. crassa. Biocontrol fungi such as Pochonia chlamydosporia have a low content of polyunsaturated free fatty acids in their plasma membranes and are resistant to chitosan. Genome sequencing of P. chlamydosporia reveals a wide gene machinery to degrade and assimilate chitosan. Chitosan increases P. chlamydosporia sporulation and enhances parasitism of plant parasitic nematodes by the fungus. Omics studies allow understanding the mode of action of chitosan and help its development as an antifungal and gene modulator. Full article

(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)

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Open AccessReview

Invasive Candidiasis in Various Patient Populations: Incorporating Non-Culture Diagnostic Tests into Rational Management Strategies

by Cornelius J. Clancy, Ryan K. Shields and M. Hong Nguyen

J. Fungi 2016, 2(1), 10; https://doi.org/10.3390/jof2010010 - 06 Feb 2016

Cited by 8 | Viewed by 4705

Abstract

Mortality rates due to invasive candidiasis remain unacceptably high, in part because the poor sensitivity and slow turn-around time of cultures delay the initiation of antifungal treatment. β-d-glucan (Fungitell) and polymerase chain reaction (PCR)-based (T2Candida) assays are FDA-approved adjuncts to cultures for diagnosing [...] Read more.

Mortality rates due to invasive candidiasis remain unacceptably high, in part because the poor sensitivity and slow turn-around time of cultures delay the initiation of antifungal treatment. β-d-glucan (Fungitell) and polymerase chain reaction (PCR)-based (T2Candida) assays are FDA-approved adjuncts to cultures for diagnosing invasive candidiasis, but their clinical roles are unclear. We propose a Bayesian framework for interpreting non-culture test results and developing rational patient management strategies, which considers test performance and types of invasive candidiasis that are most common in various patient populations. β-d-glucan sensitivity/specificity for candidemia and intra-abdominal candidiasis is ~80%/80% and ~60%/75%, respectively. In settings with 1%–10% likelihood of candidemia, anticipated β-d-glucan positive and negative predictive values are ~4%–31% and ≥97%, respectively. Corresponding values in settings with 3%–30% likelihood of intra-abdominal candidiasis are ~7%–51% and ~78%–98%. β-d-glucan is predicted to be useful in guiding antifungal treatment for wide ranges of populations at-risk for candidemia (incidence ~5%–40%) or intra-abdominal candidiasis (~7%–20%). Validated PCR-based assays should broaden windows to include populations at lower-risk for candidemia (incidence ≥~2%) and higher-risk for intra-abdominal candidiasis (up to ~40%). In the management of individual patients, non-culture tests may also have value outside of these windows. The proposals we put forth are not definitive treatment guidelines, but rather represent starting points for clinical trial design and debate by the infectious diseases community. The principles presented here will be applicable to other assays as they enter the clinic, and to existing assays as more data become available from different populations. Full article

(This article belongs to the Special Issue Yeasts Are Beasts)

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Open AccessReview

Genome Studies on Nematophagous and Entomogenous Fungi in China

by Weiwei Zhang, Xiaoli Cheng, Xingzhong Liu and Meichun Xiang

J. Fungi 2016, 2(1), 9; https://doi.org/10.3390/jof2010009 - 05 Feb 2016

Cited by 10 | Viewed by 6105

Abstract

The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several [...] Read more.

The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese medicinal fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper. Full article

(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)

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Open AccessEditorial

Acknowledgement to Reviewers of the Journal of Fungi in 2015

by Journal of Fungi Editorial Office

J. Fungi 2016, 2(1), 8; https://doi.org/10.3390/jof2010008 - 02 Feb 2016

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Abstract

The editors of the Journal of Fungi would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article

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Open AccessReview

Transcriptomic Crosstalk between Fungal Invasive Pathogens and Their Host Cells: Opportunities and Challenges for Next-Generation Sequencing Methods

by Francisco J. Enguita, Marina C. Costa, Ana Marisa Fusco-Almeida, Maria José Mendes-Giannini and Ana Lúcia Leitão

J. Fungi 2016, 2(1), 7; https://doi.org/10.3390/jof2010007 - 14 Jan 2016

Cited by 17 | Viewed by 9586

Abstract

Fungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific [...] Read more.

Fungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific transcriptional program in their host cells. The detailed knowledge of this transcriptional program will allow for a better understanding of the infection process and consequently will help in the future design of more efficient therapeutic strategies. Simultaneous transcriptomic studies of pathogen and host by high-throughput sequencing (dual RNA-seq) is an unbiased protocol to understand the intricate regulatory networks underlying the infectious process. This protocol is starting to be applied to the study of the interactions between fungal pathogens and their hosts. To date, our knowledge of the molecular basis of infection for fungal pathogens is still very limited, and the putative role of regulatory players such as non-coding RNAs or epigenetic factors remains elusive. The wider application of high-throughput transcriptomics in the near future will help to understand the fungal mechanisms for colonization and survival, as well as to characterize the molecular responses of the host cell against a fungal infection. Full article

(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)

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Open AccessArticle

Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins

by Jackson Champer, James I. Ito, Karl V. Clemons, David A. Stevens and Markus Kalkum

J. Fungi 2016, 2(1), 6; https://doi.org/10.3390/jof2010006 - 12 Jan 2016

Cited by 40 | Viewed by 9104

Abstract

We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal [...] Read more.

We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MS^E (Mass Spectrometry—Elevated Collision Energy). Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4), Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here. Full article

(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)

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Open AccessReview

Pediatric Invasive Candidiasis: Epidemiology and Diagnosis in Children

by William J. Steinbach

J. Fungi 2016, 2(1), 5; https://doi.org/10.3390/jof2010005 - 08 Jan 2016

Cited by 23 | Viewed by 5044

Abstract

Pediatric patients present with differing underlying conditions and cytotoxic therapeutic protocols, so the differing epidemiology of invasive candidiasis in children versus adults is not surprising. Understanding the Candida species epidemiology is critical, as we often begin empiric therapy or therapy before antifungal susceptibilities [...] Read more.

Pediatric patients present with differing underlying conditions and cytotoxic therapeutic protocols, so the differing epidemiology of invasive candidiasis in children versus adults is not surprising. Understanding the Candida species epidemiology is critical, as we often begin empiric therapy or therapy before antifungal susceptibilities are known. Reports with newer molecular diagnostic assays for invasive candidiasis are rare and require more study to develop firm pediatric-specific guidance. Antifungal treatment of pediatric candidiasis is reviewed in the context of larger epidemiologic studies and the few trials completed to date. Full article

(This article belongs to the Special Issue Yeasts Are Beasts)

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Open AccessReview

Severe Dermatophytosis and Acquired or Innate Immunodeficiency: A Review

by Claire Rouzaud, Roderick Hay, Olivier Chosidow, Nicolas Dupin, Anne Puel, Olivier Lortholary and Fanny Lanternier

J. Fungi 2016, 2(1), 4; https://doi.org/10.3390/jof2010004 - 31 Dec 2015

Cited by 75 | Viewed by 13535

Abstract

Dermatophytes are keratinophilic fungi responsible for benign and common forms of infection worldwide. However, they can lead to rare and severe diseases in immunocompromised patients. Severe forms include extensive and/or invasive dermatophytosis, i.e., deep dermatophytosis and Majocchi’s granuloma. They are reported in [...] Read more.

Dermatophytes are keratinophilic fungi responsible for benign and common forms of infection worldwide. However, they can lead to rare and severe diseases in immunocompromised patients. Severe forms include extensive and/or invasive dermatophytosis, i.e., deep dermatophytosis and Majocchi’s granuloma. They are reported in immunocompromised hosts with primary (autosomal recessive CARD9 deficiency) or acquired (solid organ transplantation, autoimmune diseases requiring immunosuppressive treatments, HIV infection) immunodeficiencies. The clinical manifestations of the infection are not specific. Lymph node and organ involvement may also occur. Diagnosis requires both mycological and histological findings. There is no consensus on treatment. Systemic antifungal agents such as terbinafine and azoles (itraconazole or posaconazole) are effective. However, long-term outcome and treatment management depend on the site and extent of the infection and the nature of the underlying immunodeficiency. Full article

(This article belongs to the Special Issue Cutaneous Fungal Diseases)

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Open AccessReview

Microsporidiosis in Vertebrate Companion Exotic Animals

by Claire Vergneau-Grosset and Sylvain Larrat

J. Fungi 2016, 2(1), 3; https://doi.org/10.3390/jof2010003 - 24 Dec 2015

Cited by 10 | Viewed by 6542

Abstract

Veterinarians caring for companion animals may encounter microsporidia in various host species, and diagnosis and treatment of these fungal organisms can be particularly challenging. Fourteen microsporidial species have been reported to infect humans and some of them are zoonotic; however, to date, direct [...] Read more.

Veterinarians caring for companion animals may encounter microsporidia in various host species, and diagnosis and treatment of these fungal organisms can be particularly challenging. Fourteen microsporidial species have been reported to infect humans and some of them are zoonotic; however, to date, direct zoonotic transmission is difficult to document versus transit through the digestive tract. In this context, summarizing information available about microsporidiosis of companion exotic animals is relevant due to the proximity of these animals to their owners. Diagnostic modalities and therapeutic challenges are reviewed by taxa. Further studies are needed to better assess risks associated with animal microsporidia for immunosuppressed owners and to improve detection and treatment of infected companion animals. Full article

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Open AccessReview

Colliding Epidemics and the Rise of Cryptococcosis

by Christina C. Chang and Sharon C.-A. Chen

J. Fungi 2016, 2(1), 1; https://doi.org/10.3390/jof2010001 - 23 Dec 2015

Cited by 14 | Viewed by 4400

Abstract

Discovered more than 100 years ago as a human pathogen, the Cryptococcus neoformans–Cryptococcus gattii (C. neoformans–C. gattii) complex has seen a large global resurgence in its association with clinical disease in the last 30 years. First isolated in fermenting peach juice, [...] Read more.

Discovered more than 100 years ago as a human pathogen, the Cryptococcus neoformans–Cryptococcus gattii (C. neoformans–C. gattii) complex has seen a large global resurgence in its association with clinical disease in the last 30 years. First isolated in fermenting peach juice, and identified as a human pathogen in 1894 in a patient with bone lesions, this environmental pathogen has now found niches in soil, trees, birds, and domestic pets. Cryptococcosis is well recognized as an opportunistic infection and was first noted to be associated with reticuloendothelial cancers in the 1950s. Since then, advances in transplant immunology, medical science and surgical techniques have led to increasing numbers of solid organ transplantations (SOT) and hematological stem cell transplantations being performed, and the use of biological immunotherapeutics in increasingly high-risk and older individuals, have contributed to the further rise in cryptococcosis. Globally, however, the major driver for revivification of cryptococcosis is undoubtedly the HIV epidemic, particularly in Sub-Saharan Africa where access to care and antiretroviral therapy remains limited and advanced immunodeficiency, poverty and malnutrition remains the norm. As a zoonotic disease, environmental outbreaks of both human and animal cryptococcosis have been reported, possibly driven by climate change. This is best exemplified by the resurgence of C. gattii infection in Vancouver Island, Canada, and the Pacific Northwest of the United States since 1999. Here we describe how the colliding epidemics of HIV, transplantation and immunologics, climate change and migration have contributed to the rise of cryptococcosis. Full article

(This article belongs to the Special Issue Yeasts Are Beasts)

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Open AccessReview

Phaeohyphomycosis in Transplant Patients

by Sanjay G. Revankar

J. Fungi 2016, 2(1), 2; https://doi.org/10.3390/jof2010002 - 22 Dec 2015

Cited by 15 | Viewed by 4308

Abstract

Phaeohyphomycosis is caused by a large, heterogenous group of darkly pigmented fungi. The presence of melanin in their cell walls is characteristic, and is likely an important virulence factor. These infections are being increasingly seen in a variety of clinical syndromes in both [...] Read more.

Phaeohyphomycosis is caused by a large, heterogenous group of darkly pigmented fungi. The presence of melanin in their cell walls is characteristic, and is likely an important virulence factor. These infections are being increasingly seen in a variety of clinical syndromes in both immunocompromised and normal individuals. Transplant patients are especially at risk due their prolonged immunosuppression. There are no specific diagnostic tests for these fungi, though the Fontana-Masson stain is relatively specific in tissue. They are generally seen in a worldwide distribution, though a few species are only found in specific geographic regions. Management of these infections is not standardized due to lack of clinical trials, though recommendations are available based on clinical experience from case reports and series and animal models. Superficial infections may be treated without systemic therapy. Central nervous system infections are unique in that they often affect otherwise normal individuals, and are difficult to treat. Disseminated infections carry a high mortality despite aggressive therapy, usually with multiple antifungal drugs. Considerable work is needed to determine optimal diagnostic and treatment strategies for these infections. Full article

(This article belongs to the Special Issue Fungal Infections in Transplant Recipients)

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J. Fungi, Volume 2, Issue 1 (March 2016) – 11 articles

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