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J. Fungi, Volume 5, Issue 4 (December 2019) – 31 articles

Cover Story (view full-size image): The order Mucorales currently consists of 261 species, 38 of which cause human infections. For two decades, many taxa have been revised based on molecular phylogeny followed by, in part, confusing name changes. Several phenotypic characteristics traditionally used in mucoralean taxonomy have turned out to be not informative when viewed together with molecular data. With a clear focus on medically important genera and species, this review provides an overview on state-of-the-art taxonomic concepts.View this paper.
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Article
Identification of Cryptic Species of Four Candida Complexes in a Culture Collection
J. Fungi 2019, 5(4), 117; https://doi.org/10.3390/jof5040117 - 17 Dec 2019
Cited by 6 | Viewed by 1518
Abstract
Candida spp. are one of the most common causes of fungal infections worldwide. The taxonomy of Candida is controversial and has undergone recent changes due to novel genetically related species. Therefore, some complexes of cryptic species have been proposed. In clinical settings, the [...] Read more.
Candida spp. are one of the most common causes of fungal infections worldwide. The taxonomy of Candida is controversial and has undergone recent changes due to novel genetically related species. Therefore, some complexes of cryptic species have been proposed. In clinical settings, the correct identification of Candida species is relevant since some species are associated with high resistance to antifungal drugs and increased virulence. This study aimed to identify the species of four Candida complexes (C. albicans, C. glabrata, C. parapsilosis, and C. haemulonii) by molecular methods. This is the first report of six cryptic Candida species in Honduras: C. dubliniensis, C. africana, C. duobushaemulonii, C. orthopsilosis, and C. metapsilosis, and it is also the first report of the allele hwp1-2 of C. albicans sensu stricto. It was not possible to demonstrate the existence of C. auris among the isolates of the C. haemulonii complex. We also propose a simple method based on PCR-RFLP for the discrimination of the multi-resistant pathogen C. auris within the C. haemulonii complex. Full article
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Review
Immune Parameters for Diagnosis and Treatment Monitoring in Invasive Mold Infection
J. Fungi 2019, 5(4), 116; https://doi.org/10.3390/jof5040116 - 16 Dec 2019
Cited by 8 | Viewed by 2183
Abstract
Infections caused by invasive molds, including Aspergillus spp., can be difficult to diagnose and remain associated with high morbidity and mortality. Thus, early diagnosis and targeted systemic antifungal treatment remains the most important predictive factor for a successful outcome in immunocompromised individuals with [...] Read more.
Infections caused by invasive molds, including Aspergillus spp., can be difficult to diagnose and remain associated with high morbidity and mortality. Thus, early diagnosis and targeted systemic antifungal treatment remains the most important predictive factor for a successful outcome in immunocompromised individuals with invasive mold infections. Diagnosis remains difficult due to low sensitivities of diagnostic tests including culture and other mycological tests for mold pathogens, particularly in patients on mold-active antifungal prophylaxis. As a result, antifungal treatment is rarely targeted and reliable markers for treatment monitoring and outcome prediction are missing. Thus, there is a need for improved markers to diagnose invasive mold infections, monitor response to treatment, and assist in determining when antifungal therapy should be escalated, switched, or can be stopped. This review focuses on the role of immunologic markers and specifically cytokines in diagnosis and treatment monitoring of invasive mold infections. Full article
(This article belongs to the Special Issue Antifungal Immunity and Fungal Vaccine Development)
Review
The Broad Clinical Spectrum of Disseminated Histoplasmosis in HIV-Infected Patients: A 30 Years’ Experience in French Guiana
J. Fungi 2019, 5(4), 115; https://doi.org/10.3390/jof5040115 - 13 Dec 2019
Cited by 9 | Viewed by 1738
Abstract
Histoplasmosis is a common but neglected AIDS-defining condition in endemic areas for Histoplasma capsulatum. At the advanced stage of HIV infection, the broad spectrum of clinical features may mimic other frequent opportunistic infections such as tuberculosis and makes it difficult for clinicians [...] Read more.
Histoplasmosis is a common but neglected AIDS-defining condition in endemic areas for Histoplasma capsulatum. At the advanced stage of HIV infection, the broad spectrum of clinical features may mimic other frequent opportunistic infections such as tuberculosis and makes it difficult for clinicians to diagnose histoplasmosis in a timely manner. Diagnosis of histoplasmosis is difficult and relies on a high index of clinical suspicion along with access to medical mycology facilities with the capacity to implement conventional diagnostic methods (direct examination and culture) in a biosafety level 3 laboratory as well as indirect diagnostic methods (molecular biology, antibody, and antigen detection tools in tissue and body fluids). Time to initiation of effective antifungals has an impact on the patient’s prognosis. The initiation of empirical antifungal treatment should be considered in endemic areas for Histoplasma capsulatum and HIV. Here, we report on 30 years of experience in managing HIV-associated histoplasmosis based on a synthesis of clinical findings in French Guiana with considerations regarding the difficulties in determining its differential diagnosis with other opportunistic infections. Full article
(This article belongs to the Special Issue Histoplasma and Histoplasmosis)
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Communication
The Fungal Cell Death Regulator czt-1 Is Allelic to acr-3
J. Fungi 2019, 5(4), 114; https://doi.org/10.3390/jof5040114 - 06 Dec 2019
Cited by 3 | Viewed by 1253
Abstract
Fungal infections have far-reaching implications that range from severe human disease to a panoply of disruptive agricultural and ecological effects, making it imperative to identify and understand the molecular pathways governing the response to antifungal compounds. In this context, CZT-1 (cell death-activated zinc [...] Read more.
Fungal infections have far-reaching implications that range from severe human disease to a panoply of disruptive agricultural and ecological effects, making it imperative to identify and understand the molecular pathways governing the response to antifungal compounds. In this context, CZT-1 (cell death-activated zinc cluster transcription factor) functions as a master regulator of cell death and drug susceptibility in Neurospora crassa. Here we provide evidence indicating that czt-1 is allelic to acr-3, a previously described locus that we now found to harbor a point mutation in its coding sequence. This nonsynonymous amino acid substitution in a low complexity region of CZT-1/ACR-3 caused a robust gain-of-function that led to reduced sensitivity to acriflavine and staurosporine, and increased expression of the drug efflux pump abc-3. Thus, accumulating evidence shows that CZT-1 is an important broad regulator of the cellular response to various antifungal compounds that appear to share common molecular targets. Full article
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Article
Serial Detection of Circulating Mucorales DNA in Invasive Mucormycosis: A Retrospective Multicenter Evaluation
J. Fungi 2019, 5(4), 113; https://doi.org/10.3390/jof5040113 - 03 Dec 2019
Cited by 19 | Viewed by 2247
Abstract
Invasive mucormycosis is a fungal infection with high mortality. Early diagnosis and initiation of appropriate treatment is essential to improve survival. However, current diagnostic tools suffer from low sensitivity, leading to delayed or missed diagnoses. Recently, several PCR assays for the detection of [...] Read more.
Invasive mucormycosis is a fungal infection with high mortality. Early diagnosis and initiation of appropriate treatment is essential to improve survival. However, current diagnostic tools suffer from low sensitivity, leading to delayed or missed diagnoses. Recently, several PCR assays for the detection of Mucorales DNA have been developed. We retrospectively assessed the diagnostic and kinetic properties of a commercial Mucorales PCR assay (MucorGenius®, PathoNostics) on serial blood samples from patients with culture-positive invasive mucormycosis and found an overall sensitivity of 75%. Importantly, a positive test preceded a positive culture result by up to 81 days (median eight days, inter-quartile range 1.75–16.25). After initiation of appropriate therapy, the average levels of circulating DNA decreased after one week and stabilized after two weeks. In conclusion, detection of circulating Mucorales DNA appears to be a good, fast diagnostic test that often precedes the final diagnosis by several days to weeks. This test could be especially useful in cases in which sampling for culture or histopathology is not feasible. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Fungal Infections)
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Review
Molecular Diagnostics of Mucormycosis in Hematological Patients: A Literature Review
J. Fungi 2019, 5(4), 112; https://doi.org/10.3390/jof5040112 - 29 Nov 2019
Cited by 5 | Viewed by 1428
Abstract
Objectives: to analyze the results of molecular methods applying for the diagnosis of mucormycosis in hematologic patients based on a literature review. Data sources: A systematic search in databases PubMed, Google Scholar for August 2019. Review eligibility criteria: original articles published in English, [...] Read more.
Objectives: to analyze the results of molecular methods applying for the diagnosis of mucormycosis in hematologic patients based on a literature review. Data sources: A systematic search in databases PubMed, Google Scholar for August 2019. Review eligibility criteria: original articles published in English, studies of molecular methods for the diagnosis of mucormycosis in hematologic patients. Results. We analyzed the research data from 116 hematological patients with mucormycosis, including children (6%). Patients with localized forms of mucormycosis prevailed (72%), and lung involvement was diagnosed in 58% of these cases. For molecular verification of the causative agent of mucormycosis, blood serum was most often used, less commonly postoperative and autopsy material, biopsy specimens, formalin-fixed paraffin-embedded samples and bronchoalveolar lavage, pleural fluid and sputum. The sensitivity of molecular diagnostics of mucormycosis in a cohort of hematological patients was 88.2%. Conclusion. The use of molecular techniques along with standard mycological methods will improve the diagnostics of mucormycosis in hematologic patients. However, prospective studies of the effectiveness of molecular methods for the diagnosis of mucormycosis of various etiologies in hematological patients, including children, using bronchoalveolar lavage (BAL) and cerebrospinal fluid (CSF) are needed. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Fungal Infections)
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Review
Candida auris: A Review of Recommendations for Detection and Control in Healthcare Settings
J. Fungi 2019, 5(4), 111; https://doi.org/10.3390/jof5040111 - 28 Nov 2019
Cited by 39 | Viewed by 3795
Abstract
Candida auris is an emerging multidrug-resistant fungal pathogen. Since first reported in 2009, C. auris has caused healthcare outbreaks around the world, often involving high mortality. Identification of C. auris has been a major challenge as many common conventional laboratory methods cannot accurately [...] Read more.
Candida auris is an emerging multidrug-resistant fungal pathogen. Since first reported in 2009, C. auris has caused healthcare outbreaks around the world, often involving high mortality. Identification of C. auris has been a major challenge as many common conventional laboratory methods cannot accurately detect it. Early detection and implementation of infection control practices can prevent its spread. The aim of this review is to describe recommendations for the detection and control of C. auris in healthcare settings. Full article
(This article belongs to the Special Issue Candida auris)
Conference Report
The XVIII Congress of European Mycologists: Conference Report
J. Fungi 2019, 5(4), 110; https://doi.org/10.3390/jof5040110 - 25 Nov 2019
Cited by 1 | Viewed by 1332
Abstract
The 18th Congress of European Mycologists took place from 16 to 21 September 2019 in Warsaw and Białowieża, Poland (Figure 1) [...] Full article
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Review
The Burden of Fungal Infections in Ethiopia
J. Fungi 2019, 5(4), 109; https://doi.org/10.3390/jof5040109 - 22 Nov 2019
Cited by 12 | Viewed by 2253
Abstract
The burden of severe fungal infections (FIs) is not well addressed in Ethiopia. We have estimated the burden of FIs from multiple demographic sources and by searching articles from PubMed. Opportunistic FIs were estimated using modelling and 2017 national HIV data. The burdens [...] Read more.
The burden of severe fungal infections (FIs) is not well addressed in Ethiopia. We have estimated the burden of FIs from multiple demographic sources and by searching articles from PubMed. Opportunistic FIs were estimated using modelling and 2017 national HIV data. The burdens of chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA) were estimated by using the prevalence of asthma, chronic obstructive pulmonary disease, and annual the incidence of tuberculosis. Of the 105,000,000 estimated Ethiopian population, 610,000 are thought to have HIV infection. Our estimation of HIV-related FIs were: 9900 cryptococcal meningitis (CM), 12,700 Pneumocystis jirovecii pneumonia (PCP), 76,300 oral and 56,000 oesophageal candidiasis cases. A remarkable 7,051,700 4–14-year-olds probably have tinea capitis and 1,469,000 women probably have recurrent Candida vaginitis. There were 15,200 estimated CPA cases (prevalence) and 11,500 invasive aspergillosis (IA) cases (incidence). Data are scant, but we estimated 5300 candidaemia and 800 Candida peritonitis cases. In conclusion, approximately 8% of Ethiopians suffer from FIs annually, mostly schoolchildren with tinea capitis. IA, CM and PCP are the major causes of fungal deaths. The absence of CD4 count is challenging the identification of HIV patients at risk of opportunistic FIs. There is a pressing need to improve FI diagnosis, probably including national surveillance. Full article
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Review
Antifungal Susceptibly Testing by Concentration Gradient Strip Etest Method for Fungal Isolates: A Review
J. Fungi 2019, 5(4), 108; https://doi.org/10.3390/jof5040108 - 22 Nov 2019
Cited by 13 | Viewed by 1869
Abstract
Antifungal susceptibility testing is an important tool for managing patients with invasive fungal infections, as well as for epidemiological surveillance of emerging resistance. For routine testing in clinical microbiology laboratories, ready-to-use commercial methods are more practical than homemade reference techniques. Among commercially available [...] Read more.
Antifungal susceptibility testing is an important tool for managing patients with invasive fungal infections, as well as for epidemiological surveillance of emerging resistance. For routine testing in clinical microbiology laboratories, ready-to-use commercial methods are more practical than homemade reference techniques. Among commercially available methods, the concentration gradient Etest strip technique is widely used. It combines an agar-based diffusion method with a dilution method that determinates a minimal inhibitory concentration (MIC) in µg/mL. Many studies have evaluated the agreement between the gradient strip method and the reference methods for both yeasts and filamentous fungi. This agreement has been variable depending on the antifungal, the species, and the incubation time. It has also been shown that the gradient strip method could be a valuable alternative for detection of emerging resistance (non-wild-type isolates) as Etest epidemiological cutoff values have been recently defined for several drug-species combinations. Furthermore, the Etest could be useful for direct antifungal susceptibility testing on blood samples and basic research studies (e.g., the evaluation of the in vitro activity of antifungal combinations). This review summarizes the available data on the performance and potential use of the gradient strip method. Full article
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Article
Deletion of the SKO1 Gene in a hog1 Mutant Reverts Virulence in Candida albicans
J. Fungi 2019, 5(4), 107; https://doi.org/10.3390/jof5040107 - 15 Nov 2019
Cited by 1 | Viewed by 1561
Abstract
Candida albicans displays the ability to adapt to a wide variety of environmental conditions, triggering signaling pathways and transcriptional regulation. Sko1 is a transcription factor that was previously involved in early hypoxic response, cell wall remodeling, and stress response. In the present work, [...] Read more.
Candida albicans displays the ability to adapt to a wide variety of environmental conditions, triggering signaling pathways and transcriptional regulation. Sko1 is a transcription factor that was previously involved in early hypoxic response, cell wall remodeling, and stress response. In the present work, the role of sko1 mutant in in vivo and ex vivo studies was explored. The sko1 mutant behaved as its parental wild type strain regarding the ability to colonize murine intestinal tract, ex vivo adhesion to murine gut epithelium, or systemic virulence. These observations suggest that Sko1 is expendable during commensalism or pathogenesis. Nevertheless, the study of the hog1 sko1 double mutant showed unexpected phenotypes. Previous researches reported that the deletion of the HOG1 gene led to avirulent C. albicans mutant cell, which was, therefore, unable to establish as a commensal in a gastrointestinal murine model. Here, we show that the deletion of sko1 in a hog1 background reverted the virulence of the hog1 mutant in a systemic infection model in Galleria mellonella larvae and slightly improved the ability to colonize the murine gut in a commensalism animal model compared to the hog1 mutant. These results indicate that Sko1 acts as a repressor of virulence related genes, concluding that Sko1 plays a relevant role during commensalism and systemic infection. Full article
(This article belongs to the Special Issue Pathogenesis of Candidiasis)
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Review
Updates on the Taxonomy of Mucorales with an Emphasis on Clinically Important Taxa
J. Fungi 2019, 5(4), 106; https://doi.org/10.3390/jof5040106 - 14 Nov 2019
Cited by 60 | Viewed by 3799
Abstract
Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. [...] Read more.
Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. Several taxa cause life-threatening infections, predominantly in patients with impaired immunity. The order Mucorales has now been assigned to the phylum Mucoromycota and is comprised of 261 species in 55 genera. Of these accepted species, 38 have been reported to cause infections in humans, as a clinical entity known as mucormycosis. Due to molecular phylogenetic studies, the taxonomy of the order has changed widely during the last years. Characteristics such as homothallism, the shape of the suspensors, or the formation of sporangiola are shown to be not taxonomically relevant. Several genera including Absidia, Backusella, Circinella, Mucor, and Rhizomucor have been amended and their revisions are summarized in this review. Medically important species that have been affected by recent changes include Lichtheimia corymbifera, Mucor circinelloides, and Rhizopus microsporus. The species concept of Rhizopus arrhizus (syn. R. oryzae) is still a matter of debate. Currently, species identification of the Mucorales is best performed by sequencing of the internal transcribed spacer (ITS) region. Ecologically, the Mucorales represent a diverse group but for the majority of taxa, the ecological role and the geographic distribution remain unknown. Understanding the biology of these opportunistic fungal pathogens is a prerequisite for the prevention of infections, and, consequently, studies on the ecology of the Mucorales are urgently needed. Full article
(This article belongs to the Special Issue Mucorales and Mucormycosis)
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Article
Detection of Fusarium Species in Clinical Specimens by Probe-Based Real-Time PCR
J. Fungi 2019, 5(4), 105; https://doi.org/10.3390/jof5040105 - 12 Nov 2019
Cited by 2 | Viewed by 1461
Abstract
The mold Fusarium is a ubiquitous fungus causing plant, animal and human infections. In humans, Fusarium spp. are the major cause of eye infections in patients wearing contact lenses or after local trauma. Systemic infections by Fusarium spp. mainly occur in immunosuppressed patients [...] Read more.
The mold Fusarium is a ubiquitous fungus causing plant, animal and human infections. In humans, Fusarium spp. are the major cause of eye infections in patients wearing contact lenses or after local trauma. Systemic infections by Fusarium spp. mainly occur in immunosuppressed patients and can disseminate throughout the human body. Due to high levels of resistance to antifungals a fast identification of the causative agent is an urgent need. By using a probe-based real-time PCR assay specific for the genus Fusarium we analysed several different clinical specimens detecting Fusarium spp. commonly found in clinical samples in Germany. Also, a large collection of lung fluid samples of haematological patients was analysed (n = 243). In these, two samples (0.8%) were reproducibly positive, but only one could be confirmed by sequencing. For this case of probable invasive fungal disease (IFD) culture was positive for Fusarium species. Here we describe a rapid, probe-based real-time PCR assay to specifically detect DNA from a broad range of Fusarium species and its application to clinically relevant specimens. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Fungal Infections)
Communication
Shift in Epidemiology of Cryptococcal Infections in Ottawa with High Mortality in Non-HIV Immunocompromised Patients
J. Fungi 2019, 5(4), 104; https://doi.org/10.3390/jof5040104 - 10 Nov 2019
Cited by 7 | Viewed by 1300
Abstract
Cryptococcus neoformans is a fungus that can cause life-threatening infections. While human immunodeficiency virus (HIV)-positive status historically had the highest risk for cryptococcal infection and was associated with high mortality rates, there have been changes in HIV treatment and the epidemiology of other [...] Read more.
Cryptococcus neoformans is a fungus that can cause life-threatening infections. While human immunodeficiency virus (HIV)-positive status historically had the highest risk for cryptococcal infection and was associated with high mortality rates, there have been changes in HIV treatment and the epidemiology of other acquired immunodeficiencies, such as hematological malignancies. We conducted a retrospective case series analysis of patients who had cryptococcal infections documented at the Ottawa Hospital from 2005 to 2017. The Ottawa Hospital is a tertiary care hospital and provides complex care such as chemotherapy and transplantations. There were 28 confirmed cryptococcal infections. The most common underlying condition associated with cryptococcal infection was hematological malignancy (n = 8.29%), followed by HIV (n = 5.18%) and solid organ transplantation (n = 4.14%). Furthermore, while there was a decrease in the number of cryptococcal infections in HIV patients after 2010 (four to one case), the number of cases in non-HIV immunocompromised patients increased from four in the years 2005–2010 to fourteen in 2011–2017. There were nine cryptococcal-attributable deaths. The case fatality rate was highest among patients with underlying hematological malignancies (63%), followed by solid organ transplant (50%) and HIV patients (20%). In conclusion, this study showed that there may be an epidemiological shift of cryptococcal infection in Ottawa. Additionally, infections may be associated with a worse prognosis in patients with a hematological malignancy and solid organ transplant than in patients with HIV infection in the modern era. Better prevention and/or treatment is warranted for high-risk populations. Full article
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Article
Thermogenic Characterization and Antifungal Susceptibility of Candida auris by Microcalorimetry
J. Fungi 2019, 5(4), 103; https://doi.org/10.3390/jof5040103 - 06 Nov 2019
Cited by 6 | Viewed by 1707
Abstract
Candida auris has emerged globally as a multidrug-resistant fungal pathogen. Isolates of C. auris are reported to be misidentified as Candida haemulonii. The aim of the study was to compare the heat production profiles of C. auris strains and other Candida spp. [...] Read more.
Candida auris has emerged globally as a multidrug-resistant fungal pathogen. Isolates of C. auris are reported to be misidentified as Candida haemulonii. The aim of the study was to compare the heat production profiles of C. auris strains and other Candida spp. and evaluate their antifungal susceptibility using isothermal microcalorimetry. The minimum heat inhibitory concentrations (MHIC) and the minimum biofilm fungicidal concentration (MBFC) were defined as the lowest antimicrobial concentration leading to the lack of heat flow production after 24 h for planktonic cells and 48 h for biofilm-embedded cells. C. auris exhibited a peculiar heat production profile. Thermogenic parameters of C. auris suggested a slower growth rate compared to Candida lusitaniae and a different distinct heat profile compared to that of C. haemulonii species complex strains, although they all belong to the Metschnikowiaceae clade. Amphotericin B MHIC and MBFC were 0.5 µg/mL and ≥8 µg/mL, respectively. C. auris strains were non-susceptible to fluconazole at tested concentrations (MHIC > 128 µg/mL, MBFC > 256 µg/mL). The heat curve represents a fingerprint of C. auris, which distinguished it from other species. Treatment based on amphotericin B represents a potential therapeutic option for C. auris infection. Full article
(This article belongs to the Special Issue Candida auris)
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Article
Genetic Regulators and Physiological Significance of Glycogen Storage in Candida albicans
J. Fungi 2019, 5(4), 102; https://doi.org/10.3390/jof5040102 - 30 Oct 2019
Cited by 3 | Viewed by 1250
Abstract
The dimorphic human fungal pathogen C. albicans has broad metabolic flexibility that allows it to adapt to the nutrient conditions in different host habitats. C. albicans builds large carbohydrate stores (glycogen) at the end of exponential growth and begins consumption of stored carbohydrates [...] Read more.
The dimorphic human fungal pathogen C. albicans has broad metabolic flexibility that allows it to adapt to the nutrient conditions in different host habitats. C. albicans builds large carbohydrate stores (glycogen) at the end of exponential growth and begins consumption of stored carbohydrates when nutrients become limiting. The expression of genes required for the successful transition between host environments, including the factors controlling glycogen content, is controlled by protein kinase A signaling through the transcription factor Efg1. In addition to the inability to transition to hyphal growth, C. albicans efg1 mutants have low glycogen content and reduced long-term survival, suggesting that carbohydrate storage is required for viability during prolonged culture. To test this assumption, we constructed a glycogen-deficient C. albicans mutant and assessed its viability during extended culture. Pathways and additional genetic factors controlling C. albicans glycogen synthesis were identified through the screening of mutant libraries for strains with low glycogen content. Finally, a part of the Efg1-regulon was screened for mutants with a shortened long-term survival phenotype. We found that glycogen deficiency does not affect long-term survival, growth, metabolic flexibility or morphology of C. albicans. We conclude that glycogen is not an important contributor to C. albicans fitness. Full article
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Article
Ongoing Challenges with Healthcare-Associated Candida auris Outbreaks in Oman
J. Fungi 2019, 5(4), 101; https://doi.org/10.3390/jof5040101 - 23 Oct 2019
Cited by 25 | Viewed by 2234
Abstract
Candida auris has emerged in the past decade as a multi-drug resistant public health threat causing health care outbreaks. Here we report epidemiological, clinical, and microbiological investigations of a C. auris outbreak in a regional Omani hospital between April 2018 and April 2019. [...] Read more.
Candida auris has emerged in the past decade as a multi-drug resistant public health threat causing health care outbreaks. Here we report epidemiological, clinical, and microbiological investigations of a C. auris outbreak in a regional Omani hospital between April 2018 and April 2019. The outbreak started in the intensive care areas (intensive care unit (ICU), coronary care unit (CCU), and high dependency unit) but cases were subsequently diagnosed in other medical and surgical units. In addition to the patients’ clinical and screening samples, environmental swabs from high touch areas and from the hands of 35 staff were collected. All the positive samples from patients and environmental screening were confirmed using MALDI-TOF, and additional ITS-rDNA sequencing was done for ten clinical and two environmental isolates. There were 32 patients positive for C. auris of which 14 (43.8%) had urinary tract infection, 11 (34.4%) had candidemia, and 7 (21.8%) had asymptomatic skin colonization. The median age was 64 years (14–88) with 17 (53.1%) male and 15 (46.9%) female patients. Prior to diagnosis, 21 (65.6%) had been admitted to the intensive care unit, and 11 (34.4%) had been nursed in medical or surgical wards. The crude mortality rate in our patient’s cohort was 53.1. Two swabs collected from a ventilator in two different beds in the ICU were positive for C. auris. None of the health care worker samples were positive. Molecular typing showed that clinical and environmental isolates were genetically similar and all belonged to the South Asian C. auris clade I. Most isolates had non-susceptible fluconazole (100%) and amphotericin B (33%) minimal inhibitory concentrations (MICs), but had low echinocandin and voriconazole MICs. Despite multimodal infection prevention and control measures, new cases continued to appear, challenging all the containment efforts. Full article
(This article belongs to the Special Issue Candida auris)
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Article
PdMFS1 Transporter Contributes to Penicilliun digitatum Fungicide Resistance and Fungal Virulence during Citrus Fruit Infection
J. Fungi 2019, 5(4), 100; https://doi.org/10.3390/jof5040100 - 18 Oct 2019
Cited by 16 | Viewed by 2276
Abstract
A new Penicillium digitatum major facilitator superfamily (MFS) transporter (PdMFS1) was identified and functionally characterized in order to shed more light on the mechanisms underlying fungicide resistance. PdMFS1 can play an important role in the intensification of resistance to fungicides normally [...] Read more.
A new Penicillium digitatum major facilitator superfamily (MFS) transporter (PdMFS1) was identified and functionally characterized in order to shed more light on the mechanisms underlying fungicide resistance. PdMFS1 can play an important role in the intensification of resistance to fungicides normally used in P. digitatum postharvest treatments. In the PdMFS1 disrupted mutants, a slight effect in response to chemical fungicides was observed, but fungicide sensitivity was highly affected in the overexpression mutants which became resistant to wide range of chemical fungicides. Moreover, P. digitatum knock-out mutants exhibited a lower rate of fungal virulence when infected oranges were stored at 20 °C. Disease symptoms were higher in the PdMFS1 overexpression mutants coming from the low-virulent P. digitatum parental strain. In addition, the gene expression analysis showed an induction of PdMFS1 transcription in all overexpression mutants regardless from which progenitor came from, and four-time intensification of the parental wild type strain during citrus infection reinforcing PdMFS1 role in fungal virulence. The P. digitatum MFS transporter PdMFS1 contributes not only to the acquisition of wide range of fungicide resistance but also in fungal virulence during citrus infection. Full article
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Article
First Isolation, Antifungal Susceptibility, and Molecular Characterization of Cryptococcus neoformans from the Environment in Croatia
J. Fungi 2019, 5(4), 99; https://doi.org/10.3390/jof5040099 - 12 Oct 2019
Cited by 3 | Viewed by 1509
Abstract
The purpose of this study was to investigate the presence of Cryptococcus neoformans species complex isolates from environmental sources in Croatia and to determine their molecular types and antifungal susceptibility. Swab samples of tree hollows and bird excreta in the soil beneath trees [...] Read more.
The purpose of this study was to investigate the presence of Cryptococcus neoformans species complex isolates from environmental sources in Croatia and to determine their molecular types and antifungal susceptibility. Swab samples of tree hollows and bird excreta in the soil beneath trees were collected. Samples included 472 (92.73%) samples obtained from tree hollows and 37 (7.27%) samples from bird excreta. Four C. neoformans species complex isolates were recovered from tree hollow swabs along the Mediterranean coast, while there were no isolates recovered from bird excreta or from the continental area. Three isolates were identified as molecular types VNI and one as VNIV. All tested antifungals showed high in vitro activity against the four isolates. This is the first report proving the presence of C. neoformans species complex in the environment of Croatia. The results of the study suggest a major risk of exposure for inhabitants living along the Croatian coast and that both VNI and VNIV molecular types can be expected in clinical cases of cryptococcosis. Susceptibility to antifungals confirmed that no resistance should be expected in patients with cryptococcosis at the present time. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Fungal Infections)
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Article
Evaluation of a Novel Mitochondrial Pan-Mucorales Marker for the Detection, Identification, Quantification, and Growth Stage Determination of Mucormycetes
J. Fungi 2019, 5(4), 98; https://doi.org/10.3390/jof5040098 - 11 Oct 2019
Cited by 8 | Viewed by 1660
Abstract
Mucormycosis infections are infrequent yet aggressive and serious fungal infections. Early diagnosis of mucormycosis and its discrimination from other fungal infections is required for targeted treatment and more favorable patient outcomes. The majority of the molecular assays use 18 S rDNA. In the [...] Read more.
Mucormycosis infections are infrequent yet aggressive and serious fungal infections. Early diagnosis of mucormycosis and its discrimination from other fungal infections is required for targeted treatment and more favorable patient outcomes. The majority of the molecular assays use 18 S rDNA. In the current study, we aimed to explore the potential of the mitochondrial rnl (encoding for large-subunit-ribosomal-RNA) gene as a novel molecular marker suitable for research and diagnostics. Rnl was evaluated as a marker for: (1) the Mucorales family, (2) species identification (Rhizopus arrhizus, R. microsporus, Mucor circinelloides, and Lichtheimia species complexes), (3) growth stage, and (4) quantification. Sensitivity, specificity, discriminatory power, the limit of detection (LoD), and cross-reactivity were evaluated. Assays were tested using pure cultures, spiked clinical samples, murine organs, and human paraffin-embedded-tissue (FFPE) samples. Mitochondrial markers were found to be superior to nuclear markers for degraded samples. Rnl outperformed the UMD universal® (Molyzm) marker in FFPE (71.5% positive samples versus 50%). Spiked blood samples highlighted the potential of rnl as a pan-Mucorales screening test. Fungal burden was reproducibly quantified in murine organs using standard curves. Identification of pure cultures gave a perfect (100%) correlation with the detected internal transcribed spacer (ITS) sequence. In conclusion, mitochondrial genes, such as rnl, provide an alternative to the nuclear 18 S rDNA genes and deserve further evaluation. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Fungal Infections)
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Communication
Antifungal Drugs: Special Problems Treating Central Nervous System Infections
J. Fungi 2019, 5(4), 97; https://doi.org/10.3390/jof5040097 - 11 Oct 2019
Cited by 11 | Viewed by 1675
Abstract
Treating fungal infections in the central nervous system (CNS) remains a challenge despite the availability of new antifungal agents. Therapy is limited by poor understanding of the kinetic properties of antifungal drugs in the CNS compounded by lack of data for many agents. [...] Read more.
Treating fungal infections in the central nervous system (CNS) remains a challenge despite the availability of new antifungal agents. Therapy is limited by poor understanding of the kinetic properties of antifungal drugs in the CNS compounded by lack of data for many agents. In some cases, clinical response rates do not correspond to data on drug concentrations in the cerebral spinal fluid and/or brain parenchyma. In order to better characterize the use of antifungal agents in treating CNS infections, a review of the essential principles of neuroPK are reviewed. Specific data regarding antifungal drug concentrations in the cerebral spinal fluid and brain tissue are described from human data where available. Alternative dosing regimens and the role of antifungal drug concentration monitoring in treating fungal infections in the CNS are also discussed. Having a better understanding of these key concepts will help guide clinicians in determining the best treatment courses for patients with these devastating infections. Full article
(This article belongs to the Special Issue Fungal Infections of the Central Nervous System)
Article
Construction of a Codon-Adapted Nourseotricin-Resistance Marker Gene for Efficient Targeted Gene Deletion in the Mycophenolic Acid Producer Penicillium brevicompactum
J. Fungi 2019, 5(4), 96; https://doi.org/10.3390/jof5040096 - 10 Oct 2019
Cited by 2 | Viewed by 1527
Abstract
Penicillium brevicompactum is a filamentous ascomycete used in the pharmaceutical industry to produce mycophenolic acid, an immunosuppressant agent. To extend options for genetic engineering of this fungus, we have tested two resistance markers that have not previously been applied to P. brevicompactum. [...] Read more.
Penicillium brevicompactum is a filamentous ascomycete used in the pharmaceutical industry to produce mycophenolic acid, an immunosuppressant agent. To extend options for genetic engineering of this fungus, we have tested two resistance markers that have not previously been applied to P. brevicompactum. Although a generally available phleomycin resistance marker (ble) was successfully used in DNA-mediated transformation experiments, we were not able to use a commonly applicable nourseothricin resistance cassette (nat1). To circumvent this failure, we constructed a new nat gene, considering the codon bias for P. brevicompactum. We then used this modified nat gene in subsequent transformation experiments for the targeted disruption of two nuclear genes, MAT1-2-1 and flbA. For MAT1-2-1, we obtained deletion strains with a frequency of about 10%. In the case of flbA, the frequency was about 4%, and this disruption strain also showed reduced conidiospore formation. To confirm the deletion, we used ble to reintroduce the wild-type genes. This step restored the wild-type phenotype in the flbA deletion strain, which had a sporulation defect. The successful transformation system described here substantially extends options for genetically manipulating the biotechnologically relevant fungus P. brevicompactum. Full article
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Conference Report
9th Trends in Medical Mycology Held on 11–14 October 2019, Nice, France, Organized under the Auspices of EORTC-IDG and ECMM
J. Fungi 2019, 5(4), 95; https://doi.org/10.3390/jof5040095 - 08 Oct 2019
Cited by 10 | Viewed by 4159
Abstract
Dear Friends and Colleagues,
It is a great honor and pleasure for us to invite you cordially to participate in the 9th Congress on Trends in Medical Mycology (TIMM-9) [...] Full article
Article
External Quality Assessment Evaluating the Ability of Dutch Clinical Microbiological Laboratories to Identify Candida auris
J. Fungi 2019, 5(4), 94; https://doi.org/10.3390/jof5040094 - 07 Oct 2019
Cited by 9 | Viewed by 1728
Abstract
Background: Candida auris is a yeast that is causing nosocomial outbreaks in healthcare facilities around the world. There is a risk of the misidentification of C. auris with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)—when libraries are used that lack [...] Read more.
Background: Candida auris is a yeast that is causing nosocomial outbreaks in healthcare facilities around the world. There is a risk of the misidentification of C. auris with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)—when libraries are used that lack C. auris spectra, or when conventional biochemical methods are used. Methods: We conducted an external quality assessment to evaluate the ability of Dutch clinical microbiological laboratories to identify C. auris, and to raise awareness about the risk of misidentification. Results: 35/47 participating laboratories were able to identify C. auris correctly. Only 2/14 labs that potentially misidentified C. auris with their primary identification methods specified that they would perform additional tests to exclude C. auris when appropriate. 45/47 labs used MALDI-TOF MS systems to identify Candida species. Conclusions: There was a lack of awareness about the potential misidentification of C. auris in many labs that used MALDI-TOF MS with libraries that lacked C. auris spectra, and labs that used Vitek 2. However, as the currently available MALDI-TOF MS libraries in The Netherlands contain several C. auris spectra, we expect that currently almost all participating laboratories are able to identify C. auris correctly, as 45/47 participating laboratories use MALDI-TOF MS as their primary yeast identification method. Full article
(This article belongs to the Special Issue Candida auris)
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Perspective
National Public Health Response to Candida auris in England
J. Fungi 2019, 5(4), 93; https://doi.org/10.3390/jof5040093 - 03 Oct 2019
Cited by 3 | Viewed by 1572
Abstract
This paper highlights the key steps undertaken by a national public health agency, working in close collaboration with academic partners and experienced healthcare professionals, in developing a response to the rapid emergence of a novel nosocomial pathogen. It details the key activities in [...] Read more.
This paper highlights the key steps undertaken by a national public health agency, working in close collaboration with academic partners and experienced healthcare professionals, in developing a response to the rapid emergence of a novel nosocomial pathogen. It details the key activities in national incident management team formation, surveillance activities, epidemiological investigations, laboratory developments, scientific advances, and collaborative activities. It discusses commonalities that can be adapted for dealing with the emergence of future new pathogens. Full article
(This article belongs to the Special Issue Candida auris)
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Article
Repositionable Compounds with Antifungal Activity against Multidrug Resistant Candida auris Identified in the Medicines for Malaria Venture’s Pathogen Box
J. Fungi 2019, 5(4), 92; https://doi.org/10.3390/jof5040092 - 01 Oct 2019
Cited by 27 | Viewed by 3123
Abstract
Background. Candida auris has spread rapidly around the world as a causative agent of invasive candidiasis in health care facilities and there is an urgent need to find new options for treating this emerging, often multidrug-resistant pathogen. Methods. We screened the Pathogen Box [...] Read more.
Background. Candida auris has spread rapidly around the world as a causative agent of invasive candidiasis in health care facilities and there is an urgent need to find new options for treating this emerging, often multidrug-resistant pathogen. Methods. We screened the Pathogen Box® chemical library for inhibitors of C. auris strain 0390, both under planktonic and biofilm growing conditions. Results. The primary screen identified 12 compounds that inhibited at least 60% of biofilm formation or planktonic growth. After confirmatory dose-response assays, iodoquinol and miltefosine were selected as the two main leading repositionable compounds. Iodoquinol displayed potent in vitro inhibitory activity against planktonic C. auris but showed negligible inhibitory activity against biofilms; whereas miltefosine was able to inhibit the growth of C. auris under both planktonic and biofilm-growing conditions. Subsequent experiments confirmed their activity against nine other strains C. auris clinical isolates, irrespective of their susceptibility profiles against conventional antifungals. We extended our studies further to seven different species of Candida, also with similar findings. Conclusion. Both drugs possess broad spectrum of activity against Candida spp., including multiple strains of the emergent C. auris, and may constitute promising repositionable options for the development of novel therapeutics for the treatment of candidiasis. Full article
(This article belongs to the Special Issue Candida auris)
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Case Report
The First Two Cases of Candida auris in The Netherlands
J. Fungi 2019, 5(4), 91; https://doi.org/10.3390/jof5040091 - 30 Sep 2019
Cited by 15 | Viewed by 2607
Abstract
Candida auris is a rapidly emerging multidrug-resistant pathogenic yeast. In recent years, an increasing number of C. auris invasive infections and colonized patients have been reported, and C. auris has been associated with hospital outbreaks worldwide, mainly in intensive care units (ICUs). Here, [...] Read more.
Candida auris is a rapidly emerging multidrug-resistant pathogenic yeast. In recent years, an increasing number of C. auris invasive infections and colonized patients have been reported, and C. auris has been associated with hospital outbreaks worldwide, mainly in intensive care units (ICUs). Here, we describe the first two cases of C. auris in The Netherlands. Both cases were treated in a healthcare facility in India prior to admission. The patients were routinely placed in contact precautions in a single room after admission, which is common practice in The Netherlands for patients with hospitalization outside The Netherlands. No transmission of C. auris was noticed in both hospitals. Routine admission screening both for multidrug-resistant (MDR) bacteria and MDR yeasts should be considered for patients admitted from foreign hospitals or countries with reported C. auris transmission. Full article
(This article belongs to the Special Issue Candida auris)
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Review
Identification of Mycoses in Developing Countries
J. Fungi 2019, 5(4), 90; https://doi.org/10.3390/jof5040090 - 29 Sep 2019
Cited by 31 | Viewed by 2843
Abstract
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in [...] Read more.
Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Fungal Infections)
Editorial
Special Issue: Fungal–Bacterial Interactions—Current Knowledge and Future Perspectives
J. Fungi 2019, 5(4), 89; https://doi.org/10.3390/jof5040089 - 24 Sep 2019
Cited by 1 | Viewed by 1140
Abstract
We would like to thank all the contributors to the Special Issue on Fungal–Bacterial Interactions—Current Knowledge and Future Perspectives [...] Full article
Article
Long-Chain Acyl-CoA Synthetase is Associated with the Growth of Malassezia spp.
J. Fungi 2019, 5(4), 88; https://doi.org/10.3390/jof5040088 - 21 Sep 2019
Cited by 4 | Viewed by 1435
Abstract
The lipophilic fungal pathogen Malassezia spp. must acquire long-chain fatty acids (LCFAs) from outside the cell. To clarify the mechanism of LCFA acquisition, we investigated fatty acid uptake by this fungus and identified the long-chain acyl-CoA synthetase (ACS) gene FAA1 in three Malassezia [...] Read more.
The lipophilic fungal pathogen Malassezia spp. must acquire long-chain fatty acids (LCFAs) from outside the cell. To clarify the mechanism of LCFA acquisition, we investigated fatty acid uptake by this fungus and identified the long-chain acyl-CoA synthetase (ACS) gene FAA1 in three Malassezia spp.: M. globosa, M. pachydermatis, and M. sympodialis. These FAA1 genes could compensate for the double mutation of FAA1 and FAA4 in Saccharomyces cerevisiae, suggesting that Malassezia Faa1 protein recognizes exogenous LCFAs. MgFaa1p and MpFaa1p utilized a medium-chain fatty acid, lauric acid (C12:0). Interestingly, the ACS inhibitor, triacsin C, affected the activity of the Malassezia Faa1 proteins but not that of S. cerevisiae. Triacsin C also reduced the growth of M. globosa, M. pachydermatis, and M. sympodialis. These results suggest that triacsin C and its derivatives are potential compounds for the development of new anti-Malassezia drugs. Full article
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