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Diagnosis of Human Pathogenic Fungi
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Diagnosis of Human Pathogenic Fungi

A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 7817

Special Issue Editor

Dr. Eleonora Dubljanin

E-Mail Website
Guest Editor
Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
Interests: fungi; invasive fungal infections; superficial fungal infections; laboratory diagnosis of human mycosis; onychomycosis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungal pathogens can cause a range of diseases in humans and represent an increasing global public health concern. Superficial fungal infections, such as ringworm, athlete’s foot caused by dermatophytes, or thrush, and dandruff caused by other fungi, are common worldwide and affect 20% to 25% of the world's population. Fungal infections of the skin, hair and nails are among the most common ailments of humans, while it is estimated that 3 million adults worldwide are sensitive to fungal allergens that cause considerable lung-associated pathologies. Invasive fungal diseases are recognised as an increasing global burden in immunocompromised and other seriously ill populations, with more than 300 million people affected and more than 1.5 million deaths globally per year from these diseases. The most common causes of life-threatening fungal infections are Candida spp, Aspergillus, Cryptococcus spp., Mucorales, and Pneumocystis jirovecii. The diagnosis of fungal infection by conventional methods such as culture and microscopy remains the gold standard, but this is difficult in patients with invasive fungal infections. Prompt diagnosis of invasive fungal infections is challenging and mainly relies on the detection of diagnostics biomarkers. However, the accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes.

Dr. Eleonora Dubljanin
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • invasive fungal infections
  • superficial fungal infections
  • laboratory diagnosis of human mycosis
  • fungal biomarkers
  • candidiasis
  • aspergillosis
  • mucomycosis
  • dermatomycosis

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Related Special Issue

Published Papers (7 papers)

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Research

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12 pages, 753 KiB  
Article
A Laboratory-Developed Assay for the Simultaneous Detection of Aspergillus fumigatus and Pneumocystis jirovecii Pulmonary Pathogens
by Margherita Cacaci, Debora Talamonti, Giulia Menchinelli, Damiano Squitieri, Riccardo Torelli, Elena De Carolis, Giulia De Angelis, Maurizio Sanguinetti and Brunella Posteraro
J. Fungi 2025, 11(4), 280; https://doi.org/10.3390/jof11040280 - 2 Apr 2025
Viewed by 260
Abstract
Invasive fungal diseases are a significant threat in immunocompromised patients, underscoring the need for rapid and accurate diagnostics. This study describes the development and validation of a real-time PCR-based laboratory-developed assay (LDA) on the Panther Fusion system for the simultaneous detection of Aspergillus [...] Read more.
Invasive fungal diseases are a significant threat in immunocompromised patients, underscoring the need for rapid and accurate diagnostics. This study describes the development and validation of a real-time PCR-based laboratory-developed assay (LDA) on the Panther Fusion system for the simultaneous detection of Aspergillus fumigatus (AF) and Pneumocystis jirovecii (PJ) in bronchoalveolar lavage fluid (BALF) samples. The assay was evaluated using 239 clinical BALF samples, including cases confirmed positive for AF or PJ by reference mycological methods. Rigorous optimization ensured compatibility with the automated workflow of the Panther Fusion system, which addresses challenges such as BALF viscosity and fungal DNA recovery. No cross-reactivity with non-target fungal species was observed, and the assay demonstrated high analytical sensitivity and specificity. Only two false-negative results were reported, which could plausibly be reclassified as true negatives when interpreted alongside the serum beta-d-glucan and galactomannan assay results. For PJ detection, the assay showed excellent concordance with the OLM PneumID assay, supporting its reliability in clinical settings. The dual-target approach facilitates the simultaneous detection of both pathogens within a single workflow, improving diagnostic efficiency. The AF/PJ LDA represents a robust and scalable alternative to existing molecular assays, with the potential to enhance routine diagnostics for pulmonary fungal infections. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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13 pages, 1184 KiB  
Article
Identification of Challenging Dermatophyte Species Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
by Tsung-Fu Tsai, Yun-Chen Fan, Jang-Jih Lu, Chun-Chih Chien, Hsin-Yao Wang and Pei-Lun Sun
J. Fungi 2025, 11(2), 107; https://doi.org/10.3390/jof11020107 - 31 Jan 2025
Viewed by 864
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a widely adopted technique for bacterial and yeast identification in clinical laboratories but is less frequently applied to filamentous fungi due to inconsistent performance, limitations of commercial libraries, and variability of preparation methods. This [...] Read more.
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a widely adopted technique for bacterial and yeast identification in clinical laboratories but is less frequently applied to filamentous fungi due to inconsistent performance, limitations of commercial libraries, and variability of preparation methods. This study aimed to validate the efficiency of MALDI-TOF MS-based dermatophyte identification using the Bruker Biotyper system. Focusing on species from the Trichophyton, Nannizzia, Microsporum, and Epidermophyton genera, an in-house reference library was established and evaluated with clinical isolates. The expanded library, which combined the in-house and Bruker libraries, achieved significantly higher accuracy than the Bruker library alone, correctly identifying 90.7% (107/118) of isolates at the species level compared to 16.1% (19/118) by the Bruker library. This study presents an efficient, standardized MALDI-TOF MS protocol for routine dermatophyte identification and provides a review of the current status and influencing factors in MALDI-TOF MS-based dermatophyte identification strategies. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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12 pages, 2715 KiB  
Article
Utility of Cand PCR in the Diagnosis of Vulvovaginal Candidiasis in Pregnant Women
by Eduardo García-Salazar, Paola Betancourt-Cisneros, Xóchitl Ramírez-Magaña, Hugo Díaz-Huerta, Erick Martínez-Herrera and María Guadalupe Frías-De-León
J. Fungi 2025, 11(1), 5; https://doi.org/10.3390/jof11010005 - 25 Dec 2024
Viewed by 718
Abstract
Vulvovaginal candidiasis (VVC) can lead to multiple complications when it occurs during pregnancy, so it is necessary to diagnose it promptly for effective treatment. Traditional methods for identifying Candida spp. are often too time-consuming and have limited specificity and sensitivity. In this work, [...] Read more.
Vulvovaginal candidiasis (VVC) can lead to multiple complications when it occurs during pregnancy, so it is necessary to diagnose it promptly for effective treatment. Traditional methods for identifying Candida spp. are often too time-consuming and have limited specificity and sensitivity. In this work, we evaluated the diagnostic utility of an endpoint PCR assay (Cand PCR) in vaginal swab specimens. Using a cotton swab, 108 vaginal swab samples were taken from pregnant women who consented to participate in the study. The samples were inoculated in Sabouraud agar plates (the gold standard) and subsequently used to extract DNA directly from the exudate. The yeasts isolated from the Sabouraud agar were identified in CHROMagar™ Candida. DNA extracted from vaginal swabs was amplified by Cand PCR. Based on the results of the Cand PCR and the gold standard, sensitivity (S), specificity (E), positive predictive values (PPVs), and negative predictive values (NPVs) were determined. Cand PCR presented an S = 65%, E = 100%, PPV = 100% and NPV = 91%. Cand PCR showed low sensitivity for detecting Candida spp. directly from vaginal swabs, but it was useful for identifying the etiologic agent and reducing the time to obtain the result, which is usually at least 48 h. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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15 pages, 1781 KiB  
Article
Influence of Fungal Colonization on Exacerbations in Patients with Cystic Fibrosis
by Claudia Janeth Madrid-Carbajal, Teresa Peláez-García de la Rasilla, Marta Iscar-Urrutia, Marta Solís-García, Ramón Fernández-Álvarez, Liliana Pérez-Martínez, María Soledad Zapico-González and Marta Garcia-Clemente
J. Fungi 2024, 10(12), 875; https://doi.org/10.3390/jof10120875 - 17 Dec 2024
Viewed by 812
Abstract
The importance of fungal pathogens in cystic fibrosis (CF) patients and their diagnosis remains a challenge, so our aim was to analyze the influence of the detection of fungi in sputum by using conventional culture and molecular techniques, polymerase chain reaction (PCR), lateral [...] Read more.
The importance of fungal pathogens in cystic fibrosis (CF) patients and their diagnosis remains a challenge, so our aim was to analyze the influence of the detection of fungi in sputum by using conventional culture and molecular techniques, polymerase chain reaction (PCR), lateral flow devices (LFDs), and galactomannan (GM) on exacerbations in patients with cystic fibrosis. A prospective study was conducted in patients via follow-up in the CF Unit of the Central University Hospital of Asturias from January 2021 to April 2022. Adult patients with at least one documented exacerbation were included. A complete fungal analysis of sputum samples was performed both in a period of clinical stability and in the exacerbation period. The microbiological study included conventional cultures for fungi, qPCR (polymerase chain reaction), LFDs (lateral flow devices), and galactomannan (GM) in sputum. We found that there were changes in their detection according to whether the patient is in a period of clinical stability or exacerbation; the positivity of the molecular tests and biomarkers in the period of exacerbation increased by 14%, 25%, and 21% for the analysis by qPCR, GM, and LFDs for Aspergillus and by 15% for the sputum culture for Aspergillus, which may mean that fungal isolates may play a role in the exacerbations of these patients. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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Review

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14 pages, 958 KiB  
Review
Current Analytical Methods and Challenges for the Clinical Diagnosis of Invasive Pulmonary Aspergillosis Infection
by Madeline C. R. Schwarz, Alex E. Moskaluk, Joshua B. Daniels, Sue VandeWoude and Melissa M. Reynolds
J. Fungi 2024, 10(12), 829; https://doi.org/10.3390/jof10120829 - 28 Nov 2024
Viewed by 1277
Abstract
In the last decade, pulmonary fungal infections such as invasive pulmonary aspergillosis (IPA) have increased in incidence due to the increased number of immunocompromised individuals. This increase is especially problematic when considering mortality rates associated with IPA are upwards of 70%. This high [...] Read more.
In the last decade, pulmonary fungal infections such as invasive pulmonary aspergillosis (IPA) have increased in incidence due to the increased number of immunocompromised individuals. This increase is especially problematic when considering mortality rates associated with IPA are upwards of 70%. This high mortality rate is due to, in part, the length of time it takes to diagnose a patient with IPA. When diagnosed early, mortality rates of IPA decrease by as much as 30%. In this review, we discuss current technologies employed in both medical and research laboratories to diagnose IPA, including culture, imaging, polymerase chain reaction, peptide nucleic acid–fluorescence in situ hybridization, enzyme-linked immunosorbent assay, lateral flow assay, and liquid chromatography mass spectrometry. For each technique, we discuss both promising results and potential areas for improvement that would lead to decreased diagnosis time for patients suspected of contracting IPA. Further study into methods that offer increased speed and both analytical and clinical sensitivity to decrease diagnosis time for IPA is warranted. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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34 pages, 3319 KiB  
Review
Diagnosis of Human Endemic Mycoses Caused by Thermally Dimorphic Fungi: From Classical to Molecular Methods
by Joaquina María García-Martín, Antonio Muro and Pedro Fernández-Soto
J. Fungi 2024, 10(9), 637; https://doi.org/10.3390/jof10090637 - 6 Sep 2024
Cited by 1 | Viewed by 2265
Abstract
Human endemic mycoses are potentially fatal diseases caused by a diverse group of fungi that can alter their morphology in response to an increase in temperature. These thermally dimorphic fungi affect both healthy and immunocompromised hosts, causing a substantial health and economic burden. [...] Read more.
Human endemic mycoses are potentially fatal diseases caused by a diverse group of fungi that can alter their morphology in response to an increase in temperature. These thermally dimorphic fungi affect both healthy and immunocompromised hosts, causing a substantial health and economic burden. Despite this, the diagnosis of endemic mycoses is still a formidable challenge for several reasons, including similar symptomatology, limited utility of classical diagnostic methods, inaccessibility to reliable molecular approaches in most endemic areas, and a lack of clinical suspicion out of these regions. This review summarizes essential knowledge on thermally dimorphic fungi and the life-threatening diseases they cause. The principle, advantages and limitations of the methods traditionally used for their diagnosis are also described, along with the application status and future directions for the development of alternative diagnostic strategies, which could help to reduce the disease burden in endemic areas. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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Other

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11 pages, 1182 KiB  
Case Report
Moesziomyces aphidis Bloodstream Infection in Oncologic Patient: First Report in Poland
by Beata Sulik-Tyszka, Jolanta Małyszko, Agnieszka Pęczuła and Sylwia Jarzynka
J. Fungi 2025, 11(2), 95; https://doi.org/10.3390/jof11020095 - 24 Jan 2025
Cited by 1 | Viewed by 821
Abstract
Moesziomyces spp. (Pseudozyma) is a genus recognized as a new opportunistic human pathogen, causing systemic infections including premature neonates and adult patients. These fungi’s natural resistance to caspofungin enables them to spread through vascular catheter colonization, making them a new etiological [...] Read more.
Moesziomyces spp. (Pseudozyma) is a genus recognized as a new opportunistic human pathogen, causing systemic infections including premature neonates and adult patients. These fungi’s natural resistance to caspofungin enables them to spread through vascular catheter colonization, making them a new etiological agent associated with fungal bloodstream infections (FBIs) and a significant contributor to high mortality rates. In this report, we present a case of fungemia caused by Moesziomyces aphidis species in a patient with medical history that revealed pancreatic cancer infiltrating the duodenum and bile ducts. During hospitalization, the M. aphidis was cultured twice from peripheral blood samples on Sabouraud agar. The strain was sensitive to amphotericin B and voriconazole. In vitro susceptibility testing revealed resistance to fluconazole, caspofungin, anidulafungin, and micafungin. Antifungal therapy with voriconazole resulted in the resolution of clinical symptoms associated with fungal infection. Related to M. aphidis fungemia, we reviewed a total of three cases in Europe published in the PubMed database between 2003 and 2024. To the best of our knowledge, this is the first case of M. aphidis FBI in Poland and the fourth case in an adult patient in Europe. Full article
(This article belongs to the Special Issue Diagnosis of Human Pathogenic Fungi)
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