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The Molecular Diagnosis of Fungal Disease
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The Molecular Diagnosis of Fungal Disease

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (20 January 2024) | Viewed by 11503

Special Issue Editor

Dr. P. Lewis White

E-Mail Website
Guest Editor
Public Health Wales Mycology Reference Laboratory, PHW Microbiology Cardiff, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
Interests: novel diagnostics; invasive fungal disease; novel strategies; SNPs; aspergillosis; candidosis; pneumocystosis; mucormycosis

Special Issue Information

Dear Colleagues,

The molecular diagnostic of fungal infection has taken some significant steps in the last few years, not least with PCR being incorporated into the EORTC/MSGERC consensus definitions for invasive fungal diseases. The ISHAM working group Fungal PCR Initiative has been at the forefront of standardizing Aspergillus PCR and is close to producing guidance on how best to use PCR to diagnose Pneumocystis infections as well as those caused by Mucorales.

This Special Issue of the Journal of Fungi will focus on recent achievements in the standardization but also recent/novel developments and clinical validations of molecular tests to aid in the diagnosis of these diseases. State-of-the-art reviews and research articles describing the development, standardizing and validation of molecular testing of Aspergillus, Candida, Pneumocystis, and Mucorales species as well as the detection of fungal infection specifically within tissue will be presented. Companion papers describing the laboratory and clinical aspects will be presented, including details on the challenges and pitfalls of molecular testing while also mapping out the future work that still needs to be done.

Dr. P. Lewis White
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

  • fungal PCR
  • Aspergillus
  • Candida
  • Mucorales
  • Pneumocystis
  • tissue PCR
  • molecular detection of antifungal resistance
  • next-generation sequencing
  • host genomics that predispose to fungal infection

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Published Papers (5 papers)

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Research

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13 pages, 2110 KiB  
Article
An Evaluation of the OLM PneumID Real-Time Polymerase Chain Reaction to Aid in the Diagnosis of Pneumocystis Pneumonia
by Jessica S. Price, Melissa Fallon, Raquel Posso, Matthijs Backx and P. Lewis White
J. Fungi 2023, 9(11), 1106; https://doi.org/10.3390/jof9111106 - 15 Nov 2023
Cited by 3 | Viewed by 1583
Abstract
Background: The use of the PCR to aid in the diagnosis of Pneumocystis pneumonia (PcP) has demonstrated excellent clinical performance, as evidenced through various systematic reviews and meta-analyses, yet there are concerns over the interpretation of positive results due to the potential presence [...] Read more.
Background: The use of the PCR to aid in the diagnosis of Pneumocystis pneumonia (PcP) has demonstrated excellent clinical performance, as evidenced through various systematic reviews and meta-analyses, yet there are concerns over the interpretation of positive results due to the potential presence of Pneumocystis colonization of the airways. While this can be overcome by applying designated positivity thresholds to PCR testing, the shear number of assays described limits the development of a universal threshold. Commercial assays provide the opportunity to overcome this problem, provided satisfactory performance is determined through large-scale, multi-centre evaluations. Methods: Retrospective case/control and consecutive cohort performance evaluations of the OLM PneumID real-time PCR assay were performed on DNA eluates from a range of samples sent from patients where “in-house” PCR had been performed as part of routine diagnostic testing. The clinical performance of the PneumID assay was determined before including it in a diagnostic algorithm to provide the probability of PcP (dependent on diagnostic evidence). Results: After being used to test 317 patients (32 with PcP), the overall performance of the PneumID assay was found to be excellent (Sensitivity/Specificity: 96.9%/95.1%). False positivity could be removed by applying a threshold specific to sample type (<33.1 cycles for BAL fluid; <37.0 cycles for throat swabs), whereas considering any positive respiratory samples as significant generated 100% sensitivity, making absolute negativity sufficient to exclude PcP. Incorporating the PneumID assay into diagnostic algorithms alongside (1-3)-β-D-Glucan testing provided high probabilities of PcP (up to 85.2%) when both were positive and very low probabilities (<1%) when both were negative. Conclusions: The OLM PneumID qPCR provides a commercial option for the accurate diagnosis of PcP, generating excellent sensitivity and specificity, particularly when testing respiratory specimens. The combination of PcP PCR with serum (1-3)-β-D-Glucan provides excellent clinical utility for diagnosing PcP. Full article
(This article belongs to the Special Issue The Molecular Diagnosis of Fungal Disease)
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Review

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31 pages, 480 KiB  
Review
Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches
by David Pham, Varsha Sivalingam, Helen M. Tang, James M. Montgomery, Sharon C.-A. Chen and Catriona L. Halliday
J. Fungi 2024, 10(7), 447; https://doi.org/10.3390/jof10070447 - 26 Jun 2024
Cited by 1 | Viewed by 3053
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid [...] Read more.
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation. Full article
(This article belongs to the Special Issue The Molecular Diagnosis of Fungal Disease)

Other

Jump to: Research, Review

15 pages, 547 KiB  
Systematic Review
An Overview of Systematic Reviews of Polymerase Chain Reaction (PCR) for the Diagnosis of Invasive Aspergillosis in Immunocompromised People: A Report of the Fungal PCR Initiative (FPCRI)—An ISHAM Working Group
by Mario Cruciani, P. Lewis White, Rosemary A. Barnes, Juergen Loeffler, J. Peter Donnelly, Thomas R. Rogers, Werner J. Heinz, Adilia Warris, Charles Oliver Morton, Martina Lengerova, Lena Klingspor, Boualem Sendid and Deborah E. A. Lockhart
J. Fungi 2023, 9(10), 967; https://doi.org/10.3390/jof9100967 - 26 Sep 2023
Cited by 4 | Viewed by 2921
Abstract
This overview of reviews (i.e., an umbrella review) is designed to reappraise the validity of systematic reviews (SRs) and meta-analyses related to the performance of Aspergillus PCR tests for the diagnosis of invasive aspergillosis in immunocompromised patients. The methodological quality of the SRs [...] Read more.
This overview of reviews (i.e., an umbrella review) is designed to reappraise the validity of systematic reviews (SRs) and meta-analyses related to the performance of Aspergillus PCR tests for the diagnosis of invasive aspergillosis in immunocompromised patients. The methodological quality of the SRs was assessed using the AMSTAR-2 checklist; the quality of the evidence (QOE) within each SR was appraised following the GRADE approach. Eight out of 12 SRs were evaluated for qualitative and quantitative assessment. Five SRs evaluated Aspergillus PCR on bronchoalveolar lavage fluid (BAL) and three on blood specimens. The eight SRs included 167 overlapping reports (59 evaluating PCR in blood specimens, and 108 in BAL), based on 107 individual primary studies (98 trials with a cohort design, and 19 with a case−control design). In BAL specimens, the mean sensitivity and specificity ranged from 0.57 to 0.91, and from 0.92 to 0.97, respectively (QOE: very low to low). In blood specimens (whole blood or serum), the mean sensitivity ranged from 0.57 to 0.84, and the mean specificity from 0.58 to 0.95 (QOE: low to moderate). Across studies, only a low proportion of AMSTAR-2 critical domains were unmet (1.8%), demonstrating a high quality of methodological assessment. Conclusions. Based on the overall methodological assessment of the reviews included, on average we can have high confidence in the quality of results generated by the SRs. Full article
(This article belongs to the Special Issue The Molecular Diagnosis of Fungal Disease)
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11 pages, 3698 KiB  
Case Report
Talaromyces amestolkiae Infection in an AIDS Patient with Cryptococcal Meningitis
by Li-An Wang, Yu-Chuan Chuang, Ting-Kuang Yeh, Kuan-Pei Lin, Chi-Jan Lin and Po-Yu Liu
J. Fungi 2023, 9(9), 932; https://doi.org/10.3390/jof9090932 - 15 Sep 2023
Cited by 1 | Viewed by 1299
Abstract
Concurrent infections caused by multiple fungal pathogens in immunocompromised patients can pose diagnostic and treatment challenges. Here, we presented the first reported case in Taiwan of an AIDS patient who had concurrent infection with Cryptococcus neoformans meningitis and Talaromyces amestolkiae lymphadenopathy. The patient [...] Read more.
Concurrent infections caused by multiple fungal pathogens in immunocompromised patients can pose diagnostic and treatment challenges. Here, we presented the first reported case in Taiwan of an AIDS patient who had concurrent infection with Cryptococcus neoformans meningitis and Talaromyces amestolkiae lymphadenopathy. The patient presented with an enlarged inguinal lymph node and was diagnosed with T. amestolkiae lymphadenitis. The species T. amestolkiae was identified using DNA sequencing, which had the capability of differentiating it from other Talaromyces species. The patient was discharged from the hospital following treatment with amphotericin B and subsequent administration of voriconazole. This case highlights the importance of maintaining a suspicion of co-infections and utilizing appropriate diagnostic tools, such as DNA sequencing, to identify possible pathogens. Further studies are needed to determine the optimal treatment for T. amestolkiae and other co-infecting fungal pathogens. Full article
(This article belongs to the Special Issue The Molecular Diagnosis of Fungal Disease)
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10 pages, 729 KiB  
Brief Report
Molecular Detection of Candida auris Using DiaSorin Molecular Simplexa® Detection Kit: A Diagnostic Performance Evaluation
by Juan David Ramírez, Chin Yi Wang, Deandra Bolton, Bernadette Liggayu, Sarah Schaefer, Gopi Patel, Waleed Javaid, Carlos Cordon-Cardo, Adolfo Firpo-Betancourt, Emilia Mia Sordillo and Alberto Paniz-Mondolfi
J. Fungi 2023, 9(8), 849; https://doi.org/10.3390/jof9080849 - 15 Aug 2023
Cited by 5 | Viewed by 1859
Abstract
Candida auris is a globally emerging fungal pathogen that is associated with healthcare-related infections. The accurate and rapid detection of C. auris is crucial for effective infection prevention, control, and patient management. This study aimed to validate the analytical and diagnostic performance of [...] Read more.
Candida auris is a globally emerging fungal pathogen that is associated with healthcare-related infections. The accurate and rapid detection of C. auris is crucial for effective infection prevention, control, and patient management. This study aimed to validate the analytical and diagnostic performance of the DiaSorin Molecular C. auris Detection Kit. The analytical specificity, sensitivity, and reproducibility of the assay were evaluated. The limit of detection (LOD) was determined to be 266 CFU/µL using the ZeptoMetrix Candida auris Z485 strain and standard calibration curves. The assay demonstrated high analytical specificity and showed no amplification against a diverse panel of bacteria and fungi. Clinical validation was conducted using deidentified residual axillary/groin surveillance culture specimens from C. auris culture-positive and culture-negative patients. The DiaSorin Molecular Detection Kit exhibited 100% agreement in sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) when compared to cultures coupled with MALDI-TOF identification. Intra- and inter-reproducibility testing demonstrated consistent and reliable diagnostic performance. This validated assay offers rapid and accurate detection of C. auris, facilitating timely implementation of infection control measures and appropriate patient care. The DiaSorin Molecular C. auris Detection Kit has the potential to aid in controlling the outbreaks caused by this emerging fungal pathogen. Providing a reliable diagnostic tool can contribute to the effective management and containment of C. auris infections in healthcare settings and ultimately improve patient outcomes. Full article
(This article belongs to the Special Issue The Molecular Diagnosis of Fungal Disease)
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