An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections

Jenks, Jeffrey D.; White, P. Lewis; Kidd, Sarah E.; Goshia, Tyler; Fraley, Stephanie I.; Hoenigl, Martin; Thompson, George R.

doi:10.1080/14737159.2023.2267977

Cited by 61Antifungal resistance and susceptibilityBacterial Identification and Susceptibility TestingFungal Infections and Studies

An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections

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Jenks, Jeffrey D., White, P. Lewis, Kidd, Sarah E., Goshia, Tyler, Fraley, Stephanie I., Hoenigl, Martin, Thompson, George R.·2023·Expert Review of Molecular Diagnostics

DOI 10.1080/14737159.2023.2267977PMC PMC10842420

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Abstract

BACKGROUND: Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens. AREAS COVERED: We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS). EXPERT OPINION: PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.

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The T2Candida panel is limited to five species of Candida: C. albicans, C. tropicalis, C. krusei, C. glabrata, and C. parapsilosis.
“However, the panel is only limited to five species of Candida: C. albicans, C. tropicalis, C. krusei, C. glabrata, and C. parapsilosis.”
From Epidemiology of Invasive Candidiasis (2024) · cites this paper as [19]
The T2Candida Panel does not require positive blood cultures compared to the BioFire FilmArray Blood Culture Identification Panel.
“The T2Candida Panel (T2 Biosystems, Lexington, MA, United States) does not require positive blood cultures compared to the commonly used BioFire® FilmArray® Blood Culture Identification (BCID) Panel (BioFire Diagnostics, Salt Lake City, Utah, United States).”
From Epidemiology of Invasive Candidiasis (2024) · cites this paper as [19]
The T2Candida panel has a sensitivity of 91% and a specificity of 94% across multiple studies.
“The T2Candida panel has a sensitivity of 91% and a specificity of 94% across multiple studies.19”
From Epidemiology of Invasive Candidiasis (2024) · cites this paper as [19]

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Combat-Related Invasive Fungal Wound Infections
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Incidence of invasive fungal disease after unmanipulated haploidentical stem cell transplantation was significantly higher than that after HLA-matched sibling transplantation
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(New) Methods for Detection of Aspergillus fumigatus Resistance in Clinical Samples
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Multiplex Single-Color PCR with Amplicon Melting Analysis for Identification of Aspergillus Species
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High-Resolution Melting Analysis for Identification of the Cryptococcus neoformans-Cryptococcus gattii Complex
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Locally invasive pulmonary aspergillosis occurring in a gardener: an occupational hazard?
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Detection of invasive fungal pathogens by real-time PCR and high-resolution melting analysis.
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Clinical evaluation of an in-house panfungal real-time PCR assay for the detection of fungal pathogens
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Outbreak of histoplasmosis among industrial plant workers--Nebraska, 2004.
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Multicenter Prospective Study of Biomarkers for Diagnosis of Invasive Candidiasis in Children and Adolescents
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Diagnostic accuracy of high resolution melting analysis for detection of KRAS mutations: a systematic review and meta-analysis
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Recent Advances and Novel Approaches in Laboratory-Based Diagnostic Mycology
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Rapid Detection and Identification of Aspergillus from Lower Respiratory Tract Specimens by Use of a Combined Probe–High-Resolution Melting Analysis
Alonso, M., Escribano, P., Guinea, J., Recio, S., Simón, A., Peláez, T., Bouza, E., & de Viedma, D. G. (2012) · Journal of Clinical Microbiology · doi:10.1128/jcm.00176-12 · Cited by 21 · see citing works
High-resolution melting analysis: A novel approach for clade differentiation in Pythium insidiosum and pythiosis
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Improving Quantitative Power in Digital PCR through Digital High-Resolution Melting
Aralar, A., Yuan, Y., Chen, K., Geng, Y., Velez, D. O., Sinha, M., Lawrence, S. M., & Fraley, S. I. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.00325-20 · Cited by 19 · see citing works
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Development and Validation of a High-Resolution Melting Assay To Detect Azole Resistance in Aspergillus fumigatus
Bernal‐Martínez, L., Gil, H., Rivero-Menéndez, O., Gago, S., Cuenca‐Estrella, M., Mellado, E., & Alastruey‐Izquierdo, A. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01083-17 · Cited by 18 · see citing works
Real-time PCR assay for detection and differentiation of Coccidioides immitis and Coccidioides posadasii from culture and clinical specimens
Chaturvedi, S., Victor, T. R., Marathe, A., Sidamonidze, K., Crucillo, K. L., & Chaturvedi, V. P. (2021) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0009765 · Cited by 18 · see citing works
Discrimination of three genetically close Aspergillus species by using high resolution melting analysis applied to indoor air as case study
Libert, X., Packeu, A., Bureau, F., Roosens, N. H. C., & Keersmaecker, S. C. J. D. (2017) · BMC Microbiology · doi:10.1186/s12866-017-0996-4 · Cited by 17 · see citing works
Metagenomic Next-Generation Sequencing Assists in the Diagnosis of Mediastinal Aspergillus fumigatus Abscess in an Immunocompetent Patient: A Case Report and Literature Review
Deng, W., Jiang, Y., Qin, J., Chen, G., Lv, Y., Lei, Y., Luo, J., Hong, K., Huang, B., Qin, L., et al. (2023) · Infection and Drug Resistance · doi:10.2147/idr.s399484 · Cited by 17 · see citing works
A High-Resolution Digital DNA Melting Platform for Robust Sequence Profiling and Enhanced Genotype Discrimination
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Combat Trauma–Related Invasive Fungal Wound Infections
Tribble, D. R., Ganesan, A., & Rodríguez, C. J. (2020) · Current Fungal Infection Reports · doi:10.1007/s12281-020-00385-4 · Cited by 16 · see citing works
Development of a Duplex Real-Time PCR Assay for the Differentiation of Blastomyces dermatitidis and Blastomyces gilchristii and a Retrospective Analysis of Culture and Primary Specimens from Blastomycosis Cases from New York (2005 to 2019)
Kaplan, M. S., Zhu, Y., Kus, J. V., McTaggart, L. R., Chaturvedi, V. P., & Chaturvedi, S. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.02078-20 · Cited by 16 · see citing works
Rapid detection of ERG11 polymorphism associated azole resistance in Candida tropicalis
Paul, S., Dadwal, R., Singh, S., Shaw, D., Chakrabarti, A., Rudramurthy, S. M., & Ghosh, A. K. (2021) · PLoS ONE · doi:10.1371/journal.pone.0245160 · Cited by 15 · see citing works
Transmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics
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Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report
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Diagnosis of mucormycosis using an intercalating dye-based quantitative PCR
Bigot, J., Godmer, A., Prudenté, L., Angebault, C., Brissot, É., Bigé, N., Voiriot, G., Léger, P., Petit-Hoang, C., Atallah, S., et al. (2022) · Medical Mycology · doi:10.1093/mmy/myac015 · Cited by 14 · see citing works
Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis
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Roles of the multiplex real-time PCR assay and β-D-glucan in a high-risk population for intra-abdominal candidiasis (IAC)
Fortün, J., Buitrago, M. J., Gioia, F., de la Pedrosa, E. G. G., Alvarez, M. E., Martín‐Dávila, P., Pintado, V., Cobeta, P., Martinez-Castro, N., Soriano, C., et al. (2019) · Medical Mycology · doi:10.1093/mmy/myz123 · Cited by 12 · see citing works
Diagnosis of central nervous system invasive aspergillosis in a liver transplant recipient using microbial cell‐free next generation DNA sequencing
Shishido, A. A., Vostal, A. C., Mayer, R. C., Ho, C., & Baddley, J. W. (2021) · Transplant Infectious Disease · doi:10.1111/tid.13592 · Cited by 12 · see citing works
A novel droplet digital polymerase chain reaction for diagnosis of Pneumocystis pneumonia (PCP)-a clinical performance study and survey of sulfamethoxazole-trimethoprim resistant mutations
Jitmuang, A., Nititammaluk, A., Boonsong, T., Sarasombath, P. T., Sompradeekul, S., & Chayakulkeeree, M. (2021) · Journal of Infection · doi:10.1016/j.jinf.2021.09.014 · Cited by 12 · see citing works
Development of a Droplet Digital Polymerase Chain Reaction for Sensitive Detection of Pneumocystis jirovecii in Respiratory Tract Specimens
Yi, J., Wang, N., Wu, J., Tang, Y., Zhang, J., Zhu, L., Rui, X., Guo, Y. S., & Xu, Y. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.761788 · Cited by 12 · see citing works
Use of a High-Resolution Melt Assay To Characterize Codon 54 of the cyp51A Gene of Aspergillus fumigatus on a Rotor-Gene 6000 Instrument
Tuohy, M. J., Reja, V., Park, S. Z., Perlin, D. S., Wnek, M., Procop, G. W., & Yen‐Lieberman, B. (2010) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01712-09 · Cited by 11 · see citing works
Long-term Outcomes of Patients With Fungal Infections Associated With Contaminated Methylprednisolone Injections
Malani, A. N., Kauffman, C. A., Latham, R. H., Peglow, S., Ledtke, C., Kerkering, T. M., Kaufman, D., Triplett, P., Wright, P. W., Bloch, K. C., et al. (2020) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofaa164 · Cited by 11 · see citing works
Knowledge at what cost? An audit of the utility of panfungal PCR performed on bronchoalveolar lavage fluid specimens at a tertiary mycology laboratory
Garnham, K., Halliday, C. L., Kok, J., Jayawardena, M. B., Ahuja, V., Green, W., & Chen, S. C. ‐. (2020) · Pathology · doi:10.1016/j.pathol.2020.03.013 · Cited by 11 · see citing works
An Evaluation of the OLM CandID Real-Time PCR to Aid in the Diagnosis of Invasive Candidiasis When Testing Serum Samples
Price, J. S., Fallon, M., Posso, R. B., Backx, M., & White, P. L. (2022) · Journal of Fungi · doi:10.3390/jof8090935 · Cited by 11 · see citing works
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The Use of Host Biomarkers for the Management of Invasive Fungal Disease
Griffiths, J. S., Orr, S. J., Morton, C. O., Loeffler, J., & White, P. L. (2022) · Journal of Fungi · doi:10.3390/jof8121307 · Cited by 11 · see citing works
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Rapid identification of invasive fungal species using sensitive universal primers-based PCR and restriction endonuclease digestions coupled with high-resolution melting analysis
Tsai, M.-H., Lin, L.-C., Hsu, J., Lai, M., Huang, H., Chiang, M., & Lu, J. (2019) · Journal of Microbiology Immunology and Infection · doi:10.1016/j.jmii.2019.06.001 · Cited by 9 · see citing works
Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing
Pasala, A. R., Perini, M., Piazza, A., Panelli, S., Carlo, D. D., Loretelli, C., Cafiso, A., Inglese, S., Gona, F., Cirillo, D. M., et al. (2020) · AMB Express · doi:10.1186/s13568-020-01164-7 · Cited by 9 · see citing works
Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power
Langouche, L., Aralar, A., Sinha, M., Lawrence, S. M., Fraley, S. I., & Coleman, T. P. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa1053 · Cited by 9 · see citing works
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Rapid Identification of Four Fusarium spp. Complex by High-Resolution Melting Curve Analysis and their Antifungal Susceptibility Profiles
Hou, X., Geng, Y., Dai, R., Zhao, F., He, L., & Gong, J. (2022) · Mycopathologia · doi:10.1007/s11046-022-00635-8 · Cited by 9 · see citing works
DNA Barcoding Coupled with High Resolution Melting Analysis Enables Rapid and Accurate Distinction ofAspergillusspecies
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Social Mycology: Using Social Media Networks in the Management of Aspergillosis and Other Mycoses
Stone, N. R. H. (2023) · Mycopathologia · doi:10.1007/s11046-023-00726-0 · Cited by 8 · see citing works
Application of High-Resolution Melting PCR to Detect the Genomic Fungal ITS 2 Region
Nawar, N. N., Behiry, I. K., Yousef, R., & Emara, A. M. (2019) · Laboratory Medicine · doi:10.1093/labmed/lmz034 · Cited by 7 · see citing works
Double Vision and Gait Ataxia in an Immunocompetent 9-Year-Old Girl With Intracranial Phaeohyphomycosis
Pareek, A. V., Lotze, T. E., Demmler, G. J., Mohila, C., Tran, B. H., & Shah, V. S. (2021) · Journal of Neuro-Ophthalmology · doi:10.1097/wno.0000000000001204 · Cited by 6 · see citing works
Development of a High-Resolution Melting Curve Analysis to Differentiate Candida parapsilosis Complex Species.
Shao, Y. K., Xu, J., Gong, J., & Chang, J. M. (2021) · PubMed · doi:10.3967/bes2021.064 · Cited by 1 · see citing works
S2.3c High-resolution digital DNA melting: a breakthrough in diagnosing IMI?
Goshia, T., Wiederhold, N. P., Jenks, J., Mehta, S. R., Hoenigl, M., & Goshia, T. (2022) · Medical Mycology · doi:10.1093/mmy/myac072.s2.3c · Cited by 1 · see citing works
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Novel antifungals and treatment approaches to tackle resistance and improve outcomes of invasive fungal disease
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Fungal Infections in Kidney Transplant Recipients: A Comprehensive Narrative Review
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CAF to the Rescue! Potential and Challenges of Combination Antifungal Therapy for Reducing Morbidity and Mortality in Hospitalized Patients With Serious Fungal Infections
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Universal digital high-resolution melting for the detection of pulmonary mold infections
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Presence of Microorganisms in the Environment: One Health Approach
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Recent advances in the clinical development of antifungal vaccines: a narrative review
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Invasive fungal infections in hematologic diseases: evidence, challenges, and clinical practice
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Morphed aflaxotin concentration produced by Aspergillus flavus strain VKMN22 on maize grains inoculated on agar culture
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Universal Digital High Resolution Melt for the detection of pulmonary mold infectionsPreprint
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Performance of the LIAISON PLEX yeast blood culture assay for identifying 16 invasive fungal pathogens in blood cultures
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Histoplasma capsulatum urinary antigen detection in a kidney transplant recipient with acute paracoccidioidomycosis: Case study and literature review
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Invasive cerebral aspergillosis in a pregnant woman: a rare case of intracranial giant granuloma
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Knowledge framework and emerging trends of invasive pulmonary fungal infection: A bibliometric analysis (2003–2023)
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Molecular diagnostics in fungal infections
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Authors: Jenks, J. D., White, P. L., Kidd, S. E., Goshia, T., Fraley, S. I., Hoenigl, M., & Thompson, G. R.
Affiliations: Duke University (US)
University Hospital of Wales (GB)
South Australia Pathology (AU)
University of California San Diego (US)
Medical University of Graz (AT)
University of California Davis Medical Center (US)
Corresponding author: Jenks, Jeffrey D.
ORCID: Jenks, Jeffrey D.
White, P. Lewis
Kidd, Sarah E.
Goshia, Tyler
Fraley, Stephanie I.
Hoenigl, Martin
Thompson, George R.
Venue: Expert Review of Molecular Diagnostics
Publisher: Informa UK Limited
Published: 2023-10-10
Volume: 23
Issue: 12
Pages: 1135-1152
ISSN: 1473-7159 (ISSN-L)
1744-8352
DOI: 10.1080/14737159.2023.2267977
PMC: PMC10842420
OpenAlex: W4387397825
Semantic Scholar: 0b4f4ca4b59b50126e8a4e13dfcc7dd1b5318578
Cited by: 61
References: 184
Citations by year: 2026: 26 · 2025: 18 · 2024: 16 · 2023: 1
FWCI: 2.89
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Expert Review of Molecular Diagnostics (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: National Institute of Allergy and Infectious Diseases
National Institutes of Health (R01AI134982)
Topics: Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
Health Sciences › Medicine › Epidemiology › Fungal Infections and Studies
Keywords: invasive fungal infections, molecular diagnosis, PCR, digital PCR, high-resolution melting analysis, metagenomic next-generation sequencing, endemic fungal infection, species identification
MeSH terms: Invasive Fungal Infections, Antifungal Agents, Fungi, Humans, Mycoses, Sensitivity and Specificity, Pathology, Molecular

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An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections

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