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Updated: Dec 29, 2025
Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance
Published on: December 28, 2017
A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?
Sarah E Kidd1, Sharon C-A Chen2,3, Wieland Meyer3,4,5,6
1National Mycology Reference Centre, Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, SA, Australia.
Abstract:
Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.
Insights
Molecular diagnostics rapidly detect invasive fungal diseases (IFDs) and antifungal resistance. Advances in PCR and next-generation sequencing enhance accuracy and aid in identifying drug resistance, improving patient outcomes.
Area of Science:
- Medical Mycology
- Molecular Diagnostics
- Infectious Diseases
Background:
- Invasive fungal diseases (IFDs) pose a significant global health challenge, particularly in immunocompromised patients.
- Increasing antifungal drug resistance complicates treatment and necessitates accurate diagnostic methods.
- Early and precise detection of fungal pathogens and their resistance profiles is crucial for effective patient management.
Purpose of the Study:
- To review the current landscape and advancements in molecular diagnostic approaches for IFDs.
- To highlight the utility and limitations of various PCR-based assays for fungal detection and resistance profiling.
- To discuss the role of emerging technologies like DNA barcoding and next-generation sequencing in fungal diagnostics.
Main Methods:
- Review of existing literature on molecular diagnostic techniques for IFDs.
- Analysis of performance characteristics (sensitivity, specificity, NPV, PPV) of PCR assays for specific fungal pathogens.
- Discussion of emerging technologies such as DNA barcoding and next-generation sequencing (NGS).
Main Results:
- Panfungal PCR assays offer rapid detection of fungal species with high specificity and sensitivity.
- Aspergillus PCR assays demonstrate good utility in high-risk patients, with commercial assays enabling resistance mutation detection.
- Standardization challenges exist for Candida PCR, while Mucorales and Pneumocystis jirovecii PCR show growing utility. DNA barcoding and NGS provide high accuracy for species identification and resistance characterization.
Conclusions:
- Molecular diagnostics, particularly PCR-based methods, are essential for the timely and accurate diagnosis of IFDs.
- Standardization and validation of assays are critical for widespread clinical adoption.
- Emerging technologies like NGS promise further advancements in fungal diagnostics, including outbreak investigation and drug resistance surveillance.
