Molecular Diagnostics of Fungal Infections

Fungal infections represent a growing global threat, particularly among immunocompromised populations, where traditional culture and microscopy methods often fail to provide timely and precise identification. Molecular diagnostics have transformed this landscape by harnessing nucleic acid–based techniques to detect and characterise fungal pathogens directly from clinical specimens. Polymerase chain reaction (PCR) assays targeting conserved regions such as the internal transcribed spacer (ITS) enable rapid detection of a broad spectrum of fungi, while species-specific probes provide enhanced sensitivity and specificity. Isothermal amplification methods, including loop-mediated isothermal amplification (LAMP) and multiple cross displacement amplification, offer robust, equipment-light alternatives suited to point-of-care settings. High-throughput workflows incorporating automated DNA extraction, real-time PCR and next-generation sequencing (NGS) support comprehensive pathogen profiling, including resistance markers. Emerging approaches such as nanopore sequencing, nanotechnology-based biosensors and machine learning–driven pattern recognition promise further gains. Together, these innovations are reshaping clinical mycology by delivering faster turnaround times, improved diagnostic accuracy and better patient outcomes worldwide.

Research from Nature Portfolio

A foundational review in Nature Communications examined the unique challenges of fungal identification in routine clinical laboratories, highlighting a decline in specialised mycology expertise and the limited availability of fungal-specific assays. It surveyed current molecular platforms—from broad-range PCR barcoding to NGS-based pathogen discovery—and discussed practical barriers to implementation, including assay validation, instrumentation costs and regulatory hurdles. The authors emphasised the need for standardised workflows and curated reference databases to ensure diagnostic consistency across centres.

In Scientific Reports, a study evaluated an automated 18S rDNA real-time PCR screening pipeline applied to over two hundred clinical specimens. The workflow combined robotic DNA extraction with high-throughput PCR and Sanger sequencing against a commercial fungal database. Concordance with conventional culture and ITS PCR exceeded 90%, and the method detected pathogens in culture-negative samples from patients with confirmed fungal disease. This work demonstrates the feasibility of integrating large-scale molecular assays into diagnostic algorithms for invasive mycoses.

Molecular Diagnostics of Fungal Infections publication trend

The graph below shows the total number of articles in molecular diagnostics of fungal infections across all publications each year (not limited to Nature Index journals).

Technical terms

Internal transcribed spacer (ITS): A genomic region between ribosomal RNA genes used as a universal fungal barcode for species identification.

Polymerase chain reaction (PCR): A method for exponential amplification of target DNA sequences to enable sensitive pathogen detection.

Loop-mediated isothermal amplification (LAMP): An amplification technique performed at constant temperature that yields rapid and high-yield DNA products, suited to resource-limited settings.

Next-generation sequencing (NGS): High-throughput sequencing technologies that generate large volumes of DNA sequence data for comprehensive pathogen profiling and resistance gene detection.

Lateral flow biosensor (LFB): A rapid, paper-based assay format that visually reports the presence of target nucleic acids or antigens without specialised instruments.

References

1. Diagnosis of invasive fungal infections: challenges and recent developments. Journal of Biomedical Science (2023).
2. A novel, rapid, ultrasensitive diagnosis platform for detecting Candida albicans using restriction endonuclease‐mediated real-time loop-mediated isothermal amplification. Frontiers in Cellular and Infection Microbiology (2024).
3. Molecular diagnostics in medical mycology. Nature Communications (2018).
4. Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. Scientific Reports (2018).
5. Establishment and Application of Multiple Cross Displacement Amplification Coupled With Lateral Flow Biosensor (MCDA-LFB) for Visual and Rapid Detection of Candida albicans in Clinical Samples. Frontiers in Cellular and Infection Microbiology (2019).