Molecular Typing of Fungi: Introduction, Common Molecular Typing Method, and Application

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Introduction

Molecular typing of fungi uses DNA-based methods to identify species and differentiate strains for clinical, epidemiological, and environmental studies.

Various Candida species growth on HiCrome Candida Differential Agar
Fig. Various Candida species growth on HiCrome Candida Differential Agar

Key techniques include Internal Transcribed Spacer (ITS) sequencing (the standard for identification), Multilocus Sequence Typing (MLST), restriction fragment length polymorphism (RFLP), and Whole Genome Sequencing (WGS). These methods are crucial for tracking infection outbreaks, understanding fungal taxonomy, and assessing pathogenicity. 

Main Molecular Typing Methods

  • DNA Sequencing: The most precise method, commonly using the ITS region for identification and multiple housekeeping genes for MLST.
  • PCR-Based Techniques: Techniques like RFLP, RAPD, and AFLP are used to generate fingerprint patterns for identifying specific strains.
Aspergillus fumigatus growth on Sabouraud dextrose agar (SDA) tube
Fig. Aspergillus fumigatus growth on Sabouraud dextrose agar (SDA) tube
  • Electrophoretic Karyotyping (EK): Also known as Pulsed-Field Gel Electrophoresis (PFGE), it separates entire chromosomes to differentiate species.
  • Whole Genome Sequencing (WGS): Provides the highest resolution for epidemiological studies and studying phylogenetic relationships.
  • MALDI-TOF Mass Spectrometry: Used for rapid identification by analyzing protein profiles. 
MALDI TOF MS (Vitek MS) Prime
Fig. MALDI TOF MS (Vitek MS) Prime

Applications

  • Clinical Diagnostics: Identifying fungal pathogens (e.g., Candida, Aspergillus) and tracking outbreaks in hospitals.
  • Epidemiology: Identifying the source and transmission routes of infections.
  • Taxonomy & Phylogeny: Classifying fungi and understanding their evolution.
  • Environmental Monitoring: Analyzing microbial communities in soil and air. 

Further Readings

  1. https://pubmed.ncbi.nlm.nih.gov/12667249/
  2. https://pubmed.ncbi.nlm.nih.gov/11204145/
  3. https://academic.oup.com/mmy/article/38/Supplement_1/189/1026187
  4. https://academic.oup.com/cid/article-abstract/20/6/1535/477419
  5. https://www.biotechnologia-journal.org/Molecular-typing-biodiversity-and-biological-control-of-endophytic-fungi-of-Triticum,127831,0,2.html
  6. https://pubmed.ncbi.nlm.nih.gov/15156023/
  7. https://www.sciencedirect.com/science/article/pii/S1198743X14624654
  8. https://multimedia.efsa.europa.eu/moleculartyping/index.htm
  9. https://pmc.ncbi.nlm.nih.gov/articles/PMC8443879

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