Fungal identification based on the polyphasic approach: a clinical practice guideline

Taxonomy includes classification, nomenclature, and identification. Identification assigns unknown fungi to species based on their strain characteristics. Traditionally, fungal taxonomy relied on morphological, physiological, and biochemical traits. However, advancements in molecular phylogeny, especially multilocus sequence analysis (MLSA), have revolutionized fungal taxonomy. MLSA combines phylogenetic and genetic approaches. Although effective, MLSA may not fully reflect biodiversity or distinguish between closely related species. Polyphasic taxonomy integrates genotypic, phylogenetic, chemotaxonomic, and phenotypic data into a consensus classification system. Polyphasic taxonomy was first applied to Rhodotorula glutinis in 2001 and is now widely accepted. Phenotypic traits, such as protein profiles and chemotaxonomic markers, analyzed using techniques such as matrix-assisted laser desorption ionization-time of flight mass spectrometry, are effective for yeast and filamentous fungi. Genotypic data from DNA/RNA sequencing, compared with data from databases such as Index Fungorum and MycoBank, aids species identification and synonym verification. Despite its practicality, the polyphasic approach lacks strict guidelines, resulting in varied interpretations.