Ann Clin Microbiol 2024;27(4):221-230. Fungal identification based on the polyphasic approach: a clinical practice guideline
| Categories | Contents |
|---|---|
| Phenotypic-based approach | |
| Morphological characteristics | – Sporulation organ structures (e.g., conidia, macroconidia). – Colony traits: growth rate, aerial mycelium, odor. – Cultivation conditions (e.g., medium composition, temperature). – Microscopy: with/without staining, DIC microscopy. |
| Biochemical and physiological characteristics | – Chemotaxonomic markers (e.g., polysaccharides, fatty acids). – Metabolite profiling (chromatography). – Protein fingerprints. – Multilocus enzyme electrophoresis. – Isoenzyme analysis. – Metabolite profiling. – Complementary markers (e.g., carbohydrate assimilation, colony color, growth rate). |
| Parasitism and mating ability | – Pathogenicity, aggressiveness, specialization (geography, ecology). – Mating via sexual offspring. |
| MALDI-TOF MS | – Reliable for identifying Candida, and Cryptococcus spp. – Accuracy varies for molds. – Limited database sizes, cross-identification issues, varying cultivation conditions, and inadequate QC strategies. |
| Molecular-based approach | |
| Genetic markers and database | – ITS regions, rDNA regions. – Multilocus sequence analysis. – GenBank, CBS-KNAW, ISHAM ITS, MycoBank. |
| Analytical tools | – RNA-Seq-based next-generation sequencing. – PCR-based methods (RT-PCR, nested PCR). – DNA/RNA probes (e.g., FISH, Northern blot). – Post-amplification methods (Microarray). – Isothermal amplification methods (e.g., LAMP, NASMA). – Multigenic phylogeny. |
| Resource for nomenclature | – MycoBank (http://www.mycobank.org). – Index Fungorum (http://www.indexfungorum.org/names/Names.asp). – the Mycology Online database (https://www.Mycology.adelaide.edu.au). – Fungal Taxonomy (https://www.fungaltaxonomy.org). – Clinical Fungi websites (https://www.clinicalfungi.org). |
Abbreviations: DIC, differential interference contrast; MALDI-TOF-MS, matrix-assisted laser desorption/ ionization-mass spectrometry; QC, quality control; ITS, internal transcribed spacer; PCR, polymerase chain reaction; RT-PCR, Reverse Transcription PCR; FISH, Fluorescence In Situ Hybridization; LAMP, Loop-Mediated Isothermal Amplification;NASBA, Nucleic Acid Sequence-Based Amplification.