ABSTRACT
Fungi (singular fungus, meaning “mushroom” in Latin) are a diverse group of eukaryotic organisms (ranging from yeasts, molds, mushrooms, lichens, rusts, smuts to microsporidia) that constitute one of the –ve kingdoms (i.e., Prokaryotae, Fungi, Protista, Plantae, and Animalia) in the current classi-–cation system for living organisms. Similar to other eukaryotic kingdoms (Protista, Plantae, and Animalia), fungi harbor membrane-bound nuclei with chromosomal DNA, which consists of noncoding regions (introns) and coding regions
(exons), possess membrane-bound cytoplasmic organelles (e.g., mitochondria), sterol-containing membranes, and 80S ribosomes and produce a variety of soluble carbohydrates and storage compounds, including sugar alcohols, disaccharides, and polysaccharides. Furthermore, Fungi resemble Protista and Animalia by the lack of chloroplasts and thus the requirement of preformed organic compounds as energy sources. Although both Fungi and Plantae possess a cell wall and vacuoles, reproduce by sexual as well as asexual means, generate spores (as in ferns and mosses), and have haploid nuclei (as in mosses and algae), Fungi differ from Plantae
1.1 Preamble .............................................................................................................................................................................. 1 1.2 Classi–cation, Biology, Genetics, and Clinical Presentation ............................................................................................... 2
1.2.1 Classi–cation ............................................................................................................................................................ 2 1.2.2 Biology ..................................................................................................................................................................... 4 1.2.3 Genetics ................................................................................................................................................................... 4 1.2.4 Clinical Presentation................................................................................................................................................ 5
1.3 Phenotypic Characterization................................................................................................................................................ 5 1.3.1 Sample Collection and Processing .......................................................................................................................... 5
1.3.1.1 General Guidelines for Specimen Handling ............................................................................................. 5 1.3.1.2 Sputum, Bronchial Washings, and Throat Swabs ..................................................................................... 6 1.3.1.3 Blood, Bone Marrow, and Body Fluids .................................................................................................... 6 1.3.1.4 Pus, Exudate, and Drainage ...................................................................................................................... 6 1.3.1.5 Vaginal Swabs ........................................................................................................................................... 6 1.3.1.6 Urine ......................................................................................................................................................... 6 1.3.1.7 Cerebrospinal Fluid .................................................................................................................................. 6 1.3.1.8 Tissue Biopsies from Visceral Organs ...................................................................................................... 6 1.3.1.9 Nail, Hair, Skin Scraping, and Swabs ....................................................................................................... 6
1.3.2 Microscopic Examination ........................................................................................................................................ 7 1.3.3 In Vitro Cultivation .................................................................................................................................................. 7 1.3.4 Biochemical and Antifungal Testing ..................................................................................................................... 15
1.4 Genotypic Characterization ............................................................................................................................................... 15 1.4.1 Nucleic Acid Puri–cation ....................................................................................................................................... 15 1.4.2 Target Genes .......................................................................................................................................................... 15 1.4.3 Template Ampli–cation ......................................................................................................................................... 16 1.4.4 Product Detection .................................................................................................................................................. 19
1.5 Result Interpretation, Standardization, Quality Control, and Assurance .......................................................................... 20 1.5.1 Key Performance Characteristics .......................................................................................................................... 20 1.5.2 Result Interpretation .............................................................................................................................................. 20 1.5.3 Standardization and Validation ............................................................................................................................. 21 1.5.4 Quality Control and Assurance ............................................................................................................................. 21
1.5.4.1 Quality Control ....................................................................................................................................... 21 1.5.4.2 Quality Assurance .................................................................................................................................. 21
1.6 Conclusions ........................................................................................................................................................................ 22 References ................................................................................................................................................................................... 22
by the presence of chitin (which also exists in the exoskeleton of arthropods), instead of cellulose in the cell walls, and the absence of chloroplasts. On the other hand, Fungi differ from Prokaryotae by having nuclear membrane, plasma membrane, and cell wall.
