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Classification of Fungi
Fungal disease contributes significantly to patients’ morbidity and mortality in certain clinical settings. Extensive medical interventions, immunosuppression, and a heightened awareness of fungal disease, particularly opportunistic mycoses in the setting of immune compromise, have all necessitated an increased understanding of fungal etiologic agents and their classification, identification, and clinical manifestations.
The Agents
Definition
Fungi are heterotrophic (using organic compounds as a primary source of energy and lacking chlorophyll) eukaryotic organisms surrounded by a rigid cell wall composed mostly of chitin, glucan, chitosan, mannan, and glycoproteins. They have a nucleus surrounded by a membrane, and their replication is by both mitosis (asexual) and meiosis (sexual). Fungi range from simple, single-celled organisms, mostly yeasts, to complex filamentous mold species. Yeasts typically are round to oval with budding cells (blastoconidia). Yeasts mostly are small, white to cream-colored colonies on Sabouraud dextrose agar, although some species can be pink to salmon colored. The term black yeast is applied loosely to the yeast form of the mold genus Exophiala and other closely related genera. Molds are multicellular, produce an extensive mycelium (filamentous), are variously colored, and have several modes of reproduction that may be asexual (conidiogenesis yielding conidia), sexual (sporogenesis yielding spores), or both. The classic primary mold pathogens such as Histoplasma, Coccidioides, Blastomyces , and Paracoccidioides species are thermally dimorphic in that they can exhibit both a yeast stage (spherules for Coccidioides spp.) and a filamentous phase, depending on their growth in the host or under laboratory conditions. Other molds can be referred to as pleomorphic (i.e., can demonstrate multiple morphologic forms under laboratory conditions). This pleomorphism is discussed further when considering appropriate naming of molds (taxonomy and nomenclature).
Classification
The Kingdom Fungi is arranged in a hierarchical classification system with each rank denoted by a particular ending: phylum, -mycota; subphylum, -mycotina; class, -mycetes; order, -ales; family, -aceae. Most of the clinically significant genera in the kingdom Fungi are within the phyla Ascomycota, Basidiomycota, Mucoromycota, Entomophthoromycota, and Basidiobolomycota. Herein are contained members of the order Mucorales, which includes most genera inciting mucormycosis, as well as the Entomophthorales, inciting entomophthoramycosis. An example of an abbreviated classification for the fungus Microascus cirrosus would be as follows: kingdom Fungi, subkingdom Dikarya, phylum Ascomycota, order Microascales, family Microascaceae, genus Microascus , species Microascus cirrosus . Closely related parafungal organisms in the genera Pythium and Lagenidium are in the kingdom Straminipila (Stramenopila), phylum Oomycota, whereas Rhinosporidium is in the supergroup Opisthokonta, division Holozoa.
Taxonomy and Nomenclature
Taxonomy refers to the classification of fungi in a very systematic way, and nomenclature refers to the assigning of names. These tasks now are under the auspices of the International Code of Nomenclature for algae, fungi, and plants. The Melbourne Code, implemented on January 1, 2013, introduced sweeping changes into the naming of fungi and resulted in the elimination of multiple names for the same organism that produces various morphologic forms (dimorphism or pleomorphism). Thus, for example, the use of both the teleomorph (sexual) name Pseudallescheria boydii and its anamorph name Scedosporium boydii (previously thought to be Scedosporium apiospermum ) no longer is permitted. Going forward, the accepted name is Scedosporium , and similar changes are noted for various genera. The preferred name is no longer the teleomorph state, as was previously designated, but the oldest validly published name, which may be either the anamorph or teleomorph.
Laboratory Findings and Diagnosis
Collection and Examination of Specimens
The 2021 publication by the Clinical and Laboratory Standards Institute (CLSI) entitled Principles and Procedures for Detection and Culture of Fungi in Clinical Specimens CLSI guidelines M54, 2nd ed. , is an excellent source for ensuring that the specimen being examined or cultured is appropriate for the etiologic agent being sought. Consultation with laboratory personnel before specimen collection, however, is always recommended when the clinical history suggests potentially uncommon, unusual, or atypical organisms. Specimen types, rejection criteria, and specimen processing are well defined in the CLSI document, including blood culture for fungal organisms. Although the use of homogenization or grinding of specimens often facilitates the recovery of Histoplasma, this method should never be used for member of Mucorales and for most other filamentous fungi because it is deleterious to fragile fungal hyphae. Direct examination of specimens with various stains such as the Gram stain, 10% potassium hydroxide preparations, calcofluor white fluorescent stain, India ink, and others is always recommended. Histopathologic stains—such as hematoxylin and eosin and Gomori methenamine silver stain—should be applied routinely for tissue specimens, and additional special stains should be added when indicated (e.g., Fontana-Masson stain for melanin, mucicarmine for Cryptococcus ). A comprehensive review of the histopathologic diagnosis of fungal infections is available.
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