Epidemiology

Fungal infections are an increasing threat to individuals. The number of nosocomial and community-acquired infections has increased dramatically. The major factors responsible for the increase in the number of fungal infections are alterations in the host, particularly the growing number of immunocompromised people. Whether caused by immunosuppressive agents or serious underlying diseases, these alterations may lead to infection by organisms normally nonpathogenic or part of the patient’s normal microbiota (i.e., normal flora). These infections may occur in patients with debilitating diseases, such as progressive infection with the human immunodeficiency virus (HIV) or diabetes mellitus, or in patients with impaired immunologic function resulting from corticosteroid or antimetabolite chemotherapy. Other common predisposing factors include complex surgical procedures and antibacterial therapy. More than 200,000 valid species of fungi exist, but only 100 to 150 species are generally recognized as causes of human disease, and approximately 25 species cause most human disease. Most of these organisms normally live a saprophytic existence (living on dead or decayed organic matter) in nature.

Fungal infections generally are not communicable in the usual sense, through person-to-person transmission. Humans become accidental hosts for fungi by inhaling spores or through the introduction of fungal elements into tissue by trauma. Except for disease caused by the dimorphic fungi, humans are relatively resistant to infections caused by fungi. Classic infections are now appearing in new forms in patients, and the old “harmless” saprophytic molds are now being implicated in serious diseases. This ability of normally saprophytic fungi to cause disease in the immunocompromised patient means that laboratories now must be able to identify and report a wide array of fungi.

The primary pathogens appear to have well-defined geographic locations. An example of this is the dimorphic fungi Coccidioides immitis. C. immitis is usually found only in the United States in the desert Southwest, northern Mexico, and Central America. Opportunistic pathogens such as Candida and Aspergillus spp. are found all over the world.

General Features of the Fungi

Fungi seen in the clinical laboratory generally can be categorized into two groups based on the appearance of the colonies formed. The yeasts produce moist, creamy, opaque or pasty colonies on media, whereas the filamentous fungi or molds (see Chapters 60 and 61) produce fluffy, cottony, woolly, or powdery colonies. Several systemic fungal pathogens exhibit either a yeast (or yeastlike) phase, and filamentous forms are referred to as dimorphic. When dimorphism is temperature dependent, the fungi are designated as thermally dimorphic. In general, these fungi produce a mold form at 25° to 30°C and a yeast form at 35° to 37°C under certain circumstances.

The medically important dimorphic fungi are Histoplasma capsulatum, Blastomyces dermatitidis, C. immitis, Paracoccidioides brasiliensis, Sporothrix schenckii, and Penicillium marneffei (see Chapter 60). C. immitis is not thermally dimorphic. Additionally, some of the medically important yeasts, particularly the Candida species, may produce yeasts forms, pseudohyphae, and/or true hyphae (see Chapter 62). Fungi that have more than one independent form or spore stage in their life cycle are called polymorphic fungi. The polymorphic features of this group of organisms are not temperature dependent.

Taxonomy of the Fungi

Fungi are composed of a vast array of organisms that are unique compared with plants and animals. Included among these are the mushrooms, rusts and smuts, molds and mildews, and yeasts. Despite their great variation in morphologic features, most fungi share the following characteristics:

Traditionally, the fungi have been categorized into four well-established phyla: Zygomycota, Ascomycota, Basidiomycota, and Deuteromycota. The previous phylum, Zygomycota, has contained a very diverse group of organisms. Until further distinction is resolved, the organisms have been divided into the phylum, Glomeromycota and subphylum, Mucoromycotina, and Entomophthoracortina. This diverse group of fungi includes organisms that produce sparsely septate hyphae and exhibit asexual reproduction by sporangiospores and sexual reproduction by the production of zygospores. Some of the clinically important genera in this phylum are Rhizopus, Mucor, Rhizomucor, Absidia, and Cunninghamella.

The Ascomycota include many fungi that reproduce asexually by the formation of conidia (asexual spores) and sexually by the production of ascospores. The filamentous ascomycetes are ubiquitous in nature, and all produce true septate hyphae. All exhibit a sexual form (teleomorph) but also exist in an asexual form (anamorph). Fungi that have different asexual forms of the same fungus are called synanomorphs. In general, the anamorphic form correlates well with the teleomorphic classification. However, different anamorphic forms may have the same teleomorphic form. For example, Pseudallescheria boydii (Figure 59-1), in addition to having the Scedosporium apiospermum anamorph (Figure 59-2), may exhibit a Graphium anamorph (Figure 59-3). The latter anamorph may be seen with several other fungi.

An example of another clinically important fungi that belong to the phylum Ascomycota is H. capsulatum, which has a teleomorph designated as Ajellomyces. Some species of Aspergillus have a teleomorph, Eurotium.

Numerous yeast species also belong to the Ascomycota; these include Saccharomyces spp. and some species of Candida.

The phylum Basidiomycota includes fungi that reproduce sexually through the formation of basidiospores on a specialized structure called the basidia. The basidiomycetes are generally plant pathogens or environmental organisms that rarely cause disease in humans. This group includes smuts, rusts, mushrooms, and Cryptococcus neoformans complex. The teleomorphic form of C. neoformans is Filobasidiella neoformans.

The phylum Deuteromycota includes fungi that lack a sexual reproductive cycle and are characterized by their asexual reproductive structures, primarily conidia. The organisms in this group may have sexual forms that have not yet been described. The medically important fungus, Blastomyces dermatitidis, is a dimorphic fungus that has not been assigned to a phylum and is therefore placed in the order, Incertae sedis until the taxonomic placement is resolved.

Clinical Classification of the Fungi

The botanic taxonomic schema for grouping the fungi has little value in a clinical microbiology laboratory. Table 59-1 is a simplified taxonomic schema illustrating the major groups of fungi.

For clinicians, dividing the fungi into four categories of mycoses, according to the type of infection, is much more useful. The fungi are categorized as follows:

The superficial, or cutaneous, mycoses are fungal infections that involve the hair, skin, or nails without direct invasion of the deeper tissue. The fungi in this category include the dermatophytes (agents of ringworm, athlete’s foot) and agents of infections such as tinea, tinea nigra, and piedra. All of these infect keratinized tissues.

Some fungi cause infections that are confined to the subcutaneous tissue without dissemination to distant sites. Examples of subcutaneous infections include chromoblastomycosis, mycetoma, and phaeohyphomycotic cysts (see Chapter 61).

As traditionally defined, agents of systemic fungal infections include the genera Blastomyces, Coccidioides, Histoplasma, and Paracoccidioides. Infections caused by these organisms primarily involve the lungs but also may become widely disseminated and involve any organ system. P. marneffei, a geographically limited cause of systemic mycosis in a select patient population, may also be considered a part of this group.

Any of the fungi could be considered an opportunistic pathogen in the appropriate clinical setting. The list of uncommon fungi found to cause disease in humans expands every year. Fungi previously thought to be nonpathogenic may be the cause of infections. The infections these organisms cause occur primarily in patients with some type of compromise of the immune system. This may occur secondary to an underlying disease process, such as diabetes mellitus, or it may be caused by an immunosuppressive agent. Although any fungus potentially can cause disease in these patients, the most commonly encountered genera in this group are Aspergillus, Candida, and Cryptococcus, among others. All of these organisms may cause disseminated (systemic) disease. Some of the dematiaceous fungi may cause deeply invasive phaeohyphomycoses (i.e., produce brown-pigmented structures) in this patient population.

Classification by type of infection allows the clinician to attempt to categorize organisms in a logical fashion into groups having clinical relevance. Table 59-2 presents an example of a clinical classification of infections and their etiologic agents that is useful to clinicians.

Pathogeneis and Spectrum of Disease

Fungal infection is caused by either primary pathogens or opportunistic pathogens. Infections caused by primary pathogens usually occur in immunocompetent hosts, are not always as virulent, and may lead to subclinical disease. Opportunistic pathogens infect immunocompromised hosts. Opportunistic pathogens include almost any fungus present in the environment. An increase in the number of opportunistic fungal infections in humans is due in large part to the immunocompromised nature of the host. However, certain factors, called virulence factors, make invading tissues and causing disease easier for these organisms. Some virulence factors have been known for years:

Most of the fungi exist in environmental niches as saprophytic organisms (Table 59-4). Perhaps the fungi that cause disease in humans have developed various mechanisms that allow them to establish disease in the human host. Table 59-5 describes the known or speculative virulence factors of the fungi known to be pathogenic for humans.

The diagnosis of fungal infections depends entirely on the selection and collection of an appropriate clinical specimen for microscopic analysis and culture. Many fungal infections are similar clinically to mycobacterial infections, and often the same specimen is cultured for both fungi and mycobacteria. Many infections have a primary focus in the lungs; respiratory tract secretions are almost always included among the specimens selected for culture. It should be emphasized that dissemination to distant body sites may occur, and fungi may be recovered from nonrespiratory sites.

Proper collection of specimens and rapid transport to the clinical laboratory are crucial to the recovery of fungi. Specimens often contain not only the etiologic agent, but also contaminating bacteria or fungi that rapidly overgrow some of the slower-growing pathogenic fungi. The viability of fungi decreases over time. If processing will be delayed, specimens can be refrigerated for a short time, except for dermatologic specimens (skin, hair, nails), blood, and cerebrospinal fluid (CSF). Yeasts (e.g., Candida spp.) commonly are recovered on routine bacteriology media and fungal culture media. A few specific comments concerning specimen collection and culturing are included in this chapter.

Respiratory Tract Secretions

Respiratory tract secretions (sputum, induced sputum, bronchial washings, bronchoalveolar lavage, and tracheal aspirations) are perhaps the most common specimens collected for fungal culture. To ensure optimal recovery of fungi and prevent overgrowth by contaminants, antibacterial antibiotics should be included in the battery of media used. The antifungal agent cycloheximide prevents overgrowth by rapidly growing molds and should be included in at least one of the culture media. As much specimen as possible (0.5 mL) should be used to inoculate each medium.

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