Selection of appropriate specimens for culture and microscopic examination is based on the results of clinical and radiographic examination and consideration of the most likely fungal pathogen that may cause such an infection. Specimens should be collected under aseptic conditions or after appropriate cleaning and decontamination of the collection site and rapidly transported to the clinical mycology laboratory. Unfortunately many specimens submitted to the laboratory are either of insufficient amount or of poor quality and are inadequate to make a correct diagnosis.
The clinical information is very important in guiding the laboratory efforts in terms of specimen processing and interpretation of results. This is especially important when dealing with specimens from non-sterile sites such as sputum, bronchial washings and skin. Furthermore, it is the only way of effectively altering the laboratory personnel that they may be dealing with a potentially dangerous pathogen such as Histoplasma capsulatum or the Coccidioides immitis complex.
Most fungi can be recovered from specimens submitted in bacteriologic transport media, although direct microscopic examination of such material is not recommended because the transport medium components can hinder the observation of the fungi. In general, if a delay in processing is unavoidable, the specimen for the fungal culture may be safely stored at 4 degree centigrade for a short time.
Some specimens are better than others for the diagnosis of fungal infections. Swab specimens are inappropriate for mycologic culture and microscopic examination. Cultures of blood, cerebrospinal fluid (CSF) and other normally sterile body fluids should be performed if clinical signs and symptoms are suggestive of hematogenous dissemination or involvement of these sites. Diagnosis of oral or vaginal mucosal infections may be better established by clinical presentation and direct microscopic examination of secretions or mucosal scrapings. Diagnosis of fungal infections of the gastrointestinal tract is better established by biopsy and histopathologic examination of involved tissue than by culture alone. Care should be taken in collecting lower respiratory and urine specimens to minimize contamination with normal oral and periurethral flora, respectively. Twenty four hour collections of sputum or urine are inappropriate for mycologic examination because they typically become overgrown with both bacterial and fungal contaminants.