Diagnostic molecular mycology

Fungal identification has become more urgent than ever due to the increasing number of fungal species that are found to be pathogenic for humans. While the major fungal pathogens probably do not exceed 50 commonly encountered species, a growing immunosuppressed patient population and increasingly aggressive medical therapies predispose patients to a broader spectrum of fungi capable of causing disease than ever before. While clinical microbiology laboratories can identify the common fungi using classical methods such as biochemistry and morphology, the rarer fungi need more complex identification methods. These methods are drawn from the field of molecular biology. Fungi offer unique problems that must be addressed before existing molecular methods can be applied to clinical specimens. Fortunately, molecular mycology is accelerating in the rate of diagnostic assay development as several molecular assays have been FDA approved, and many more have been commercialized and are now available. These assays can be focused on single species, major pathogens from one genus, and, in some cases, pan fungal. Fungal molecular diagnostics has advanced from PCR to whole-genome sequencing, and many assays are incorporating emerging technologies. While still lagging behind bacterial and viral diagnostics, the increasing number of commercial and approved fungal diagnostic assays will be welcome additions to the clinical microbiology laboratory.