Clinical and Laboratory Standards Institute guideline M54—Principles and Procedures for Detection and Culture of Fungi in Clinical Specimens describes recommended processes for plating and examining fungal cultures as well as principles and procedures for the direct detection of fungi in clinical specimens, including criteria for performing and interpreting direct microscopic examinations. Safety considerations unique to mycology laboratories and a discussion of appropriate levels of laboratory service (eg, when to refer samples to more experienced laboratories) are highlighted. Specimen collection, transport, and processing recommendations, including rejection criteria, are provided to guide the collection of high-quality specimens for direct examinations and fungal cultures. Fungal stains and interpretive criteria appropriate for detecting and characterizing fungal elements in direct microscopic examinations are emphasized as critical components for rapid detection of fungi. Descriptions of serological and antigen-based testing and molecular assays are also provided. Media selection, incubation conditions, and other growth requirements for fungal cultures are provided with suggested culture examination schedules, interpretations for growth on positive cultures, and reporting criteria.

This guideline replaces the previous edition of the approved guideline, M54-A, published in 2012. Several changes were made in this edition, including: • Updating information, including current fungal taxonomy and nomenclature • Expanding tables and consolidating text • Adding new subchapters on antibody, antigen, and molecular testing • Adding new figures, including new photographs

This guideline provides recommendations to laboratories on procedures for collecting, processing, and handling fungal specimens and interpreting direct stain examinations and culture results. In addition, methods for direct or indirect detection from patient specimens, such as antigen, antibody, and molecular testing, are included. Because the relative importance of any fungus isolated from a patient specimen depends on the pathogenic potential of the fungus and the clinical setting in which it is isolated, these issues as well as factors to consider regarding the isolate's clinical significance are discussed. Fungal taxonomy has been updated in this edition of M54. Direct molecular methods to detect fungi in clinical specimens are also discussed, such as the use of magnetic resonance to detect Candida spp. in blood and the use of PCR to detect Pneumocystis jirovecii in respiratory specimens, other fungal pathogens, and the emerging pathogen Candida auris. This guideline considers individualized quality control plan (IQCP) issues related to fungal media and includes a table listing the differential diagnosis of various yeasts and yeast-like organisms on direct examination. Antigen and antibody detection of fungi and the extent of identification needed to provide clinical and therapeutic guidance are also discussed. The intended users of this guideline are laboratorians who process specimens for fungal culture, perform fungal direct microscopic examinations, and/or perform antibody, antigen, or molecular testing for fungi. Antifungal susceptibility testing methods (see CLSI documents M27, M38, M44, M51, M60, and M61) are not discussed in this guideline. Although Nocardia spp. and other aerobic actinomycetes can be encountered growing on mycology media, methods for detecting these organisms are not discussed in this guideline. Additionally, definitive fungal identification from culture growth (eg, examination of cellulose tape preparation, matrix-assisted laser desorption/ionization time of flight mass spectrometry [MALDI-TOF MS], or DNA sequencing) is outside this guideline's scope (see CLSI documents M58 and MM18).