The information presented in this document is intended for use with molecular diagnostic testing procedures published in CLSI guideline MM3 and CLSI/NCCLS guideline MM9. The guidelines contain information about the development, evaluation, and application of nucleic acid-based testing for infectious diseases and chemistries for diagnostic laboratories. Laboratories often receive clinical isolates for bacterial and fungal identification that have ambiguous biochemical profiles by conventional testing.

The identification of microorganisms historically has relied on phenotypic methods. Because of the growing microbial diversity with emergence of common pathogens having rare or unique phenotypic characteristics and new pathogenic microorganisms with poorly defined phenotypes, conventional methods often cannot fully characterize bacterial or fungal isolates, and laboratories are now relying on broad-range DNA sequencing for microorganism identification. The information here represents the most current information for microbial classification by DNA target sequencing, with particular emphasis on interpretation and reporting results.