CLSI Guideline Provides Interpretive Criteria for Microorganism Identification by DNA Target Sequencing

Clinical and Laboratory Standards Institute (CLSI) has recently published a new document, Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline (MM18-A), which provides the most current information for microbial classification by gene sequencing, with particular emphasis on interpretation and reporting results.

This document establishes guidelines for the systematic approach to classify bacteria and fungi by broad-range DNA sequencing.

Topics covered in the guideline include:

• Selection of DNA targets and size of targets for amplification and sequencing;

• Establishment of quality control parameters for amplification and sequencing;

• Measurement of quality of sequence;

• Assessment of reference sequences and databases;

• Comparison of sequences for identification;

• Establishment of interpretive criteria for identity scores generated by gene sequencing;

• Reporting strategies that are clinically relevant for specific groups of microorganisms; and

• Limitations of gene sequencing for microbial identification.

This guideline specifies recommendations for clinical laboratories that employ amplification and Sanger-based (dideoxy-termination) sequencing of broad-range DNA targets for the identification of bacteria, mycobacteria, and fungi from cultured clinical isolates.

Partial and full gene sequencing with 16S rRNA gene for identification of bacteria and mycobacteria, and internal transcribed spacer regions ITS1 and ITS2 regions for identification of fungi, are addressed with inclusion of alternative DNA targets when appropriate.