New CLSI Guideline Provides Interpretive Criteria for ID by DNA Target Sequencing
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 broadrange DNA sequencing for microorganism identification.
The Clinical and Laboratory Standards Institute (CLSI) has recently published a new document, Interpretive Criteria for Identification of Bacteria and Fungi by DNA TargetSequencing;
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;
- 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.
Click here for more details | |
