Updated:Wed, 22 Mar 2017

Interpretive Criteria for Microoganism Identification by DNA Target Sequencing

Wayne, Pennsylvania, USA—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.
Clinical and Laboratory Standards Institute (CLSI) has recently published a new document, Interpretive Criteria for Microorganism Identification by DNA Target Sequencing; Proposed Guideline (MM18-P), 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.
The information presented in this document is intended for use with molecular diagnostic testing procedures published in the following CLSI approved guidelines: Molecular Diagnostic Methods for Infectious Diseases; Approved Guideline—Second Edition (MM3-A2); and Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline (MM9-A). The guidelines contain information about the development, evaluation, and application of nucleic acid-based testing for infectious diseases and chemistries for diagnostic laboratories.
For additional information on CLSI or for further information regarding this release, visit our website at http://www.clsi.org or call +610.688.0100.
CLSI, formerly NCCLS, is a global, nonprofit, membership-based organization dedicated to developing standards and guidelines for the health care and medical testing community. CLSI’s unique consensus process facilitates the creation of standards and guidelines that are reliable, practical, and achievable for an effective quality system.