Interpretive Criteria for Identification of Bacteria and Fungi by Targeted DNA Sequencing
|Publication Date:||1 July 2018|
This guideline specifies recommendations for interpreting and reporting results of Sanger-based (dideoxynucleotide chain termination) sequencing of broad-range DNA targets for identifying pure isolates of bacteria, mycobacteria, and fungi from cultured patient isolates. Partial- and full-gene sequencing with 16S ribosomal RNA (rRNA) genes for bacterial and mycobacterial identification, as well as internal transcribed spacer (ITS) regions (ie, ITS-1 and ITS-2) for fungal identification are covered, including alternative DNA targets when appropriate. Although massively parallel (next-generation) sequencing technologies are rapidly emerging, this guideline's scope is limited to Sanger-based targeted DNA sequencing.
To assist the medical laboratory, guidance is provided for:
- Selecting DNA targets and sizes for amplification and sequencing
- Establishing QC parameters for amplification and sequencing
- Measuring sequence quality
- Assessing reference sequences and databases
- Comparing sequences for identification
- Establishing interpretive criteria for identity scores generated by targeted DNA sequencing
- Developing clinically relevant reporting strategies for specific microorganism groups
- Identifying the limitations of targeted DNA sequencing for microbial identification
The intended users of this guideline are medical laboratories and laboratories performing amplification and Sanger-based (dideoxynucleotide chain termination) sequencing of broad-range DNA targets for identifying bacteria, mycobacteria, and fungi from cultured patient isolates.
This guideline does not:
- Include procedures for performing microbial sequencing.
- Include RNA targets for sequencing.
- Provide guidance on definitive taxonomical criteria for microorganism classification or identification methods for novel microorganisms.
- Cover alternative sequencing systems or specific molecular assays designed with these broad-range DNA targets.
- Discuss typing strains for epidemiological purposes.
- Discuss virus or parasite identification.
- Discuss amplification and sequencing directly from patient specimens.