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CLSI MM18

Interpretive Criteria for Identification of Bacteria and Fungi by Targeted DNA Sequencing

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Organization: CLSI
Publication Date: 1 July 2018
Status: active
Page Count: 168
scope:

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.

Document History

CLSI MM18
July 1, 2018
Interpretive Criteria for Identification of Bacteria and Fungi by Targeted DNA Sequencing
This guideline specifies recommendations for interpreting and reporting results of Sanger-based (dideoxynucleotide chain termination) sequencing of broad-range DNA targets for identifying pure...
April 1, 2008
Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline
This guideline specifies recommendations for clinical laboratories that employ amplification and Sangerbased (dideoxy-termination) sequencing of broad-range DNA targets for the identification of...

References

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