Usage of curated species- specific databases of MLSTs allows the epidemiologist to place the strain at hand in global and local outbreak histories. The PCR and Sanger sequencing steps are now routinely replaced by the more cost efficient and faster whole genome shotgun sequencing for which this tool is designed. In the CLC Microbial Genomics Module we offer a number of tools in connection to NGS-MLST:
- Download of existing MLST schemes from PubMLST, MLST.net or other sources.
- Creation of a new MLST scheme.
- Merge of available MLST schemes.
- Addition of sequence to MLST scheme.
- Identification of MLST based on read mapping.
In the CLC Microbial Genomics Module, an MLST scheme can be created in two ways:
- Downloaded from a database.
- Created from sequence data imported into the workbench.
For NGS-MLST typing and summary of analysis results, we recommend using the Type a Known Species or Type among Multiple Species template workflows as described in the chapter Workflow templates.