In outbreak analysis, Multilocus Sequence Typing (MLST) is a central tool for identification of isolated pathogenic bacteria. Typing requires a defined MLST scheme for the targeted species which is based on a number of loci (typically 7). These fragments are usually chosen to lie in conserved regions such as housekeeping genes across all species members. For each locus, the scheme consists of a list of the known alleles. Each allele is assigned a number, and by using this numbering system each new isolate can be matched to known or new allelic profiles or sequence types (STs).

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:

In the CLC Microbial Genomics Module, an MLST scheme can be created in two ways:

The schemes downloaded from a database will already have information about many sequence types, whereas this information needs to be accumulated by the user for self-made schemes.

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.