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Multilocus sequence typing (MLST) is a standard method for categorising genomes (M. C. Maiden et al., 1998) based on variation in a small set of conserved house keeping genes. It allows for rapid identification of genomes into high level categories and is extremely useful for epidemiological investigations (R. Urwin & Maiden, 2003) making it a key tool for public health reference laboratories. Whilst MLST is more commonly associated with classical sequencing methods, it is possible to extract the same information from Next Generation Sequencing data, in particular from de novo assemblies which are generated routinely for bacterial sequencing data (Page et al., 2016).

Multilocus sequence typing by blast from de novo assemblies against PubMLST