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Genomes identified by _diphtOscan_ as belonging to the _C. diphtheriae_ species complex are subjected to MLST using the 7-locus scheme described initially by Bolt et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020856/) and hosted at [BIGSdb-Pasteur _C. diphtheriae_ database](https://bigsdb.pasteur.fr/diphtheria/). Note that this scheme is not specific to _C. diphtheriae_ sensu stricto but covers the whole _C. diphtheriae_ species complex, including _C. ulcerans_.
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A copy of the MLST alleles and ST definitions is stored in the [data directory](https://gitlab.pasteur.fr/BEBP/diphtoscan/data) of this repository. The update can be executed with the `-u` option.
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Notes on diphtOscan's MLST calls:
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* _diphtOscan_ makes an effort to report the closest matching ST if a precise match is not found.
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* Imprecise allele matches are indicated with a `\*`.
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* Imprecise ST calls are indicated with `-nLV`, where n indicates the number of loci that disagree with the ST reported. So `377-1LV` indicates a single-locus variant (SLV) of ST377, i.e. 6/7 loci match with ST377. |
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\ No newline at end of file |
