Reported schema not found in scheme_species_map.tab

[miguelpmachado]

Hi,
I'm running L. monocytogenes samples and noticed that the reported schema (listeria_2) is not found in scheme_species_map.tab.
scheme_species_map.tab still has lmonocytogenes but db/pubmlst has listeria_2.
I just wanted to let you know about this small difference.
Thanks,
Miguel

[JayanthiGangiredla]

Hi,

In addition to the posted request above, we would like to know how can we identify L.innocula based on lineage and ST matches? Other than calling all of them as Listeria_2 schema? Please give us your thoughts on it.

Thanks,
Jayanthi Gangiredla

[evezeyl]

The updated version of MLST indeed include the "Listeria_2 scheme", whereas the previous versions included a "lmonocytogenes" scheme that corresponded to the BIGSdb (Pasteur) Listeria monocytogenes MLST scheme.

I am kind of confused about the "Listeria_2 scheme", when using it for typing, it detects several alleles at the dapE gene, while this was not detected using the previous scheme. I tested for eventual intra-specific contamination using confindr -rMLST scheme on the listeria isolates I was using, and could not detect anything significant.
So, either the scheme is different or default parameters for detecting new alleles are different ?

This is confusing as I cannot trace back the origin of this new scheme (could you add information about the scheme source ?). (detecting, likely incorectly several alleles at a gene is problematic, as thus STs are not assigned, and thus CC groups not identified).

Could you provide additonal information ?

Best regards
Eve