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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Reported schema not found in scheme_species_map.tab #128

Open miguelpmachado opened 1 year ago

miguelpmachado commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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