Update `microorganisms` data set to latest taxonomy about amr

[msberends]

Remember to add the taxons mentioned in #131

[silverfoxdoc]

hopefully will be fixed by an update to microorganism data set but can't seem to match Clavispora (Candida) lusitaniae. Also hoping that Nakaseomyces glabratus and Pichia kudriavzevii will arrive with update and their old names redirected to these new names, as lab are moving over to these new names.

[msberends]

That’s true, it’s a discussion at our lab as well. Do you know if it’s formal already? Meaning, accepted by authoritative taxonomy sources? I’m well aware of the publications suggesting these changes, but do you know whether they are formally adopted already?

[silverfoxdoc]

Afraid I don't know for sure about the International Taxonomy groups definitely accepting all these changes. This is a useful paper detailing the most common changes from a medical perspective if you've not already seen it https://doi.org/10.1093/ofid/ofac559

It may well be a moving target unfortunately...

[msberends]

Yes, I know that one. Unfortunately, Open Forum Infectious Diseases is ‘just’ a journal, not a taxonomically reliable source. The results/propositions of such papers must be ratified by taxonomic sources first.

But I found on MycoBank, a great and reliable taxonomic source for fungi, that they do have new names for many Candida species already. I found a couple of inconsistencies though, I’ll share them here and hope that we both could have a look at it. Will be later this week probably.