Teleomorph vs anamorph ID of yeasts

[send2dan]

Hello,

as.mo() struggles a bit with yeasts.

Some yeasts may have two names that correlate to the growth state of the fungus: an anamorph name associated with asexual growth and replication (mitosis only) of the fungus and a teleomorph name associated with the sexual growth and replication. Examples of dual names are listed in the reference below [1].

Notably, for many yeasts the MALDI-TOF now only reports the teleomorph name, which may not include "Candida" even though the organism can be reasonably classified to that genus [1].

In practice, in Newcastle, since approx. Aug 2023, the MALDI-TOF has never once reported e.g. Candida lusitaniae or Candida krusei, but has continued to report e.g. Candida albicans and Candida parapsilosis.

While CLSI recommends using the anamorph name (e.g., "Candida krusei") for common fungi in reports due to clinician preference [1], MALDI-TOF's innate reporting of the teleomorph presents a practical challenge. At some stage, the teleomorph name given by the MALDI-TOF needs to be changed to the anamorph name (e.g. Pichia kudriavzevii changed to Candida krusei).

Can the AMR package be updated to reflect alternate names for select Candida species/yeast?

Teleomorph name Anamorph name Wickerhamomyces anomalus Candida pelliculosa Clavispora lusitaniae Candida lusitaniae Meyerozyma guilliermondii Candida guilliermondii Kluyveromyces marxianus Candida kefyr Pichia kudriavzevii Candida krusei Pichia caribbica/Meyerozyma caribbica Candida fermentati Kodamaea ohmeri Candida guilliermondii var membranifaciens Yarrowia lipolytica Candida lipolytica Cyberlindnera fabianii Candida fabianii Debaryozyma hansenii Candida famata Pichia fermentans Candida lambica Pichia norvegensis Candida norvegensis Cyberlindnera jadinii Candida utilis

References [1] https://www.cdc.gov/candidiasis/hcp/anamorph-and-teleomorph-names/index.html

[send2dan]

Noted #135 may help answer my request here, thanks :)

[msberends]

Ahhh, I think you are -really- going to like the update I’ve been working on for the past 4-6 weeks! I’m currently implementing MycoBank that has both teleomorph name anamorph names available. Though sadly enough, they don’t register which are which in a structured way, but keep rather standardised taxonomic status names.

Take for example their query page (https://www.mycobank.org/Simple%20names%20search) and type in “Candida krusei”. You’ll see that they consider Pichia as its ‘current name’. I’m currently exploring the best ways to implement all useful details.

First indications show that the AMR package will gain about 10,000 new fungi and the latest taxonomic info on existing ones.

I’ll try to wrap it up over the next weeks. It’s in my ‘spare’ working hours, but I’ll have a lot more of them now that colleagues start to go on holidays :)

For this topic, and especially for your expertise regarding this topic, we perhaps could have a video call? That would probably help me better in choosing the right angles which this complex part of microbial taxonomy. I’ve always been more of a bacteriologist to be frank 😊

[send2dan]

Thanks Matthijs, happy to help if you want a second opinion on this subject – I’ve been away on leave a bit myself, but will be fully up and running again from 9/9/24.

From: Matthijs Berends @.> Sent: Wednesday, July 10, 2024 5:54 PM To: msberends/AMR @.> Cc: WEIAND, Daniel (THE NEWCASTLE UPON TYNE HOSPITALS NHS FOUNDATION TRUST) @.>; Author @.> Subject: Re: [msberends/AMR] Teleomorph vs anamorph ID of yeasts (Issue #157)

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Ahhh, I think you are -really- going to like the update I’ve been working on for the past 4-6 weeks! I’m currently implementing MycoBankhttps://www.mycobank.org/ that has both teleomorph name anamorph names available. Though sadly enough, they don’t register which are which in a structured way, but keep rather standardised taxonomic status names.

Take for example their query page (https://www.mycobank.org/Simple%20names%20search) and type in “Candida krusei”. You’ll see that they consider Pichia as its ‘current name’. I’m currently exploring the best ways to implement all useful details.

First indications show that the AMR package will gain about 10,000 new fungi and the latest taxonomic info on existing ones.

I’ll try to wrap it up over the next weeks. It’s in my ‘spare’ working hours, but I’ll have a lot more of them now that colleagues start to go on holidays :)

For this topic, and especially for your expertise regarding this topic, we perhaps could have a video call? That would probably help me better in choosing the right angles which this complex part of microbial taxonomy. I’ve always been more of a bacteriologist to be frank 😊

— Reply to this email directly, view it on GitHubhttps://github.com/msberends/AMR/issues/157#issuecomment-2221014478, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVYNORJYZWJYBLBLA4M7AW3ZLVRJJAVCNFSM6AAAAABKU4RRFWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRRGAYTINBXHA. You are receiving this because you authored the thread.Message ID: @.**@.>>

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