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arpcard / amr_curation

A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.
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Is OXA-1 a carbapenamase? #86

Closed flashton2003 closed 8 months ago

flashton2003 commented 1 year ago

Hello,

I'm not very familiar with CARD, and I'm not an AMR expert, so I could be misinterpreting things here.

However, OXA-1 seems to be called as a carbapenemase in CARD - https://card.mcmaster.ca/ontology/37796

But, from what I can read, OXA-1 isn't a carbapenemase? https://academic.oup.com/jac/article/74/2/326/5156209

Am I getting something wrong here?

Thanks,

Phil

arpcard commented 1 year ago

Hi Phil, you are correct that OXA-1 is not a carbapenemase - what's going on here is the way CARD handles confers_resistance_to_drug_class is based on any member of the AMR Gene Family (in this case OXA beta-lactamases https://card.mcmaster.ca/ontology/36026). However this is still confusing on our part because it would be more correct to say some OXA beta-lactamases confer resistance to drug class carbapenem (as is the case with OXA-23 for example).

The good news is your question has prompted a discussion among the curation team on how to better define and show this in CARD and we believe we have a good solution. The bad news is it will take some time to implement and so won't be ready in time for our next release. I suspect it will be introduced in the following release some time before the end of the year.

Thanks for bringing this to our attention!

flashton2003 commented 1 year ago

Great, thanks for the comprehensive action and the update.

On Mon, Sep 25, 2023 at 3:50 PM Comprehensive Antibiotic Resistance Database @.***> wrote:

Hi Phil, you are correct that OXA-1 is not a carbapenemase - what's going on here is the way CARD handles confers_resistance_to_drug_class is based on any member of the AMR Gene Family (in this case OXA beta-lactamases https://card.mcmaster.ca/ontology/36026). However this is still confusing on our part because it would be more correct to say some OXA beta-lactamases confer resistance to drug class carbapenem (as is the case with OXA-23 for example).

The good news is your question has prompted a discussion among the curation team on how to better define and show this in CARD and we believe we have a good solution. The bad news is it will take some time to implement and so won't be ready in time for our next release. I suspect it will be introduced in the following release some time before the end of the year.

Thanks for bringing this to our attention!

  • Brian

— Reply to this email directly, view it on GitHub https://github.com/arpcard/amr_curation/issues/86#issuecomment-1733875371, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAT6FEUSXABGI7XNE2S4KGLX4GK3BANCNFSM6AAAAAA4F7PBSE . You are receiving this because you authored the thread.Message ID: @.***>

bpalcock commented 8 months ago

Hi Phil, just to let you know the most recent release of CARD completed this past month includes the changes to the OXA beta-lactamase ontology that should fix this issue

thanks Brian

flashton2003 commented 8 months ago

Great! Thanks Brian!

On Thu, Feb 29, 2024 at 5:45 PM brian @.***> wrote:

Hi Phil, just to let you know the most recent release of CARD completed this past month includes the changes to the OXA beta-lactamase ontology that should fix this issue

thanks Brian

— Reply to this email directly, view it on GitHub https://github.com/arpcard/amr_curation/issues/86#issuecomment-1971419505, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAT6FEUPA3ZQOX3PUEK7RLDYV5GJ7AVCNFSM6AAAAAA4F7PBSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZRGQYTSNJQGU . You are receiving this because you authored the thread.Message ID: @.***>