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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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blaSHV carbapenemase activity? #105

Open cgonzalezz opened 2 months ago

cgonzalezz commented 2 months ago

We have a concern about the drug classes listed for SHV-beta lactamases in CARD. We find "carbapenem" listed for the family as a whole, however the publications you list do not appear to indicate SHV having carbapenemase activity. We currently license CARD for use in software and provide drug metadata based on this drug information, and we have had software users raise this concern about SHV as well. Can you provide any insight into this drug classification or let us know if this is going to be updated in a future version of CARD?

bpalcock commented 2 months ago

Thank you for bringing this to our attention. This was a straightforward error in our curation and I've gone ahead and corrected it. We'll be releasing a new version of CARD in early August where this will no longer appear.

I will add that sometimes the semantic relationship confers_resistance_to_drug_class is added to an AMR gene family (such as SHVs) when some but not all members match that criteria. This is incorrect, or at least ambiguous, but arises because of pre-existing rules which we are currently planning to overhaul in the coming weeks for beta-lactamase curation. This is something we recently resolved for the OXA beta-lactamases in our February 2024 release, but hasn't yet been generalized for all Bla families.

That was a bit tangential but I wanted to add some context as your concern is a known issue. Regardless, in this case it was simply an error for the blaSHV family and I have gone ahead and corrected it. I will leave this issue open until I have confirmed the fix has been made after the next release.

Thanks again, Brian