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Published 20 hours ago • verified publisher icon tseemann

Consistify nomenclature of RESISTANCE phenotypes

Open tseemann opened this issue 4 years ago • 4 comments

ncbi, resfinder, card all use diff names maybe use 3 letter codes? like FUS, KAN, VAN etc

tseemann avatar Sep 10 '19 00:09 tseemann

EUCAST Antimicrobial agent abbreviations - they have a guidance document and table!

EUCAST_system_for_antimicrobial_abbreviations.pdf

tseemann avatar Oct 24 '19 00:10 tseemann

Will you adding this as a separate column? I ran abricate with card database option and the output for product is sentence (without the antibiotic class like penicillin ( I do see beta lactamase gene in the input) but having the antibiotic spelled out would be helpful.

darwinbandoy avatar Oct 28 '19 23:10 darwinbandoy

CARD uses sentences for its products unfortunately, not simple gene names. I can't fix that. Complain to them directly at https://github.com/arpcard/amr_curation :-)

You should get normal looking RESISTANCE column in the current abricate. Are you using an old version? See https://github.com/tseemann/abricate/releases/tag/v0.9.8

tseemann avatar Oct 29 '19 02:10 tseemann

We've been meaning to incorporate these and we could give them a unique flag in the CARD json so they are easy to extract.

arpcard avatar Nov 06 '19 22:11 arpcard