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msberends / AMR

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

Home Page:https://msberends.github.io/AMR/

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Errors in CLSI interpretation

a-cienfuegos opened this issue · comments

commented

There are some errors in the clinical breakpoint CLSI interpretation. Eg. In E. coli MIC=16 is interpreted as S instead I. I checked the dataset and the susceptible breakpoint was set at 16 instead of 8. Can you correct this issue?

commented

Hi, many thanks for bringing this up! We'll look into it. Do you happen to have a screenshot of the CLSI 2023 table where Gram-negatives (or at least, E. coli) is mentioned? And which antibiotic do you mean?

commented

Hi Dr. Berends, I attached a screenshot of the CLSI 2023 (Table 2A) and the clinical breakpoints table from the AMR package. The antibiotic is ampicillin-sulbactam. Thanks for your help.

CB.pdf

commented

Hi, many thanks for finding this. It appeared to be an error in the WHONET interpretation files that we used. We'll let them know.

Best,
Matthijs