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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.
https://msberends.github.io/AMR/
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MIssing/extra veterinary breakpoints #143

Open samueljpearce opened 5 months ago

samueljpearce commented 5 months ago

As mentioned in issue #141, the feline E. coli urinary tract breakpoint for ampicillin is missing from the clinical breakpoints dataset, even though it is in the 2023 CLSI VET01S document.

I have just found that the clinical breakpoints dataset contains an extra breakpoint for dogs for Staphylococcus spp. and amoxicillin-clavulanate for urinary tract infections that does not exist in the 2023 CLSI VET01S document. These breakpoints are higher than the combined soft tissue and urinary tract infection breakpoint in the document.

samueljpearce commented 5 months ago

Cefazolin for Pasteurella multocida in dogs is also incorrectly given urinary and genital tract sites (should only be for skin, soft tissue and respiratory).

msberends commented 2 months ago

As mentioned in issue https://github.com/msberends/AMR/issues/141, the feline E. coli urinary tract breakpoint for ampicillin is missing from the clinical breakpoints dataset, even though it is in the 2023 CLSI VET01S document.

image

Apparently it is in the CLSI 2024 data that we imported from WHONET, but not in older guidelines. I'll check the other ones too.