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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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Wrong MIC interpretation of carbapenems in *Morganella morganii* #44

Closed msberends closed 3 years ago

msberends commented 3 years ago

During an ECCMID 2021 talk, it was discovered by someone that the MIC of at least imipenem is wrongly interpreted for M. morganii.

Test using:

as.rsi(x = as.mic(c(0.0125, 0.5, 1, 2, 4, 8)),
       mo = "Morganella morganii", 
       ab = "Imipenem",
       guideline = "EUCAST") 

# or coloured plotting
plot(as.mic(c(0.0125, 0.5, 1, 2, 4, 8)),
     mo = "Morganella morganii", 
     ab = "Imipenem",
     guideline = "EUCAST")
msberends commented 3 years ago

Found the error, one line of the Excel file distributed by EUCAST was not read in correctly. This bug only applies to taxonomic members of the Morganellaceae family, including the genera Morganella and Proteus.

This error is for Proteus not present when using the EUCAST 2020 guideline.

msberends commented 3 years ago

(this is an automated reply)

The development version nows contains the fix to this issue. You can try the latest version yourself using:

install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")