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(v2.1.1.9247) CLSI/EUCAST 2025!

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dr. M.S. (Matthijs) Berends
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@ -16,11 +16,11 @@
\source{
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
\itemize{
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
}
}
\usage{
@ -84,7 +84,7 @@ sir_interpretation_history(clean = FALSE)
\item{ab}{A vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
\item{guideline}{A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see \emph{Details}. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.}
\item{guideline}{A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see \emph{Details}. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.}
\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
@ -146,9 +146,9 @@ Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC
These breakpoints are currently implemented:
\itemize{
\item For \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024;
\item For \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024;
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
}
All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
@ -196,9 +196,14 @@ your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_species",
\subsection{Supported Guidelines}{
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024, and for \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024.
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:
\itemize{
\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
}
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2024"} or \code{"CLSI 2024"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.
The \code{guideline} argument must be set to e.g., \code{"EUCAST 2025"} or \code{"CLSI 2025"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.
You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.