AMR/man/clinical_breakpoints.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{clinical_breakpoints}
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 61 393 observations and 15 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"}
\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either \code{"ECOFF"}, \code{"aquatic"}, \code{"cats"}, \code{"cattle"}, \code{"dogs"}, \code{"horse"}, \code{"human"}, \code{"poultry"}, or \code{"swine"}
\item \code{method}\cr Testing method, either \code{"DISK"} or \code{"MIC"}
\item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
\item \code{rank_index}\cr Taxonomic rank index of \code{mo}, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., \emph{Streptococcus} group A), 3 for genus, 4 for family, 5 for order, 6 for other groups (e.g., Gram-negative or anaerobic bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see \emph{Details}) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence.
\item \code{ab}\cr Antimicrobial code as used by this package, EARS-Net and WHONET, see \code{\link[=as.ab]{as.ab()}}
\item \code{ref_tbl}\cr Info about where the guideline rule can be found
\item \code{disk_dose}\cr Dose of the used disk diffusion method
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S", is \code{NA} for blocking rows (see \emph{Details}). EUCAST's off-scale MIC breakpoint of 0.001 mg/L, which indicates that there is no S category, is stored as 0.0001 to keep all isolates out of "S".
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA}
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 72 breakpoints.
\item \code{note}\cr Notes from the guideline that apply to the breakpoint, if available
}
}
\usage{
clinical_breakpoints
}
\description{
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.

These breakpoints are currently implemented:
\itemize{
\item For \strong{clinical microbiology}: EUCAST 2011-2026 and CLSI 2011-2026;
\item For \strong{veterinary microbiology}: EUCAST 2021-2026 and CLSI 2019-2026;
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.
}

Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
}
\details{
\subsection{Different Types of Breakpoints}{

Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.

The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. Use \code{\link[=as.sir]{as.sir(..., breakpoint_type = ...)}} to interpret raw data using a specific breakpoint type, e.g. \code{as.sir(..., breakpoint_type = "ECOFF")} to use ECOFFs.
}

\subsection{Blocking Rows}{

Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", breakpoints in brackets, an organism excluded with "except", or no S category for a zone diameter), \code{\link[=as.sir]{as.sir()}} must not fall back to the breakpoint of a broader taxon, such as the breakpoint for \emph{Vibrio} spp. where EUCAST gives "IE" for \emph{V. fluvialis}. Such cases are included as "blocking rows": rows in which \code{breakpoint_S} and \code{breakpoint_R} are both \code{NA} and the \code{note} starts with \code{"[No breakpoint]"} followed by the reason. \code{\link[=as.sir]{as.sir()}} returns \code{NA} for these. This currently applies to 15 660 rows. Remove them with \code{subset(clinical_breakpoints, !is.na(breakpoint_S))} if only actual breakpoints are needed.

Where another guideline has no S category for a zone diameter, such as CLSI for fluconazole in \emph{C. glabrata} (SDD and R only), only \code{breakpoint_R} is given, and the \code{note} starts with \code{"[No S category]"}. \code{\link[=as.sir]{as.sir()}} then returns R where applicable, and \code{NA} otherwise.
}

\subsection{Imported From WHONET}{

Some breakpoints in this package were validated through and imported from \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}. The developers of WHONET and this \code{AMR} package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.

From WHONET, imported were:
\itemize{
\item All CLSI breakpoints, including ECOFF
\item All non-human EUCAST breakpoints, including ECOFF
\item Human EUCAST breakpoints between 2011 and 2018
\item Human EUCAST antifungal breakpoints between 2019 and 2025
}

Human EUCAST breakpoints from 2019 onwards (antifungal breakpoints from 2026 onwards) were retrieved directly from the EUCAST Clinical Breakpoint Tables published on \url{https://www.eucast.org}, using \href{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R}{this script}.

Our WHONET import script can be \href{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R}{found here}.
}

\subsection{Response From CLSI and EUCAST}{

The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this \code{AMR} package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this \code{AMR} package.
}

\subsection{Download Note}{

This \code{AMR} package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the \link{microorganisms.groups} data set). It is important that this is considered when implementing the breakpoints for own use.
}
}
\section{Download Our Reference Data}{

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw/datasets}{our GitHub repository}.
}

\examples{
clinical_breakpoints
}
\seealso{
\link{intrinsic_resistant}
}
\keyword{datasets}