AMR/man/mdro.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mdro.R
\name{mdro}
\alias{mdro}
\alias{MDR}
\alias{XDR}
\alias{PDR}
\alias{BRMO}
\alias{3MRGN}
\alias{4MRGN}
\alias{brmo}
\alias{mrgn}
\alias{mdr_tb}
\alias{mdr_cmi2012}
\alias{eucast_exceptional_phenotypes}
\title{Determine Multidrug-Resistant Organisms (MDRO)}
\usage{
mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
  carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
  info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
  verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)

brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)

mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)

mdr_tb(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)

mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
  ...)

eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
  verbose = FALSE, ...)
}
\arguments{
\item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}

\item{guideline}{A specific guideline to follow, see sections \emph{Supported international / national guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}

\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}

\item{esbl}{\link{logical} values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins).}

\item{carbapenemase}{\link{logical} values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins).}

\item{mecA}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{mecA} gene (or production of its proteins).}

\item{mecC}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{mecC} gene (or production of its proteins).}

\item{vanA}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{vanA} gene (or production of its proteins).}

\item{vanB}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{vanB} gene (or production of its proteins).}

\item{info}{A \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.}

\item{pct_required_classes}{Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}

\item{combine_SI}{A \link{logical} to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{\link[=mdro]{mdro()}} function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.}

\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}

\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}

\item{...}{In case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antimicrobials} below.}

\item{as_factor}{A \link{logical} to indicate whether the returned value should be an ordered \link{factor} (\code{TRUE}, default), or otherwise a \link{character} vector.}
}
\value{
\itemize{
\item If \code{verbose} is set to \code{TRUE}:\cr
A \link{data.frame} containing columns \code{row_number}, \code{microorganism}, \code{MDRO}, \code{reason}, \code{all_nonsusceptible_columns}, \code{guideline}
\item CMI 2012 paper - function \code{\link[=mdr_cmi2012]{mdr_cmi2012()}} or \code{\link[=mdro]{mdro()}}:\cr
Ordered \link{factor} with levels \code{Negative} < \code{Multi-drug-resistant (MDR)} < \verb{Extensively drug-resistant (XDR)} < \code{Pandrug-resistant (PDR)}
\item TB guideline - function \code{\link[=mdr_tb]{mdr_tb()}} or \code{\link[=mdro]{mdro(..., guideline = "TB")}}:\cr
Ordered \link{factor} with levels \code{Negative} < \code{Mono-resistant} < \code{Poly-resistant} < \code{Multi-drug-resistant} < \verb{Extensively drug-resistant}
\item German guideline - function \code{\link[=mrgn]{mrgn()}} or \code{\link[=mdro]{mdro(..., guideline = "MRGN")}}:\cr
Ordered \link{factor} with levels \code{Negative} < \verb{3MRGN} < \verb{4MRGN}
\item Everything else, except for custom guidelines:\cr
Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed} < \code{Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests
}
}
\description{
Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
}
\details{
These functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.

For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).

\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named \emph{order} Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
\subsection{Supported International / National Guidelines}{

Please suggest to implement guidelines by \href{https://github.com/msberends/AMR/issues/new?template=2-feature-request.yml&title=Add\%20new\%20MDRO\%20guideline}{letting us know}.

Currently supported guidelines are (case-insensitive):
\itemize{
\item \code{guideline = "CMI 2012"} (default)

Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\doi{10.1111/j.1469-0691.2011.03570.x})
\item \code{guideline = "EUCAST 3.3"} (or simply \code{guideline = "EUCAST"})

The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{link})

Also:
\itemize{
\item \code{guideline = "EUCAST 3.2"}

The former European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link})
\item \code{guideline = "EUCAST 3.1"}

The former European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
}
\item \code{guideline = "TB"}

The international guideline for multi-drug resistant tuberculosis - World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/publications/i/item/9789241548809}{link})
\item \code{guideline = "MRGN"}

The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}
\item \code{guideline = "BRMO 2024"} (or simply \code{guideline = "BRMO"})

The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (\href{https://www.sri-richtlijnen.nl/brmo}{link})

Also:
\itemize{
\item \code{guideline = "BRMO 2017"}

The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)"
}
}
}

\subsection{Using Custom Guidelines}{

Using a custom MDRO guideline is of importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.

Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}} function.
}
}
\section{Antimicrobials}{

To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use \code{\link[=guess_ab_col]{guess_ab_col()}} to find them.

To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
}

\section{Interpretation of SIR}{

In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/newsiandr}).

This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}

\examples{
out <- mdro(example_isolates)
str(out)
table(out)

out <- mdro(example_isolates, guideline = "EUCAST 3.3")
table(out)

\donttest{
if (require("dplyr")) {
  # no need to define `x` when used inside dplyr verbs:
  example_isolates \%>\%
    mutate(MDRO = mdro()) \%>\%
    count(MDRO)
}
}
}
\seealso{
\code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}
}