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(v0.8.0.9004) added MDR guideline by Magiorakos et al.
This commit is contained in:
419
R/mdro.R
419
R/mdro.R
@ -23,13 +23,14 @@
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#'
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#' Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.
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#' @param x table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
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#' @param guideline a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.
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#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.
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#' @param info print progress
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#' @inheritParams eucast_rules
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#' @param verbose print additional info: missing antibiotic columns per parameter
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#' @inheritSection eucast_rules Antibiotics
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#' @details Currently supported guidelines are (case-insensitive):
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#' \itemize{
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#' \item{\code{guideline = "CMI2012"}: 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) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})}
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#' \item{\code{guideline = "EUCAST"}: The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})}
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#' \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/tb/publications/pmdt_companionhandbook/en/}{link})}
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#' \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}
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@ -38,24 +39,26 @@
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#'
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#' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
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#' @return \itemize{
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#' \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensive drug-resistant}}
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#' \item{CMI 2012 paper - function \code{mdr_cmi2012()} or \code{mdro()}:\cr Ordered factor with levels \code{Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR)}}
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#' \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant}}
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#' \item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
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#' \item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < 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. molecular) tests}
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#' }
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#' @rdname mdro
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#' @importFrom dplyr %>%
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#' @importFrom crayon red blue bold
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#' @importFrom dplyr %>% filter_all
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#' @importFrom crayon blue bold italic
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @source
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#' EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
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#'
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#' World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (\href{https://www.who.int/tb/publications/pmdt_companionhandbook/en/}{link})
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#'
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#' Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
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#' Please see Details for the list of publications used for this function.
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#' @examples
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#' library(dplyr)
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#'
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#'
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#' example_isolates %>%
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#' mdro() %>%
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#' freq()
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#'
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#' \donttest{
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#' example_isolates %>%
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#' mutate(EUCAST = mdro(.),
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#' BRMO = brmo(.),
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@ -65,6 +68,7 @@
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#' rename(PIP = TZP) %>% # no piperacillin, so take piperacillin/tazobactam
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#' mrgn() %>% # check German guideline
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#' freq() # check frequencies
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#' }
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mdro <- function(x,
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guideline = NULL,
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col_mo = NULL,
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@ -86,7 +90,8 @@ mdro <- function(x,
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}
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if (is.null(guideline)) {
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guideline <- "eucast"
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# default to the paper by Magiorakos et al. (2012)
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guideline <- "cmi2012"
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}
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if (tolower(guideline) == "nl") {
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guideline <- "BRMO"
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@ -94,7 +99,7 @@ mdro <- function(x,
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if (tolower(guideline) == "de") {
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guideline <- "MRGN"
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}
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if (!tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb")) {
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if (!tolower(guideline) %in% c("brmo", "mrgn", "eucast", "tb", "cmi2012")) {
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stop("invalid guideline: ", guideline, call. = FALSE)
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}
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guideline <- list(code = tolower(guideline))
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@ -114,7 +119,13 @@ mdro <- function(x,
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stop("`col_mo` must be set.", call. = FALSE)
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}
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if (guideline$code == "eucast") {
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if (guideline$code == "cmi2012") {
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guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
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guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
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guideline$version <- "N/A"
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guideline$source <- "Magiorakos et al. (2012) Clinical Microbiology and Infection 18:3. DOI: 10.1111/j.1469-0691.2011.03570.x"
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} else if (guideline$code == "eucast") {
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guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Exceptional Phenotypes Tables\""
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guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
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guideline$version <- "3.1"
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@ -129,9 +140,10 @@ mdro <- function(x,
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# support per country:
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} else if (guideline$code == "mrgn") {
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guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
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guideline$author <- "J. M\u00fcller, A. Voss, R. K\u00f6ck, ..., W.V. Kern, C. Wendt, A.W. Friedrich"
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guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
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guideline$version <- "N/A"
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guideline$source <- "M\u00fcller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6"
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} else if (guideline$code == "brmo") {
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guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
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guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
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@ -141,16 +153,126 @@ mdro <- function(x,
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stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
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}
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if (info == TRUE) {
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cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
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"Guideline: ", red(guideline$name), "\n",
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"Version: ", red(guideline$version), "\n",
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"Author: ", red(guideline$author), "\n",
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"Source: ", blue(guideline$source), "\n",
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"\n", sep = "")
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}
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if (guideline$code == "tb") {
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if (guideline$code == "cmi2012") {
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cols_ab <- get_column_abx(x = x,
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soft_dependencies = c(
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# table 1 (S aureus):
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"GEN",
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"RIF",
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"CPT",
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"OXA",
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"CIP",
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"MFX",
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"SXT",
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"FUS",
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"VAN",
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"TEC",
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"TLV",
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"TGC",
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"CLI",
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"DAP",
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"ERY",
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"LNZ",
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"CHL",
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"FOS",
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"QDA",
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"TCY",
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"DOX",
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"MNO",
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# table 2 (Enterococcus)
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"GEH",
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"STH",
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"IPM",
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"MEM",
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"DOR",
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"CIP",
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"LVX",
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"MFX",
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"VAN",
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"TEC",
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"TGC",
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"DAP",
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"LNZ",
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"AMP",
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"QDA",
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"DOX",
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"MNO",
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# table 3 (Enterobacteriaceae)
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"GEN",
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"TOB",
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"AMK",
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"NET",
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"CPT",
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"TCC",
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"TZP",
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"ETP",
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"IPM",
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"MEM",
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"DOR",
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"CZO",
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"CXM",
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"CTX",
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"CAZ",
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"FEP",
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"FOX",
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"CTT",
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"CIP",
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"SXT",
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"TGC",
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"ATM",
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"AMP",
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"AMC",
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"SAM",
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"CHL",
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"FOS",
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"COL",
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"TCY",
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"DOX",
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"MNO",
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# table 4 (Pseudomonas)
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"GEN",
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"TOB",
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"AMK",
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"NET",
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"IPM",
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"MEM",
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"DOR",
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"CAZ",
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"FEP",
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"CIP",
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"LVX",
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"TCC",
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"TZP",
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"ATM",
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"FOS",
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"COL",
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"PLB",
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# table 5 (Acinetobacter)
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"GEN",
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"TOB",
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"AMK",
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"NET",
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"IPM",
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"MEM",
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"DOR",
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"CIP",
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"LVX",
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"TZP",
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"TCC",
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"CTX",
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"CRO",
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"CAZ",
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"FEP",
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"SXT",
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"SAM",
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"COL",
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"PLB",
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"TCY",
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"DOX",
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"MNO"
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),
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verbose = verbose, ...)
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} else if (guideline$code == "tb") {
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cols_ab <- get_column_abx(x = x,
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soft_dependencies = c("CAP",
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"ETH",
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@ -188,11 +310,14 @@ mdro <- function(x,
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CLI <- cols_ab["CLI"]
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CLR <- cols_ab["CLR"]
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COL <- cols_ab["COL"]
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CPT <- cols_ab["CPT"]
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CRO <- cols_ab["CRO"]
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CTT <- cols_ab["CTT"]
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CTX <- cols_ab["CTX"]
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CXM <- cols_ab["CXM"]
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CZO <- cols_ab["CZO"]
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DAP <- cols_ab["DAP"]
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DOR <- cols_ab["DOR"]
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DOX <- cols_ab["DOX"]
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ERY <- cols_ab["ERY"]
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ETP <- cols_ab["ETP"]
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@ -201,6 +326,7 @@ mdro <- function(x,
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FOS <- cols_ab["FOS"]
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FOX <- cols_ab["FOX"]
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FUS <- cols_ab["FUS"]
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GEH <- cols_ab["GEH"]
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GEN <- cols_ab["GEN"]
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IPM <- cols_ab["IPM"]
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KAN <- cols_ab["KAN"]
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@ -219,6 +345,7 @@ mdro <- function(x,
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NOR <- cols_ab["NOR"]
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NOV <- cols_ab["NOV"]
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OFX <- cols_ab["OFX"]
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OXA <- cols_ab["OXA"]
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PEN <- cols_ab["PEN"]
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PIP <- cols_ab["PIP"]
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PLB <- cols_ab["PLB"]
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@ -227,12 +354,16 @@ mdro <- function(x,
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RID <- cols_ab["RID"]
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RIF <- cols_ab["RIF"]
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RXT <- cols_ab["RXT"]
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SAM <- cols_ab["SAM"]
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SIS <- cols_ab["SIS"]
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STH <- cols_ab["STH"]
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SXT <- cols_ab["SXT"]
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TCC <- cols_ab["TCC"]
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TCY <- cols_ab["TCY"]
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TEC <- cols_ab["TEC"]
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TGC <- cols_ab["TGC"]
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TIC <- cols_ab["TIC"]
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TLV <- cols_ab["TLV"]
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TMP <- cols_ab["TMP"]
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TOB <- cols_ab["TOB"]
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TZP <- cols_ab["TZP"]
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@ -251,10 +382,22 @@ mdro <- function(x,
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if (guideline$code == "tb" & length(abx_tb) == 0) {
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stop("No antimycobacterials found in data set.", call. = FALSE)
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}
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if (info == TRUE) {
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cat("\nDetermining multidrug-resistant organisms (MDRO), according to:\n",
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bold("Guideline: "), italic(guideline$name), "\n",
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bold("Version: "), guideline$version, "\n",
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bold("Author: "), guideline$author, "\n",
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bold("Source: "), guideline$source, "\n",
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"\n", sep = "")
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}
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ab_missing <- function(ab) {
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isTRUE(ab %in% c(NULL, NA)) | length(ab) == 0
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}
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ab_NA <- function(x) {
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x[!is.na(x)]
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}
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# antibiotic classes
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aminoglycosides <- c(TOB, GEN)
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@ -280,16 +423,211 @@ mdro <- function(x,
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x[rows, "MDRO"] <<- to
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}
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}
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trans_tbl2 <- function(txt, rows, lst) {
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# function specific for the CMI paper of 2012 (Magiorakos et al.)
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lst_vector <- unlist(lst)[!is.na(unlist(lst))]
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x$total_groups <- NA_integer_
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x$affected_groups <- NA_integer_
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x[rows, "total_groups"] <- length(lst)
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# now the hard part - using two sapply()s for super fast results:
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# [1] run through all `rows` with sapply()
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# [2] within each row, run through all antibiotic groups with another sapply()
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# [3] determine for each antibiotic group in that row if at least 1 drug is R of I
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# [4] sum the number of TRUEs of this determination
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x[rows, "affected_groups"] <- sapply(rows,
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function(row, group_tbl = lst) {
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sum(sapply(group_tbl,
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function(group) {
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any(x[row, group[!is.na(group)]] == "R") |
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any(x[row, group[!is.na(group)]] == "I")
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}),
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na.rm = TRUE)
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})
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# now set MDROs:
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# MDR (=2): >=3 groups affected
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x[which(x$row_number %in% rows & x$affected_groups >= 3), "MDRO"] <<- 2
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# XDR (=3): all but <=2 groups affected
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x[which(x$row_number %in% rows & x$total_groups - x$affected_groups <= 2), "MDRO"] <<- 3
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# PDR (=4): all agents are R
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x[filter_at(x[rows, ],
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vars(lst_vector),
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all_vars(. %in% c("R", "I")))$row_number,
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"MDRO"] <<- 4
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}
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x <- x %>%
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mutate_at(vars(col_mo), as.mo) %>%
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# join to microorganisms data set
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left_join_microorganisms(by = col_mo) %>%
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# add unconfirmed to where genus is available
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mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_)) %>%
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mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
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row_number = 1:nrow(x)) %>%
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# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
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as.data.frame(stringsAsFactors = FALSE)
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if (guideline$code == "cmi2012") {
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# CMI, 2012 ---------------------------------------------------------------
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# Non-susceptible = R and I
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# (see header 'Approaches to Creating Definitions for MDR, XDR and PDR' in paper)
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# take amoxicillin if ampicillin is unavailable
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if (is.na(AMP) & !is.na(AMX)) AMP <- AMX
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# take ceftriaxone if cefotaxime is unavailable and vice versa
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if (is.na(CRO) & !is.na(CTX)) CRO <- CTX
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if (is.na(CTX) & !is.na(CRO)) CTX <- CRO
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# intrinsic resistant must not be considered for the determination of MDR,
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# so let's just remove them, meticulously following the paper
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x[which(x$genus == "Enterococcus" & x$species == "faecium"), ab_NA(IPM)] <- NA
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x[which(x$genus == "Enterococcus" & x$species == "faecalis"), ab_NA(QDA)] <- NA
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x[which((x$genus == "Providencia" & x$species == "rettgeri")
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| (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(c(GEN, TOB, NET))] <- NA
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x[which(x$genus == "Escherichia" & x$species == "hermannii"), ab_NA(c(TCC, TZP))] <- NA
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x[which((x$genus == "Citrobacter" & x$species == "freundii")
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| (x$genus == "Enterobacter" & x$species == "aerogenes")
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| (x$genus == "Enterobacter" & x$species == "cloacae")
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| (x$genus == "Hafnia" & x$species == "alvei")
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||||
| (x$genus == "Morganella" & x$species == "morganii")
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||||
| (x$genus == "Proteus" & x$species == "penneri")
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||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(CZO)] <- NA
|
||||
x[which((x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Proteus" & x$species == "penneri")
|
||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(CXM)] <- NA
|
||||
x[which((x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Proteus" & x$species == "mirabilis")
|
||||
| (x$genus == "Proteus" & x$species == "penneri")
|
||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(TGC)] <- NA
|
||||
x[which((x$genus == "Citrobacter" & x$species == "koseri")
|
||||
| (x$genus == "Citrobacter" & x$species == "freundii")
|
||||
| (x$genus == "Enterobacter" & x$species == "aerogenes")
|
||||
| (x$genus == "Enterobacter" & x$species == "cloacae")
|
||||
| (x$genus == "Escherichia" & x$species == "hermannii")
|
||||
| (x$genus == "Hafnia" & x$species == "alvei")
|
||||
| (x$genus == "Klebsiella")
|
||||
| (x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Proteus" & x$species == "penneri")
|
||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Providencia" & x$species == "stuartii")
|
||||
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMP)] <- NA
|
||||
x[which((x$genus == "Citrobacter" & x$species == "freundii")
|
||||
| (x$genus == "Enterobacter" & x$species == "aerogenes")
|
||||
| (x$genus == "Enterobacter" & x$species == "cloacae")
|
||||
| (x$genus == "Hafnia" & x$species == "alvei")
|
||||
| (x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Providencia" & x$species == "stuartii")
|
||||
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMC)] <- NA
|
||||
x[which((x$genus == "Citrobacter" & x$species == "freundii")
|
||||
| (x$genus == "Citrobacter" & x$species == "koseri")
|
||||
| (x$genus == "Enterobacter" & x$species == "aerogenes")
|
||||
| (x$genus == "Enterobacter" & x$species == "cloacae")
|
||||
| (x$genus == "Hafnia" & x$species == "alvei")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(SAM)] <- NA
|
||||
x[which((x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Proteus" & x$species == "mirabilis")
|
||||
| (x$genus == "Proteus" & x$species == "penneri")
|
||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Providencia" & x$species == "stuartii")
|
||||
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(COL)] <- NA
|
||||
x[which((x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Proteus" & x$species == "mirabilis")
|
||||
| (x$genus == "Proteus" & x$species == "penneri")
|
||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(TCY)] <- NA
|
||||
x[which((x$genus == "Morganella" & x$species == "morganii")
|
||||
| (x$genus == "Proteus" & x$species == "penneri")
|
||||
| (x$genus == "Proteus" & x$species == "vulgaris")
|
||||
| (x$genus == "Providencia" & x$species == "rettgeri")
|
||||
| (x$genus == "Providencia" & x$species == "stuartii")), ab_NA(c(DOX, MNO))] <- NA
|
||||
|
||||
# now add the MDR levels to the data
|
||||
trans_tbl(2,
|
||||
which(x$genus == "Staphylococcus" & x$species == "aureus"),
|
||||
c(OXA, FOX),
|
||||
"any")
|
||||
trans_tbl2(paste("Table 1 -", italic("S. aureus")),
|
||||
which(x$genus == "Staphylococcus" & x$species == "aureus"),
|
||||
list(GEN,
|
||||
RIF,
|
||||
CPT,
|
||||
c(OXA, FOX),
|
||||
c(CIP, MFX),
|
||||
SXT,
|
||||
FUS,
|
||||
c(VAN, TEC, TLV),
|
||||
TGC,
|
||||
CLI,
|
||||
DAP,
|
||||
ERY,
|
||||
LNZ,
|
||||
CHL,
|
||||
FOS,
|
||||
QDA,
|
||||
c(TCY, DOX, MNO)))
|
||||
trans_tbl2(paste("Table 2 -", italic("Enterococcus"), "spp"),
|
||||
which(x$genus == "Enterococcus"),
|
||||
list(GEH,
|
||||
STH,
|
||||
c(IPM, MEM, DOR),
|
||||
c(CIP, LVX, MFX),
|
||||
c(VAN, TEC),
|
||||
TGC,
|
||||
DAP,
|
||||
LNZ,
|
||||
AMP,
|
||||
QDA,
|
||||
c(DOX, MNO)))
|
||||
trans_tbl2(paste("Table 3 -", italic("Enterobacteriaceae")),
|
||||
which(x$family == "Enterobacteriaceae"),
|
||||
list(c(GEN, TOB, AMK, NET),
|
||||
CPT,
|
||||
c(TCC, TZP),
|
||||
c(ETP, IPM, MEM, DOR),
|
||||
CZO,
|
||||
CXM,
|
||||
c(CTX, CAZ, FEP),
|
||||
c(FOX, CTT),
|
||||
CIP,
|
||||
SXT,
|
||||
TGC,
|
||||
ATM,
|
||||
AMP,
|
||||
c(AMC, SAM),
|
||||
CHL,
|
||||
FOS,
|
||||
COL,
|
||||
c(TCY, DOX, MNO)))
|
||||
trans_tbl2(paste("Table 4 -", italic("Pseudomonas aeruginosa")),
|
||||
which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
|
||||
list(c(GEN, TOB, AMK, NET),
|
||||
c(IPM, MEM, DOR),
|
||||
c(CAZ, FEP),
|
||||
c(CIP, LVX),
|
||||
c(TCC, TZP),
|
||||
ATM,
|
||||
FOS,
|
||||
c(COL, PLB)))
|
||||
trans_tbl2(paste("Table 5 -", italic("Acinetobacter"), "spp"),
|
||||
which(x$genus == "Acinetobacter"),
|
||||
list(c(GEN, TOB, AMK, NET),
|
||||
c(IPM, MEM, DOR),
|
||||
c(CIP, LVX),
|
||||
c(TZP, TCC),
|
||||
c(CTX, CRO, CAZ, FEP),
|
||||
SXT,
|
||||
SAM,
|
||||
c(COL, PLB),
|
||||
c(TCY, DOX, MNO)))
|
||||
}
|
||||
|
||||
if (guideline$code == "eucast") {
|
||||
# EUCAST ------------------------------------------------------------------
|
||||
# Table 5
|
||||
@ -534,20 +872,32 @@ mdro <- function(x,
|
||||
second = ifelse(drug_is_R(CAP) | drug_is_R(KAN) | drug_is_R(AMK),
|
||||
TRUE, FALSE),
|
||||
xdr = ifelse(mdr & xdr & second, TRUE, FALSE)) %>%
|
||||
mutate(mdr_tb = case_when(xdr ~ 5,
|
||||
mutate(MDRO = case_when(xdr ~ 5,
|
||||
mdr ~ 4,
|
||||
poly ~ 3,
|
||||
mono ~ 2,
|
||||
TRUE ~ 1),
|
||||
# keep all real TB, make other species NA
|
||||
mdr_tb = ifelse(x$fullname == "Mycobacterium tuberculosis", mdr_tb, NA_real_))
|
||||
MDRO = ifelse(x$fullname == "Mycobacterium tuberculosis", MDRO, NA_real_))
|
||||
}
|
||||
|
||||
if (info == TRUE) {
|
||||
cat(bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " MDROs out of ", sum(!is.na(x$MDRO)),
|
||||
" possible cases (", percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO))), ")")))
|
||||
}
|
||||
|
||||
# return results
|
||||
if (guideline$code == "tb") {
|
||||
factor(x = x$mdr_tb,
|
||||
if (guideline$code == "cmi2012") {
|
||||
factor(x = x$MDRO,
|
||||
levels = 1:4,
|
||||
labels = c("Negative", "Multi-drug-resistant (MDR)",
|
||||
"Extensively drug-resistant (XDR)", "Pandrug-resistant (PDR)"),
|
||||
ordered = TRUE)
|
||||
} else if (guideline$code == "tb") {
|
||||
factor(x = x$MDRO,
|
||||
levels = 1:5,
|
||||
labels = c("Negative", "Mono-resistant", "Poly-resistant", "Multi-drug-resistant", "Extensive drug-resistant"),
|
||||
labels = c("Negative", "Mono-resistant", "Poly-resistant",
|
||||
"Multi-drug-resistant", "Extensively drug-resistant"),
|
||||
ordered = TRUE)
|
||||
} else if (guideline$code == "mrgn") {
|
||||
factor(x = x$MDRO,
|
||||
@ -580,6 +930,13 @@ mdr_tb <- function(x, guideline = "TB", ...) {
|
||||
mdro(x = x, guideline = "TB", ...)
|
||||
}
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
mdr_cmi2012 <- function(x, guideline = "CMI2012", ...) {
|
||||
mdro(x = x, guideline = "CMI2012", ...)
|
||||
}
|
||||
|
||||
|
||||
#' @rdname mdro
|
||||
#' @export
|
||||
eucast_exceptional_phenotypes <- function(x, guideline = "EUCAST", ...) {
|
||||
|
||||
Reference in New Issue
Block a user