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support for Dutch national MDR guideline
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R/mdro.R
217
R/mdro.R
@ -29,7 +29,7 @@
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#' Determine Multidrug-Resistant Organisms (MDRO)
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#'
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#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
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#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
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#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank for automatic determination.
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#' @param guideline a specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
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#' @param ... in case of [custom_mdro_guideline()]: a set of rules, see section *Using Custom Guidelines* below. Otherwise: column name of an antibiotic, see section *Antibiotics* below.
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@ -76,9 +76,15 @@
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#'
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#' * `guideline = "BRMO"`
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#'
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#' The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" ([link](https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh))
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#' The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" ([link](https://www.sri-richtlijnen.nl/brmo))
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#'
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#' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
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#' Also:
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#'
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#' * `guideline = "BRMO 2017"`
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#'
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#' The former Dutch national guideline - Werkgroep Infectiepreventie (WIP), RIVM, last revision as of 2017: "Bijzonder Resistente Micro-Organismen (BRMO)"
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#'
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#' Please suggest to implement guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
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#'
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#' @section Using Custom Guidelines:
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#'
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@ -333,7 +339,7 @@ mdro <- function(x = NULL,
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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 <- NA
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guideline$version <- NA_character_
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guideline$source_url <- paste0("Clinical Microbiology and Infection 18:3, 2012; ", font_url("https://doi.org/10.1111/j.1469-0691.2011.03570.x", "doi: 10.1111/j.1469-0691.2011.03570.x"))
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guideline$type <- "MDRs/XDRs/PDRs"
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} else if (guideline$code == "eucast3.1") {
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@ -365,14 +371,21 @@ mdro <- function(x = NULL,
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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$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
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guideline$version <- NA
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guideline$version <- NA_character_
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guideline$source_url <- paste0("Antimicrobial Resistance and Infection Control 4:7, 2015; ", font_url("https://doi.org/10.1186/s13756-015-0047-6", "doi: 10.1186/s13756-015-0047-6"))
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guideline$type <- "MRGNs"
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} else if (guideline$code == "brmo") {
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combine_SI <- TRUE # I must not be considered resistant
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guideline$name <- "Bijzonder Resistente Micro-organismen (BRMO)"
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guideline$author <- "Samenwerkingsverband Richtlijnen Infectiepreventie (SRI)"
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guideline$version <- "November 2024"
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guideline$source_url <- font_url("https://www.sri-richtlijnen.nl/brmo", "Direct link")
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guideline$type <- "BRMOs"
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} else if (guideline$code == "brmo2017") {
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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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guideline$version <- "Revision as of December 2017"
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guideline$source_url <- font_url("https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH", "Direct download")
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guideline$version <- "Last revision (December 2017) - since 2024 superseded by SRI guideline"
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guideline$source_url <- NA_character_
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guideline$type <- "BRMOs"
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} else {
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stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
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@ -429,6 +442,17 @@ mdro <- function(x = NULL,
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fn = "mdro",
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...
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)
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} else if (guideline$code == "brmo") {
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# Dutch 2024 guideline
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cols_ab <- get_column_abx(
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x = x,
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soft_dependencies = c("SXT", "GEN", "TOB", "AMK", "IPM", "MEM", "CIP", "LVX", "NOR", "PIP", "CAZ", "VAN", "PEN", "AMX", "AMP", "FLC", "OXA", "FOX", "FOX1"),
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verbose = verbose,
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info = info,
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only_sir_columns = only_sir_columns,
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fn = "mdro",
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...
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)
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} else if (guideline$code == "mrgn") {
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cols_ab <- get_column_abx(
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x = x,
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@ -524,6 +548,7 @@ mdro <- function(x = NULL,
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FLE <- cols_ab["FLE"]
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FOS <- cols_ab["FOS"]
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FOX <- cols_ab["FOX"]
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FOX1 <- cols_ab["FOX1"]
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FUS <- cols_ab["FUS"]
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GAT <- cols_ab["GAT"]
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GEH <- cols_ab["GEH"]
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@ -651,7 +676,7 @@ mdro <- function(x = NULL,
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# nolint end
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# helper function for editing the table
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trans_tbl <- function(to, rows, cols, any_all) {
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trans_tbl <- function(to, rows, cols, any_all, reason = NULL) {
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cols <- cols[!ab_missing(cols)]
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 && length(cols) > 0) {
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@ -696,14 +721,18 @@ mdro <- function(x = NULL,
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)
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rows_affected <- x[which(rows_affected), "row_number", drop = TRUE]
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rows_to_change <- rows[rows %in% rows_affected]
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x[rows_to_change, "MDRO"] <<- to
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x[rows_to_change, "reason"] <<- paste0(
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any_all,
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rows_not_to_change <- rows[!rows %in% c(rows_affected, rows_to_change)]
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rows_not_to_change <- rows_not_to_change[is.na(x[rows_not_to_change, "reason"])]
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if (is.null(reason)) {
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reason <- paste0(any_all,
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" of the required antibiotics ",
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ifelse(any_all == "any", "is", "are"),
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" R",
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ifelse(!isTRUE(combine_SI), " or I", "")
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)
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ifelse(!isTRUE(combine_SI), " or I", ""))
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}
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x[rows_to_change, "MDRO"] <<- to
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x[rows_to_change, "reason"] <<- reason
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x[rows_not_to_change, "reason"] <<- "guideline criteria not met"
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}
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}
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@ -784,7 +813,7 @@ mdro <- function(x = NULL,
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x <- left_join_microorganisms(x, by = col_mo)
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x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
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x$row_number <- seq_len(nrow(x))
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x$reason <- paste0("not covered by ", toupper(guideline$code), " guideline")
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x$reason <- NA_character_
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x$columns_nonsusceptible <- ""
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if (guideline$code == "cmi2012") {
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@ -1402,7 +1431,147 @@ mdro <- function(x = NULL,
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}
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if (guideline$code == "brmo") {
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# Netherlands -------------------------------------------------------------
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# Netherlands 2024 --------------------------------------------------------
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aminoglycosides <- c(GEN, TOB, AMK) # note 4: gentamicin or tobramycin or amikacin
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aminoglycosides_serratia_marcescens <- GEN # note 4: TOB and AMK do not count towards S. marcescens
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fluoroquinolones <- c(CIP, NOR, LVX) # note 5: ciprofloxacin or norfloxacin or levofloxacin
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carbapenems <- carbapenems[!is.na(carbapenems)]
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carbapenems_without_imipenem <- carbapenems[carbapenems != IPM]
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amino <- AMX %or% AMP
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third <- CAZ %or% CTX
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ESBLs <- c(amino, third)
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ESBLs <- ESBLs[!is.na(ESBLs)]
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if (length(ESBLs) != 2) {
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ESBLs <- character(0)
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}
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# Enterobacterales
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if (length(ESBLs) > 0) {
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trans_tbl(
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2, # positive, unconfirmed
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which(x$order == "Enterobacterales" & x[[ESBLs[1]]] == "R" & x[[ESBLs[2]]] == "R"),
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c(AMX %or% AMP, cephalosporins_3rd),
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"all",
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reason = "Enterobacterales: ESBL"
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)
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}
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trans_tbl(
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3, # positive
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which(x$order == "Enterobacterales" & (x$genus %in% c("Proteus", "Providencia") | paste(x$genus, x$species) %in% c("Serratia marcescens", "Morganella morganii"))),
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carbapenems_without_imipenem,
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"any",
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reason = "Enterobacterales: carbapenem or carbapenemase"
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)
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trans_tbl(
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3,
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which(x$order == "Enterobacterales" & !(x$genus %in% c("Proteus", "Providencia") | paste(x$genus, x$species) %in% c("Serratia marcescens", "Morganella morganii"))),
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carbapenems,
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"any",
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reason = "Enterobacterales: carbapenem or carbapenemase"
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)
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trans_tbl(
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3,
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which(x[[SXT]] == "R" &
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(x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
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(x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
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(x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
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c(SXT, aminoglycosides, fluoroquinolones),
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"any",
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reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"
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)
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trans_tbl(
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3,
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which(x[[SXT]] == "R" &
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x[[GEN]] == "R" &
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(x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
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paste(x$genus, x$species) == "Serratia marcescens"),
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c(SXT, aminoglycosides_serratia_marcescens, fluoroquinolones),
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"any",
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reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"
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)
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# Acinetobacter baumannii-calcoaceticus complex
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trans_tbl(
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3,
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which((x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
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(x[[CIP]] == "R" | x[[LVX]] == "R") &
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x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"]),
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c(aminoglycosides, CIP, LVX),
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"any",
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reason = "A. baumannii-calcoaceticus complex: aminoglycoside + ciprofloxacin or levofloxacin"
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)
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trans_tbl(
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2, # unconfirmed
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which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"]),
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carbapenems,
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"any",
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reason = "A. baumannii-calcoaceticus complex: carbapenemase"
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)
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# Pseudomonas aeruginosa
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if (ab_missing(PIP) && !ab_missing(TZP)) {
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# take pip/tazo if just pip is not available - many labs only test for pip/tazo because of availability on a Vitek card
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PIP <- TZP
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}
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if (!ab_missing(MEM) && !ab_missing(IPM) &&
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!ab_missing(GEN) && !ab_missing(TOB) &&
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!ab_missing(CIP) &&
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!ab_missing(CAZ) &&
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!ab_missing(PIP)) {
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x$psae <- 0
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x[which(x[, MEM, drop = TRUE] == "R" | x[, IPM, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, MEM, drop = TRUE] == "R" | x[, IPM, drop = TRUE] == "R"), "psae"]
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x[which(x[, GEN, drop = TRUE] == "R" & x[, TOB, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, GEN, drop = TRUE] == "R" & x[, TOB, drop = TRUE] == "R"), "psae"]
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x[which(x[, CIP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CIP, drop = TRUE] == "R"), "psae"]
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x[which(x[, CAZ, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, CAZ, drop = TRUE] == "R"), "psae"]
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x[which(x[, PIP, drop = TRUE] == "R"), "psae"] <- 1 + x[which(x[, PIP, drop = TRUE] == "R"), "psae"]
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} else {
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x$psae <- 0
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}
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trans_tbl(
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3,
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which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
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c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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"all", # this will set all negatives to "guideline criteria not met" instead of "not covered by guideline"
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reason = "P. aeruginosa: at least 3 classes contain R"
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)
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trans_tbl(
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3,
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which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3),
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c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
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"any", # this is the actual one, changing the ones with x$psae >= 3
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reason = "P. aeruginosa: at least 3 classes contain R"
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)
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# Enterococcus faecium
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trans_tbl(
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3,
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which(x$genus == "Enterococcus" & x$species == "faecium"),
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c(PEN %or% AMX %or% AMP, VAN),
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"all",
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reason = "E. faecium: vancomycin or vanA/vanB gene + penicillin group"
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)
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# Staphylococcus aureus
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trans_tbl(
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2,
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which(x$genus == "Staphylococcus" & x$species == "aureus"),
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c(PEN, AMX, AMP, FLC, OXA, FOX, FOX1),
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"any",
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reason = "S. aureus: MRSA"
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)
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# Candida auris
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trans_tbl(
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3,
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which(x$genus == "Candida" & x$species == "auris"),
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character(0),
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"any",
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reason = "C. auris: regardless of resistance"
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)
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}
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if (guideline$code == "brmo2017") {
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# Netherlands 2017 --------------------------------------------------------
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aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
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fluoroquinolones <- fluoroquinolones[!is.na(fluoroquinolones)]
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carbapenems <- carbapenems[!is.na(carbapenems)]
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@ -1477,10 +1646,7 @@ mdro <- function(x = NULL,
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c(CAZ, CIP, GEN, IPM, MEM, TOB, TZP),
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"any"
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)
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x[which(
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x$genus == "Pseudomonas" & x$species == "aeruginosa" &
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x$psae >= 3
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), "reason"] <- paste0("at least 3 classes contain R", ifelse(!isTRUE(combine_SI), " or I", ""))
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x[which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3), "reason"] <- paste0("at least 3 classes contain R", ifelse(!isTRUE(combine_SI), " or I", ""))
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# Table 3
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trans_tbl(
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@ -1580,7 +1746,7 @@ mdro <- function(x = NULL,
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" (3 required for MDR)"
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)
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} else {
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x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
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#x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
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}
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}
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@ -1610,12 +1776,14 @@ mdro <- function(x = NULL,
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if (isTRUE(info.bak)) {
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cat(font_italic(paste0(" (", length(rows_empty), " isolates had no test results)\n")))
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}
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x[rows_empty, "MDRO"] <- NA
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x[rows_empty, "reason"] <- "none of the antibiotics have test results"
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} else if (isTRUE(info.bak)) {
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cat("\n")
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}
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if (isTRUE(info.bak) && !isTRUE(verbose)) {
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cat("\nRerun with 'verbose = TRUE' to retrieve detailed info and reasons for every MDRO classification.\n")
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}
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# Results ----
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if (guideline$code == "cmi2012") {
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if (any(x$MDRO == -1, na.rm = TRUE)) {
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@ -1663,7 +1831,12 @@ mdro <- function(x = NULL,
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)
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}
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if (isTRUE(verbose)) {
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# fill in empty reasons
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x$reason[is.na(x$reason)] <- "not covered by guideline"
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x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)")
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# format data set
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colnames(x)[colnames(x) == col_mo] <- "microorganism"
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x$microorganism <- mo_name(x$microorganism, language = NULL)
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x[, c(
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13
man/mdro.Rd
13
man/mdro.Rd
@ -77,7 +77,7 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed}
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}
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}
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\description{
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Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
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Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
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}
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\details{
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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}.
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@ -111,10 +111,17 @@ The international guideline for multi-drug resistant tuberculosis - World Health
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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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\item \code{guideline = "BRMO"}
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The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (\href{https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh}{link})
|
||||
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)"
|
||||
}
|
||||
}
|
||||
|
||||
Please suggest your own (country-specific) guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}.
|
||||
Please suggest to implement guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}.
|
||||
}
|
||||
|
||||
\section{Using Custom Guidelines}{
|
||||
|
||||
Loading…
Reference in New Issue
Block a user