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(v0.7.1.9096) German guideline for mdro()

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dr. M.S. (Matthijs) Berends
2019-10-07 14:32:06 +02:00
parent 1e260d85c8
commit 4e9c4c1b4e
22 changed files with 514 additions and 410 deletions
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2
R/eucast_rules.R
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@ -41,7 +41,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' @section Antibiotics:
#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
#'
#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{ATC code})', sorted by name:
#'
#' \strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
#' \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),

102
R/mdro.R
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@ -28,18 +28,20 @@
#' @inheritParams eucast_rules
#' @param verbose print additional info: missing antibiotic columns per parameter
#' @inheritSection eucast_rules Antibiotics
#' @details Currently supported guidelines are:
#' @details Currently supported guidelines are (case-insensitive):
#' \itemize{
#' \item{\code{guideline = "EUCAST"}: 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})}
#' \item{\code{guideline = "TB"}: 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})}
#' \item{\code{guideline = "MRGN"}: (work in progress)}
#' \item{\code{guideline = "BRMO"}: 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})}
#' \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})}
#' \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})}
#' \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"}: The Dutch national guideline - 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})}
#' }
#'
#' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
#' @return For TB (\code{mdr_tb()}): Ordered factor with levels \code{Negative < Mono-resistance < Poly-resistance < Multidrug resistance < Extensive drug resistance}.
#'
#' For everything else: 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.
#' @return \itemize{
#' \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}}
#' \item{German guideline - function \code{mrgn()} or \code{mdro(..., guideline = "MRGN")}:\cr Ordered factor with levels \code{Negative < 3MRGN < 4MRGN}}
#' \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}
#' }
#' @rdname mdro
#' @importFrom dplyr %>%
#' @importFrom crayon red blue bold
@ -56,7 +58,13 @@
#'
#' example_isolates %>%
#' mutate(EUCAST = mdro(.),
#' BRMO = brmo(.))
#' BRMO = brmo(.),
#' MRGN = mrgn(.))
#'
#' example_isolates %>%
#' rename(PIP = TZP) # no piperacillin, so take piperacillin/tazobactam
#' mrgn() %>% # check German guideline
#' freq() # check frequencies
mdro <- function(x,
guideline = NULL,
col_mo = NULL,
@ -120,10 +128,10 @@ mdro <- function(x,
# support per country:
} else if (guideline$code == "mrgn") {
guideline$name <- "Germany"
guideline$name <- ""
guideline$version <- ""
guideline$source <- ""
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
guideline$author <- "J. M\u00fcller, A. Voss, R. K\u00f6ck, ..., W.V. Kern, C. Wendt, A.W. Friedrich"
guideline$version <- "N/A"
guideline$source <- "M\u00fcller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6"
} else if (guideline$code == "brmo") {
guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
@ -153,6 +161,15 @@ mdro <- function(x,
"RIB",
"RFP"),
verbose = verbose, ...)
} else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("PIP",
"CTX",
"CAZ",
"IPM",
"MEM",
"CIP"),
verbose = verbose, ...)
} else {
cols_ab <- get_column_abx(x = x, verbose = verbose, ...)
}
@ -269,7 +286,9 @@ mdro <- function(x,
# join to microorganisms data set
left_join_microorganisms(by = col_mo) %>%
# add unconfirmed to where genus is available
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_))
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_)) %>%
# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
as.data.frame(stringsAsFactors = FALSE)
if (guideline$code == "eucast") {
# EUCAST ------------------------------------------------------------------
@ -302,7 +321,7 @@ mdro <- function(x,
"any")
# Table 6
trans_tbl(3,
which(x$fullname %like% "^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)"),
which(x$fullname %like% "^(Coagulase-negative|Staphylococcus (aureus|epidermidis|hominis|haemolyticus|intermedius|pseudointermedius))"),
c(VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
@ -314,7 +333,7 @@ mdro <- function(x,
c(carbapenems, VAN, TEC, DAP, LNZ, QDA, TGC, RIF),
"any")
trans_tbl(3, # Sr. groups A/B/C/G
which(x$fullname %like% "^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)"),
which(x$fullname %like% "^Streptococcus (group (A|B|C|G)|pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)"),
c(PEN, cephalosporins, VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
@ -338,7 +357,51 @@ mdro <- function(x,
if (guideline$code == "mrgn") {
# Germany -----------------------------------------------------------------
stop("We are still working on German guidelines in this beta version.", call. = FALSE)
CTX_or_CAZ <- CTX %or% CAZ
IPM_or_MEM <- IPM %or% MEM
x$missing <- NA_character_
if (is.na(PIP)) PIP <- "missing"
if (is.na(CTX_or_CAZ)) CTX_or_CAZ <- "missing"
if (is.na(IPM_or_MEM)) IPM_or_MEM <- "missing"
if (is.na(IPM)) IPM <- "missing"
if (is.na(MEM)) MEM <- "missing"
if (is.na(CIP)) CIP <- "missing"
# Table 1
x[which((x$family == "Enterobacteriaceae" |
x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
x[, IPM_or_MEM] == "S" &
x[, CIP] == "R"),
"MDRO"] <- 2 # 2 = 3MRGN
x[which((x$family == "Enterobacteriaceae" |
x$fullname %like% "^Acinetobacter baumannii") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
x[, IPM_or_MEM] == "R" &
x[, CIP] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, overwrites 3MRGN if applicable
x[which((x$family == "Enterobacteriaceae" |
x$fullname %like% "^Acinetobacter baumannii") &
x[, IPM] == "R" | x[, MEM] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN, always when imipenem or meropenem is R
x[which(x$fullname %like% "^Pseudomonas aeruginosa" &
(x[, PIP] == "S") +
(x[, CTX_or_CAZ] == "S") +
(x[, IPM_or_MEM] == "S") +
(x[, CIP] == "S") == 1),
"MDRO"] <- 2 # 2 = 3MRGN, if only 1 group is S
x[which((x$fullname %like% "^Pseudomonas aeruginosa") &
x[, PIP] == "R" &
x[, CTX_or_CAZ] == "R" &
x[, IPM_or_MEM] == "R" &
x[, CIP] == "R"),
"MDRO"] <- 3 # 3 = 4MRGN
}
if (guideline$code == "brmo") {
@ -486,6 +549,11 @@ mdro <- function(x,
levels = 1:5,
labels = c("Negative", "Mono-resistant", "Poly-resistant", "Multi-drug-resistant", "Extensive drug-resistant"),
ordered = TRUE)
} else if (guideline$code == "mrgn") {
factor(x = x$MDRO,
levels = 1:3,
labels = c("Negative", "3MRGN", "4MRGN"),
ordered = TRUE)
} else {
factor(x = x$MDRO,
levels = 1:3,