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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Determine multidrug-resistant organisms (MDRO)
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
#' @param x table with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
#' @param country country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
#' @param info print progress
#' @inheritParams eucast_rules
#' @param verbose print additional info: missing antibiotic columns per parameter
#' @inheritSection eucast_rules Antibiotics
#' @details When \code{country} will be left blank, guidelines will be taken from 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}).
#' @return Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
#' @rdname mdro
#' @importFrom dplyr %>%
#' @importFrom crayon red blue bold
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' library(dplyr)
#'
#' septic_patients %>%
#' mutate(EUCAST = mdro(.),
#' BRMO = brmo(.))
mdro <- function(x,
country = NULL,
col_mo = NULL,
info = TRUE,
verbose = FALSE,
...) {
tbl_ <- x
if (!is.data.frame(tbl_)) {
stop("`x` must be a data frame.", call. = FALSE)
}
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(tbl = tbl_, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
if (length(country) > 1) {
stop('`country` must be a length one character string.', call. = FALSE)
}
if (is.null(country)) {
country <- 'EUCAST'
}
country <- trimws(country)
if (tolower(country) != 'eucast' & !country %like% '^[a-z]{2}$') {
stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?mdro.', call. = FALSE)
}
# create list and make country code case-independent
guideline <- list(country = list(code = tolower(country)))
if (guideline$country$code == 'eucast') {
guideline$country$name <- '(European guidelines)'
guideline$name <- 'EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables"'
guideline$version <- 'Version 3.1'
guideline$source <- 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'
# support per country:
} else if (guideline$country$code == 'de') {
guideline$country$name <- 'Germany'
guideline$name <- ''
guideline$version <- ''
guideline$source <- ''
} else if (guideline$country$code == 'nl') {
guideline$country$name <- 'The Netherlands'
guideline$name <- 'WIP-Richtlijn BRMO'
guideline$version <- 'Revision as of December 2017'
guideline$source <- 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'
# add here more countries like this:
# } else if (country$code == 'xx') {
# country$name <- 'country name'
} else {
stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
}
if (info == TRUE) {
cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
"Guideline: ", red(paste0(guideline$name, ", ", guideline$version, "\n")),
"Country : ", red(paste0(guideline$country$name, "\n")),
"Source : ", blue(paste0(guideline$source, "\n")),
"\n", sep = "")
}
cols_ab <- get_column_abx(x = x, verbose = verbose)
AMC <- cols_ab['AMC']
AMK <- cols_ab['AMK']
AMP <- cols_ab['AMP']
AMX <- cols_ab['AMX']
ATM <- cols_ab['ATM']
AZL <- cols_ab['AZL']
AZM <- cols_ab['AZM']
CAZ <- cols_ab['CAZ']
CED <- cols_ab['CED']
CHL <- cols_ab['CHL']
CIP <- cols_ab['CIP']
CLI <- cols_ab['CLI']
CLR <- cols_ab['CLR']
COL <- cols_ab['COL']
CRO <- cols_ab['CRO']
CTX <- cols_ab['CTX']
CXM <- cols_ab['CXM']
CZO <- cols_ab['CZO']
DAP <- cols_ab['DAP']
DOX <- cols_ab['DOX']
ERY <- cols_ab['ERY']
ETP <- cols_ab['ETP']
FEP <- cols_ab['FEP']
FLC <- cols_ab['FLC']
FOS <- cols_ab['FOS']
FOX <- cols_ab['FOX']
FUS <- cols_ab['FUS']
GEN <- cols_ab['GEN']
IPM <- cols_ab['IPM']
KAN <- cols_ab['KAN']
LIN <- cols_ab['LIN']
LNZ <- cols_ab['LNZ']
LVX <- cols_ab['LVX']
MEM <- cols_ab['MEM']
MEZ <- cols_ab['MEZ']
MTR <- cols_ab['MTR']
MFX <- cols_ab['MFX']
MNO <- cols_ab['MNO']
NAL <- cols_ab['NAL']
NEO <- cols_ab['NEO']
NET <- cols_ab['NET']
NIT <- cols_ab['NIT']
NOR <- cols_ab['NOR']
NOV <- cols_ab['NOV']
OFX <- cols_ab['OFX']
PEN <- cols_ab['PEN']
PIP <- cols_ab['PIP']
PLB <- cols_ab['PLB']
PRI <- cols_ab['PRI']
QDA <- cols_ab['QDA']
RID <- cols_ab['RID']
RIF <- cols_ab['RIF']
RXT <- cols_ab['RXT']
SIS <- cols_ab['SIS']
SXT <- cols_ab['SXT']
TCY <- cols_ab['TCY']
TEC <- cols_ab['TEC']
TGC <- cols_ab['TGC']
TIC <- cols_ab['TIC']
TMP <- cols_ab['TMP']
TOB <- cols_ab['TOB']
TZP <- cols_ab['TZP']
VAN <- cols_ab['VAN']
ab_missing <- function(ab) {
isTRUE(ab %in% c(NULL, NA)) | length(ab) == 0
}
# antibiotic classes
aminoglycosides <- c(TOB, GEN)
cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
cephalosporins_3rd <- c(CTX, CRO, CAZ)
carbapenems <- c(ETP, IPM, MEM)
fluoroquinolones <- c(OFX, CIP, LVX, MFX)
# helper function for editing the table
trans_tbl <- function(to, rows, cols, any_all) {
cols <- cols[!ab_missing(cols)]
cols <- cols[!is.na(cols)]
if (length(rows) > 0 & length(cols) > 0) {
if (any_all == "any") {
col_filter <- which(tbl_[, cols] == 'R')
} else if (any_all == "all") {
col_filter <- tbl_ %>%
mutate(index = 1:nrow(.)) %>%
filter_at(vars(cols), all_vars(. == "R")) %>%
pull((index))
}
rows <- rows[rows %in% col_filter]
tbl_[rows, 'MDRO'] <<- to
}
}
tbl_ <- tbl_ %>%
mutate_at(vars(col_mo), as.mo) %>%
# 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_))
if (guideline$country$code == 'eucast') {
# EUCAST ------------------------------------------------------------------
# Table 5
trans_tbl(3,
which(tbl_$family == 'Enterobacteriaceae'
| tbl_$fullname %like% '^Pseudomonas aeruginosa'
| tbl_$genus == 'Acinetobacter'),
COL,
"all")
trans_tbl(3,
which(tbl_$fullname %like% '^Salmonella Typhi'),
c(carbapenems, fluoroquinolones),
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Haemophilus influenzae'),
c(cephalosporins_3rd, carbapenems, fluoroquinolones),
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Moraxella catarrhalis'),
c(cephalosporins_3rd, fluoroquinolones),
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Neisseria meningitidis'),
c(cephalosporins_3rd, fluoroquinolones),
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Neisseria gonorrhoeae'),
AZM,
"any")
# Table 6
trans_tbl(3,
which(tbl_$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
c(VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
which(tbl_$genus == 'Corynebacterium'),
c(VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Streptococcus pneumoniae'),
c(carbapenems, VAN, TEC, DAP, LNZ, QDA, TGC, RIF),
"any")
trans_tbl(3, # Sr. groups A/B/C/G
which(tbl_$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
c(PEN, cephalosporins, VAN, TEC, DAP, LNZ, QDA, TGC),
"any")
trans_tbl(3,
which(tbl_$genus == 'Enterococcus'),
c(DAP, LNZ, TGC, TEC),
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Enterococcus faecalis'),
c(AMP, AMX),
"any")
# Table 7
trans_tbl(3,
which(tbl_$genus == 'Bacteroides'),
MTR,
"any")
trans_tbl(3,
which(tbl_$fullname %like% '^Clostridium difficile'),
c( MTR, VAN),
"any")
}
if (guideline$country$code == 'de') {
# Germany -----------------------------------------------------------------
stop("We are still working on German guidelines in this beta version.", call. = FALSE)
}
if (guideline$country$code == 'nl') {
# Netherlands -------------------------------------------------------------
aminoglycosides <- aminoglycosides[!ab_missing(aminoglycosides)]
fluoroquinolones <- fluoroquinolones[!ab_missing(fluoroquinolones)]
carbapenems <- carbapenems[!ab_missing(carbapenems)]
# Table 1
trans_tbl(3,
which(tbl_$family == 'Enterobacteriaceae'),
c(aminoglycosides, fluoroquinolones),
"all")
trans_tbl(2,
which(tbl_$family == 'Enterobacteriaceae'),
c(carbapenems),
"any")
# Table 2
trans_tbl(2,
which(tbl_$genus == 'Acinetobacter'),
c(carbapenems),
"any")
trans_tbl(3,
which(tbl_$genus == 'Acinetobacter'),
c(aminoglycosides, fluoroquinolones),
"all")
trans_tbl(3,
which(tbl_$fullname %like% '^Stenotrophomonas maltophilia'),
SXT,
"all")
if (!ab_missing(MEM) & !ab_missing(IPM)
& !ab_missing(GEN) & !ab_missing(TOB)
& !ab_missing(CIP)
& !ab_missing(CAZ)
& !ab_missing(TZP) ) {
tbl_$psae <- 0
tbl_[which(tbl_[, MEM] == "R" | tbl_[, IPM] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, MEM] == "R" | tbl_[, IPM] == "R"), "psae"]
tbl_[which(tbl_[, GEN] == "R" & tbl_[, TOB] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, GEN] == "R" & tbl_[, TOB] == "R"), "psae"]
tbl_[which(tbl_[, CIP] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, CIP] == "R"), "psae"]
tbl_[which(tbl_[, CAZ] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, CAZ] == "R"), "psae"]
tbl_[which(tbl_[, TZP] == "R"), "psae"] <- 1 + tbl_[which(tbl_[, TZP] == "R"), "psae"]
} else {
tbl_$psae <- 0
}
tbl_[which(
tbl_$fullname %like% 'Pseudomonas aeruginosa'
& tbl_$psae >= 3
), 'MDRO'] <- 3
# Table 3
trans_tbl(3,
which(tbl_$fullname %like% 'Streptococcus pneumoniae'),
PEN,
"all")
trans_tbl(3,
which(tbl_$fullname %like% 'Streptococcus pneumoniae'),
VAN,
"all")
trans_tbl(3,
which(tbl_$fullname %like% 'Enterococcus faecium'),
c(PEN, VAN),
"all")
}
factor(x = tbl_$MDRO,
levels = 1:3,
labels = c('Negative', 'Positive, unconfirmed', 'Positive'),
ordered = TRUE)
}
#' @rdname mdro
#' @export
brmo <- function(..., country = "nl") {
mdro(..., country = "nl")
}
#' @rdname mdro
#' @export
mrgn <- function(x, country = "de", ...) {
mdro(x = x, country = "de", ...)
}
#' @rdname mdro
#' @export
eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
mdro(x = x, country = "EUCAST", ...)
}
# is_ESBL <- function(x, col_mo = NULL, ...) {
# get_ab_col <- function(columns, ab) {
# columns[names(columns) == ab]
# }
# col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
# cols_ab <- get_column_abx(tbl = x,
# soft_dependencies = c("AMX", "AMP"),
# hard_dependencies = c("CAZ"),
# ...)
#
# if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
# # both ampicillin and amoxicillin are missing
# generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
# return(rep(NA, nrow(x)))
# }
#
# ESBLs <- rep(NA, nrow(x))
#
# # first make all eligible cases FALSE
# ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
# & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
# )] <- FALSE
# # now make the positives cases TRUE
# ESBLs[which(!is.na(ESBLs)
# & x[, get_ab_col(cols_ab, "AMX")] == "R"
# & x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
# ESBLs
#
# }
#
# is_3MRGN <- function(x, ...) {
#
# }
#
# is_4MRGN <- function(x, ...) {
#
# }
get_column_mo <- function(tbl, col_mo = NULL) {
# throws a blue note about which column will be used if guessed
if (is.null(col_mo)) {
col_mo <- search_type_in_df(tbl = tbl, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
col_mo
}
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