AMR/R/mdro.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Determine multidrug-resistant organisms (MDRO)
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @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
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#' @inheritParams EUCAST_rules
#' @param metr column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
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#' @param ... parameters that are passed on to methods
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#' @inheritSection EUCAST_rules Antibiotics
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#' @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" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
#' @return Ordered factor with levels \code{Unknown < Negative < Unconfirmed < Positive}.
#' @rdname MDRO
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#' @importFrom dplyr %>%
#' @importFrom crayon red blue
#' @export
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#' @examples
#' library(dplyr)
#'
#' septic_patients %>%
#' mutate(EUCAST = MDRO(.),
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#' BRMO = BRMO(.))
MDRO <- function(tbl,
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country = NULL,
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col_mo = NULL,
info = TRUE,
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amcl = 'amcl',
amik = 'amik',
amox = 'amox',
ampi = 'ampi',
azit = 'azit',
aztr = 'aztr',
cefa = 'cefa',
cfra = 'cfra',
cfep = 'cfep',
cfot = 'cfot',
cfox = 'cfox',
cfta = 'cfta',
cftr = 'cftr',
cfur = 'cfur',
chlo = 'chlo',
cipr = 'cipr',
clar = 'clar',
clin = 'clin',
clox = 'clox',
coli = 'coli',
czol = 'czol',
dapt = 'dapt',
doxy = 'doxy',
erta = 'erta',
eryt = 'eryt',
fosf = 'fosf',
fusi = 'fusi',
gent = 'gent',
imip = 'imip',
kana = 'kana',
levo = 'levo',
linc = 'linc',
line = 'line',
mero = 'mero',
metr = 'metr',
mino = 'mino',
moxi = 'moxi',
nali = 'nali',
neom = 'neom',
neti = 'neti',
nitr = 'nitr',
novo = 'novo',
norf = 'norf',
oflo = 'oflo',
peni = 'peni',
pita = 'pita',
poly = 'poly',
qida = 'qida',
rifa = 'rifa',
roxi = 'roxi',
siso = 'siso',
teic = 'teic',
tetr = 'tetr',
tica = 'tica',
tige = 'tige',
tobr = 'tobr',
trim = 'trim',
trsu = 'trsu',
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vanc = 'vanc',
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col_bactid = NULL) {
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if (!is.data.frame(tbl)) {
stop("`tbl` must be a data frame.", call. = FALSE)
}
# try to find columns based on type
# -- mo
if (!is.null(col_bactid)) {
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col_mo <- col_bactid
warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
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} else if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"]
message("NOTE: Using column `", col_mo, "` as input for `col_mo`.")
} else if (!col_mo %in% colnames(tbl)) {
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stop('Column ', col_mo, ' not found.', call. = FALSE)
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}
# strip whitespaces
if (length(country) > 1) {
stop('`country` must be a length one character string.', call. = FALSE)
}
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if (is.null(country)) {
country <- 'EUCAST'
}
country <- trimws(country)
if (country != 'EUCAST' & !country %like% '^[a-z]{2}$') {
stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?MDRO.', call. = FALSE)
}
# create list and make country code case-independent
guideline <- list(country = list(code = tolower(country)))
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if (guideline$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$version <- 'Revision of December 2017'
guideline$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:
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# } 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) {
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cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
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"Guideline: ", red(paste0(guideline$name, ", ", guideline$version, "\n")),
"Country : ", red(paste0(guideline$country$name, "\n")),
"Source : ", blue(paste0(guideline$source, "\n")),
"\n", sep = "")
}
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# check columns
col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot,
cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
levo, linc, line, mero, metr, mino, moxi, nali, neom, neti, nitr,
novo, norf, oflo, peni, pita, poly, qida, rifa, roxi, siso,
teic, tetr, tica, tige, tobr, trim, trsu, vanc)
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
amcl <- col.list[amcl]
amik <- col.list[amik]
amox <- col.list[amox]
ampi <- col.list[ampi]
azit <- col.list[azit]
aztr <- col.list[aztr]
cefa <- col.list[cefa]
cfra <- col.list[cfra]
cfep <- col.list[cfep]
cfot <- col.list[cfot]
cfox <- col.list[cfox]
cfta <- col.list[cfta]
cftr <- col.list[cftr]
cfur <- col.list[cfur]
chlo <- col.list[chlo]
cipr <- col.list[cipr]
clar <- col.list[clar]
clin <- col.list[clin]
clox <- col.list[clox]
coli <- col.list[coli]
czol <- col.list[czol]
dapt <- col.list[dapt]
doxy <- col.list[doxy]
erta <- col.list[erta]
eryt <- col.list[eryt]
fosf <- col.list[fosf]
fusi <- col.list[fusi]
gent <- col.list[gent]
imip <- col.list[imip]
kana <- col.list[kana]
levo <- col.list[levo]
linc <- col.list[linc]
line <- col.list[line]
mero <- col.list[mero]
metr <- col.list[metr]
mino <- col.list[mino]
moxi <- col.list[moxi]
nali <- col.list[nali]
neom <- col.list[neom]
neti <- col.list[neti]
nitr <- col.list[nitr]
novo <- col.list[novo]
norf <- col.list[norf]
oflo <- col.list[oflo]
peni <- col.list[peni]
pita <- col.list[pita]
poly <- col.list[poly]
qida <- col.list[qida]
rifa <- col.list[rifa]
roxi <- col.list[roxi]
siso <- col.list[siso]
teic <- col.list[teic]
tetr <- col.list[tetr]
tica <- col.list[tica]
tige <- col.list[tige]
tobr <- col.list[tobr]
trim <- col.list[trim]
trsu <- col.list[trsu]
vanc <- col.list[vanc]
# antibiotic classes
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aminoglycosides <- c(tobr, gent) # can also be kana but that one is often intrinsic R
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cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
cephalosporins_3rd <- c(cfot, cftr, cfta)
carbapenems <- c(erta, imip, mero)
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fluoroquinolones <- c(oflo, cipr, levo, moxi)
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# helper function for editing the table
trans_tbl <- function(to, rows, cols) {
cols <- cols[!is.na(cols)]
if (length(rows) > 0 & length(cols) > 0) {
col_filter <- which(tbl[, cols] == 'R')
rows <- rows[rows %in% col_filter]
tbl[rows, 'MDRO'] <<- to
}
}
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if (!tbl %>% pull(col_mo) %>% is.mo()) {
tbl[, col_mo] <- as.mo(tbl[, col_mo])
}
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tbl <- tbl %>%
# 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_))
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if (guideline$country$code == 'eucast') {
# EUCAST ------------------------------------------------------------------
# Table 5
trans_tbl(4,
which(tbl$family == 'Enterobacteriaceae'
| tbl$fullname %like% '^Pseudomonas aeruginosa'
| tbl$genus == 'Acinetobacter'),
coli)
trans_tbl(4,
which(tbl$fullname %like% '^Salmonella Typhi'),
c(carbapenems, fluoroquinolones))
trans_tbl(4,
which(tbl$fullname %like% '^Haemophilus influenzae'),
c(cephalosporins_3rd, carbapenems, fluoroquinolones))
trans_tbl(4,
which(tbl$fullname %like% '^Moraxella catarrhalis'),
c(cephalosporins_3rd, fluoroquinolones))
trans_tbl(4,
which(tbl$fullname %like% '^Neisseria meningitidis'),
c(cephalosporins_3rd, fluoroquinolones))
trans_tbl(4,
which(tbl$fullname %like% '^Neisseria gonorrhoeae'),
azit)
# Table 6
trans_tbl(4,
which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
c(vanc, teic, dapt, line, qida, tige))
trans_tbl(4,
which(tbl$genus == 'Corynebacterium'),
c(vanc, teic, dapt, line, qida, tige))
trans_tbl(4,
which(tbl$fullname %like% '^Streptococcus pneumoniae'),
c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa))
trans_tbl(4, # Sr. groups A/B/C/G
which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige))
trans_tbl(4,
which(tbl$genus == 'Enterococcus'),
c(dapt, line, tige, teic))
trans_tbl(4,
which(tbl$fullname %like% '^Enterococcus faecalis'),
c(ampi, amox))
# Table 7
trans_tbl(4,
which(tbl$genus == 'Bacteroides'),
metr)
trans_tbl(4,
which(tbl$fullname %like% '^Clostridium difficile'),
c(metr, vanc))
}
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if (guideline$country$code == 'de') {
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# Germany -----------------------------------------------------------------
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stop("We are still working on German guidelines in this beta version.", call. = FALSE)
}
if (guideline$country$code == 'nl') {
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# Netherlands -------------------------------------------------------------
aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
fluoroquinolones <- fluoroquinolones[!is.na(fluoroquinolones)]
carbapenems <- carbapenems[!is.na(carbapenems)]
# Table 1
tbl[which(
tbl$family == 'Enterobacteriaceae'
& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
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& rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
), 'MDRO'] <- 4
tbl[which(
tbl$family == 'Enterobacteriaceae'
& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
), 'MDRO'] <- 3
# rest is negative
tbl[which(
tbl$family == 'Enterobacteriaceae'
& tbl$MDRO == 1
), 'MDRO'] <- 2
# Table 2
tbl[which(
tbl$genus == 'Acinetobacter'
& rowSums(tbl[, carbapenems] == 'R', na.rm = TRUE) >= 1
), 'MDRO'] <- 3
tbl[which(
tbl$genus == 'Acinetobacter'
& rowSums(tbl[, aminoglycosides] == 'R', na.rm = TRUE) >= 1
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& rowSums(tbl[, fluoroquinolones] == 'R', na.rm = TRUE) >= 1
), 'MDRO'] <- 4
# rest of Acinetobacter is negative
tbl[which(
tbl$genus == 'Acinetobacter'
& tbl$MDRO == 1
), 'MDRO'] <- 2
tbl[which(
tbl$fullname %like% 'Stenotrophomonas maltophilia'
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& tbl[, trsu] == 'R'
), 'MDRO'] <- 4
# rest of Stenotrophomonas is negative
tbl[which(
tbl$fullname %like% 'Stenotrophomonas maltophilia'
& tbl$MDRO == 1
), 'MDRO'] <- 2
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tbl <- tbl %>% mutate(
psae = 0,
psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
psae = ifelse(cipr == "R", psae + 1, psae),
psae = ifelse(cfta == "R", psae + 1, psae),
psae = ifelse(pita == "R", psae + 1, psae),
psae = ifelse(is.na(psae), 0, psae)
)
tbl[which(
tbl$fullname %like% 'Pseudomonas aeruginosa'
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& tbl$psae >= 3
), 'MDRO'] <- 4
# rest of Pseudomonas is negative
tbl[which(
tbl$fullname %like% 'Pseudomonas aeruginosa'
& tbl$MDRO == 1
), 'MDRO'] <- 2
# Table 3
tbl[which(
tbl$fullname %like% 'Streptococcus pneumoniae'
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& tbl[, peni] == 'R'
), 'MDRO'] <- 4
tbl[which(
tbl$fullname %like% 'Streptococcus pneumoniae'
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& tbl[, vanc] == 'R'
), 'MDRO'] <- 4
# rest of Streptococcus pneumoniae is negative
tbl[which(
tbl$fullname %like% 'Streptococcus pneumoniae'
& tbl$MDRO == 1
), 'MDRO'] <- 2
tbl[which(
tbl$fullname %like% 'Enterococcus faecium'
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& rowSums(tbl[, c(peni, vanc)] == 'R', na.rm = TRUE) >= 1
), 'MDRO'] <- 4
# rest of Enterococcus faecium is negative
tbl[which(
tbl$fullname %like% 'Enterococcus faecium'
& tbl$MDRO == 1
), 'MDRO'] <- 2
}
factor(x = tbl$MDRO,
levels = c(1:4),
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labels = c('Not evaluated', 'Negative', 'Unconfirmed', 'Positive'),
ordered = TRUE)
}
#' @rdname MDRO
#' @export
BRMO <- function(tbl, country = "nl", ...) {
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MDRO(tbl = tbl, country = "nl", ...)
}
#' @rdname MDRO
#' @export
MRGN <- function(tbl, country = "de", ...) {
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MDRO(tbl = tbl, country = "de", ...)
}
#' @rdname MDRO
#' @export
EUCAST_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
MDRO(tbl = tbl, country = "EUCAST", ...)
}