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(v1.3.0.9026) eucast expert rules 3.2

new-mo-algorithm
parent
commit
c19095a3d5
  1. 4
      DESCRIPTION
  2. 14
      NEWS.md
  3. 25
      R/aa_helper_functions.R
  4. 10
      R/ab.R
  5. 2
      R/ab_class_selectors.R
  6. 2
      R/data.R
  7. 979
      R/eucast_rules.R
  8. 2
      R/filter_ab_class.R
  9. 44
      R/guess_ab_col.R
  10. 12
      R/like.R
  11. 19
      R/mdro.R
  12. 2
      R/mo.R
  13. 2
      R/mo_matching_score.R
  14. 4
      R/mo_source.R
  15. 14
      R/rsi.R
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      R/sysdata.rda
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      data-raw/ab.md5
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      data-raw/antibiotics.txt
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      data-raw/antibiotics.xlsx
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      data-raw/eucast_rules.tsv
  25. 26
      data-raw/internals.R
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      data-raw/intrinsic_resistant.dta
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      data-raw/intrinsic_resistant.md5
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      data-raw/intrinsic_resistant.txt
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      data-raw/intrinsic_resistant.xlsx
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      data-raw/reproduction_of_antibiotics.R
  34. 12
      data-raw/reproduction_of_intrinsic_resistant.R
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      data-raw/rsi.md5
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      data-raw/rsi_translation.dta
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      data/antibiotics.rda
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      data/example_isolates.rda
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      data/intrinsic_resistant.rda
  45. 2
      docs/404.html
  46. 2
      docs/LICENSE-text.html
  47. 218
      docs/articles/datasets.html
  48. 2
      docs/articles/index.html
  49. 2
      docs/authors.html
  50. 2
      docs/index.html
  51. 26
      docs/news/index.html
  52. 2
      docs/pkgdown.yml
  53. 2
      docs/reference/WHONET.html
  54. 2
      docs/reference/ab_from_text.html
  55. 2
      docs/reference/ab_property.html
  56. 2
      docs/reference/age_groups.html
  57. 10
      docs/reference/antibiotics.html
  58. 2
      docs/reference/as.ab.html
  59. 2
      docs/reference/as.disk.html
  60. 2
      docs/reference/as.mic.html
  61. 4
      docs/reference/as.mo.html
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      docs/reference/as.rsi.html
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      docs/reference/atc_online.html
  64. 2
      docs/reference/availability.html
  65. 4
      docs/reference/bug_drug_combinations.html
  66. 2
      docs/reference/catalogue_of_life_version.html
  67. 2
      docs/reference/count.html
  68. 145
      docs/reference/eucast_rules.html
  69. 2
      docs/reference/example_isolates.html
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      docs/reference/example_isolates_unclean.html
  71. 2
      docs/reference/first_isolate.html
  72. 2
      docs/reference/ggplot_rsi.html
  73. 2
      docs/reference/guess_ab_col.html
  74. 4
      docs/reference/index.html
  75. 6
      docs/reference/intrinsic_resistant.html
  76. 2
      docs/reference/join.html
  77. 2
      docs/reference/kurtosis.html
  78. 2
      docs/reference/like.html
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      docs/reference/mdro.html
  80. 2
      docs/reference/microorganisms.codes.html
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      docs/reference/microorganisms.html
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      docs/reference/microorganisms.old.html
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      docs/reference/mo_matching_score.html
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      docs/reference/mo_property.html
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      docs/reference/mo_source.html
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      docs/reference/proportion.html
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      docs/reference/resistance_predict.html
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      docs/reference/rsi_translation.html
  89. 2
      docs/reference/skewness.html
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      docs/survey.html
  91. 4
      man/antibiotics.Rd
  92. 2
      man/as.mo.Rd
  93. 3
      man/as.rsi.Rd
  94. 2
      man/bug_drug_combinations.Rd
  95. 138
      man/eucast_rules.Rd
  96. 4
      man/intrinsic_resistant.Rd
  97. 86
      man/mdro.Rd
  98. 2
      man/mo_matching_score.Rd
  99. 2
      man/mo_source.Rd
  100. 12
      tests/testthat/test-eucast_rules.R
  101. Some files were not shown because too many files have changed in this diff Show More

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.3.0.9025
Date: 2020-09-19
Version: 1.3.0.9026
Date: 2020-09-24
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

14
NEWS.md

@ -1,9 +1,10 @@ @@ -1,9 +1,10 @@
# AMR 1.3.0.9025
## <small>Last updated: 19 September 2020</small>
# AMR 1.3.0.9026
## <small>Last updated: 24 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
### New
* Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the parameters `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2.
* A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
@ -45,7 +46,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th @@ -45,7 +46,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
* Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using `mo_*` functions like `mo_name()` on microoganism IDs.
* Added parameter `ignore_pattern` to `as.mo()` which can also be given to `mo_*` functions like `mo_name()`, to exclude known non-relevant input from analysing. This can also be set with the option `AMR_ignore_pattern`.
* `get_locale()` now uses at default `Sys.getenv("LANG")` or, if `LANG` is not set, `Sys.getlocale()`. This can be overwritten by setting the option `AMR_locale`.
* Speed improvement for `eucast_rules()`
* Big speed improvement for `eucast_rules()`
* Overall speed improvement by tweaking joining functions
* Function `mo_shortname()` now returns the genus for input where the species is unknown
* BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus"
@ -55,7 +56,12 @@ Note: some changes in this version were suggested by anonymous reviewers from th @@ -55,7 +56,12 @@ Note: some changes in this version were suggested by anonymous reviewers from th
* Small `as.ab()` algorithm improvements
* Fix for combining MIC values with raw numbers, i.e. `c(as.mic(2), 2)` previously failed but now returns a valid MIC class
* `ggplot_rsi()` and `geom_rsi()` gained parameters `minimum` and `language`, to influence the internal use of `rsi_df()`
* Added abbreviation "piptazo" to piperacillin/tazobactam (TZP)
* Changes in the `antibiotics` data set:
* Updated oral and parental DDDs from the WHOCC
* Added abbreviation "piptazo" to 'Piperacillin/tazobactam' (TZP)
* 'Penicillin G' (for intravenous use) is now named 'Benzylpenicillin' (code `PEN`)
* 'Penicillin V' (for oral use, code `PNV`) was removed, since its actual entry 'Phenoxymethylpenicillin' (code `PHN`) already existed
* The group name (`antibiotics$group`) of 'Linezolid' (`LNZ`), 'Cycloserine' (`CYC`), 'Tedizolid' (`TZD`) and 'Thiacetazone' (`THA`) is now "Oxazolidinones" instead of "Other antibacterials"
### Other
* Removed unnecessary references to the `base` package

25
R/aa_helper_functions.R

@ -87,6 +87,8 @@ check_dataset_integrity <- function() { @@ -87,6 +87,8 @@ check_dataset_integrity <- function() {
data_in_pkg <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
data_in_globalenv <- ls(envir = globalenv())
overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
# exception for example_isolates
overwritten <- overwritten[overwritten != "example_isolates"]
stop_if(length(overwritten) > 0,
"the following data set is overwritten by your global environment and prevents the AMR package from working correctly:\n",
paste0("'", overwritten, "'", collapse = ", "),
@ -110,7 +112,7 @@ check_dataset_integrity <- function() { @@ -110,7 +112,7 @@ check_dataset_integrity <- function() {
invisible(TRUE)
}
search_type_in_df <- function(x, type) {
search_type_in_df <- function(x, type, info = TRUE) {
# try to find columns based on type
found <- NULL
@ -187,7 +189,7 @@ search_type_in_df <- function(x, type) { @@ -187,7 +189,7 @@ search_type_in_df <- function(x, type) {
}
}
if (!is.null(found)) {
if (!is.null(found) & info == TRUE) {
msg <- paste0("NOTE: Using column `", font_bold(found), "` as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
@ -197,6 +199,11 @@ search_type_in_df <- function(x, type) { @@ -197,6 +199,11 @@ search_type_in_df <- function(x, type) {
found
}
is_possibly_regex <- function(x) {
sapply(strsplit(x, ""),
function(y) any(y %in% c("$", "(", ")", "*", "+", "-", ".", "?", "[", "]", "^", "{", "|", "}", "\\"), na.rm = TRUE))
}
stop_ifnot_installed <- function(package) {
# no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
# https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
@ -259,7 +266,7 @@ stop_if <- function(expr, ..., call = TRUE) { @@ -259,7 +266,7 @@ stop_if <- function(expr, ..., call = TRUE) {
}
stop_ifnot <- function(expr, ..., call = TRUE) {
if (!isTRUE(expr)) {
if (isFALSE(expr)) {
if (isTRUE(call)) {
call <- -1
}
@ -317,6 +324,18 @@ dataset_UTF8_to_ASCII <- function(df) { @@ -317,6 +324,18 @@ dataset_UTF8_to_ASCII <- function(df) {
df
}
create_ab_documentation <- function(ab) {
ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
ab <- ab[order(ab_names)]
ab_names <- ab_names[order(ab_names)]
atcs <- ab_atc(ab)
atcs[!is.na(atcs)] <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab[!is.na(atcs)]), ")")
atcs[is.na(atcs)] <- "no ATC code"
out <- paste0(ab_names, " (`", ab, "`, ", atcs, ")", collapse = ", ")
substr(out, 1, 1) <- toupper(substr(out, 1, 1))
out
}
has_colour <- function() {
# this is a base R version of crayon::has_color
enabled <- getOption("crayon.enabled")

10
R/ab.R

@ -110,8 +110,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) { @@ -110,8 +110,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
note_if_more_than_one_found <- function(found, index, from_text) {
if (initial_search == TRUE & isTRUE(length(from_text) > 1)) {
message(font_blue(paste0("NOTE: more than one result was found for item ", index, ": ",
paste0(ab_name(from_text, tolower = TRUE, initial_search = FALSE), collapse = ", "))))
abnames <- ab_name(from_text, tolower = TRUE, initial_search = FALSE)
if (ab_name(found[1L], language = NULL) %like% "clavulanic acid") {
abnames <- abnames[!abnames == "clavulanic acid"]
}
if (length(abnames) > 1) {
message(font_blue(paste0("NOTE: more than one result was found for item ", index, ": ",
paste0(abnames, collapse = ", "))))
}
}
found[1L]
}

2
R/ab_class_selectors.R

@ -149,7 +149,7 @@ ab_selector <- function(ab_class, function_name) { @@ -149,7 +149,7 @@ ab_selector <- function(ab_class, function_name) {
vars_vct <- peek_vars_tidyselect(fn = function_name)
vars_df <- data.frame(as.list(vars_vct))[0, , drop = FALSE]
colnames(vars_df) <- vars_vct
ab_in_data <- suppressMessages(get_column_abx(vars_df))
ab_in_data <- get_column_abx(vars_df, info = FALSE)
if (length(ab_in_data) == 0) {
message(font_blue("NOTE: no antimicrobial agents found."))

2
R/data.R

@ -254,7 +254,7 @@ catalogue_of_life <- list( @@ -254,7 +254,7 @@ catalogue_of_life <- list(
#' - `antibiotic`\cr Name of the antibiotic drug
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
#'
#' This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
#' This data set is based on '`r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$title`', `r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$version_txt` from `r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$year`.
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @examples

979
R/eucast_rules.R

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2
R/filter_ab_class.R

@ -93,7 +93,7 @@ filter_ab_class <- function(x, @@ -93,7 +93,7 @@ filter_ab_class <- function(x,
stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: 'any', 'all'")
# get all columns in data with names that resemble antibiotics
ab_in_data <- suppressMessages(get_column_abx(x))
ab_in_data <- get_column_abx(x, info = FALSE)
if (length(ab_in_data) == 0) {
message(font_blue("NOTE: no columns with class <rsi> found (see ?as.rsi), data left unchanged."))
return(x.bak)

44
R/guess_ab_col.R

@ -110,16 +110,21 @@ get_column_abx <- function(x, @@ -110,16 +110,21 @@ get_column_abx <- function(x,
soft_dependencies = NULL,
hard_dependencies = NULL,
verbose = FALSE,
info = TRUE,
...) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)
if (info == TRUE) {
message(font_blue("NOTE: Auto-guessing columns suitable for analysis"), appendLF = FALSE)
}
x <- as.data.frame(x, stringsAsFactors = FALSE)
if (NROW(x) > 10000) {
# only test maximum of 10,000 values per column
message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE)
if (info == TRUE) {
message(font_blue(paste0(" (using only ", font_bold("the first 10,000 rows"), ")...")), appendLF = FALSE)
}
x <- x[1:10000, , drop = FALSE]
} else {
} else if (info == TRUE) {
message(font_blue("..."), appendLF = FALSE)
}
x_bak <- x
@ -130,8 +135,8 @@ get_column_abx <- function(x, @@ -130,8 +135,8 @@ get_column_abx <- function(x,
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x_columns <- sapply(colnames(x), function(col, df = x_bak) {
if (toupper(col) %in% vectr_antibiotics |
is.rsi(as.data.frame(df)[, col]) |
is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5)) {
is.rsi(as.data.frame(df)[, col, drop = TRUE]) |
is.rsi.eligible(as.data.frame(df)[, col, drop = TRUE], threshold = 0.5)) {
return(col)
} else {
return(NA_character_)
@ -142,7 +147,7 @@ get_column_abx <- function(x, @@ -142,7 +147,7 @@ get_column_abx <- function(x,
df_trans <- data.frame(colnames = colnames(x),
abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)))
df_trans <- df_trans[!is.na(df_trans$abcode), ]
df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode
@ -166,7 +171,9 @@ get_column_abx <- function(x, @@ -166,7 +171,9 @@ get_column_abx <- function(x,
}
if (length(x) == 0) {
message(font_blue("No columns found."))
if (info == TRUE) {
message(font_blue("No columns found."))
}
return(x)
}
@ -178,14 +185,16 @@ get_column_abx <- function(x, @@ -178,14 +185,16 @@ get_column_abx <- function(x,
x <- x[order(names(x), x)]
# succeeded with auto-guessing
message(font_blue("OK."))
if (info == TRUE) {
message(font_blue("OK."))
}
for (i in seq_len(length(x))) {
if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
}
if (names(x[i]) %in% names(duplicates)) {
if (info == TRUE & names(x[i]) %in% names(duplicates)) {
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns.")),
@ -206,14 +215,19 @@ get_column_abx <- function(x, @@ -206,14 +215,19 @@ get_column_abx <- function(x,
}
if (!is.null(soft_dependencies)) {
soft_dependencies <- unique(soft_dependencies)
if (!all(soft_dependencies %in% names(x))) {
if (info == TRUE & !all(soft_dependencies %in% names(x))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing_txt <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"),
missing_msg <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", missing, ")"),
collapse = ", ")
message(font_blue("NOTE: Reliability would be improved if these antimicrobial results would be available too:",
missing_txt))
missing_msg <- paste("NOTE: Reliability would be improved if these antimicrobial results would be available too:",
missing_msg)
wrapped <- strwrap(missing_msg,
width = 0.95 * getOption("width"),
exdent = 6)
wrapped <- gsub("\\((.*?)\\)", paste0("(", font_bold("\\1"), ")"), wrapped) # add bold abbreviations
message(font_blue(wrapped, collapse = "\n"))
}
}
x

12
R/like.R

@ -64,7 +64,7 @@ @@ -64,7 +64,7 @@
#' }
like <- function(x, pattern, ignore.case = TRUE) {
# set to fixed if no regex found
fixed <- all(!grepl("[\\[$.^*?+-}{|)(]", pattern))
fixed <- !any(is_possibly_regex(pattern))
if (ignore.case == TRUE) {
# set here, otherwise if fixed = TRUE, this warning will be thrown: argument 'ignore.case = TRUE' will be ignored
x <- tolower(x)
@ -140,3 +140,13 @@ like <- function(x, pattern, ignore.case = TRUE) { @@ -140,3 +140,13 @@ like <- function(x, pattern, ignore.case = TRUE) {
"%like_case%" <- function(x, pattern) {
like(x, pattern, ignore.case = FALSE)
}
# don't export his one, it's just for convenience in eucast_rules()
# match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
"%like_perl%" <- function(x, pattern) {
grepl(x = tolower(x),
pattern = tolower(pattern),
perl = TRUE,
fixed = FALSE,
ignore.case = TRUE)
}

19
R/mdro.R

@ -141,7 +141,7 @@ mdro <- function(x, @@ -141,7 +141,7 @@ mdro <- function(x,
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
}
if (is.null(col_mo) & guideline$code == "tb") {
message(font_blue("NOTE: No column found as input for `col_mo`,",
@ -303,7 +303,9 @@ mdro <- function(x, @@ -303,7 +303,9 @@ mdro <- function(x,
"TCY",
"DOX",
"MNO"),
verbose = verbose, ...)
verbose = verbose,
info = info,
...)
} else if (guideline$code == "tb") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("CAP",
@ -314,7 +316,9 @@ mdro <- function(x, @@ -314,7 +316,9 @@ mdro <- function(x,
"RIF",
"RIB",
"RFP"),
verbose = verbose, ...)
info = info,
verbose = verbose,
...)
} else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("PIP",
@ -323,9 +327,14 @@ mdro <- function(x, @@ -323,9 +327,14 @@ mdro <- function(x,
"IPM",
"MEM",
"CIP"),
verbose = verbose, ...)
verbose = verbose,
info = info,
...)
} else {
cols_ab <- get_column_abx(x = x, verbose = verbose, ...)
cols_ab <- get_column_abx(x = x,
verbose = verbose,
info = info,
...)
}
AMC <- cols_ab["AMC"]

2
R/mo.R

@ -109,7 +109,7 @@ @@ -109,7 +109,7 @@
#' 3. The level of uncertainty \eqn{U} needed to get to the result, as stated above (1 to 3);
#' 4. The [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
#'
#' \deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F}
#' \deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}
#'
#' The final matching score \eqn{M} is calculated as:
#' \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}

2
R/mo_matching_score.R

@ -32,7 +32,7 @@ @@ -32,7 +32,7 @@
#' 3. The level of uncertainty \eqn{U} that is needed to get to a result (1 to 3, see [as.mo()]);
#' 4. The [Levenshtein distance](https://en.wikipedia.org/wiki/Levenshtein_distance) \eqn{L} is the distance between the user input and all taxonomic full names, with the text length of the user input being the maximum distance. A modified version of the Levenshtein distance \eqn{L'} based on the text length of the full name \eqn{F} is calculated as:
#'
#' \deqn{L' = F - \frac{0.5L}{F}}{L' = (F - 0.5L) / F}
#' \deqn{L' = 1 - \frac{0.5L}{F}}{L' = 1 - ((0.5 * L) / F)}
#'
#' The final matching score \eqn{M} is calculated as:
#' \deqn{M = L' \times \frac{1}{P K U} = \frac{F - 0.5L}{F P K U}}{M = L' * (1 / (P * K * U)) = (F - 0.5L) / (F * P * K * U)}

4
R/mo_source.R

@ -35,7 +35,7 @@ @@ -35,7 +35,7 @@
#'
#' The created compressed data file `"~/.mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location of the original file will be saved as an R option with `options(mo_source = path)`. Its timestamp will be saved with `options(mo_source_datetime = ...)`.
#'
#' The function [get_mo_source()] will return the data set by reading `"~/.mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the aforementioned options `mo_source` and `mo_source_datetime`), it will call [set_mo_source()] to update the data file automatically.
#' The function [get_mo_source()] will return the data set by reading `"~/.mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the aforementioned options `mo_source` and `mo_source_datetime`), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
#'
#' Reading an Excel file (`.xlsx`) with only one row has a size of 8-9 kB. The compressed file created with [set_mo_source()] will then have a size of 0.1 kB and can be read by [get_mo_source()] in only a couple of microseconds (millionths of a second).
#'
@ -224,7 +224,7 @@ get_mo_source <- function() { @@ -224,7 +224,7 @@ get_mo_source <- function() {
set_mo_source("")
return(NULL)
}
if (new_time != old_time) {
if (interactive() && new_time != old_time) {
# set updated source
set_mo_source(getOption("mo_source"))
}

14
R/rsi.R

@ -187,7 +187,6 @@ is.rsi <- function(x) { @@ -187,7 +187,6 @@ is.rsi <- function(x) {
#' @export
is.rsi.eligible <- function(x, threshold = 0.05) {
stop_if(NCOL(x) > 1, "`x` must be a one-dimensional vector.")
if (any(c("logical",
"numeric",
"integer",
@ -226,15 +225,12 @@ as.rsi.default <- function(x, ...) { @@ -226,15 +225,12 @@ as.rsi.default <- function(x, ...) {
class = c("rsi", "ordered", "factor"))
} else {
ab <- deparse(substitute(x))
if (!any(x %like% "(R|S|I)", na.rm = TRUE)) {
if (!is.na(suppressWarnings(as.ab(ab)))) {
# check if they are actually MICs or disks now that the antibiotic name is valid
if (all_valid_mics(x)) {
as.rsi(as.mic(x), ab = ab, ...)
} else if (all_valid_disks(x)) {
as.rsi(as.disk(x), ab = ab, ...)
}
# check if they are actually MICs or disks now that the antibiotic name is valid
if (all_valid_mics(x)) {
warning("The input seems to be MIC values. Transform them with as.mic() before running as.rsi() to interpret them.")
} else if (all_valid_disks(x)) {
warning("The input seems to be disk diffusion values. Transform them with as.disk() before running as.rsi() to interpret them.")
}
}

BIN
R/sysdata.rda

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2
data-raw/ab.md5

@ -1 +1 @@ @@ -1 +1 @@
8f2f30e72f9d7c318439abe04073bece
a30faa0e4475d440d1bb8e44e6857062

BIN
data-raw/antibiotics.dta

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BIN
data-raw/antibiotics.rds

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BIN
data-raw/antibiotics.sas

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data-raw/antibiotics.sav

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43
data-raw/antibiotics.txt

@ -7,14 +7,14 @@ @@ -7,14 +7,14 @@
"AMK" "J01GB06" 37768 "Amikacin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")" "c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")" 1 "g" "c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")"
"AKF" "Amikacin/fosfomycin" "Aminoglycosides" "" "" ""
"AMX" "J01CA04" 33613 "Amoxicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"ac\", \"amox\", \"amx\")" "c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\",
\"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")" 1.5 "g" 1 "g" "c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")"
\"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")" 1.5 "g" 3 "g" "c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")"
"AMC" "J01CR02" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")" "c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")" 1.5 "g" 3 "g" "character(0)"
"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
"AMB" "J02AA01" 5280965 "Amphotericin B" "Antifungals/antimycotics" "Antimycotics for systemic use" "Antibiotics" "c(\"amfb\", \"amph\")" "c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")" 35 "mg" "c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")"
"AMH" "Amphotericin B-high" "Aminoglycosides" "c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")" "" ""
"AMP" "J01CA01" 6249 "Ampicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"am\", \"amp\", \"ampi\")" "c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\",
\"binotal\", \"bonapicillin\", \"britacil\", \"campicillin\", \"copharcilin\", \"delcillin\", \"deripen\", \"divercillin\", \"doktacillin\", \"duphacillin\", \"grampenil\", \"guicitrina\", \"guicitrine\", \"lifeampil\", \"marcillin\", \"morepen\", \"norobrittin\", \"nuvapen\", \"olin kid\", \"omnipen\", \"orbicilina\", \"pen a oral\", \"pen ampil\", \"penbristol\", \"penbritin\", \"penbritin paediatric\", \"penbritin syrup\", \"penbrock\", \"penicline\", \"penimic\", \"pensyn\", \"pentrex\", \"pentrexl\", \"pentrexyl\", \"pentritin\", \"pfizerpen a\", \"polycillin\", \"polyflex\",
\"ponecil\", \"princillin\", \"principen\", \"qidamp\", \"racenacillin\", \"rosampline\", \"roscillin\", \"semicillin\", \"semicillin r\", \"servicillin\", \"sumipanto\", \"synpenin\", \"texcillin\", \"tokiocillin\", \"tolomol\", \"totacillin\", \"totalciclina\", \"totapen\", \"trifacilina\", \"ukapen\", \"ultrabion\", \"ultrabron\", \"vampen\", \"viccillin\", \"viccillin s\", \"vidocillin\", \"wypicil\")" 2 "g" 2 "g" "c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")"
\"ponecil\", \"princillin\", \"principen\", \"qidamp\", \"racenacillin\", \"rosampline\", \"roscillin\", \"semicillin\", \"semicillin r\", \"servicillin\", \"sumipanto\", \"synpenin\", \"texcillin\", \"tokiocillin\", \"tolomol\", \"totacillin\", \"totalciclina\", \"totapen\", \"trifacilina\", \"ukapen\", \"ultrabion\", \"ultrabron\", \"vampen\", \"viccillin\", \"viccillin s\", \"vidocillin\", \"wypicil\")" 2 "g" 6 "g" "c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")"
"SAM" "J01CR01" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")" "" 6 "g" ""
"AMR" 73341 "Amprolium" "Other antibacterials" "" "c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")" "character(0)"
"ANI" "J02AX06" 166548 "Anidulafungin" "Antifungals/antimycotics" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid" "c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")" 0.1 "g" "58420-1"
@ -63,7 +63,7 @@ @@ -63,7 +63,7 @@
"CDR" "J01DD15" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")" "c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")" 0.6 "g" "character(0)"
"DIT" "J01DD16" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn" "cefditoren" 0.4 "g" "character(0)"
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")" "character(0)"
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 2 "g" "38363-8"
"FEP" "J01DE01" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")" "c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")" 4 "g" "38363-8"
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "c(\"cicl\", \"xpml\")" "" ""
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "" "" ""
"FPZ" "Cefepime/zidebactam" "Other antibacterials" "" "" ""
@ -103,11 +103,11 @@ @@ -103,11 +103,11 @@
"CRD" "J01DB11" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")" 2.1 "character(0)"
"CFS" "J01DD03" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfsl\", \"cfsu\")" "c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")" 4 "g" "c(\"131-3\", \"25242-9\")"
"CSU" 68718 "Cefsumide" "Cephalosporins (unclassified gen.)" "" "c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")" "character(0)"
"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" "character(0)"
"CPT" "J01DI02" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "c(\"\", \"cfro\")" "c(\"teflaro\", \"zinforo\")" 1.2 "character(0)"
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "" "" ""
"CAZ" "J01DD02" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")" "c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")" 4 "g" "c(\"21151-6\", \"3449-6\", \"80960-8\")"
"CZA" "Ceftazidime/avibactam" "Cephalosporins (3rd gen.)" "c(\"\", \"cfav\")" "" ""
"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" ""
"CCV" "J01DD52" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"czcl\", \"xtzl\")" "" 6 ""
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "" "c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")" "character(0)"
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "" "c(\"cefteram pivoxil\", \"tomiron\")" "character(0)"
"CTL" "J01DB12" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "Other beta-lactam antibacterials" "First-generation cephalosporins" "" "c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")" 3 "g" "character(0)"
@ -115,9 +115,9 @@ @@ -115,9 +115,9 @@
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "" "c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")" "character(0)"
"CZX" "J01DD07" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")" "c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")" 4 "g" "c(\"25243-7\", \"3450-4\")"
"CZP" 9578661 "Ceftizoxime alapivoxil" "Cephalosporins (3rd gen.)" "" "" ""
"BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" "character(0)"
"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" ""
"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" ""
"BPR" "J01DI01" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "" "ceftobiprole" 1.5 "character(0)"
"CFM1" "J01DI01" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" 1.5 ""
"CEI" "J01DI54" "Ceftolozane/enzyme inhibitor" "Cephalosporins (5th gen.)" "Other beta-lactam antibacterials" "Other cephalosporins" "" "" 3 ""
"CZT" "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "" "" ""
"CRO" "J01DD04" 5479530 "Ceftriaxone" "Cephalosporins (3rd gen.)" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")" "c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")" 2 "g" "c(\"25244-5\", \"3451-2\", \"80957-4\")"
"CXM" "J01DC02" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")" "c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")" 0.5 "g" 3 "g" "c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
@ -141,7 +141,7 @@ @@ -141,7 +141,7 @@
"CIX" "D01AE14" 47472 "Ciclopirox" "Antifungals/antimycotics" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")" "character(0)"
"CIN" "J01MB06" 2762 "Cinoxacin" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"cino\", \"cnox\")" "c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")" 1 "g" "character(0)"
"CIP" "J01MA02" 2764 "Ciprofloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"ci\", \"cip\", \"cipr\", \"cp\")" "c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\",
\"citopcin\", \"corsacin\", \"cyprobay\", \"fimoflox\", \"flociprin\", \"ipiflox\", \"italnik\", \"linhaliq\", \"otiprio\", \"probiox\", \"proflaxin\", \"quinolid\", \"quintor\", \"rancif\", \"roxytal\", \"septicide\", \"sophixin ofteno\", \"spitacin\", \"superocin\", \"velmonit\", \"velomonit\", \"zumaflox\")" 1 "g" 0.5 "g" "c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")"
\"citopcin\", \"corsacin\", \"cyprobay\", \"fimoflox\", \"flociprin\", \"ipiflox\", \"italnik\", \"linhaliq\", \"otiprio\", \"probiox\", \"proflaxin\", \"quinolid\", \"quintor\", \"rancif\", \"roxytal\", \"septicide\", \"sophixin ofteno\", \"spitacin\", \"superocin\", \"velmonit\", \"velomonit\", \"zumaflox\")" 1 "g" 0.8 "g" "c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")"
"CLR" "J01FA09" 84029 "Clarithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")" "c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\",
\"kofron\", \"mabicrol\", \"macladin\", \"maclar\", \"veclam\", \"vikrol\", \"zeclar\")" 0.5 "g" 1 "g" "c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")"
"CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "" "c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")" "character(0)"
@ -154,10 +154,10 @@ @@ -154,10 +154,10 @@
"CTR" "G01AF02" 2812 "Clotrimazole" "Antifungals/antimycotics" "clot" "c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\",
\"lotrimin solution\", \"monobaycuten\", \"mycelax\", \"mycelex\", \"mycelex cream\", \"mycelex g\", \"mycelex otc\", \"mycelex solution\", \"mycelex troches\", \"mycelex twin pack\", \"myclo cream\", \"myclo solution\", \"myclo spray solution\", \"mycofug\", \"mycosporin\", \"mykosporin\", \"nalbix\", \"otomax\", \"pedisafe\", \"rimazole\", \"stiemazol\", \"tibatin\", \"trimysten\", \"veltrim\")" "character(0)"
"CLO" "J01CF02" 6098 "Cloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"clox\")" "c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")" 2 "g" 2 "g" "c(\"16628-0\", \"25250-2\")"
"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 3 "MU" "c(\"16645-4\", \"29493-4\")"
"COL" "J01XB01" 5311054 "Colistin" "Polymyxins" "Other antibacterials" "Polymyxins" "c(\"cl\", \"coli\", \"cs\", \"ct\")" "c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")" 9 "MU" "c(\"16645-4\", \"29493-4\")"
"COP" "Colistin/polysorbate" "Other antibacterials" "" "" ""
"CYC" "J04AB01" 6234 "Cycloserine" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")"
"DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" "character(0)"
"CYC" "J04AB01" 6234 "Cycloserine" "Oxazolidinones" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl" "c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")" 0.75 "g" "c(\"16702-3\", \"25251-0\", \"3519-6\")"
"DAL" "J01XA04" 23724878 "Dalbavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "dalb" "c(\"dalbavancin\", \"dalvance\")" 1.5 "character(0)"
"DAN" 71335 "Danofloxacin" "Quinolones" "" "c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")" "character(0)"
"DPS" "J04BA02" 2955 "Dapsone" "Other antibacterials" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "" "c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\",
\"slphadione\", \"sulfadione\", \"sulfona\", \"sulfone ucb\", \"sulfonyldianiline\", \"sulphadione\", \"sulphonyldianiline\", \"sumicure s\", \"tarimyl\", \"udolac\", \"wln: zr dswr dz\")" 50 "mg" "9747-7"
@ -169,7 +169,7 @@ @@ -169,7 +169,7 @@
"DIC" "J01CF01" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "c(\"\", \"dicl\")" "c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")" 2 "g" 2 "g" "c(\"10984-3\", \"16769-2\", \"25252-8\")"
"DIF" 56206 "Difloxacin" "Quinolones" "" "difloxacin" "character(0)"
"DIR" "J01FA13" 6473883 "Dirithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "" "c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")" 0.5 "g" "character(0)"
"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" "character(0)"
"DOR" "J01DH04" 73303 "Doripenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "dori" "c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")" 1.5 "character(0)"
"DOX" "J01AA02" 54671203 "Doxycycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "c(\"dox\", \"doxy\")" "c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")" 0.1 "g" 0.1 "g" "c(\"10986-8\", \"21250-6\", \"26902-7\")"
"ECO" "J01XDXX" 3198 "Econazole" "Antifungals/antimycotics" "econ" "c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")" "character(0)"
"ENX" "J01MA04" 3229 "Enoxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"enox\")" "c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")" 0.8 "g" "c(\"16816-1\", \"3590-7\")"
@ -248,7 +248,7 @@ @@ -248,7 +248,7 @@
"LND" 9850038 "Levonadifloxacin" "Quinolones" "" "levonadifloxacin" "character(0)"
"LSP" "Linco-spectin (lincomycin/spectinomycin)" "Other antibacterials" "" "" ""
"LIN" "J01FF02" 3000540 "Lincomycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc" "c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")" 1.8 "g" 1.8 "g" "87597-1"
"LNZ" "J01XX08" 441401 "Linezolid" "Other antibacterials" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")"
"LNZ" "J01XX08" 441401 "Linezolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "c(\"line\", \"lnz\", \"lz\", \"lzd\")" "c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")" 1.2 "g" 1.2 "g" "c(\"34202-2\", \"80609-1\")"
"LFE" "Linoprist-flopristin" "Other antibacterials" "" "" ""
"LOM" "J01MA07" 3948 "Lomefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"lmf\", \"lom\", \"lome\")" "c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")" 0.4 "character(0)"
"LOR" "J01DC08" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "c(\"\", \"lora\")" "c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")" 0.6 "g" "character(0)"
@ -257,7 +257,7 @@ @@ -257,7 +257,7 @@
"MAR" 60651 "Marbofloxacin" "Quinolones" "" "c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")" "character(0)"
"MEC" "J01CA11" 36273 "Mecillinam (Amdinocillin)" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")" 1.2 "g" "character(0)"
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "" "" ""
"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 2 "g" "41406-0"
"MEM" "J01DH02" 441130 "Meropenem" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")" "c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")" 3 "g" "41406-0"
"MNC" "Meropenem/nacubactam" "Carbapenems" "" "" ""
"MEV" "J01DH52" "Meropenem/vaborbactam" "Carbapenems" "Other beta-lactam antibacterials" "Carbapenems" "" "" ""
"MES" 176886 "Mesulfamide" "Other antibacterials" "" "c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")" "character(0)"
@ -328,9 +328,8 @@ @@ -328,9 +328,8 @@
"PAZ" "J01MA18" 65957 "Pazufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")" 1 "g" "character(0)"
"PEF" "J01MA03" 51081 "Pefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"pefl\")" "c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")" 0.8 "g" 0.8 "g" "3906-5"
"PNM" "J01CE06" 10250769 "Penamecillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")" 1.05 "g" "character(0)"
"PEN" "J01CE01" 5904 "Penicillin G" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"p\", \"pen\", \"peni\", \"pv\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
"PEN" "J01CE01" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
)" 3.6 "g" "3913-1"
"PNV" "J01CE01" 6869 "Penicillin V" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"bepe\", \"p\", \"pen\", \"pv\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 3.6 "g" "3914-9"
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "" "" ""
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
"PNM1" "J01AA10" 54686187 "Penimepicycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")" "character(0)"
@ -338,7 +337,7 @@ @@ -338,7 +337,7 @@
"PTZ" 55250256 "Pentizidone" "Other antibacterials" "" "" ""
"PEX" 16132253 "Pexiganan" "Other antibacterials" "" "pexiganan" "character(0)"
"PHE" "J01CE05" 272833 "Phenethicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fene\")" "c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")" 1 "g" "41471-4"
"PHN" "J01CE02" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"\", \"fepe\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 2 "g" "character(0)"
"PHN" "J01CE02" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "c(\"fepe\", \"peni v\", \"penicillin v\", \"pnv\", \"pv\")" "c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")" 2 "g" "character(0)"
"PMR" 5284447 "Pimaricin (Natamycin)" "Antifungals/antimycotics" "" "c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")" "character(0)"
"PPA" "J01MB04" 4831 "Pipemidic acid" "Quinolones" "Quinolone antibacterials" "Other quinolones" "c(\"pipz\", \"pizu\")" "c(\"acide pipemidique\", \"acido pipemidico\", \"acidum pipemidicum\", \"deblaston\", \"dolcol\", \"pipedac\", \"pipemid\", \"pipemidic\", \"pipemidic acid\", \"pipemidicacid\", \"pipram\", \"uromidin\")" 0.8 "g" "character(0)"
"PIP" "J01CA12" 43672 "Piperacillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"pi\", \"pip\", \"pipc\", \"pipe\", \"pp\")" "c(\"isipen\", \"pentcillin\", \"peperacillin\", \"peracin\", \"piperacilina\", \"piperacillin\", \"piperacillin na\", \"piperacillin sodium\", \"piperacilline\", \"piperacillinum\", \"pipercillin\", \"pipracil\", \"pipril\")" 14 "g" "c(\"25268-4\", \"3972-7\")"
@ -369,7 +368,7 @@ @@ -369,7 +368,7 @@
"RAM" 16132338 "Ramoplanin" "Glycopeptides" "" "ramoplanin" "character(0)"
"RZM" 10993211 "Razupenem" "Carbapenems" "" "razupenem" "character(0)"
"RTP" "A07AA11" 6918462 "Retapamulin" "Other antibacterials" "Intestinal antiinfectives" "Antibiotics" "" "c(\"altabax\", \"altargo\", \"retapamulin\")" 0.6 "g" "character(0)"
"RBC" "J02AC05" 44631912 "Ribociclib" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "c(\"kisqali\", \"ribociclib\")" 0.2 "character(0)"
"RBC" "J02AC05" 44631912 "Ribociclib" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "c(\"kisqali\", \"ribociclib\")" 0.2 0.2 "character(0)"
"RST" "J01GB10" 33042 "Ribostamycin" "Aminoglycosides" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")" 1 "g" "character(0)"
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "" "ridinilazole" "character(0)"
"RIB" "J04AB04" 135398743 "Rifabutin" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")" 0.15 "g" "24032-5"
@ -458,13 +457,13 @@ @@ -458,13 +457,13 @@
"TLP" 163307 "Talmetoprim" "Other antibacterials" "" "talmetoprim" "character(0)"
"TAZ" "J01CG02" 123630 "Tazobactam" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo" "c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")" "character(0)"
"TBP" 9800194 "Tebipenem" "Carbapenems" "" "" ""
"TZD" "J01XX11" 11234049 "Tedizolid" "Other antibacterials" "Other antibacterials" "Other antibacterials" "tedi" "c(\"tedizolid\", \"torezolid\")" 0.2 "character(0)"
"TZD" "J01XX11" 11234049 "Tedizolid" "Oxazolidinones" "Other antibacterials" "Other antibacterials" "tedi" "c(\"tedizolid\", \"torezolid\")" 0.2 0.2 "character(0)"
"TEC" "J01XA02" 16131923 "Teicoplanin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")" "c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")" 0.4 "g" "c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
"TCM" "Teicoplanin-macromethod" "Glycopeptides" "" "" ""
"TLV" "J01XA03" 3081362 "Telavancin" "Glycopeptides" "Other antibacterials" "Glycopeptide antibacterials" "tela" "c(\"telavancin\", \"vibativ\")" "character(0)"
"TLT" "J01FA15" 3002190 "Telithromycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Macrolides" "c(\"\", \"teli\")" "levviax" 0.8 "g" "character(0)"
"TMX" "J01MA05" 60021 "Temafloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"tema\")" "c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")" 0.8 "g" "character(0)"
"TEM" "J01CA17" 171758 "Temocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"\", \"temo\")" "c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")" 2 "g" "character(0)"
"TEM" "J01CA17" 171758 "Temocillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "c(\"\", \"temo\")" "c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")" 4 "g" "character(0)"
"TRB" "D01BA02" 1549008 "Terbinafine" "Antifungals/antimycotics" "Antifungals for systemic use" "Antifungals for systemic use" "c(\"\", \"terb\")" "c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")" 0.25 "g" "character(0)"
"TRC" 441383 "Terconazole" "Antifungals/antimycotics" "" "c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")" "character(0)"
"TRZ" "J04AK03" 65720 "Terizidone" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")" "character(0)"
@ -472,7 +471,7 @@ @@ -472,7 +471,7 @@
\"orlycycline\", \"panmycin\", \"piracaps\", \"polycycline\", \"polyotic\", \"purocyclina\", \"resteclin\", \"robitet\", \"roviciclina\", \"sigmamycin\", \"solvocin\", \"sumycin\", \"sumycin syrup\", \"tetrabon\", \"tetrachel\", \"tetraciclina\", \"tetracycl\", \"tetracyclin\", \"tetracycline\", \"tetracycline base\", \"tetracycline i\", \"tetracycline ii\", \"tetracyclinum\", \"tetracyn\", \"tetradecin\", \"tetrafil\", \"tetramed\", \"tetrasure\", \"tetraverine\", \"tetrazyklin\", \"tetrex\", \"topicycline\", \"tsiklomistsin\", \"tsiklomitsin\", \"veracin\", \"vetacyclinum\"
)" 1 "g" 1 "g" "c(\"25272-6\", \"4045-1\", \"87590-6\")"
"TET" 65450 "Tetroxoprim" "Other antibacterials" "" "c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")" "character(0)"
"THA" 9568512 "Thiacetazone" "Antimycobacterials" "" "c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\",
"THA" 9568512 "Thiacetazone" "Oxazolidinones" "" "c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\",
\"thibon\", \"thibone\", \"thioacetazon\", \"thioacetazone\", \"thioacetazonum\", \"thioazetazone\", \"thiocarbazil\", \"thiomicid\", \"thionicid\", \"thioparamizon\", \"thioparamizone\", \"thiosemicarbarzone\", \"thiosemicarbazone\", \"thiotebesin\", \"thiotebezin\", \"thiotebicina\", \"thizone\", \"tiacetazon\", \"tibicur\", \"tibion\", \"tibione\", \"tibizan\", \"tibone\", \"tioacetazon\", \"tioacetazona\", \"tioatsetazon\", \"tiobicina\", \"tiocarone\", \"tiosecolo\", \"tubercazon\", \"tubigal\")" "character(0)"
"THI" "J01BA02" 27200 "Thiamphenicol" "Amphenicols" "Amphenicols" "Amphenicols" "" "c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")" 1.5 "g" 1.5 "g" "character(0)"
"THI1" "J04AM04" "Thioacetazone/isoniazid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "" "" ""

BIN
data-raw/antibiotics.xlsx

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data-raw/eucast_rules.tsv

@ -1,191 +1,301 @@ @@ -1,191 +1,301 @@
# -------------------------------------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins'
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins',
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# -------------------------------------------------------------------------------------------------------------------------------
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints
genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints
genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints
genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints
genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints
genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints
genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints
genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints
genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints
genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints
genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S MFX S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX I Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints
genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints
genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints
genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints
genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints
genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints
genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints
genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints
genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints
genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints
genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints
genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints
genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints
genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints
genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints
genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints
genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints
genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints
genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints
genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints
genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints
genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints
genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints
genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints
genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints
genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints
genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints
genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints
genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints
genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints
genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints
genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Enterobacter aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Escherichia hermanni aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordatella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus capitis CAZ, FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus aureus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus epidermidis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus coagulase-negative CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus hominis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules
genus like .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus like .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus like .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules
order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version note
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 10
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 10
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 10
genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints 10
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints 10
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 10
genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints 10
genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints 10
genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints 10
genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints 10
genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints 10
genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 10
genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 10
genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 10
genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 10
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 10
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 10
genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 10
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints 10
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 10
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 10
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints 10
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints 10
genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 10
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 10
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 10
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 10
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints 10
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints 10
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints 10
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints 10
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints 10
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints 10
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 10
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 10
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 10
genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints 10
genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints 10
genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints 10
genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints 10
genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints 10
genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints 10
genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints 10
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 10
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 10
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 10
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 10
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 10
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 10
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 10
genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints 10
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 10
genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints 10
genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints 10
genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 10
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus capitis CAZ, FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus aureus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus epidermidis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus coagulase-negative CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus hominis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules 3.1
genus like .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1
genus like .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1
genus like .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1
genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1
genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Yersinia pseudotuberculosis polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas hydrophila aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Ochrobactrum anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, TMP, tetracyclines, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, DOX, TCY, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Haemophilus influenzae FUS, streptogramins R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Moraxella catarrhalis TMP R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus is Neisseria TMP R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus aureus CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus coagulase-negative CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides
genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
fullname like ^Enterococcus (gallinarum|casseliflavus) FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides
genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations
genus is Corynebacterium FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus one_of Leuconostoc, Pediococcus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus is Lactobacillus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
fullname like ^Clostridium (ramosum|innocuum) VAN R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rules on Enterobacterales Expert Rules 3.2
genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.2
fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.2
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.2
genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Metakosakonia, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp.
fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.2
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 R all_betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 S all_betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.2 all penicillins without beta-lactamse inhibitor
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus LVX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus MFX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus TCY S DOX, MNO, TGC S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus TCY R DOX, MNO R Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus VAN S lipoglycopeptides S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus LNZ S TZD S Expert Rules on Staphylococcus Expert Rules 3.2
fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.2
fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.2
genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.2
genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.2
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2
genus_species is Haemophilus influenzae PEN S all_betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.2
genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.2
genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.2
genus_species is Campylobacter ERY R CLR, AZM R Expert Rules on Campylobacter Expert Rules 3.2

Can't render this file because it contains an unexpected character in line 6 and column 96.

26
data-raw/internals.R

@ -24,21 +24,25 @@ @@ -24,21 +24,25 @@
# --------------------------------------------------------------------------
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
library(dplyr, warn.conflicts = FALSE)
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
skip = 10,
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
strip.white = TRUE,
na = c(NA, "", NULL))
# take the order of the reference.rule_group column in the original data file
eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group,
levels = unique(eucast_rules_file$reference.rule_group),
ordered = TRUE)
eucast_rules_file <- dplyr::arrange(eucast_rules_file,
reference.rule_group,
reference.rule)
eucast_rules_file$reference.rule_group <- as.character(eucast_rules_file$reference.rule_group)
na = c(NA, "", NULL)) %>%
# take the order of the reference.rule_group column in the original data file
mutate(reference.rule_group = factor(reference.rule_group,
levels = unique(reference.rule_group),
ordered = TRUE),
sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)) %>%
arrange(reference.rule_group,
reference.version,
sorting_rule,
reference.rule) %>%
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
select(-sorting_rule)
# Translations ----
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
@ -72,7 +76,9 @@ rm(microorganisms.translation) @@ -72,7 +76,9 @@ rm(microorganisms.translation)
# Save to raw data to repository ----
write_md5 <- function(object) {
writeLines(digest::digest(object, "md5"), file(paste0("data-raw/", deparse(substitute(object)), ".md5")))
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
writeLines(digest::digest(object, "md5"), conn)
close(conn)
}
changed_md5 <- function(object) {
tryCatch({

BIN
data-raw/intrinsic_resistant.dta

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2
data-raw/intrinsic_resistant.md5

@ -1 +1 @@ @@ -1 +1 @@
6915f562bd64e546e1d57741a2a5ad27
b6de75043ef27eabd6fff22f04638225

BIN
data-raw/intrinsic_resistant.rds

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data-raw/intrinsic_resistant.sas

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BIN
data-raw/intrinsic_resistant.sav

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48774
data-raw/intrinsic_resistant.txt

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