diff --git a/DESCRIPTION b/DESCRIPTION index 3c1626582..c4c2f3074 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9055 +Version: 3.0.1.9056 Date: 2026-04-30 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NAMESPACE b/NAMESPACE index c8e953a0d..c6ec41018 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -49,6 +49,7 @@ S3method(as.data.frame,mo) S3method(as.double,mic) S3method(as.double,sir) S3method(as.list,custom_eucast_rules) +S3method(as.list,custom_interpretive_rules) S3method(as.list,custom_mdro_guideline) S3method(as.list,mic) S3method(as.matrix,mic) @@ -66,6 +67,7 @@ S3method(c,ab) S3method(c,amr_selector) S3method(c,av) S3method(c,custom_eucast_rules) +S3method(c,custom_interpretive_rules) S3method(c,custom_mdro_guideline) S3method(c,disk) S3method(c,mic) @@ -96,6 +98,7 @@ S3method(print,amr_selector) S3method(print,av) S3method(print,bug_drug_combinations) S3method(print,custom_eucast_rules) +S3method(print,custom_interpretive_rules) S3method(print,custom_mdro_guideline) S3method(print,deprecated_amr_dataset) S3method(print,disk) @@ -228,6 +231,7 @@ export(count_df) export(count_resistant) export(count_susceptible) export(custom_eucast_rules) +export(custom_interpretive_rules) export(custom_mdro_guideline) export(eucast_dosage) export(eucast_exceptional_phenotypes) diff --git a/NEWS.md b/NEWS.md index a67994555..f694ac103 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9055 +# AMR 3.0.1.9056 This will become release v3.1.0, intended for launch end of May. @@ -45,6 +45,7 @@ This will become release v3.1.0, intended for launch end of May. * Fixed `as.sir()` ignoring `info = FALSE` for columns with no breakpoints (e.g. cefoxitin against *E. coli*) ### Updates +* Renamed `custom_eucast_rules()` to `custom_interpretive_rules()`; old function is now a deprecated wrapper. Renamed `data-raw/eucast_rules.tsv` to `interpretive_rules.tsv` and added `rule.provider` column for multi-guideline (EUCAST/CLSI) support. `clsi_rules()` no longer throws an error (#268) * `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (#239) * Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265) * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable). diff --git a/R/aa_globals.R b/R/aa_globals.R index 436f8ce89..a12de1b2b 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -27,7 +27,7 @@ # how to conduct AMR data analysis: https://amr-for-r.org # # ==================================================================== # -# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints +# add new version numbers here, and add the rules themselves to "data-raw/interpretive_rules.tsv" and clinical_breakpoints # (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file) EUCAST_VERSION_BREAKPOINTS <- list( "16.0" = list( @@ -221,6 +221,7 @@ globalVariables(c( "reference.rule", "reference.rule_group", "reference.version", + "rule.provider", "rowid", "rule_group", "rule_name", diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R old mode 100644 new mode 100755 diff --git a/R/amr_course.R b/R/amr_course.R old mode 100644 new mode 100755 diff --git a/R/antibiogram.R b/R/antibiogram.R index dc4e707e0..39bc5ea7e 100755 --- a/R/antibiogram.R +++ b/R/antibiogram.R @@ -762,7 +762,9 @@ antibiogram.default <- function(x, # precompute priors per group and build (group, chunk) job list jobs <- unlist(lapply(unique_groups, function(g) { params_g <- wisca_parameters[wisca_parameters$group == g, , drop = FALSE] - if (sum(params_g$n_tested, na.rm = TRUE) == 0L) return(NULL) + if (sum(params_g$n_tested, na.rm = TRUE) == 0L) { + return(NULL) + } priors_g <- create_wisca_priors(params_g) lapply(seq_along(chunk_sizes), function(ch) { list(group = g, priors = priors_g, n_sims = chunk_sizes[ch]) @@ -788,7 +790,6 @@ antibiogram.default <- function(x, } if (isTRUE(info)) message_(font_green_bg(" DONE "), as_note = FALSE) - } else { progress <- progress_ticker( n = length(unique_groups) * simulations, @@ -1115,7 +1116,9 @@ antibiogram.grouped_df <- function(x, x_df <- as.data.frame(x) run_group <- function(i) { rows <- unlist(groups[i, ]$.rows) - if (length(rows) == 0L) return(NULL) + if (length(rows) == 0L) { + return(NULL) + } antibiogram(x_df[rows, , drop = FALSE], antimicrobials = antimicrobials, mo_transform = NULL, @@ -1136,7 +1139,7 @@ antibiogram.grouped_df <- function(x, conf_interval = conf_interval, interval_side = interval_side, info = FALSE, - parallel = FALSE # never nest parallelism in workers + parallel = FALSE # never nest parallelism in workers ) } diff --git a/R/custom_eucast_rules.R b/R/custom_interpretive_rules.R similarity index 79% rename from R/custom_eucast_rules.R rename to R/custom_interpretive_rules.R index f047cdb9d..be2a61c78 100755 --- a/R/custom_eucast_rules.R +++ b/R/custom_interpretive_rules.R @@ -27,27 +27,27 @@ # how to conduct AMR data analysis: https://amr-for-r.org # # ==================================================================== # -#' Define Custom EUCAST Rules +#' Define Custom Interpretive Rules #' -#' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()]. +#' Define custom interpretive rules for your organisation or specific analysis and use the output of this function in [interpretive_rules()]. #' @param ... Rules in [formula][base::tilde] notation, see below for instructions, and in *Examples*. #' @details -#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function. +#' Some organisations have their own adoption of interpretive rules. This function can be used to define custom rules to be used in the [interpretive_rules()] function. #' #' ### Basics #' #' If you are familiar with the [`case_when()`][dplyr::case_when()] function of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written *before* the tilde (`~`) and the consequence of the rule is written *after* the tilde: #' #' ```r -#' x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S", -#' TZP == "R" ~ aminopenicillins == "R") +#' x <- custom_interpretive_rules(TZP == "S" ~ aminopenicillins == "S", +#' TZP == "R" ~ aminopenicillins == "R") #' ``` #' -#' These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work: +#' These are two custom interpretive rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work: #' #' ```r #' x -#' #> A set of custom EUCAST rules: +#' #> A set of custom interpretive rules: #' #> #' #> 1. If TZP is "S" then set to S : #' #> amoxicillin (AMX), ampicillin (AMP) @@ -68,11 +68,11 @@ #' #> 1 Escherichia coli R S S #' #> 2 Klebsiella pneumoniae R S S #' -#' eucast_rules(df, -#' rules = "custom", -#' custom_rules = x, -#' info = FALSE, -#' overwrite = TRUE) +#' interpretive_rules(df, +#' rules = "custom", +#' custom_rules = x, +#' info = FALSE, +#' overwrite = TRUE) #' #> mo TZP ampi cipro #' #> 1 Escherichia coli R R S #' #> 2 Klebsiella pneumoniae R R S @@ -83,16 +83,16 @@ #' There is one exception in columns used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), sort = FALSE, documentation = TRUE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`: #' #' ```r -#' y <- custom_eucast_rules( +#' y <- custom_interpretive_rules( #' TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S", #' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R" #' ) #' -#' eucast_rules(df, -#' rules = "custom", -#' custom_rules = y, -#' info = FALSE, -#' overwrite = TRUE) +#' interpretive_rules(df, +#' rules = "custom", +#' custom_rules = y, +#' info = FALSE, +#' overwrite = TRUE) #' #> mo TZP ampi cipro #' #> 1 Escherichia coli R S S #' #> 2 Klebsiella pneumoniae R R S @@ -109,9 +109,9 @@ #' Rules can also be applied to multiple antimicrobials and antimicrobial groups simultaneously. Use the `c()` function to combine multiple antimicrobials. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R": #' #' ```r -#' x <- custom_eucast_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R") +#' x <- custom_interpretive_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R") #' x -#' #> A set of custom EUCAST rules: +#' #> A set of custom interpretive rules: #' #> #' #> 1. If TZP is "R" then set to "R": #' #> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP) @@ -123,7 +123,7 @@ #' @returns A [list] containing the custom rules #' @export #' @examples -#' x <- custom_eucast_rules( +#' x <- custom_interpretive_rules( #' AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", #' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I" #' ) @@ -141,24 +141,24 @@ #' # combine rule sets #' x2 <- c( #' x, -#' custom_eucast_rules(TZP == "R" ~ carbapenems == "R") +#' custom_interpretive_rules(TZP == "R" ~ carbapenems == "R") #' ) #' x2 -custom_eucast_rules <- function(...) { +custom_interpretive_rules <- function(...) { dots <- tryCatch(list(...), error = function(e) "error" ) stop_if( identical(dots, "error"), - "rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}" + "rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun custom_interpretive_rules}](AMR::custom_interpretive_rules)}" ) n_dots <- length(dots) - stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}.") + stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun custom_interpretive_rules}](AMR::custom_interpretive_rules)}.") out <- vector("list", n_dots) for (i in seq_len(n_dots)) { stop_ifnot( inherits(dots[[i]], "formula"), - "rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}" + "rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun custom_interpretive_rules}](AMR::custom_interpretive_rules)}" ) # Query @@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) { result <- dots[[i]][[3]] stop_ifnot( deparse(result) %like% "==", - "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}" + "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help [{.fun custom_interpretive_rules}](AMR::custom_interpretive_rules)}" ) result_group <- as.character(result)[[2]] result_group <- as.character(str2lang(result_group)) @@ -230,13 +230,13 @@ custom_eucast_rules <- function(...) { } names(out) <- paste0("rule", seq_len(n_dots)) - set_clean_class(out, new_class = c("custom_eucast_rules", "list")) + set_clean_class(out, new_class = c("custom_interpretive_rules", "list")) } -#' @method c custom_eucast_rules +#' @method c custom_interpretive_rules #' @noRd #' @export -c.custom_eucast_rules <- function(x, ...) { +c.custom_interpretive_rules <- function(x, ...) { if (length(list(...)) == 0) { return(x) } @@ -245,21 +245,21 @@ c.custom_eucast_rules <- function(x, ...) { out <- c(out, unclass(e)) } names(out) <- paste0("rule", seq_len(length(out))) - set_clean_class(out, new_class = c("custom_eucast_rules", "list")) + set_clean_class(out, new_class = c("custom_interpretive_rules", "list")) } -#' @method as.list custom_eucast_rules +#' @method as.list custom_interpretive_rules #' @noRd #' @export -as.list.custom_eucast_rules <- function(x, ...) { +as.list.custom_interpretive_rules <- function(x, ...) { c(x, ...) } -#' @method print custom_eucast_rules +#' @method print custom_interpretive_rules #' @export #' @noRd -print.custom_eucast_rules <- function(x, ...) { - cat("A set of custom EUCAST rules:\n") +print.custom_interpretive_rules <- function(x, ...) { + cat("A set of custom interpretive rules:\n") for (i in seq_len(length(x))) { rule <- x[[i]] rule$query <- format_custom_query_rule(rule$query) @@ -291,3 +291,19 @@ print.custom_eucast_rules <- function(x, ...) { cat("\n ", rule_if, "\n", rule_then, "\n", sep = "") } } + +# Backward-compat S3 dispatch for objects created with the old custom_eucast_rules() function +#' @method c custom_eucast_rules +#' @noRd +#' @export +c.custom_eucast_rules <- function(x, ...) c.custom_interpretive_rules(x, ...) + +#' @method as.list custom_eucast_rules +#' @noRd +#' @export +as.list.custom_eucast_rules <- function(x, ...) as.list.custom_interpretive_rules(x, ...) + +#' @method print custom_eucast_rules +#' @export +#' @noRd +print.custom_eucast_rules <- function(x, ...) print.custom_interpretive_rules(x, ...) diff --git a/R/first_isolate.R b/R/first_isolate.R old mode 100644 new mode 100755 diff --git a/R/get_episode.R b/R/get_episode.R old mode 100644 new mode 100755 diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R index 0e333d415..8a3338864 100755 --- a/R/interpretive_rules.R +++ b/R/interpretive_rules.R @@ -62,17 +62,17 @@ format_eucast_version_nr <- function(version, markdown = TRUE) { #' @param x A data set with antimicrobials columns, such as `amox`, `AMX` and `AMC`. #' @param info A [logical] to indicate whether progress should be printed to the console - the default is only print while in interactive sessions. #' @param guideline A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option [`AMR_guideline`][AMR-options]. -#' @param rules A [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_interpretive_rules`][AMR-options]: `options(AMR_interpretive_rules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()]. +#' @param rules A [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_interpretive_rules`][AMR-options]: `options(AMR_interpretive_rules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_interpretive_rules()]. #' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time. #' @param version_breakpoints The version number to use for the EUCAST Clinical Breakpoints guideline. Can be `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), documentation = TRUE, reverse = TRUE)`. #' @param version_expected_phenotypes The version number to use for the EUCAST Expected Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_EXPECTED_PHENOTYPES), documentation = TRUE, reverse = TRUE)`. #' @param version_expertrules The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), documentation = TRUE, reverse = TRUE)`. -#' @param ampc_cephalosporin_resistance (only applies when `rules` contains `"expert"` or `"all"`) a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these versions of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`. +#' @param ampc_cephalosporin_resistance (only applies when `rules` contains `"expert"` or `"all"`) a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these versions of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(INTERPRETIVE_RULES_DF[which(INTERPRETIVE_RULES_DF$reference.version %in% c(3.2, 3.3) & INTERPRETIVE_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`. #' @param ... Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; [guess_ab_col()] will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. `AMX = "amoxicillin"`. To skip a specific antimicrobial, set it to `NULL`, e.g. `TIC = NULL` to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning. #' @param ab Any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]. #' @param administration Route of administration, either `r vector_or(dosage$administration, documentation = TRUE)`. #' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be included that were transformed to class [sir][as.sir()] on beforehand. Defaults to `FALSE` if no columns of `x` have a class [sir][as.sir()]. -#' @param custom_rules Custom rules to apply, created with [custom_eucast_rules()]. +#' @param custom_rules Custom rules to apply, created with [custom_interpretive_rules()]. #' @param overwrite A [logical] indicating whether to overwrite existing SIR values (default: `FALSE`). When `FALSE`, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant". #' @param add_if_missing A [logical] indicating whether rules should also be applied to missing (`NA`) values (default: `TRUE`). When `FALSE`, rules are only applied to cells that already contain an SIR value; cells with `NA` are left untouched. This is particularly useful when using `overwrite = TRUE` with custom rules and you want to update reported results without imputing values for untested drugs. #' @inheritParams first_isolate @@ -80,17 +80,17 @@ format_eucast_version_nr <- function(version, markdown = TRUE) { #' **Note:** This function does not translate MIC or disk values to SIR values. Use [as.sir()] for that. \cr #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr #' -#' The file containing all EUCAST rules is located here: . **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms]. +#' The file containing all interpretive rules is located here: . **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms]. #' #' ### Custom Rules #' -#' Custom rules can be created using [custom_eucast_rules()], e.g.: +#' Custom rules can be created using [custom_interpretive_rules()], e.g.: #' #' ```r -#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", -#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I") +#' x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", +#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I") #' -#' eucast_rules(example_isolates, rules = "custom", custom_rules = x) +#' interpretive_rules(example_isolates, rules = "custom", custom_rules = x) #' ``` #' #' ### 'Other' Rules @@ -102,7 +102,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) { #' #' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set. #' -#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_interpretive_rules`][AMR-options], i.e. run `options(AMR_interpretive_rules = "all")`. +#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `interpretive_rules(..., rules = "all")`. You can also set the package option [`AMR_interpretive_rules`][AMR-options], i.e. run `options(AMR_interpretive_rules = "all")`. #' @aliases EUCAST #' @rdname interpretive_rules #' @export @@ -184,7 +184,7 @@ interpretive_rules <- function(x, meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES))) meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE) meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) - meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE) + meet_criteria(custom_rules, allow_class = c("custom_interpretive_rules", "custom_eucast_rules"), allow_NULL = TRUE) meet_criteria(overwrite, allow_class = "logical", has_length = 1) meet_criteria(add_if_missing, allow_class = "logical", has_length = 1) @@ -193,11 +193,6 @@ interpretive_rules <- function(x, "Either set {.arg overwrite} or {.arg add_if_missing} to {.code TRUE}, or both." ) - stop_if( - guideline == "CLSI", - "CLSI guideline is not yet supported." - ) - stop_if( !is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules), "For the {.arg ampc_cephalosporin_resistance} argument to work, the {.arg rules} argument must contain {.code \"expert\"} or {.code \"all\"}." @@ -205,8 +200,14 @@ interpretive_rules <- function(x, add_MO_lookup_to_AMR_env() + if (guideline %like% "EUCAST") { + guideline <- "EUCAST" + } else if (guideline %like% "CLSI") { + guideline <- "CLSI" + } + if ("custom" %in% rules && is.null(custom_rules)) { - warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: no custom rules were set with the {.arg custom_rules} argument", + warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: no custom rules were set with the {.arg custom_rules} argument", immediate = TRUE ) rules <- rules[rules != "custom"] @@ -229,13 +230,13 @@ interpretive_rules <- function(x, if (interactive() && isTRUE(verbose) && isTRUE(info)) { txt <- paste0( - "WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with comprehensive info about which rows and columns would be effected and in which way.", + "WARNING: In Verbose mode, the interpretive_rules() function does not apply rules to the data, but instead returns a data set in logbook form with comprehensive info about which rows and columns would be effected and in which way.", "\n\nThis may overwrite your existing data if you use e.g.:", - "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?" + "\ndata <- interpretive_rules(data, verbose = TRUE)\n\nDo you want to continue?" ) showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE) if (!is.null(showQuestion)) { - q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt) + q_continue <- showQuestion("Using verbose = TRUE with interpretive_rules()", txt) } else { q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt) } @@ -330,7 +331,7 @@ interpretive_rules <- function(x, verbose = verbose, info = info, only_sir_columns = only_sir_columns, - fn = "eucast_rules", + fn = "interpretive_rules", ... ) @@ -489,7 +490,7 @@ interpretive_rules <- function(x, "Rules by the ", font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)), " (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"), - "), see {.help [{.fun eucast_rules}](AMR::eucast_rules)}\n" + "), see {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}\n" ) )) cat("\n\n") @@ -611,59 +612,62 @@ interpretive_rules <- function(x, if (!any(c("all", "custom") %in% rules) && !is.null(custom_rules)) { if (isTRUE(info)) { - message_("Skipping custom EUCAST rules, since the {.arg rules} argument does not contain {.code \"custom\"}.") + message_("Skipping custom interpretive rules, since the {.arg rules} argument does not contain {.code \"custom\"}.") } custom_rules <- NULL } - # >>> Apply Official EUCAST rules <<< --------------------------------------------------- + # >>> Apply Official interpretive rules <<< --------------------------------------------------- eucast_notification_shown <- FALSE - if (!is.null(list(...)$eucast_rules_df)) { - # this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF |> filter(is.na(have_these_values))) - eucast_rules_df_total <- list(...)$eucast_rules_df + if (!is.null(list(...)$interpretive_rules_df)) { + # this allows: interpretive_rules(x, interpretive_rules_df = AMR:::INTERPRETIVE_RULES_DF |> filter(is.na(have_these_values))) + interpretive_rules_df_total <- list(...)$interpretive_rules_df + } else if (!is.null(list(...)$eucast_rules_df)) { + # deprecated parameter name kept for backward compatibility + interpretive_rules_df_total <- list(...)$eucast_rules_df } else { - # otherwise internal data file, created in data-raw/_pre_commit_checks.R - eucast_rules_df_total <- EUCAST_RULES_DF + # internal data file, created in data-raw/_pre_commit_checks.R + interpretive_rules_df_total <- INTERPRETIVE_RULES_DF } - ## filter on user-set guideline versions ---- - eucast_rules_df <- data.frame() + ## filter on guideline provider and user-set guideline versions ---- + interpretive_rules_df <- data.frame() if (any(c("all", "breakpoints") %in% rules)) { - eucast_rules_df <- eucast_rules_df %pm>% - rbind_AMR(eucast_rules_df_total %pm>% - subset(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)) + interpretive_rules_df <- interpretive_rules_df %pm>% + rbind_AMR(interpretive_rules_df_total %pm>% + subset(rule.provider == guideline & reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)) } if (any(c("all", "expected_phenotypes") %in% rules)) { - eucast_rules_df <- eucast_rules_df %pm>% - rbind_AMR(eucast_rules_df_total %pm>% - subset(reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes)) + interpretive_rules_df <- interpretive_rules_df %pm>% + rbind_AMR(interpretive_rules_df_total %pm>% + subset(rule.provider == guideline & reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes)) } if (any(c("all", "expert") %in% rules)) { - eucast_rules_df <- eucast_rules_df %pm>% - rbind_AMR(eucast_rules_df_total %pm>% - subset(reference.rule_group %like% "expert" & reference.version == version_expertrules)) + interpretive_rules_df <- interpretive_rules_df %pm>% + rbind_AMR(interpretive_rules_df_total %pm>% + subset(rule.provider == guideline & reference.rule_group %like% "expert" & reference.version == version_expertrules)) } ## filter out AmpC de-repressed cephalosporin-resistant mutants ---- # no need to filter on version number here - the rules contain these version number, so are inherently filtered # cefotaxime, ceftriaxone, ceftazidime if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) { - eucast_rules_df <- subset( - eucast_rules_df, + interpretive_rules_df <- subset( + interpretive_rules_df, reference.rule %unlike% "ampc" ) } else { if (isTRUE(ampc_cephalosporin_resistance)) { ampc_cephalosporin_resistance <- "R" } - if (!is.null(eucast_rules_df$reference.rule)) { - eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance) + if (!is.null(interpretive_rules_df$reference.rule)) { + interpretive_rules_df[which(interpretive_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance) } } # sometimes, the screenings are missing but the names are actually available - # we only hints on remaining rows in `eucast_rules_df` + # we only hints on remaining rows in `interpretive_rules_df` screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")]) - screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(EUCAST_RULES_DF$and_these_antibiotics[!is.na(EUCAST_RULES_DF$and_these_antibiotics)], ", *")))] + screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(interpretive_rules_df_total$and_these_antibiotics[!is.na(interpretive_rules_df_total$and_these_antibiotics)], ", *")))] if (isTRUE(info)) { cat("\n") } @@ -682,12 +686,12 @@ interpretive_rules <- function(x, } ## Go over all rules and apply them ---- - for (i in seq_len(nrow(eucast_rules_df))) { - rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE] - rule_current <- eucast_rules_df[i, "reference.rule", drop = TRUE] - rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule", drop = TRUE] - rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE] - rule_group_current <- eucast_rules_df[i, "reference.rule_group", drop = TRUE] + for (i in seq_len(nrow(interpretive_rules_df))) { + rule_previous <- interpretive_rules_df[max(1, i - 1), "reference.rule", drop = TRUE] + rule_current <- interpretive_rules_df[i, "reference.rule", drop = TRUE] + rule_next <- interpretive_rules_df[min(nrow(interpretive_rules_df), i + 1), "reference.rule", drop = TRUE] + rule_group_previous <- interpretive_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE] + rule_group_current <- interpretive_rules_df[i, "reference.rule_group", drop = TRUE] # don't apply rules if user doesn't want to apply them if (rule_group_current %like% "breakpoint" && !any(c("all", "breakpoints") %in% rules)) { next @@ -702,16 +706,16 @@ interpretive_rules <- function(x, if (isFALSE(info) || isFALSE(verbose)) { rule_text <- "" } else { - if (is.na(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE])) { - rule_text <- paste0("always report as '", eucast_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])) + if (is.na(interpretive_rules_df[i, "and_these_antibiotics", drop = TRUE])) { + rule_text <- paste0("always report as '", interpretive_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(interpretive_rules_df[i, "then_change_these_antibiotics", drop = TRUE])) } else { rule_text <- paste0( - "report as '", eucast_rules_df[i, "to_value", drop = TRUE], "' when ", + "report as '", interpretive_rules_df[i, "to_value", drop = TRUE], "' when ", format_antibiotic_names( - ab_names = get_antibiotic_names(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]), - ab_results = eucast_rules_df[i, "have_these_values", drop = TRUE] + ab_names = get_antibiotic_names(interpretive_rules_df[i, "and_these_antibiotics", drop = TRUE]), + ab_results = interpretive_rules_df[i, "have_these_values", drop = TRUE] ), ": ", - get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]) + get_antibiotic_names(interpretive_rules_df[i, "then_change_these_antibiotics", drop = TRUE]) ) } } @@ -720,7 +724,7 @@ interpretive_rules <- function(x, rule_previous <- "" rule_group_previous <- "" } - if (i == nrow(eucast_rules_df)) { + if (i == nrow(interpretive_rules_df)) { rule_next <- "" } @@ -789,13 +793,13 @@ interpretive_rules <- function(x, } ## Get rule from file ------------------------------------------------------ - if_mo_property <- trimws(eucast_rules_df[i, "if_mo_property", drop = TRUE]) - like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE]) - mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE]) - source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE] - source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE))) - target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE] - target_value <- eucast_rules_df[i, "to_value", drop = TRUE] + if_mo_property <- trimws(interpretive_rules_df[i, "if_mo_property", drop = TRUE]) + like_is_one_of <- trimws(interpretive_rules_df[i, "like.is.one_of", drop = TRUE]) + mo_value <- trimws(interpretive_rules_df[i, "this_value", drop = TRUE]) + source_antibiotics <- interpretive_rules_df[i, "and_these_antibiotics", drop = TRUE] + source_value <- trimws(unlist(strsplit(interpretive_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE))) + target_antibiotics <- interpretive_rules_df[i, "then_change_these_antibiotics", drop = TRUE] + target_value <- interpretive_rules_df[i, "to_value", drop = TRUE] # if amo_value contains a group name, expand that name with all species in it if (any(trimws(strsplit(mo_value, ",")[[1]]) %in% AMR::microorganisms.groups$mo_group_name, na.rm = TRUE)) { @@ -894,7 +898,7 @@ interpretive_rules <- function(x, if (!is.null(custom_rules)) { if (isTRUE(info)) { cat("\n") - cat(font_bold("Custom EUCAST rules, set by user"), "\n") + cat(font_bold("Custom interpretive rules, set by user"), "\n") } for (i in seq_len(length(custom_rules))) { rule <- custom_rules[[i]] @@ -929,8 +933,8 @@ interpretive_rules <- function(x, to = target_value, rule = c( rule_text, - "Custom EUCAST rules", - paste0("Custom EUCAST rule ", i), + "Custom interpretive rules", + paste0("Custom interpretive rule ", i), paste0( "Object '", deparse(substitute(custom_rules)), "' consisting of ", length(custom_rules), " custom rules" @@ -1075,7 +1079,7 @@ interpretive_rules <- function(x, warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))] warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)] warning_( - "in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: not all columns with antimicrobial results are of class {.cls sir}. Transform them on beforehand, e.g.:\n\n", + "in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: not all columns with antimicrobial results are of class {.cls sir}. Transform them on beforehand, e.g.:\n\n", "\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0(x_deparsed, " |> as.sir(", ifelse(length(warn_lacking_sir_class) == 1, warn_lacking_sir_class, paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)]) @@ -1177,7 +1181,7 @@ edit_sir <- function(x, new_edits[rows, cols] == "NS") non_SIR <- !isSIR if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) { - warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: some columns had SIR values which were not overwritten, since {.code overwrite = FALSE}.") + warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: some columns had SIR values which were not overwritten, since {.code overwrite = FALSE}.") } # determine which cells to modify based on overwrite and add_if_missing if (isTRUE(overwrite)) { @@ -1211,7 +1215,7 @@ edit_sir <- function(x, }) suppressWarnings(do_assign()) warning_( - "in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: value \"", to, "\" added to the factor levels of column", + "in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"), " ", vector_and(cols, quotes = "`", sort = FALSE), " because this value was not an existing factor level." @@ -1219,7 +1223,7 @@ edit_sir <- function(x, txt_warning() warned <<- FALSE } else { - warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: ", w$message) + warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: ", w$message) txt_warning() } }, diff --git a/R/mic.R b/R/mic.R old mode 100644 new mode 100755 diff --git a/R/proportion.R b/R/proportion.R old mode 100644 new mode 100755 diff --git a/R/sysdata.rda b/R/sysdata.rda index d95f3a50c..397e8cd86 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/R/tidymodels.R b/R/tidymodels.R old mode 100644 new mode 100755 diff --git a/R/zz_deprecated.R b/R/zz_deprecated.R index fb9b7c1dc..66f4076db 100755 --- a/R/zz_deprecated.R +++ b/R/zz_deprecated.R @@ -70,6 +70,13 @@ as.data.frame.deprecated_amr_dataset <- function(x, ...) { # - `antibiotics` in `antibiogram()` # - `converse_capped_values` in `as.sir()` +#' @rdname AMR-deprecated +#' @export +custom_eucast_rules <- function(...) { + deprecation_warning("custom_eucast_rules", "custom_interpretive_rules", is_function = TRUE) + custom_interpretive_rules(...) +} + #' @rdname AMR-deprecated #' @export ab_class <- function(...) { diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index 6a083863d..60c776fdf 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -42,9 +42,9 @@ pre_commit_lst <- list() usethis::ui_info(paste0("Updating internal package data")) -# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file -pre_commit_lst$EUCAST_RULES_DF <- utils::read.delim( - file = "data-raw/eucast_rules.tsv", +# See 'data-raw/interpretive_rules.tsv' for the interpretive rules reference file +pre_commit_lst$INTERPRETIVE_RULES_DF <- utils::read.delim( + file = "data-raw/interpretive_rules.tsv", skip = 9, sep = "\t", stringsAsFactors = FALSE, @@ -364,7 +364,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c( ) # antibiotic groups -# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv) +# (these will also be used for interpretive_rules() and understanding data-raw/interpretive_rules.tsv) pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>% filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>% pull(ab) diff --git a/data-raw/interpretive_rules.tsv b/data-raw/interpretive_rules.tsv new file mode 100644 index 000000000..8c5c22473 --- /dev/null +++ b/data-raw/interpretive_rules.tsv @@ -0,0 +1,1533 @@ +# ------------------------------------------------------------------------------------------------------------------------------- +# For editing this interpretive rules reference file, these values can all be used for targeting antibiotics: +# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, betalactams_with_inhibitor, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins +# and all separate EARS-Net letter codes such as 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'. If 'this_value' exists in AMR::microorganisms.groups$mo_group_name it will be expanded in interpretive_rules() to all relevant species occuring in microorganisms.groups$mo_name before further processing of the line in this file. +# 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 and later +# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 9 LINES SKIPPED <<<<< +# ------------------------------------------------------------------------------------------------------------------------------- +rule.provider reference.rule_group reference.version reference.rule if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value note +EUCAST Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S +EUCAST Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I +EUCAST Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R +EUCAST Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP S LVX S +EUCAST Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP I LVX I +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus sanguinicola CIP R LVX R +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae NOR S fluoroquinolones S +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae NOR I fluoroquinolones I +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae NOR R fluoroquinolones R +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 10 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S +EUCAST Breakpoints 10 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I +EUCAST Breakpoints 10 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R +EUCAST Breakpoints 10 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S +EUCAST Breakpoints 10 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I +EUCAST Breakpoints 10 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R +EUCAST Breakpoints 10 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY S DOX S +EUCAST Breakpoints 10 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY I DOX I +EUCAST Breakpoints 10 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY R DOX R +EUCAST Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli ERY S AZM, CLR S +EUCAST Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli ERY I AZM, CLR I +EUCAST Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli ERY R AZM, CLR R +EUCAST Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli TCY S DOX S +EUCAST Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli TCY I DOX I +EUCAST Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli TCY R DOX R +EUCAST Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 10 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 10 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 10 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 10 Enterococcus genus is Enterococcus AMP S AMX, AMC, PIP, TZP S +EUCAST Breakpoints 10 Enterococcus genus is Enterococcus AMP I AMX, AMC, PIP, TZP I +EUCAST Breakpoints 10 Enterococcus genus is Enterococcus AMP R AMX, AMC, PIP, TZP R +EUCAST Breakpoints 10 Enterococcus genus is Enterococcus NOR S CIP, LVX S +EUCAST Breakpoints 10 Enterococcus genus is Enterococcus NOR I CIP, LVX I +EUCAST Breakpoints 10 Enterococcus genus is Enterococcus NOR R CIP, LVX R +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMP S AMX, PIP S +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMP I AMX, PIP I +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMP R AMX, PIP R +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S TZP S +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I TZP I +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R TZP R +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae TCY I DOX I +EUCAST Breakpoints 10 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 10 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 10 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 10 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus PEN, FOX R, S OXA, FLC S +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus FOX R betalactams R +EUCAST Breakpoints 10 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R +EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G 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 +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S MFX S +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX I +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +EUCAST Breakpoints 10 Viridans group streptococci 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 +EUCAST Breakpoints 10 Viridans group streptococci 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 +EUCAST Breakpoints 10 Viridans group streptococci 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 +EUCAST Breakpoints 10 Viridans group streptococci 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 +EUCAST Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S +EUCAST Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I +EUCAST Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R +EUCAST Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP S LVX S +EUCAST Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP I LVX I +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus sanguinicola CIP R LVX R +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae NOR S fluoroquinolones S +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae NOR I fluoroquinolones I +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae NOR R fluoroquinolones R +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 11 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TIC S +EUCAST Breakpoints 11 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TIC I +EUCAST Breakpoints 11 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TIC R +EUCAST Breakpoints 11 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TIC S +EUCAST Breakpoints 11 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TIC I +EUCAST Breakpoints 11 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TIC R +EUCAST Breakpoints 11 Bacillus genus is Bacillus NOR S fluoroquinolones S added in 11 +EUCAST Breakpoints 11 Bacillus genus is Bacillus NOR I fluoroquinolones I added in 11 +EUCAST Breakpoints 11 Bacillus genus is Bacillus NOR R fluoroquinolones R added in 11 +EUCAST Breakpoints 11 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY S DOX S +EUCAST Breakpoints 11 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY I DOX I +EUCAST Breakpoints 11 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY R DOX R +EUCAST Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli ERY S AZM, CLR S +EUCAST Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli ERY I AZM, CLR I +EUCAST Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli ERY R AZM, CLR R +EUCAST Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli TCY S DOX S +EUCAST Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli TCY I DOX I +EUCAST Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli TCY R DOX R +EUCAST Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 11 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 11 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 11 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 11 Enterococcus genus is Enterococcus AMP S AMX, AMC, PIP, TZP S +EUCAST Breakpoints 11 Enterococcus genus is Enterococcus AMP I AMX, AMC, PIP, TZP I +EUCAST Breakpoints 11 Enterococcus genus is Enterococcus AMP R AMX, AMC, PIP, TZP R +EUCAST Breakpoints 11 Enterococcus genus is Enterococcus NOR S CIP, LVX S +EUCAST Breakpoints 11 Enterococcus genus is Enterococcus NOR I CIP, LVX I +EUCAST Breakpoints 11 Enterococcus genus is Enterococcus NOR R CIP, LVX R +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMP S AMX, PIP S +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMP I AMX, PIP I +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMP R AMX, PIP R +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S TZP S +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I TZP I +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R TZP R +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae TCY I DOX I +EUCAST Breakpoints 11 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 11 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 11 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 11 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus PEN, FOX R, S OXA, FLC S +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus FOX R betalactams R +EUCAST Breakpoints 11 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R +EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S +EUCAST Breakpoints 11 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G 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 +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S MFX S +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX I +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +EUCAST Breakpoints 11 Viridans group streptococci 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 +EUCAST Breakpoints 11 Viridans group streptococci 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 +EUCAST Breakpoints 11 Viridans group streptococci 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 +EUCAST Breakpoints 11 Viridans group streptococci 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 +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +EUCAST Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +EUCAST Breakpoints 12 Bacillus genus is Bacillus NOR-S S CIP, LVX I +EUCAST Breakpoints 12 Bacillus genus is Bacillus NOR-S R CIP, LVX R +EUCAST Breakpoints 12 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +EUCAST Breakpoints 12 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +EUCAST Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 12 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 12 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 12 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 12 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +EUCAST Breakpoints 12 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +EUCAST Breakpoints 12 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +EUCAST Breakpoints 12 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +EUCAST Breakpoints 12 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +EUCAST Breakpoints 12 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +EUCAST Breakpoints 12 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +EUCAST Breakpoints 12 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +EUCAST Breakpoints 12 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 12 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I +EUCAST Breakpoints 12 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R +EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 12 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis BLA-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R penicillins()[!penicillins() %in% betalactams_with_inhibitor()] +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +EUCAST Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +EUCAST Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +EUCAST Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +EUCAST Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +EUCAST Breakpoints 12 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +EUCAST Breakpoints 12 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +EUCAST Breakpoints 12 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +EUCAST Breakpoints 12 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +EUCAST Breakpoints 12 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +EUCAST Breakpoints 12 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +EUCAST Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +EUCAST Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S R penicillins R See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus NOR-S S MFX S +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S MRSA isolates are in this file safely denoted as FOX resistant +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S +EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio ERY S AZM S +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio ERY I AZM I +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio ERY R AZM R +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio TCY-S S DOX S +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio TCY-S I DOX I +EUCAST Breakpoints 12 Vibrio spp. genus is Vibrio TCY-S R DOX R +EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +EUCAST Breakpoints 13 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP S AMX S +EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP I AMX I +EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP R AMX R +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +EUCAST Breakpoints 14 Bacillus genus is Bacillus NOR-S S CIP, LVX I +EUCAST Breakpoints 14 Bacillus genus is Bacillus NOR-S R CIP, LVX R +EUCAST Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis PEN I AMX S +EUCAST Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis PEN R AMX R +EUCAST Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis TCY-S S DOX S +EUCAST Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis TCY-S R DOX R +EUCAST Breakpoints 14 Brucella melitensis genus_species is Brucella melitensis TCY-S S DOX S +EUCAST Breakpoints 14 Brucella melitensis genus_species is Brucella melitensis TCY-S R DOX R +EUCAST Breakpoints 14 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +EUCAST Breakpoints 14 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +EUCAST Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +EUCAST Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +EUCAST Breakpoints 14 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 14 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 14 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 14 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +EUCAST Breakpoints 14 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +EUCAST Breakpoints 14 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +EUCAST Breakpoints 14 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +EUCAST Breakpoints 14 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +EUCAST Breakpoints 14 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +EUCAST Breakpoints 14 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +EUCAST Breakpoints 14 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +EUCAST Breakpoints 14 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 14 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I +EUCAST Breakpoints 14 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R +EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 14 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis BLA-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R penicillins()[!penicillins() %in% betalactams_with_inhibitor()] +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +EUCAST Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +EUCAST Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +EUCAST Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +EUCAST Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +EUCAST Breakpoints 14 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +EUCAST Breakpoints 14 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +EUCAST Breakpoints 14 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +EUCAST Breakpoints 14 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +EUCAST Breakpoints 14 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +EUCAST Breakpoints 14 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +EUCAST Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +EUCAST Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S R penicillins R See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus NOR-S S MFX S +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus coagulase-negative VAN, TEC S, S DAL S +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S MRSA isolates are in this file safely denoted as FOX resistant +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S +EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio ERY S AZM S +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio ERY I AZM I +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio ERY R AZM R +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio TCY-S S DOX S +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio TCY-S I DOX I +EUCAST Breakpoints 14 Vibrio spp. genus is Vibrio TCY-S R DOX R +EUCAST Breakpoints 14 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S will be expanded in eucast_rules() +EUCAST Breakpoints 14 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R will be expanded in eucast_rules() +EUCAST Breakpoints 14 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S will be expanded in eucast_rules() +EUCAST Breakpoints 14 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I will be expanded in eucast_rules() +EUCAST Breakpoints 14 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R will be expanded in eucast_rules() +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP S AMX S +EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP I AMX I +EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP R AMX R +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +EUCAST Breakpoints 15 Bacillus genus is Bacillus NOR-S S CIP, LVX I +EUCAST Breakpoints 15 Bacillus genus is Bacillus NOR-S R CIP, LVX R +EUCAST Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis PEN I AMX S +EUCAST Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis PEN R AMX R +EUCAST Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis TCY-S S DOX S +EUCAST Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis TCY-S R DOX R +EUCAST Breakpoints 15 Brucella melitensis genus_species is Brucella melitensis TCY-S S DOX S +EUCAST Breakpoints 15 Brucella melitensis genus_species is Brucella melitensis TCY-S R DOX R +EUCAST Breakpoints 15 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +EUCAST Breakpoints 15 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +EUCAST Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +EUCAST Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +EUCAST Breakpoints 15 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 15 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 15 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 15 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +EUCAST Breakpoints 15 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +EUCAST Breakpoints 15 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +EUCAST Breakpoints 15 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +EUCAST Breakpoints 15 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +EUCAST Breakpoints 15 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +EUCAST Breakpoints 15 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +EUCAST Breakpoints 15 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX S +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX I +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX R +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus AMP R AMX, AMC R +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 15 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis BLA-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R penicillins()[!penicillins() %in% betalactams_with_inhibitor()] +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +EUCAST Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +EUCAST Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +EUCAST Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +EUCAST Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +EUCAST Breakpoints 15 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +EUCAST Breakpoints 15 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +EUCAST Breakpoints 15 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +EUCAST Breakpoints 15 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +EUCAST Breakpoints 15 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +EUCAST Breakpoints 15 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +EUCAST Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +EUCAST Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S R penicillins R See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S S MFX S +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S +EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio ERY S AZM S +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio ERY I AZM I +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio ERY R AZM R +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio TCY-S S DOX S +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio TCY-S I DOX I +EUCAST Breakpoints 15 Vibrio spp. genus is Vibrio TCY-S R DOX R +EUCAST Breakpoints 15 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 15 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 15 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 15 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 15 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP S AMX S +EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP I AMX I +EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP R AMX R +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +EUCAST Breakpoints 16 Bacillus genus is Bacillus NOR-S S CIP, LVX I +EUCAST Breakpoints 16 Bacillus genus is Bacillus NOR-S R CIP, LVX R +EUCAST Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis PEN I AMX S +EUCAST Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis PEN R AMX R +EUCAST Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis TCY-S S DOX S +EUCAST Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis TCY-S R DOX R +EUCAST Breakpoints 16 Brucella melitensis genus_species is Brucella melitensis TCY-S S DOX S +EUCAST Breakpoints 16 Brucella melitensis genus_species is Brucella melitensis TCY-S R DOX R +EUCAST Breakpoints 16 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +EUCAST Breakpoints 16 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +EUCAST Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +EUCAST Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +EUCAST Breakpoints 16 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 16 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 16 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 16 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +EUCAST Breakpoints 16 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +EUCAST Breakpoints 16 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +EUCAST Breakpoints 16 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +EUCAST Breakpoints 16 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +EUCAST Breakpoints 16 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +EUCAST Breakpoints 16 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +EUCAST Breakpoints 16 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX S +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX I +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX R +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus AMP R AMX, AMC R +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 16 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis BLA-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R penicillins()[!penicillins() %in% betalactams_with_inhibitor()] +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +EUCAST Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +EUCAST Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +EUCAST Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +EUCAST Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +EUCAST Breakpoints 16 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +EUCAST Breakpoints 16 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +EUCAST Breakpoints 16 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +EUCAST Breakpoints 16 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +EUCAST Breakpoints 16 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +EUCAST Breakpoints 16 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +EUCAST Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +EUCAST Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +EUCAST Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus FOX-S R penicillins R See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins +EUCAST Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +EUCAST Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 16 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S S CZO, FEP, CTX, CRO, CXM I +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTA, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FEP, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("CZO", "FEP", "CTX", "CRO", "CXM", "cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "cefiderocol", "ceftolozan/tazobactam"))])) |> toString() +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTA, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FEP, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "cefiderocol", "ceftolozan/tazobactam"))])) |> toString() +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTA, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FEP, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "cefiderocol", "ceftolozan/tazobactam"))])) |> toString() +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus OXA-S S CZO, FEP, CTX, CRO, CXM I +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTA, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FEP, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("CZO", "FEP", "CTX", "CRO", "CXM", "cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "cefiderocol", "ceftolozan/tazobactam"))])) |> toString() +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTA, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FEP, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "cefiderocol", "ceftolozan/tazobactam"))])) |> toString() +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTA, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FEP, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "cefiderocol", "ceftolozan/tazobactam"))])) |> toString() +EUCAST Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +EUCAST Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S S MFX S +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S +EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio ERY S AZM S +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio ERY I AZM I +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio ERY R AZM R +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio TCY-S S DOX S +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio TCY-S I DOX I +EUCAST Breakpoints 16 Vibrio spp. genus is Vibrio TCY-S R DOX R +EUCAST Breakpoints 16 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 16 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 16 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 16 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 16 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R MO group name will be expanded in eucast_rules() +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP S AMX S +EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP I AMX I +EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP R AMX R +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +EUCAST Breakpoints 13.1 Bacillus genus is Bacillus NOR-S S CIP, LVX I +EUCAST Breakpoints 13.1 Bacillus genus is Bacillus NOR-S R CIP, LVX R +EUCAST Breakpoints 13.1 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +EUCAST Breakpoints 13.1 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +EUCAST Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +EUCAST Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +EUCAST Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +EUCAST Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +EUCAST Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +EUCAST Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I +EUCAST Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +EUCAST Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +EUCAST Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +EUCAST Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +EUCAST Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +EUCAST Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +EUCAST Breakpoints 13.1 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +EUCAST Breakpoints 13.1 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +EUCAST Breakpoints 13.1 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +EUCAST Breakpoints 13.1 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +EUCAST Breakpoints 13.1 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +EUCAST Breakpoints 13.1 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I +EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R +EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae TCY S DOX S +EUCAST Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae TCY R DOX R +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis BLA-S R AMP, AMX, APL, APX, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CLO, CRB, CRN, DIC, EPC, FLC, HET, LEN, MEC, MET, MEZ, MTM, NAF, OXA, PEN, PHE, PHN, PIP, PME, PNM, PRB, PRC, PRP, PVM, SBC, SLT6, SRX, TAL, TEM, TIC R penicillins()[!penicillins() %in% betalactams_with_inhibitor()] +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +EUCAST Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +EUCAST Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +EUCAST Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +EUCAST Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +EUCAST Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +EUCAST Breakpoints 13.1 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +EUCAST Breakpoints 13.1 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +EUCAST Breakpoints 13.1 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +EUCAST Breakpoints 13.1 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +EUCAST Breakpoints 13.1 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +EUCAST Breakpoints 13.1 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +EUCAST Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +EUCAST Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +EUCAST Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +EUCAST Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +EUCAST Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S R penicillins R See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP S sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP I sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R BPR, CAC, CAT, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CID, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPT, CPX, CRD, CRO, CSE, CSL, CSU, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZD, CZL, CZO, CZP, CZX, DIT, DIX, DIZ, FDC, FEP, FNC, FOV, FOX, FOX-S, FPT, FPZ, HAP, LOR, LTM, MAN, RID, TIO, ZOP R sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus NOR-S S MFX S +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S +EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S MRSA isolates are in this file safely denoted as FOX resistant +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN S AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP S penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN I AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP I penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species is Streptococcus Group B PEN R AMC, AMP, AMX, APL, APX, AXS, AZD, AZL, BAM, BNB, BNP, CIC, CLM, CRB, CRN, EPC, HET, LEN, MEC, MEZ, MSU, MTM, NAF, PEN, PHE, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, SAM, SBC, SLT6, SRX, TAL, TCC, TEM, TIC, TZP R penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S +EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R does not explicitly state that it is for other fluoroquinolones +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio ERY S AZM S +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio ERY I AZM I +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio ERY R AZM R +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio TCY-S S DOX S +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio TCY-S I DOX I +EUCAST Breakpoints 13.1 Vibrio spp. genus is Vibrio TCY-S R DOX R +EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S will be expanded in eucast_rules() +EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R will be expanded in eucast_rules() +EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S will be expanded in eucast_rules() +EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I will be expanded in eucast_rules() +EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R will be expanded in eucast_rules() +EUCAST Breakpoints Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints Anaerobic bacteria genus is Prevotella AMP S AMX S +EUCAST Breakpoints Anaerobic bacteria genus is Prevotella AMP I AMX I +EUCAST Breakpoints Anaerobic bacteria genus is Prevotella AMP R AMX R +EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I +EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species one_of Citrobacter koseri, Citrobacter amalonaticus AMP, AMX, TIC R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Citrobacter freundii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species one_of Enterobacter cloacae complex AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii AMP, AMX, TIC R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Hafnia alvei AMP, AMX, PLB, COL R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Klebsiella aerogenes AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species one_of Klebsiella pneumoniae complex AMX, AMP, TIC R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca AMX, AMP, TIC R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Morganella morganii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides AMX, AMP, SAM R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Proteus mirabilis tetracyclines, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Proteus penneri AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Proteus vulgaris AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Providencia rettgeri AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Providencia stuartii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus is Raoultella AMP, AMX, TIC R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Serratia marcescens AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Yersinia enterocolitica AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis PLB, COL R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila AMP, AMX, SAM R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii AMP, AMX, SAM, TIC R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis AMP, AMX, SAM, FOX R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae AMP, AMX, SAM R +EUCAST Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas jandaei AMP, AMX, SAM, TIC R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus one_of Acinetobacter, Achromobacter, Burkholderia, Elizabethkingia, Elizabethkingia, Ochrobactrum, Pseudomonas, Stenotrophomonas, Chryseobacterium PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species one_of Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter nosocomialis AMP, AMX, AMC, CTX, CRO, ATM, ETP, TMP, FOS, TCY, DOX R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species is Achromobacter xylosoxidans AMP, AMX, CTX, CRO, ATM, ETP R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species one_of Burkholderia cepacia complex AMP, AMX, AMC, SAM, TIC, TCC, PIP, TZP, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, PLB, COL R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species is Elizabethkingia meningoseptica AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, PLB, COL R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species is Elizabethkingia anophelis AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species is Ochrobactrum anthropi AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species is Pseudomonas aeruginosa AMP, AMX, AMC, SAM, CTX, CRO, ETP, CHL, TMP, KAN, NEO, tetracyclines, TGC R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus_species is Stenotrophomonas maltophilia AMP, AMX, AMC, SAM, TIC, PIP, TZP, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R +EUCAST Expected phenotypes 1.2 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria genus is Chryseobacterium AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, PLB, COL R +EUCAST Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins R +EUCAST Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species is Moraxella catarrhalis TMP R +EUCAST Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus is Neisseria TMP R +EUCAST Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R +EUCAST Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species one_of Campylobacter jejuni, Campylobacter coli FUS, streptogramins, TMP R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria gramstain is Gram-positive ATM, TEM, PLB, COL, NAL R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species one_of Coagulase-negative Staphylococcus (CoNS), Staphylococcus aureus CAZ R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, sulfonamides R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species one_of Enterococcus gallinarum, Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, sulfonamides R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, sulfonamides R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus is Corynebacterium FOS R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, FOS R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Lactobacillus casei VAN, FOS R +EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria fullname is Lactobacillus casei rhamnosus VAN, FOS R +EUCAST Expected phenotypes 1.2 Table 5: Expected resistant phenotype in anaerobes genus_species one_of Clostridium ramosum, Clostridium innocuum VAN R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Escherichia hermannii aminopenicillins, TIC R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus is Klebsiella aminopenicillins, TIC R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Morganella morganii aminopenicillins, AMC, CZO, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Proteus penneri aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus is Raoultella aminopenicillins, TIC R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R +EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Yersinia pseudotuberculosis PLB, COL R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria 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 +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Brucella anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, DOX, MNO, TCY, TGC R +EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides_except_lipo, LIN, DAP, LNZ R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Moraxella catarrhalis TMP R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus is Neisseria TMP R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter jejuni FUS, streptogramins, TMP R +EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter coli FUS, streptogramins, TMP R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria gramstain is Gram-positive ATM, polymyxins, NAL R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus aureus CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus epidermidis CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus hominis CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus haemolyticus CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus intermedius CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus pseudintermedius CAZ R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Corynebacterium FOS R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Listeria monocytogenes cephalosporins R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Lactobacillus glycopeptides_except_lipo R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Clostridium ramosum VAN R +EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Clostridium innocuum VAN R +EUCAST Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S +EUCAST Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus is Enterococcus AMP R ureidopenicillins, carbapenems R +EUCAST Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus is Enterococcus AMX R ureidopenicillins, carbapenems R +EUCAST Expert Rules 3.1 Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) order is Enterobacterales TIC, PIP R, S PIP R +EUCAST Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY S AZM, CLR S +EUCAST Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY I AZM, CLR I +EUCAST Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY R AZM, CLR R +EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides genus is Staphylococcus TOB R KAN, AMK R +EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides genus is Staphylococcus GEN R aminoglycosides R +EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides order is Enterobacterales GEN, TOB I, S GEN R +EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides order is Enterobacterales GEN, TOB R, I TOB R +EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus is Staphylococcus MFX R fluoroquinolones R +EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R +EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones order is Enterobacterales CIP R fluoroquinolones R +EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R +EUCAST Expert Rules 3.2 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S +EUCAST Expert Rules 3.2 Expert Rules on Campylobacter genus_species is Campylobacter ERY R CLR, AZM R +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales 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, 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 This is Enterobacterales except Salmonella spp. +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Morganella morganii) TGC R +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.2 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R +EUCAST Expert Rules 3.2 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R +EUCAST Expert Rules 3.2 Expert Rules on Enterococcus genus is Enterococcus NOR S CIP, LVX S +EUCAST Expert Rules 3.2 Expert Rules on Enterococcus genus is Enterococcus VAN S lipoglycopeptides S +EUCAST Expert Rules 3.2 Expert Rules on Enterococcus genus_species is Enterococcus faecium CLI R +EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae PEN S betalactams S +EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL S fluoroquinolones S +EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R +EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Expert Rules 3.2 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S fluoroquinolones S +EUCAST Expert Rules 3.2 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL R fluoroquinolones R +EUCAST Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella cephalosporins_2nd R +EUCAST Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella aminoglycosides R +EUCAST Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella PEF R CIP R +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R betalactams R +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus 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 all penicillins without beta-lactamse inhibitor +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus ERY, CLI S macrolides, lincosamides S +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus LVX R fluoroquinolones R +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus MFX R fluoroquinolones R +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus TCY S DOX, MNO, TGC S +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus TCY R DOX, MNO R +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus VAN S lipoglycopeptides S +EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus LNZ S TZD S +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX, MFX S +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR R LVX, MFX R +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY R DOX, MNO R +EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S +EUCAST Expert Rules 3.2 Expert Rules on Viridans Group Streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii aminopenicillins, TIC R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca aminopenicillins, TIC R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus is Raoultella aminopenicillins, TIC R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis polymyxins R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila aminopenicillins, AMC, SAM, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R +EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus is Acinetobacter DOX, TCY R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria 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 Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria gramstain is Gram-positive ATM, TEM, polymyxins, NAL R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus aureus CAZ R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Corynebacterium FOS R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, TEC R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Lactobacillus VAN, TEC R +EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Clostridium (ramosum|innocuum) VAN R +EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S +EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus_species is Campylobacter ERY R CLR, AZM R +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales 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, 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 This is Enterobacterales except Salmonella spp. +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Morganella morganii) TGC R +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +EUCAST Expert Rules 3.3 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R +EUCAST Expert Rules 3.3 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R +EUCAST Expert Rules 3.3 Expert Rules on Enterococcus genus is Enterococcus NOR S CIP, LVX S +EUCAST Expert Rules 3.3 Expert Rules on Enterococcus genus is Enterococcus VAN S lipoglycopeptides S +EUCAST Expert Rules 3.3 Expert Rules on Enterococcus genus_species is Enterococcus faecium CLI R +EUCAST Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae PEN S betalactams S +EUCAST Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL S fluoroquinolones S +EUCAST Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R +EUCAST Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +EUCAST Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +EUCAST Expert Rules 3.3 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S fluoroquinolones S +EUCAST Expert Rules 3.3 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL R fluoroquinolones R +EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella cephalosporins_2nd R +EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella aminoglycosides R +EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella PEF R CIP R +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R betalactams R +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus 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 all penicillins without beta-lactamse inhibitor +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus ERY, CLI S macrolides, lincosamides S +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus LVX R fluoroquinolones R +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus MFX R fluoroquinolones R +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus TCY S DOX, MNO, TGC S +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus TCY R DOX, MNO R +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus VAN S lipoglycopeptides S +EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus LNZ S TZD S +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX, MFX S +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR R LVX, MFX R +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY R DOX, MNO R +EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S +EUCAST Expert Rules 3.3 Expert Rules on Viridans Group Streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii aminopenicillins, TIC R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Hafnia alvei aminopenicillins, AMC, polymyxins R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca aminopenicillins, TIC R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus is Raoultella aminopenicillins, TIC R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis polymyxins R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila aminopenicillins, SAM R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii aminopenicillins, SAM, TIC R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis aminopenicillins, SAM, FOX R +EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae aminopenicillins, SAM R +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus is Acinetobacter DOX, TCY R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP, ATM R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria 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 Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Elizabethkingia anophelis aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus is Chryseobacterium aminopenicillins, AMC, SAM, TIC, TCC, CRO, CTX, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, polymyxins R Additional rules from header added in separate rule (genus is one of…) +EUCAST Expert Rules 3.3 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.3 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.3 Table 3: Intrinsic resistance in other gram-negative bacteria genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.3 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.3 Table 3: Intrinsic resistance in other gram-negative bacteria fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria gramstain is Gram-positive ATM, TEM, polymyxins, NAL R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus aureus CAZ R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus is Corynebacterium FOS R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, TEC R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus is Lactobacillus VAN, TEC R +EUCAST Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Clostridium (ramosum|innocuum) VAN R diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd index fa51804a8..8e28e757d 100644 --- a/man/AMR-deprecated.Rd +++ b/man/AMR-deprecated.Rd @@ -2,10 +2,13 @@ % Please edit documentation in R/zz_deprecated.R \name{AMR-deprecated} \alias{AMR-deprecated} +\alias{custom_eucast_rules} \alias{ab_class} \alias{ab_selector} \title{Deprecated Functions, Arguments, or Datasets} \usage{ +custom_eucast_rules(...) + ab_class(...) ab_selector(...) diff --git a/man/custom_eucast_rules.Rd b/man/custom_interpretive_rules.Rd similarity index 93% rename from man/custom_eucast_rules.Rd rename to man/custom_interpretive_rules.Rd index 355578f88..5ee3b9ec0 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_interpretive_rules.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/custom_eucast_rules.R -\name{custom_eucast_rules} -\alias{custom_eucast_rules} -\title{Define Custom EUCAST Rules} +% Please edit documentation in R/custom_interpretive_rules.R +\name{custom_interpretive_rules} +\alias{custom_interpretive_rules} +\title{Define Custom Interpretive Rules} \usage{ -custom_eucast_rules(...) +custom_interpretive_rules(...) } \arguments{ \item{...}{Rules in \link[base:tilde]{formula} notation, see below for instructions, and in \emph{Examples}.} @@ -13,22 +13,22 @@ custom_eucast_rules(...) A \link{list} containing the custom rules } \description{ -Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in \code{\link[=eucast_rules]{eucast_rules()}}. +Define custom interpretive rules for your organisation or specific analysis and use the output of this function in \code{\link[=interpretive_rules]{interpretive_rules()}}. } \details{ -Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the \code{\link[=eucast_rules]{eucast_rules()}} function. +Some organisations have their own adoption of interpretive rules. This function can be used to define custom rules to be used in the \code{\link[=interpretive_rules]{interpretive_rules()}} function. \subsection{Basics}{ If you are familiar with the \code{\link[dplyr:case-and-replace-when]{case_when()}} function of the \code{dplyr} package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written \emph{before} the tilde (\code{~}) and the consequence of the rule is written \emph{after} the tilde: -\if{html}{\out{
}}\preformatted{x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S", - TZP == "R" ~ aminopenicillins == "R") +\if{html}{\out{
}}\preformatted{x <- custom_interpretive_rules(TZP == "S" ~ aminopenicillins == "S", + TZP == "R" ~ aminopenicillins == "R") }\if{html}{\out{
}} -These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work: +These are two custom interpretive rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work: \if{html}{\out{
}}\preformatted{x -#> A set of custom EUCAST rules: +#> A set of custom interpretive rules: #> #> 1. If TZP is "S" then set to S : #> amoxicillin (AMX), ampicillin (AMP) @@ -48,11 +48,11 @@ df #> 1 Escherichia coli R S S #> 2 Klebsiella pneumoniae R S S -eucast_rules(df, - rules = "custom", - custom_rules = x, - info = FALSE, - overwrite = TRUE) +interpretive_rules(df, + rules = "custom", + custom_rules = x, + info = FALSE, + overwrite = TRUE) #> mo TZP ampi cipro #> 1 Escherichia coli R R S #> 2 Klebsiella pneumoniae R R S @@ -63,16 +63,16 @@ eucast_rules(df, There is one exception in columns used for the rules: all column names of the \link{microorganisms} data set can also be used, but do not have to exist in the data set. These column names are: \code{"mo"}, \code{"fullname"}, \code{"status"}, \code{"kingdom"}, \code{"phylum"}, \code{"class"}, \code{"order"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"subspecies"}, \code{"rank"}, \code{"ref"}, \code{"oxygen_tolerance"}, \code{"source"}, \code{"lpsn"}, \code{"lpsn_parent"}, \code{"lpsn_renamed_to"}, \code{"mycobank"}, \code{"mycobank_parent"}, \code{"mycobank_renamed_to"}, \code{"gbif"}, \code{"gbif_parent"}, \code{"gbif_renamed_to"}, \code{"prevalence"}, and \code{"snomed"}. Thus, this next example will work as well, despite the fact that the \code{df} data set does not contain a column \code{genus}: -\if{html}{\out{
}}\preformatted{y <- custom_eucast_rules( +\if{html}{\out{
}}\preformatted{y <- custom_interpretive_rules( TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S", TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R" ) -eucast_rules(df, - rules = "custom", - custom_rules = y, - info = FALSE, - overwrite = TRUE) +interpretive_rules(df, + rules = "custom", + custom_rules = y, + info = FALSE, + overwrite = TRUE) #> mo TZP ampi cipro #> 1 Escherichia coli R S S #> 2 Klebsiella pneumoniae R R S @@ -90,9 +90,9 @@ You can define antimicrobial groups instead of single antimicrobials for the rul Rules can also be applied to multiple antimicrobials and antimicrobial groups simultaneously. Use the \code{c()} function to combine multiple antimicrobials. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R": -\if{html}{\out{
}}\preformatted{x <- custom_eucast_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R") +\if{html}{\out{
}}\preformatted{x <- custom_interpretive_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R") x -#> A set of custom EUCAST rules: +#> A set of custom interpretive rules: #> #> 1. If TZP is "R" then set to "R": #> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP) @@ -147,7 +147,7 @@ These 43 antimicrobial groups are allowed in the rules (case-insensitive) and ca } } \examples{ -x <- custom_eucast_rules( +x <- custom_interpretive_rules( AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I" ) @@ -165,7 +165,7 @@ eucast_rules(example_isolates, # combine rule sets x2 <- c( x, - custom_eucast_rules(TZP == "R" ~ carbapenems == "R") + custom_interpretive_rules(TZP == "R" ~ carbapenems == "R") ) x2 } diff --git a/man/g.test.Rd b/man/g.test.Rd index dc82a0dee..39a42bc1f 100644 --- a/man/g.test.Rd +++ b/man/g.test.Rd @@ -45,8 +45,9 @@ A list with class \code{"htest"} containing the following \item{residuals}{the Pearson residuals, \code{(observed - expected) / sqrt(expected)}.} \item{stdres}{standardized residuals, - \code{(observed - expected) / sqrt(V)}, where \code{V} is the residual cell variance (Agresti, 2007, - section 2.4.5 for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).} + \code{(observed - expected) / sqrt(V)}, where \code{V} is the + residual cell variance (Agresti, 2007, section 2.4.5 + for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).} } \description{ \code{\link[=g.test]{g.test()}} performs chi-squared contingency table tests and goodness-of-fit tests, just like \code{\link[=chisq.test]{chisq.test()}} but is more reliable (1). A \emph{G}-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a \strong{\emph{G}-test of goodness-of-fit}), or to see whether the proportions of one variable are different for different values of the other variable (called a \strong{\emph{G}-test of independence}). diff --git a/man/interpretive_rules.Rd b/man/interpretive_rules.Rd index 341196f17..62198917e 100644 --- a/man/interpretive_rules.Rd +++ b/man/interpretive_rules.Rd @@ -46,7 +46,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15) \item{info}{A \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.} -\item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}: \code{options(AMR_interpretive_rules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.} +\item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}: \code{options(AMR_interpretive_rules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}.} \item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.} @@ -62,7 +62,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15) \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.} -\item{custom_rules}{Custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.} +\item{custom_rules}{Custom rules to apply, created with \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}.} \item{overwrite}{A \link{logical} indicating whether to overwrite existing SIR values (default: \code{FALSE}). When \code{FALSE}, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, \strong{this should remain} \code{FALSE}, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".} @@ -86,15 +86,15 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive \strong{Note:} This function does not translate MIC or disk values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr -The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until June 24th, 2024, see \link{microorganisms}. +The file containing all interpretive rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until June 24th, 2024, see \link{microorganisms}. \subsection{Custom Rules}{ -Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.: +Custom rules can be created using \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}, e.g.: -\if{html}{\out{
}}\preformatted{x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", - AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I") +\if{html}{\out{
}}\preformatted{x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", + AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I") -eucast_rules(example_isolates, rules = "custom", custom_rules = x) +interpretive_rules(example_isolates, rules = "custom", custom_rules = x) }\if{html}{\out{
}} } @@ -108,7 +108,7 @@ Before further processing, two non-EUCAST rules about drug combinations can be a Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set. -Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}, i.e. run \code{options(AMR_interpretive_rules = "all")}. +Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{interpretive_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}, i.e. run \code{options(AMR_interpretive_rules = "all")}. } } \section{Download Our Reference Data}{ diff --git a/man/pca.Rd b/man/pca.Rd index 163c65e2f..5e88c1efc 100644 --- a/man/pca.Rd +++ b/man/pca.Rd @@ -32,7 +32,7 @@ pca(x, ..., retx = TRUE, center = TRUE, scale. = TRUE, tol = NULL, standard deviations are less than or equal to \code{tol} times the standard deviation of the first component.) With the default null setting, no components are omitted (unless \code{rank.} is specified - less than \code{min(dim(x))}.). Other settings for tol could be + less than \code{min(dim(x))}.). Other settings for \code{tol} could be \code{tol = 0} or \code{tol = sqrt(.Machine$double.eps)}, which would omit essentially constant components.} diff --git a/tests/testthat/test-_deprecated.R b/tests/testthat/test-_deprecated.R index bf08e57f7..656f9f8ef 100644 --- a/tests/testthat/test-_deprecated.R +++ b/tests/testthat/test-_deprecated.R @@ -32,4 +32,11 @@ test_that("test-_deprecated.R", { expect_warning(example_isolates[, ab_class("mycobact")]) expect_warning(example_isolates[, ab_selector(name %like% "trim")]) + + # deprecated custom_interpretive_rules() still works and emits a warning + expect_warning( + x_old <- custom_eucast_rules(AMC == "R" ~ aminopenicillins == "R"), + regexp = "custom_eucast_rules" + ) + expect_inherits(x_old, "custom_interpretive_rules") }) diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index daa7070e6..7d4afb8f0 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -53,12 +53,12 @@ test_that("test-data.R", { expect_false(anyNA(microorganisms.codes$mo)) expect_true(all(dosage$ab %in% AMR::antimicrobials$ab)) expect_true(all(dosage$name %in% AMR::antimicrobials$name)) - eucast_abx <- AMR:::EUCAST_RULES_DF$and_these_antibiotics - eucast_abx <- unique(unlist(strsplit(eucast_abx[!is.na(eucast_abx)], ", +"))) - expect_true(all(eucast_abx %in% AMR::antimicrobials$ab), + interpretive_abx <- AMR:::INTERPRETIVE_RULES_DF$and_these_antibiotics + interpretive_abx <- unique(unlist(strsplit(interpretive_abx[!is.na(interpretive_abx)], ", +"))) + expect_true(all(interpretive_abx %in% AMR::antimicrobials$ab), info = paste0( "Missing in `antimicrobials` data set: ", - toString(eucast_abx[which(!eucast_abx %in% AMR::antimicrobials$ab)]) + toString(interpretive_abx[which(!interpretive_abx %in% AMR::antimicrobials$ab)]) ) ) diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-interpretive_rules.R similarity index 78% rename from tests/testthat/test-eucast_rules.R rename to tests/testthat/test-interpretive_rules.R index e4dfbabea..f29fda12d 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/tests/testthat/test-interpretive_rules.R @@ -27,13 +27,14 @@ # how to conduct AMR data analysis: https://amr-for-r.org # # ==================================================================== # -test_that("test-eucast_rules.R", { +test_that("test-interpretive_rules.R", { skip_on_cran() # thoroughly check input table expect_equal( - sort(colnames(AMR:::EUCAST_RULES_DF)), + sort(colnames(AMR:::INTERPRETIVE_RULES_DF)), sort(c( + "rule.provider", "if_mo_property", "like.is.one_of", "this_value", "and_these_antibiotics", "have_these_values", "then_change_these_antibiotics", "to_value", @@ -42,7 +43,7 @@ test_that("test-eucast_rules.R", { "note" )) ) - MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value) + MOs_mentioned <- unique(AMR:::INTERPRETIVE_RULES_DF$this_value) MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE)))) MOs_test <- suppressWarnings( trimws(paste( @@ -54,19 +55,19 @@ test_that("test-eucast_rules.R", { MOs_test[MOs_test == ""] <- mo_fullname(MOs_mentioned[MOs_test == ""], keep_synonyms = TRUE, language = NULL) expect_equal(MOs_mentioned, MOs_test) - expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing"))) - expect_error(eucast_rules(x = "text")) - expect_error(eucast_rules(data.frame(a = "test"))) - expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set")) + expect_error(suppressWarnings(interpretive_rules(example_isolates, col_mo = "Non-existing"))) + expect_error(interpretive_rules(x = "text")) + expect_error(interpretive_rules(data.frame(a = "test"))) + expect_error(interpretive_rules(data.frame(mo = "test"), rules = "invalid rules set")) - # expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE))) + # expect_warning(interpretive_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE))) expect_identical( colnames(example_isolates), - colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))) + colnames(suppressWarnings(interpretive_rules(example_isolates, info = FALSE))) ) - expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE))) + expect_output(suppressMessages(interpretive_rules(example_isolates, info = TRUE))) a <- data.frame( mo = c( @@ -86,8 +87,8 @@ test_that("test-eucast_rules.R", { amox = "R", # Amoxicillin stringsAsFactors = FALSE ) - expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b) - expect_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE)))) + expect_identical(suppressWarnings(interpretive_rules(a, "mo", info = FALSE)), b) + expect_output(suppressMessages(suppressWarnings(interpretive_rules(a, "mo", info = TRUE)))) a <- data.frame( mo = c( @@ -105,7 +106,7 @@ test_that("test-eucast_rules.R", { COL = "R", # Colistin stringsAsFactors = FALSE ) - expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b) + expect_equal(suppressWarnings(interpretive_rules(a, "mo", info = FALSE)), b) # piperacillin must be R in Enterobacteriaceae when tica is R if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { @@ -117,7 +118,7 @@ test_that("test-eucast_rules.R", { TIC = as.sir("R"), PIP = as.sir("S") ) %>% - eucast_rules(col_mo = "mo", version_expertrules = 3.1, rules = "expert", info = FALSE, overwrite = TRUE) %>% + interpretive_rules(col_mo = "mo", version_expertrules = 3.1, rules = "expert", info = FALSE, overwrite = TRUE) %>% pull(PIP) %>% unique() %>% as.character() @@ -127,7 +128,7 @@ test_that("test-eucast_rules.R", { } # azithromycin and clarythromycin must be equal to Erythromycin - a <- suppressWarnings(as.sir(eucast_rules( + a <- suppressWarnings(as.sir(interpretive_rules( data.frame( mo = example_isolates$mo, ERY = example_isolates$ERY, @@ -149,7 +150,7 @@ test_that("test-eucast_rules.R", { # amox is inferred by benzylpenicillin in Kingella kingae expect_equal( suppressWarnings( - as.list(eucast_rules( + as.list(interpretive_rules( data.frame( mo = as.mo("Kingella kingae"), PEN = "S", @@ -164,16 +165,16 @@ test_that("test-eucast_rules.R", { # also test norf if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { - expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE))) + expect_output(suppressWarnings(interpretive_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE))) } # check verbose output - expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE))) + expect_output(suppressWarnings(interpretive_rules(example_isolates, verbose = TRUE, rules = "all", info = TRUE))) # AmpC de-repressed cephalo mutants expect_identical( - eucast_rules( + interpretive_rules( data.frame( mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.sir(c("S", "S")) @@ -187,7 +188,7 @@ test_that("test-eucast_rules.R", { ) expect_identical( - eucast_rules( + interpretive_rules( data.frame( mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.sir(c("S", "S")) @@ -201,7 +202,7 @@ test_that("test-eucast_rules.R", { ) expect_identical( - eucast_rules( + interpretive_rules( data.frame( mo = c("Escherichia coli", "Enterobacter cloacae"), cefotax = as.sir(c("S", "S")) @@ -219,7 +220,7 @@ test_that("test-eucast_rules.R", { expect_inherits(eucast_dosage(c("tobra", "genta", "cipro")), "data.frame") - x <- custom_eucast_rules( + x <- custom_interpretive_rules( AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I", AMX == "S" ~ AMC == "S" @@ -230,7 +231,7 @@ test_that("test-eucast_rules.R", { # this custom rules makes 8 changes expect_equal( - nrow(eucast_rules(example_isolates, + nrow(interpretive_rules(example_isolates, rules = "custom", custom_rules = x, info = FALSE, @@ -240,4 +241,10 @@ test_that("test-eucast_rules.R", { 8, tolerance = 0.5 ) + + # clsi_rules() no longer errors (returns data unchanged until CLSI rows are added) + expect_identical( + suppressWarnings(clsi_rules(example_isolates, info = FALSE)), + example_isolates + ) })