diff --git a/DESCRIPTION b/DESCRIPTION index b65463d0e..33bfb6767 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 3.0.1.9041 -Date: 2026-03-30 +Version: 3.0.1.9042 +Date: 2026-04-02 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 1a2977f12..ba4fc855f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9041 +# AMR 3.0.1.9042 ### New * Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations. diff --git a/R/aa_globals.R b/R/aa_globals.R index b70d24217..436f8ce89 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -30,6 +30,12 @@ # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints # (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file) EUCAST_VERSION_BREAKPOINTS <- list( + "16.0" = list( + version_txt = "v16.0", + year = 2026, + title = "'EUCAST Clinical Breakpoint Tables'", + url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" + ), "15.0" = list( version_txt = "v15.0", year = 2025, diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 261d7fd0a..46f9ef8c8 100644 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -359,9 +359,9 @@ stop_ifnot_installed <- function(package) { if (any(!installed) && any(package == "rstudioapi")) { stop("This function only works in RStudio when using R >= 3.2.", call. = FALSE) } else if (any(!installed)) { - stop("This requires the ", vector_and(package[!installed]), " package.", - "\nTry to install with install.packages().", - call. = FALSE + stop_( + "This requires the ", vector_and(paste0("{.pkg ", package[!installed], "}"), quotes = FALSE), " package.", + "\nTry to install with {.fun install.packages}." ) } else { return(invisible()) @@ -747,7 +747,7 @@ format_included_data_number <- function(data) { paste0(ifelse(rounder == 0, "", "~"), format(round(n, rounder), decimal.mark = ".", big.mark = " ")) } -vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") { +vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ", documentation = FALSE) { # makes unique and sorts, and this also removed NAs v <- unique(v) has_na <- anyNA(v) @@ -761,17 +761,25 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca v <- rev(v) } if (isTRUE(quotes)) { - quotes <- '"' + if (isTRUE(documentation)) { + quotes <- '"' + } else { + # use cli to format as values + quotes <- c("{.val ", "}") + } } else if (isFALSE(quotes)) { quotes <- "" } else { quotes <- quotes[1L] } + if (length(quotes) == 1) { + quotes <- c(quotes, quotes) + } if (isTRUE(initial_captital)) { v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE) } if (length(v) <= 1) { - return(paste0(quotes, v, quotes)) + return(paste0(quotes[1], v, quotes[2])) } if (identical(v, c("I", "R", "S"))) { # class 'sir' should be sorted like this @@ -790,7 +798,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca if (is.numeric(v)) { v <- trimws(vapply(FUN.VALUE = character(1), v, format, scientific = FALSE)) } - quoted <- paste0(quotes, v, quotes) + quoted <- paste0(quotes[1], v, quotes[2]) quoted[NAs] <- "NA" # all commas except for last item, so will become '"val1", "val2", "val3" or "val4"' paste0( @@ -799,10 +807,11 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca ) } -vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) { +vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, documentation = FALSE) { vector_or( v = v, quotes = quotes, reverse = reverse, sort = sort, - initial_captital = initial_captital, last_sep = " and " + initial_captital = initial_captital, documentation = documentation, + last_sep = " and " ) } diff --git a/R/amr_selectors.R b/R/amr_selectors.R index 1e14bec38..183115405 100755 --- a/R/amr_selectors.R +++ b/R/amr_selectors.R @@ -857,7 +857,7 @@ all_any_amr_selector <- function(type, ..., na.rm = TRUE) { cols_ab <- c(...) result <- cols_ab[toupper(cols_ab) %in% VALID_SIR_LEVELS] if (length(result) == 0) { - message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"') + message_("Filtering ", type, " of columns ", vector_and(paste0("{.field ", font_bold(cols_ab, collapse = NULL), "}"), quotes = FALSE), " to only contain values ", vector_or(VALID_SIR_LEVELS)) result <- VALID_SIR_LEVELS } cols_ab <- cols_ab[!cols_ab %in% result] diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index c5846506e..f047cdb9d 100755 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -80,7 +80,7 @@ #' #' ### Using taxonomic properties in rules #' -#' 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)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`: +#' 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( diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R index 7b092fdf8..abeb0909f 100755 --- a/R/interpretive_rules.R +++ b/R/interpretive_rules.R @@ -76,7 +76,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) { #' @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". #' @inheritParams first_isolate #' @details -#' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr +#' **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]. @@ -163,7 +163,7 @@ interpretive_rules <- function(x, rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"), verbose = FALSE, - version_breakpoints = 15.0, + version_breakpoints = 16.0, version_expected_phenotypes = 1.2, version_expertrules = 3.3, ampc_cephalosporin_resistance = NA, diff --git a/R/mo.R b/R/mo.R index af1b5ba8e..d0d98d838 100755 --- a/R/mo.R +++ b/R/mo.R @@ -249,7 +249,7 @@ as.mo <- function(x, if (length(which(ind)) > 0 && isTRUE(info) && message_not_thrown_before("as.mo_microorganisms.codes", is.na(out), toupper(x))) { message_( "Retrieved value", ifelse(sum(ind) > 1, "s", ""), - " from the {.help [microorganisms.codes](AMR::microorganisms.codes)} data set for ", vector_and(paste0("{.val ", toupper(x)[ind], "}"), quotes = FALSE), "." + " from the {.help [microorganisms.codes](AMR::microorganisms.codes)} data set for ", vector_and(toupper(x)[ind]), "." ) } # From SNOMED ---- diff --git a/R/sir.R b/R/sir.R index 641501f7d..644355dcb 100755 --- a/R/sir.R +++ b/R/sir.R @@ -1079,8 +1079,8 @@ get_guideline <- function(guideline, reference_data) { guideline_param[guideline_param %unlike% " "] <- gsub("([a-z]+)([0-9]+)", "\\1 \\2", guideline_param[guideline_param %unlike% " "], ignore.case = TRUE) stop_ifnot(guideline_param %in% reference_data$guideline, - "invalid guideline: '", guideline, - "'.\nValid guidelines are: ", vector_and(reference_data$guideline, quotes = TRUE, reverse = TRUE), + "invalid guideline: {.val ", guideline, + "}.\nValid guidelines are: ", vector_and(reference_data$guideline, reverse = TRUE), call = FALSE ) diff --git a/R/sysdata.rda b/R/sysdata.rda index d7eacd65f..826394232 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R index 2d2efbc83..a1b46f741 100644 --- a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R +++ b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R @@ -386,18 +386,39 @@ breakpoints_new <- breakpoints_new |> filter(!wrong) # There's a problem with C. diff in EUCAST where breakpoint_R is missing - they are listed as normal human breakpoints but are ECOFF # 2025-04-20/ fixed now -# determine rank again now that some changes were made on taxonomic level (genus -> species) -breakpoints_new <- breakpoints_new |> - mutate(rank_index = case_when( - mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1, - mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2, - mo_rank(mo, keep_synonyms = TRUE) == "species group" ~ 2.5, - mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3, - mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4, - mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5, - mo != "UNKNOWN" ~ 6, # for B_ANAER, etc. - TRUE ~ 7 - )) +# WHONET sets for EUCAST 2026 TMP breakpoints for all Klebsiella, but this is now only for non-aerogenes species +kleb_spp <- microorganisms |> filter(rank == "species", genus == "Klebsiella", !species %in% c("", "aerogenes")) |> pull(mo) +kleb_tmp_mic <- breakpoints_new |> + filter(guideline == "EUCAST 2026", method == "MIC", ab == "TMP", mo == as.mo("Klebsiella")) |> + uncount(length(kleb_spp)) |> + mutate(mo = kleb_spp) +kleb_tmp_disk <- breakpoints_new |> + filter(guideline == "EUCAST 2026", method == "DISK", ab == "TMP", mo == as.mo("Klebsiella")) |> + uncount(length(kleb_spp)) |> + mutate(mo = kleb_spp) +breakpoints_new <- breakpoints_new |> + filter(!(guideline == "EUCAST 2026" & method == "MIC" & ab == "TMP" & mo == as.mo("Klebsiella"))) |> + bind_rows(kleb_tmp_mic, + kleb_tmp_disk) + +# WHONET contains wrong EUCAST breakpoints for enterococci/SXT: disk should be 23/23, not 21/50, and MIC should be 1/1, not 0.032/1 +# applies to all previous years, since v11 (2011) +breakpoints_new |> filter(guideline %like% "EUCAST", ab == "SXT", mo == as.mo("Enterococcus"), type == "human") +breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 23 +breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 23 +breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1 +breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "SXT" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1 +# Also wrong EUCAST breakpoints for enterococci/TMP: disk should be 21/21, not 21/50, and MIC should be 1/1, not 0.032/1 +breakpoints_new |> filter(guideline %like% "EUCAST", ab == "TMP", mo == as.mo("Enterococcus"), type == "human") +breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 21 +breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "DISK"] <- 21 +breakpoints_new$breakpoint_S[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1 +breakpoints_new$breakpoint_R[breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$ab == "TMP" & breakpoints_new$mo == as.mo("Enterococcus") & breakpoints_new$type == "human" & breakpoints_new$method == "MIC"] <- 1 + +# WHONET still contains PK/PD rules for EUCAST >= 2024, but this was ended from v14 (2024) on +breakpoints_new <- breakpoints_new |> + filter(!(guideline %like% "EUCAST (2024|2025|2026)" & ref_tbl == "PK/PD")) + # WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales: # EUCAST 2023 guideline: S <= 8 and R > 8 @@ -418,6 +439,7 @@ breakpoints_new <- breakpoints_new |> breakpoint_R )) + # check the strange duplicates breakpoints_new |> mutate(id = paste(guideline, type, host, method, site, mo, ab, uti)) %>% @@ -430,9 +452,8 @@ breakpoints_new <- breakpoints_new |> distinct(guideline, type, host, method, site, mo, ab, uti, .keep_all = TRUE) -# CHECKS AND SAVE TO PACKAGE ---- +# CHECKS ---- -# check again breakpoints_new |> filter(guideline == "EUCAST 2026", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC") # compare with current version clinical_breakpoints |> filter(guideline == "EUCAST 2025", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC") @@ -444,6 +465,24 @@ breakpoints_new |> filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAS dim(breakpoints_new) dim(clinical_breakpoints) + +# SAVE TO PACKAGE ---- + +# determine rank again now that some changes were made on taxonomic level (genus -> species) +breakpoints_new <- breakpoints_new |> + mutate(rank_index = case_when( + mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1, + mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2, + mo_rank(mo, keep_synonyms = TRUE) == "species group" ~ 2.5, + mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3, + mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4, + mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5, + mo != "UNKNOWN" ~ 6, # for B_ANAER, etc. + TRUE ~ 7 + )) |> + # and arrange + arrange(desc(guideline), mo, ab, type, host, method) + clinical_breakpoints <- breakpoints_new clinical_breakpoints <- clinical_breakpoints |> dataset_UTF8_to_ASCII() usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2) diff --git a/data-raw/clin_break.md5 b/data-raw/clin_break.md5 index 17e205028..8379b485d 100644 --- a/data-raw/clin_break.md5 +++ b/data-raw/clin_break.md5 @@ -1 +1 @@ -c43a990cf91f959913d207e5a85e2bd5 +45068afc4cd9770dea329782c1aed045 diff --git a/data-raw/datasets/clinical_breakpoints.dta b/data-raw/datasets/clinical_breakpoints.dta index ecc3a7151..2a7f177d6 100644 Binary files a/data-raw/datasets/clinical_breakpoints.dta and b/data-raw/datasets/clinical_breakpoints.dta differ diff --git a/data-raw/datasets/clinical_breakpoints.feather b/data-raw/datasets/clinical_breakpoints.feather index 73d29e94c..8afb09f75 100644 Binary files a/data-raw/datasets/clinical_breakpoints.feather and b/data-raw/datasets/clinical_breakpoints.feather differ diff --git a/data-raw/datasets/clinical_breakpoints.parquet b/data-raw/datasets/clinical_breakpoints.parquet index f89ea2a5d..955ffb2ea 100644 Binary files a/data-raw/datasets/clinical_breakpoints.parquet and b/data-raw/datasets/clinical_breakpoints.parquet differ diff --git a/data-raw/datasets/clinical_breakpoints.rds b/data-raw/datasets/clinical_breakpoints.rds index 609bfbe62..5d1ba2749 100644 Binary files a/data-raw/datasets/clinical_breakpoints.rds and b/data-raw/datasets/clinical_breakpoints.rds differ diff --git a/data-raw/datasets/clinical_breakpoints.sav b/data-raw/datasets/clinical_breakpoints.sav index 6c7d2cbf2..825d95a2c 100644 Binary files a/data-raw/datasets/clinical_breakpoints.sav and b/data-raw/datasets/clinical_breakpoints.sav differ diff --git a/data-raw/datasets/clinical_breakpoints.txt b/data-raw/datasets/clinical_breakpoints.txt index e187c1a26..a00bd27f4 100644 --- a/data-raw/datasets/clinical_breakpoints.txt +++ b/data-raw/datasets/clinical_breakpoints.txt @@ -593,14 +593,14 @@ "EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2026" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2026" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2026" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2026" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2026" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 20 20 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2026" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 15 15 FALSE FALSE "EUCAST 2026" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_ENTRC_FACM" 2 "AMP" "ECOFF" 4 4 FALSE FALSE @@ -1173,7 +1173,6 @@ "EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL" 3 "TEM" "Enterobacterales" "30 mcg" 50 17 TRUE FALSE "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL" 3 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE "EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL" 3 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE -"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL" 3 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_AERG" 2 "AMK" "ECOFF" 8 8 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_AERG" 2 "CAZ" "ECOFF" "10 mcg" 20 20 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_AERG" 2 "CAZ" "ECOFF" 1 1 FALSE FALSE @@ -1206,8 +1205,30 @@ "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_AERG" 2 "TOB" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_AERG" 2 "TZP" "ECOFF" "30/6 mcg" 17 17 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_AERG" 2 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_AFRC" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_AFRC" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_ALBA" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_ALBA" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_ELCT" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_ELCT" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_GRMN" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_GRMN" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_GRNL" 2 "TEM" "Enterobacterales" "30 mcg" 50 17 TRUE FALSE "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_GRNL" 2 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_GRNL" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_GRNL" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_HXNS" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_HXNS" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_INDC" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_INDC" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_MBLS" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_MBLS" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_MCHG" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_MCHG" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_NNSS" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_NNSS" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_ORNT" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_ORNT" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_OXYT" 2 "AMK" "ECOFF" 8 8 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_OXYT" 2 "CAZ" "ECOFF" "10 mcg" 22 22 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_OXYT" 2 "CAZ" "ECOFF" 0.5 0.5 FALSE FALSE @@ -1246,10 +1267,16 @@ "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_OXYT" 2 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_OXYT" 2 "TGC" "ECOFF" 1 1 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_OXYT" 2 "TMP" "ECOFF" "5 mcg" 21 21 FALSE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_OXYT" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_OXYT" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_OXYT" 2 "TOB" "ECOFF" "10 mcg" 15 15 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_OXYT" 2 "TOB" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_OXYT" 2 "TZP" "ECOFF" "30/6 mcg" 18 18 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_OXYT" 2 "TZP" "ECOFF" 8 8 FALSE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_OZAN" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_OZAN" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_PLNT" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_PLNT" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_PNMN" 2 "AMC" "ECOFF" "20/10 mcg" 17 17 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_PNMN" 2 "AMK" "ECOFF" "30 mcg" 16 16 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_PNMN" 2 "AMK" "ECOFF" 8 8 FALSE FALSE @@ -1314,6 +1341,8 @@ "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_PNMN" 2 "TIO" "ECOFF" 1 1 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_PNMN" 2 "TMP" "ECOFF" "5 mcg" 18 18 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_PNMN" 2 "TMP" "ECOFF" 2 2 FALSE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_PNMN" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_PNMN" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_PNMN" 2 "TOB" "ECOFF" "10 mcg" 15 15 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_KLBSL_PNMN" 2 "TOB" "ECOFF" 2 2 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "DISK" "B_KLBSL_PNMN" 2 "TZP" "ECOFF" "30/6 mcg" 17 17 FALSE FALSE @@ -1322,10 +1351,28 @@ "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_PNMN_OZAN" 1 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE "EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_PNMN_RHNS" 1 "TEM" "Enterobacterales" "30 mcg" 50 17 TRUE FALSE "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_PNMN_RHNS" 1 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_PSTR" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_PSTR" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_QSPN" 2 "TEM" "Enterobacterales" "30 mcg" 50 17 TRUE FALSE "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_QSPN" 2 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_QSPN" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_QSPN" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_QSVR" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_QSVR" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_RHNS" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_RHNS" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_SNGP" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_SNGP" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_SPLL" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_SPLL" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_TRRG" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_TRRG" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_TRVS" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_TRVS" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_VRCL" 2 "TEM" "Enterobacterales" "30 mcg" 50 17 TRUE FALSE "EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_VRCL" 2 "TEM" "Enterobacterales" 1e-04 16 TRUE FALSE +"EUCAST 2026" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_KLBSL_VRCL" 2 "TMP" "Enterobacterales" "5 mcg" 15 15 TRUE FALSE +"EUCAST 2026" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_KLBSL_VRCL" 2 "TMP" "Enterobacterales" 2 2 TRUE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_LCTBC_RHMN" 2 "AMP" "ECOFF" 4 4 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_LCTBC_RHMN" 2 "GEN" "ECOFF" 16 16 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "B_LCTBC_RHMN" 2 "TCY" "ECOFF" 4 4 FALSE FALSE @@ -3085,44 +3132,6 @@ "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "ITR" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "TRB" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE "EUCAST 2026" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "VOR" "Antifungal ECOFFs" 0.125 0.125 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 1 1 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "AMX" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "ATM" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "BPR" "PK/PD" 4 4 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CAZ" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CIP" "PK/PD" 0.25 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CPT" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CRO" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CTX" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CXM" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CZA" "PK/PD" 8 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CZO" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "CZT" "PK/PD" 4 4 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "DAL" "PK/PD" 0.25 0.25 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "ETP" "PK/PD" 0.5 1 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "FEP" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "FLU" "PK/PD" 2 4 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "GEN" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "IMR" "PK/PD" 2 2 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "IPM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "LNZ" "PK/PD" 2 2 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "LVX" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "MEM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "MEV" "PK/PD" 8 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "MFX" "PK/PD" 0.25 0.25 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "NET" "PK/PD" 2 4 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "OFX" "PK/PD" 0.25 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "ORI" "PK/PD" 0.125 0.125 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "PEN" "PK/PD" 0.25 2 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "PIP" "PK/PD" 4 16 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "SAM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "TCC" "PK/PD" 8 16 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "TGC" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "TIC" "PK/PD" 8 16 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "TOB" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2026" "human" "human" "MIC" "UNKNOWN" 7 "TZP" "PK/PD" 4 16 FALSE FALSE "EUCAST 2025" "human" "human" "DISK" "B_ACHRMB_XYLS" 2 "MEM" "A. xylosoxidans" "10 mcg" 26 20 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "B_ACHRMB_XYLS" 2 "MEM" "A. xylosoxidans" 1 4 FALSE FALSE "EUCAST 2025" "human" "human" "DISK" "B_ACHRMB_XYLS" 2 "SXT" "A. xylosoxidans" "1.25/23.75 mcg" 26 26 FALSE FALSE @@ -3717,14 +3726,14 @@ "EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2025" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2025" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2025" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2025" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2025" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 20 20 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2025" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2025" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2025" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2025" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 15 15 FALSE FALSE "EUCAST 2025" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "B_ENTRC_FACM" 2 "AMP" "ECOFF" 4 4 FALSE FALSE @@ -6189,44 +6198,6 @@ "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "ITR" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "TRB" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE "EUCAST 2025" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "VOR" "Antifungal ECOFFs" 0.125 0.125 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 1 1 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "AMX" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "ATM" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "BPR" "PK/PD" 4 4 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CAZ" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CIP" "PK/PD" 0.25 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CPT" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CRO" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CTX" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CXM" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CZA" "PK/PD" 8 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CZO" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "CZT" "PK/PD" 4 4 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "DAL" "PK/PD" 0.25 0.25 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "ETP" "PK/PD" 0.5 1 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "FEP" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "FLU" "PK/PD" 2 4 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "GEN" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "IMR" "PK/PD" 2 2 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "IPM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "LNZ" "PK/PD" 2 2 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "LVX" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "MEM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "MEV" "PK/PD" 8 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "MFX" "PK/PD" 0.25 0.25 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "NET" "PK/PD" 2 4 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "OFX" "PK/PD" 0.25 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "ORI" "PK/PD" 0.125 0.125 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "PEN" "PK/PD" 0.25 2 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "PIP" "PK/PD" 4 16 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "SAM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "TCC" "PK/PD" 8 16 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "TGC" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "TIC" "PK/PD" 8 16 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "TOB" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2025" "human" "human" "MIC" "UNKNOWN" 7 "TZP" "PK/PD" 4 16 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_ACHRMB_XYLS" 2 "MEM" "A. xylosoxidans" "10 mcg" 26 20 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_ACHRMB_XYLS" 2 "MEM" "A. xylosoxidans" 1 4 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_ACHRMB_XYLS" 2 "SXT" "A. xylosoxidans" "1.25/23.75 mcg" 26 26 FALSE FALSE @@ -6623,14 +6594,14 @@ "EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2024" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2024" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 18 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.25 FALSE FALSE -"EUCAST 2024" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2024" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2024" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2024" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2024" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_ENTRC_FACM" 2 "AMP" "ECOFF" "2 mcg" 10 10 FALSE FALSE @@ -7431,7 +7402,6 @@ "EUCAST 2024" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 23 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2024" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 17 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 21 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_STPHY" 3 "QDA" "Staphs" 1 1 FALSE FALSE @@ -7580,6 +7550,7 @@ "EUCAST 2024" "human" "human" "MIC" "Screen" "B_STPHY_SPRP" 2 "FOX" "Staphs" 8 8 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_STPHY_SPRP" 2 "NIT" "ECOFF" "100 mcg" 16 16 FALSE FALSE "EUCAST 2024" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2024" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_STPHY_SPRP" 2 "NOR" "ECOFF" "10 mcg" 18 18 FALSE FALSE "EUCAST 2024" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "DISK" "B_STPHY_SPRP" 2 "TMP" "ECOFF" "5 mcg" 23 23 FALSE FALSE @@ -8102,44 +8073,6 @@ "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "ITR" "Antifungal ECOFFs" 0.25 0.25 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "TRB" "Antifungal ECOFFs" 0.032 0.032 FALSE FALSE "EUCAST 2024" "ECOFF" "ECOFF" "MIC" "F_TRCHP_RBRM" 2 "VOR" "Antifungal ECOFFs" 0.125 0.125 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "AMC" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "AMK" "PK/PD" 1 1 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "AMP" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "AMX" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "ATM" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "BPR" "PK/PD" 4 4 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CAZ" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CIP" "PK/PD" 0.25 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CPT" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CRO" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CTX" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CXM" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CZA" "PK/PD" 8 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CZO" "PK/PD" 1 2 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "CZT" "PK/PD" 4 4 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "DAL" "PK/PD" 0.25 0.25 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "ETP" "PK/PD" 0.5 1 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "FEP" "PK/PD" 4 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "FLU" "PK/PD" 2 4 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "GEN" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "IMR" "PK/PD" 2 2 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "IPM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "LNZ" "PK/PD" 2 2 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "LVX" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "MEM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "MEV" "PK/PD" 8 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "MFX" "PK/PD" 0.25 0.25 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "NET" "PK/PD" 2 4 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "OFX" "PK/PD" 0.25 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "ORI" "PK/PD" 0.125 0.125 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "PEN" "PK/PD" 0.25 2 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "PIP" "PK/PD" 4 16 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "SAM" "PK/PD" 2 8 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "TCC" "PK/PD" 8 16 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "TGC" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "TIC" "PK/PD" 8 16 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "TOB" "PK/PD" 0.5 0.5 FALSE FALSE -"EUCAST 2024" "human" "human" "MIC" "UNKNOWN" 7 "TZP" "PK/PD" 4 16 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ACHRMB_XYLS" 2 "MEM" "A. xylosoxidans" "10 mcg" 26 20 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_ACHRMB_XYLS" 2 "MEM" "A. xylosoxidans" 1 4 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ACHRMB_XYLS" 2 "SXT" "A. xylosoxidans" "1.25/23.75 mcg" 26 26 FALSE FALSE @@ -8426,14 +8359,14 @@ "EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2023" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2023" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 18 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.25 FALSE FALSE -"EUCAST 2023" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2023" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2023" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2023" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_ENTRC_FACM" 2 "ERV" "Enterococcus" "20 mcg" 24 24 FALSE FALSE @@ -9093,7 +9026,6 @@ "EUCAST 2023" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 23 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 0.5 FALSE FALSE -"EUCAST 2023" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2023" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 17 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 21 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_STPHY" 3 "QDA" "Staphs" 1 1 FALSE FALSE @@ -9182,6 +9114,7 @@ "EUCAST 2023" "human" "human" "DISK" "B_STPHY_SPRP" 2 "AMP" "Staphs" "2 mcg" 18 18 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "Screen" "B_STPHY_SPRP" 2 "FOX" "Staphs" 8 8 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2023" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2023" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2023" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.25 FALSE FALSE "EUCAST 2023" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CLI" "Strep A, B, C, G" "2 mcg" 17 17 FALSE FALSE @@ -9857,14 +9790,14 @@ "EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2022" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2022" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 18 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.25 FALSE FALSE -"EUCAST 2022" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2022" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2022" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2022" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2022" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_ENTRC_FACM" 2 "ERV" "Enterococcus" "20 mcg" 24 24 FALSE FALSE @@ -10494,7 +10427,6 @@ "EUCAST 2022" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 23 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 0.5 FALSE FALSE -"EUCAST 2022" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2022" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 17 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 18 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_STPHY" 3 "QDA" "Staphs" 1 2 FALSE FALSE @@ -10581,6 +10513,7 @@ "EUCAST 2022" "human" "human" "DISK" "B_STPHY_SPRP" 2 "AMP" "Staphs" "2 mcg" 18 18 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "Screen" "B_STPHY_SPRP" 2 "FOX" "Staphs" 8 8 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2022" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2022" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2022" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2022" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE @@ -11387,14 +11320,14 @@ "EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2021" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2021" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 18 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.25 FALSE FALSE -"EUCAST 2021" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2021" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2021" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2021" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_ENTRC" 3 "VAN" "ECOFF" 4 4 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE @@ -12384,7 +12317,6 @@ "EUCAST 2021" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 23 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 0.5 FALSE FALSE -"EUCAST 2021" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2021" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 18 FALSE FALSE "EUCAST 2021" "human" "human" "MIC" "B_STPHY" 3 "QDA" "Staphs" 1 2 FALSE FALSE @@ -12597,6 +12529,7 @@ "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "MFX" "ECOFF" 0.25 0.25 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "NIT" "ECOFF" 32 32 FALSE FALSE "EUCAST 2021" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2021" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "RXT" "ECOFF" 1 1 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "VAN" "ECOFF" 4 4 FALSE FALSE "EUCAST 2021" "ECOFF" "ECOFF" "MIC" "B_STPHY_WRNR" 2 "CIP" "ECOFF" 1 1 FALSE FALSE @@ -13531,14 +13464,14 @@ "EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2020" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2020" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 18 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.25 FALSE FALSE -"EUCAST 2020" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2020" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2020" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2020" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_ENTRC" 3 "VAN" "ECOFF" 4 4 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE @@ -14481,7 +14414,6 @@ "EUCAST 2020" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 23 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 0.5 FALSE FALSE -"EUCAST 2020" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2020" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2020" "human" "human" "MIC" "B_STPHY" 3 "ORI" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 18 FALSE FALSE @@ -14733,6 +14665,7 @@ "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "MFX" "ECOFF" 0.25 0.25 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "NIT" "ECOFF" 32 32 FALSE FALSE "EUCAST 2020" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2020" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2020" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "RXT" "ECOFF" 1 1 FALSE FALSE "EUCAST 2020" "ECOFF" "ECOFF" "MIC" "B_STPHY_SPRP" 2 "VAN" "ECOFF" 4 4 FALSE FALSE @@ -15447,14 +15380,14 @@ "EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2019" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2019" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 18 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.25 FALSE FALSE -"EUCAST 2019" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2019" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2019" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2019" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2019" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Enterococcus" "100 mcg" 15 15 TRUE FALSE @@ -15764,7 +15697,6 @@ "EUCAST 2019" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 20 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 1 FALSE FALSE -"EUCAST 2019" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2019" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_STPHY" 3 "ORI" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 18 FALSE FALSE @@ -15843,6 +15775,7 @@ "EUCAST 2019" "human" "human" "DISK" "B_STPHY_SPRP" 2 "FOX" "Staphs" "30 mcg" 22 22 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_STPHY_SPRP" 2 "FOX" "Staphs" 8 8 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2019" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2019" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2019" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2019" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE @@ -16275,14 +16208,14 @@ "EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2018" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2018" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 15 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.5 FALSE FALSE -"EUCAST 2018" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2018" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2018" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2018" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2018" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Enterococcus" "100 mcg" 15 15 TRUE FALSE @@ -16592,7 +16525,6 @@ "EUCAST 2018" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 20 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 1 FALSE FALSE -"EUCAST 2018" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2018" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_STPHY" 3 "ORI" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 18 FALSE FALSE @@ -16670,6 +16602,7 @@ "EUCAST 2018" "human" "human" "DISK" "B_STPHY_SPRP" 2 "FOX" "Staphs" "30 mcg" 22 22 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_STPHY_SPRP" 2 "FOX" "Staphs" 8 8 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2018" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2018" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2018" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2018" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE @@ -17078,14 +17011,14 @@ "EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2017" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2017" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 15 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.5 FALSE FALSE -"EUCAST 2017" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2017" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2017" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2017" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2017" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Enterococcus" "100 mcg" 15 15 TRUE FALSE @@ -17400,7 +17333,6 @@ "EUCAST 2017" "human" "human" "MIC" "B_STPHY" 3 "LNZ" "Staphs" 4 4 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "B_STPHY" 3 "MNO" "Staphs" "30 mcg" 23 20 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 1 FALSE FALSE -"EUCAST 2017" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2017" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_STPHY" 3 "ORI" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "B_STPHY" 3 "QDA" "Staphs" "15 mcg" 21 18 FALSE FALSE @@ -17476,6 +17408,7 @@ "EUCAST 2017" "human" "human" "DISK" "B_STPHY_SPRP" 2 "FOX" "Staphs" "30 mcg" 22 22 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_STPHY_SPRP" 2 "FOX" "Staphs" 8 8 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2017" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2017" "human" "human" "MIC" "B_STPHY_SPRP" 2 "OXA" "Staphs" 2 2 FALSE FALSE "EUCAST 2017" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2017" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE @@ -17868,14 +17801,14 @@ "EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 14 14 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2016" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2016" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 15 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.5 FALSE FALSE -"EUCAST 2016" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2016" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2016" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2016" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2016" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Enterococcus" "100 mcg" 15 15 TRUE FALSE @@ -18170,8 +18103,6 @@ "EUCAST 2016" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 1 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_STPHY" 3 "MUP" "Staphs" "200 mcg" 30 18 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_STPHY" 3 "MUP" "Staphs" 1 256 FALSE FALSE -"EUCAST 2016" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE -"EUCAST 2016" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2016" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_STPHY" 3 "OFX" "Staphs" "5 mcg" 20 20 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_STPHY" 3 "OFX" "Staphs" 1 1 FALSE FALSE @@ -18222,6 +18153,8 @@ "EUCAST 2016" "human" "human" "MIC" "B_STPHY_LGDN" 2 "PEN" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "Screen" "B_STPHY_PSDN" 2 "FOX" "Staphs" "30 mcg" 35 35 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_STPHY_SPRP" 2 "AMP" "Staphs" "2 mcg" 18 18 FALSE FALSE +"EUCAST 2016" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2016" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2016" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2016" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE "EUCAST 2016" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" 8 8 FALSE FALSE @@ -18604,14 +18537,14 @@ "EUCAST 2015" "human" "human" "DISK" "B_ENTRC" 3 "QDA" "Enterococcus" "15 mcg" 22 20 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "QDA" "Enterococcus" 1 4 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "SAM" "Enterococcus" 4 8 FALSE FALSE -"EUCAST 2015" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2015" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 15 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.5 FALSE FALSE -"EUCAST 2015" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2015" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2015" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2015" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2015" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Enterococcus" "100 mcg" 15 15 TRUE FALSE @@ -18901,8 +18834,6 @@ "EUCAST 2015" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 1 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "B_STPHY" 3 "MUP" "Staphs" "200 mcg" 30 18 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_STPHY" 3 "MUP" "Staphs" 1 256 FALSE FALSE -"EUCAST 2015" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE -"EUCAST 2015" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2015" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "B_STPHY" 3 "OFX" "Staphs" "5 mcg" 20 20 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_STPHY" 3 "OFX" "Staphs" 1 1 FALSE FALSE @@ -18949,6 +18880,8 @@ "EUCAST 2015" "human" "human" "MIC" "B_STPHY_LGDN" 2 "PEN" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "Screen" "B_STPHY_PSDN" 2 "FOX" "Staphs" "30 mcg" 35 35 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "B_STPHY_SPRP" 2 "AMP" "Staphs" "2 mcg" 18 18 FALSE FALSE +"EUCAST 2015" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2015" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2015" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2015" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE "EUCAST 2015" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" 8 8 FALSE FALSE @@ -19322,14 +19255,14 @@ "EUCAST 2014" "human" "human" "DISK" "B_ENTRC" 3 "QDA" "Enterococcus" "15 mcg" 22 20 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "QDA" "Enterococcus" 1 4 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "SAM" "Enterococcus" 4 8 FALSE FALSE -"EUCAST 2014" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2014" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 15 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.5 FALSE FALSE -"EUCAST 2014" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2014" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2014" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2014" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2014" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Enterococcus" "100 mcg" 15 15 TRUE FALSE @@ -19619,8 +19552,6 @@ "EUCAST 2014" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Staphs" 0.5 1 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "B_STPHY" 3 "MUP" "Staphs" "200 mcg" 30 18 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_STPHY" 3 "MUP" "Staphs" 1 256 FALSE FALSE -"EUCAST 2014" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE -"EUCAST 2014" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2014" "human" "human" "DISK" "Screen" "B_STPHY" 3 "NOR" "Staphs" "10 mcg" 17 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "B_STPHY" 3 "OFX" "Staphs" "5 mcg" 20 20 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_STPHY" 3 "OFX" "Staphs" 1 1 FALSE FALSE @@ -19667,6 +19598,8 @@ "EUCAST 2014" "human" "human" "MIC" "B_STPHY_LGDN" 2 "PEN" "Staphs" 0.125 0.125 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "Screen" "B_STPHY_PSDN" 2 "FOX" "Staphs" "30 mcg" 35 35 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "B_STPHY_SPRP" 2 "AMP" "Staphs" "2 mcg" 18 18 FALSE FALSE +"EUCAST 2014" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" "100 mcg" 13 13 TRUE FALSE +"EUCAST 2014" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_STPHY_SPRP" 2 "NIT" "Staphs" 64 64 TRUE FALSE "EUCAST 2014" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "AZM" "Strep A, B, C, G" 0.25 0.5 FALSE FALSE "EUCAST 2014" "human" "human" "DISK" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" "30 mcg" 19 19 FALSE FALSE "EUCAST 2014" "human" "human" "MIC" "B_STRPT_ABCG" 2.5 "CHL" "Strep A, B, C, G" 8 8 FALSE FALSE @@ -20017,14 +19950,14 @@ "EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Enterococcus" 512 512 FALSE FALSE "EUCAST 2013" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Enterococcus" "300 mcg" 19 19 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Enterococcus" 512 512 FALSE FALSE -"EUCAST 2013" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 0.032 1 FALSE FALSE +"EUCAST 2013" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Enterococcus" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Enterococcus" 1 1 FALSE FALSE "EUCAST 2013" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Enterococcus" "30 mcg" 16 16 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Enterococcus" 2 2 FALSE FALSE "EUCAST 2013" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Enterococcus" "15 mcg" 18 15 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Enterococcus" 0.25 0.5 FALSE FALSE -"EUCAST 2013" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2013" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 0.032 1 TRUE FALSE +"EUCAST 2013" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2013" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Enterococcus" 1 1 TRUE FALSE "EUCAST 2013" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Enterococcus" "5 mcg" 12 12 FALSE FALSE "EUCAST 2013" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Enterococcus" 4 4 FALSE FALSE "EUCAST 2013" "human" "human" "DISK" "B_ENTRC_FACM" 2 "QDA" "Enterococcus" "15 mcg" 22 20 FALSE FALSE @@ -20706,14 +20639,14 @@ "EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "STH" "Unknown" 512 512 FALSE FALSE "EUCAST 2012" "human" "human" "DISK" "B_ENTRC" 3 "STR" "Unknown" "300 mcg" 19 19 FALSE FALSE "EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "STR" "Unknown" 512 512 FALSE FALSE -"EUCAST 2012" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Unknown" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Unknown" 0.032 1 FALSE FALSE +"EUCAST 2012" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Unknown" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Unknown" 1 1 FALSE FALSE "EUCAST 2012" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Unknown" "30 mcg" 16 16 FALSE FALSE "EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Unknown" 2 2 FALSE FALSE "EUCAST 2012" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Unknown" "15 mcg" 18 15 FALSE FALSE "EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Unknown" 0.25 0.5 FALSE FALSE -"EUCAST 2012" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Unknown" "5 mcg" 50 21 TRUE FALSE -"EUCAST 2012" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Unknown" 0.032 1 TRUE FALSE +"EUCAST 2012" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Unknown" "5 mcg" 21 21 TRUE FALSE +"EUCAST 2012" "human" "human" "MIC" "Uncomplicated urinary tract infection" "B_ENTRC" 3 "TMP" "Unknown" 1 1 TRUE FALSE "EUCAST 2012" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Unknown" "5 mcg" 12 12 FALSE FALSE "EUCAST 2012" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Unknown" 4 4 FALSE FALSE "EUCAST 2012" "human" "human" "DISK" "Uncomplicated urinary tract infection" "B_ENTRC_FCLS" 2 "NIT" "Unknown" "100 mcg" 15 15 TRUE FALSE @@ -21222,14 +21155,14 @@ "EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "NIT" "Unknown" "100 mcg" 15 15 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "NIT" "Unknown" 64 64 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "SAM" "Unknown" 4 8 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Unknown" "1.25/23.75 mcg" 50 21 FALSE FALSE -"EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Unknown" 0.32 1 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "SXT" "Unknown" "1.25/23.75 mcg" 23 23 FALSE FALSE +"EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "SXT" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "TEC" "Unknown" "30 mcg" 16 16 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "TEC" "Unknown" 2 2 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "TGC" "Unknown" "15 mcg" 18 15 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "TGC" "Unknown" 0.25 0.5 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "TMP" "Unknown" "5 mcg" 50 21 FALSE FALSE -"EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "TMP" "Unknown" 0.32 1 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "TMP" "Unknown" "5 mcg" 21 21 FALSE FALSE +"EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "TMP" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_ENTRC" 3 "VAN" "Unknown" "5 mcg" 12 12 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_ENTRC" 3 "VAN" "Unknown" 4 4 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_ENTRC_FACM" 2 "QDA" "Unknown" 1 4 FALSE FALSE @@ -21461,8 +21394,6 @@ "EUCAST 2011" "human" "human" "MIC" "B_STPHY" 3 "MFX" "Unknown" 0.5 1 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STPHY" 3 "MNO" "Unknown" 0.5 1 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STPHY" 3 "NET" "Unknown" 1 1 FALSE FALSE -"EUCAST 2011" "human" "human" "DISK" "B_STPHY_SPRP" 2 "NIT" "Unknown" "100 mcg" 13 13 FALSE FALSE -"EUCAST 2011" "human" "human" "MIC" "B_STPHY_SPRP" 2 "NIT" "Unknown" 64 64 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_STPHY" 3 "NOR" "Unknown" "10 mcg" 17 17 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STPHY" 3 "OFX" "Unknown" 1 1 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STPHY" 3 "OXA" "Unknown" 0.25 0.25 FALSE FALSE @@ -21490,6 +21421,8 @@ "EUCAST 2011" "human" "human" "DISK" "B_STPHY_LGDN" 2 "FOX" "Unknown" "30 mcg" 22 22 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STPHY_LGDN" 2 "OXA" "Unknown" 2 2 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STPHY_LGDN" 2 "TEC" "Unknown" 2 2 FALSE FALSE +"EUCAST 2011" "human" "human" "DISK" "B_STPHY_SPRP" 2 "NIT" "Unknown" "100 mcg" 13 13 FALSE FALSE +"EUCAST 2011" "human" "human" "MIC" "B_STPHY_SPRP" 2 "NIT" "Unknown" 64 64 FALSE FALSE "EUCAST 2011" "human" "human" "DISK" "B_STRPT" 3 "AMP" "Unknown" "2 mcg" 21 15 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT" 3 "AMP" "Unknown" 0.5 2 FALSE FALSE "EUCAST 2011" "human" "human" "MIC" "B_STRPT" 3 "AMX" "Unknown" 0.5 2 FALSE FALSE diff --git a/data-raw/datasets/clinical_breakpoints.xlsx b/data-raw/datasets/clinical_breakpoints.xlsx index a41b5eda9..0798152b6 100644 Binary files a/data-raw/datasets/clinical_breakpoints.xlsx and b/data-raw/datasets/clinical_breakpoints.xlsx differ diff --git a/data-raw/eucast_rules.tsv b/data-raw/eucast_rules.tsv index 45dd84c86..83529029f 100644 --- a/data-raw/eucast_rules.tsv +++ b/data-raw/eucast_rules.tsv @@ -7,1333 +7,1527 @@ # 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 <<<<< # ------------------------------------------------------------------------------------------------------------------------------- -if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version note -order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10 -order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10 -order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10 -genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S Staphylococcus Breakpoints 10 -genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10 -genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 10 -genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10 -genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 10 -genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 10 -genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints 10 -genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints 10 -genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 10 -genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints 10 -genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints 10 -genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints 10 -genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints 10 -genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints 10 -genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 10 -genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 10 -genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 10 -genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 10 -genus_species 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 Streptococcus groups A, B, C, G Breakpoints 10 -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 Streptococcus groups A, B, C, G Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 10 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 10 -genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 10 -genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints 10 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 10 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 10 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints 10 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints 10 -genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 10 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 10 -genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 10 -genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 10 -genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints 10 -genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints 10 -genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints 10 -genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints 10 -genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints 10 -genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints 10 -genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 10 -genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 10 -genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 10 -genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints 10 -genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints 10 -genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints 10 -genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints 10 -genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints 10 -genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints 10 -genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints 10 -genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints 10 -genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints 10 -genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints 10 -genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints 10 -genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints 10 -genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints 10 -genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints 10 -genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints 10 -genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints 10 -genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints 10 -genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints 10 -genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints 10 -genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints 10 -genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints 10 -genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints 10 -genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints 10 -genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints 10 -genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 10 -genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 10 -genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 10 -genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 10 -genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 10 -genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 10 -genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 10 -genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints 10 -genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 10 -genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints 10 -genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints 10 -genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 10 -order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 11 -order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 11 -order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 11 -genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S Staphylococcus Breakpoints 11 -genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 11 -genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 11 -genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 11 -genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 11 -genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 11 -genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints 11 -genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints 11 -genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 11 -genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints 11 -genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints 11 -genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints 11 -genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints 11 -genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints 11 -genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 11 -genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 11 -genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 11 -genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 11 -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 Streptococcus groups A, B, C, G Breakpoints 11 -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 Streptococcus groups A, B, C, G Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 11 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 11 -genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 11 -genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints 11 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 11 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 11 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints 11 -genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints 11 -genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 11 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 11 -genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 11 -genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 11 -genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TIC S Anaerobic Gram-positives Breakpoints 11 -genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TIC I Anaerobic Gram-positives Breakpoints 11 -genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TIC R Anaerobic Gram-positives Breakpoints 11 -genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TIC S Anaerobic Gram-negatives Breakpoints 11 -genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TIC I Anaerobic Gram-negatives Breakpoints 11 -genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TIC R Anaerobic Gram-negatives Breakpoints 11 -genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 11 -genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 11 -genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 11 -genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints 11 -genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints 11 -genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints 11 -genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints 11 -genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints 11 -genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints 11 -genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints 11 -genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints 11 -genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints 11 -genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints 11 -genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints 11 -genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints 11 -genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints 11 -genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints 11 -genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints 11 -genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints 11 -genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints 11 -genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints 11 -genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints 11 -genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints 11 -genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints 11 -genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints 11 -genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints 11 -genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints 11 -genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 11 -genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 11 -genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 11 -genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 11 -genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 11 -genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 11 -genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 11 -genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints 11 -genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 11 -genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints 11 -genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints 11 -genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 11 -genus is Bacillus NOR S fluoroquinolones S Bacillus Breakpoints 11 added in 11 -genus is Bacillus NOR I fluoroquinolones I Bacillus Breakpoints 11 added in 11 -genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11 -order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 12 -order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 12 -order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 12 -order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 12 -order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 12 -genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 12 -genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 12 -genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 12 -genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 12 -genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 12 -genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 12 -genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 12 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins -genus_species is Staphylococcus aureus "PEN, FOX-S" "S, S" penicillins S Staphylococcus Breakpoints 12 -genus_species is Staphylococcus aureus "PEN, FOX-S" "R, S" "betalactams_with_inhibitor, isoxazolylpenicillins, NAF" S Staphylococcus Breakpoints 12 -genus is Staphylococcus FOX-S R "PEN, PHN, AMP, AMX, PIP, TIC" R Staphylococcus Breakpoints 12 -genus_species is Staphylococcus saprophyticus AMP S "AMP, SAM, AMX, AMC, PIP, TZP" S Staphylococcus Breakpoints 12 -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 Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))" -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 Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))" -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 Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))" -genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R "PEN, PHN, AMP, AMX, PIP, TIC" R Staphylococcus Breakpoints 12 -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 Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))" -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 Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))" -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 Staphylococcus Breakpoints 12 "sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(""cefalexin"", ""ceftazidim"", ""ceftazidim/avibactam"", ""ceftibuten"", ""ceftolozan/tazobactam""))]))" -genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 12 -genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 12 -genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 12 -genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 12 -genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 12 -genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S S carbapenems S Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method" -genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S I carbapenems I Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method" -genus_species one_of "Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans" OXA-S R carbapenems R Staphylococcus Breakpoints 12 "Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method" -genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 12 -genus is Staphylococcus NOR-S S "CIP, LVX" I Staphylococcus Breakpoints 12 -genus_species is Staphylococcus aureus VAN S "DAL, ORI" S Staphylococcus Breakpoints 12 -genus_species is Staphylococcus aureus "FOX-S, VAN" "R, S" TLV S Staphylococcus Breakpoints 12 MRSA isolates are in this file safely denoted as FOX resistant -genus is Staphylococcus ERY S "AZM, CLR, RXT" S Staphylococcus Breakpoints 12 -genus is Staphylococcus TCY-S S "DOX, MNO" S Staphylococcus Breakpoints 12 -genus is Enterococcus AMP S "AMP, SAM, AMX, AMC, PIP, TZP" S Enterococcus Breakpoints 12 -genus is Enterococcus AMP I "AMP, SAM, AMX, AMC, PIP, TZP" I Enterococcus Breakpoints 12 -genus is Enterococcus AMP R "AMP, SAM, AMX, AMC, PIP, TZP" R Enterococcus Breakpoints 12 -genus is Enterococcus NOR-S S "CIP, LVX" S Enterococcus Breakpoints 12 -genus is Enterococcus NOR-S I "CIP, LVX" I Enterococcus Breakpoints 12 -genus is Enterococcus NOR-S R "CIP, LVX" R Enterococcus Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN S penicillins S "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN I penicillins I "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group C, Streptococcus Group G" PEN R penicillins R "Streptococcus groups A, B, C, G" Breakpoints 12 -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 "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]" -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 "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]" -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 "Streptococcus groups A, B, C, G" Breakpoints 12 "penicillins()[!penicillins() %in% c(""PHN"", isoxazolylpenicillins())]" -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN S cephalosporins S "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN I cephalosporins I "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN R cephalosporins R "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN S carbapenems S "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN I carbapenems I "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" PEN R carbapenems R "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S S MFX S "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S S LVX I "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" NOR-S R "MFX, LVX" R "Streptococcus groups A, B, C, G" Breakpoints 12 does not explicitly state that it is for other fluoroquinolones -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" VAN S "DAL, ORI" S "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" ERY S "AZM, CLR, RXT" S "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" ERY R "AZM, CLR, RXT" R "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" TCY-S S "DOX, MNO" S "Streptococcus groups A, B, C, G" Breakpoints 12 -genus_species one_of "Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G" TCY-S R "DOX, MNO" R "Streptococcus groups A, B, C, G" Breakpoints 12 -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 Streptococcus pneumoniae Breakpoints 12 "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""))" -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 Streptococcus pneumoniae Breakpoints 12 "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""))" -genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae OXA-S R "PEN, PHN" R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 12 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae AMP S "AMX, AMC, SAM, PIP, TZP" S Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae AMP I "AMX, AMC, SAM, PIP, TZP" I Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae AMP R "AMX, AMC, SAM, PIP, TZP" R Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S R "MFX, LVX" R Streptococcus pneumoniae Breakpoints 12 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae ERY S "AZM, CLR, RXT" S Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae ERY R "AZM, CLR, RXT" R Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae TCY-S S "DOX, MNO" S Streptococcus pneumoniae Breakpoints 12 -genus_species is Streptococcus pneumoniae TCY-S R "DOX, MNO" R Streptococcus pneumoniae Breakpoints 12 -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 Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")" -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 Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")" -genus_species one_of "Viridans Group Streptococcus (VGS)" AMP S "AMX, AMC, SAM, PIP, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")" -genus_species one_of "Viridans Group Streptococcus (VGS)" AMP I "AMX, AMC, SAM, PIP, TZP" I Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")" -genus_species one_of "Viridans Group Streptococcus (VGS)" AMP R "AMX, AMC, SAM, PIP, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")" -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 Haemophilus influenzae Breakpoints 12 "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()])" -genus_species is Haemophilus influenzae "PEN-S, BLA-S" "R, R" "AMP, AMX, PIP" R Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae NAL-S S "CIP, LVX, MFX, OFX" S Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae NAL-S I "CIP, LVX, MFX, OFX" I Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae NAL-S R "CIP, LVX, MFX, OFX" R Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae TCY S "DOX, MNO" S Haemophilus influenzae Breakpoints 12 -genus_species is Haemophilus influenzae TCY R "DOX, MNO" R Haemophilus influenzae Breakpoints 12 -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 Moraxella catarrhalis Breakpoints 12 penicillins()[!penicillins() %in% betalactams_with_inhibitor()] -genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis NAL-S S "CIP, LVX, MFX, OFX" S Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis NAL-S R "CIP, LVX, MFX, OFX" R Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis ERY S "AZM, CLR, RXT" S Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis ERY R "AZM, CLR, RXT" R Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis TCY S "DOX, MNO" S Moraxella catarrhalis Breakpoints 12 -genus_species is Moraxella catarrhalis TCY R "DOX, MNO" R Moraxella catarrhalis Breakpoints 12 -genus_species is Neisseria gonorrhoeae BLA-S R "AMP, AMX" R Neisseria gonorrhoeae Breakpoints 12 -genus_species is Neisseria gonorrhoeae "BLA-S, PEN" "S, S" "AMP, AMX" S Neisseria gonorrhoeae Breakpoints 12 -genus_species is Neisseria gonorrhoeae "BLA-S, PEN" "S, I" "AMP, AMX" I Neisseria gonorrhoeae Breakpoints 12 -genus_species is Neisseria gonorrhoeae "BLA-S, PEN" "S, R" "AMP, AMX" R Neisseria gonorrhoeae Breakpoints 12 -genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 12 -genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 12 -genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 12 -genus is Prevotella PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "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()])" -genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints -genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints -genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints -genus_species is Fusobacterium necrophorum PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2023"" & clinical_breakpoints$mo == as.mo(""Fusobacterium necrophorum""))]), ""AMP"", ""SAM"", ""AMX"", ""AMC"", ""PIP"", ""ETP"", ""IPM""); sort(x[x %in% betalactams()])" -genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints -genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints -genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints -genus_species is Clostridium perfringens PEN S "AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "x <- c(unique(clinical_breakpoints$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()])" -genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints -genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints -genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints -genus_species is Cutibacterium acnes PEN S "AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP" S Anaerobic bacteria Breakpoints "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()])" -genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints -genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints -genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints -genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints -genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints -genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints -genus_species is Pasteurella multocida PEN S "AMP, AMX" S Pasteurella multocida Breakpoints 12 -genus_species is Pasteurella multocida PEN I "AMP, AMX" I Pasteurella multocida Breakpoints 12 -genus_species is Pasteurella multocida PEN R "AMP, AMX" R Pasteurella multocida Breakpoints 12 -genus_species is Pasteurella multocida NAL-S S "CIP, LVX" S Pasteurella multocida Breakpoints 12 -genus_species is Pasteurella multocida NAL-S R "CIP, LVX" R Pasteurella multocida Breakpoints 12 -genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 12 -genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 12 -genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 12 -genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY S "AZM, CLR" S Campylobacter coli/jejuni Breakpoints 12 -genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY I "AZM, CLR" I Campylobacter coli/jejuni Breakpoints 12 -genus_species one_of "Campylobacter coli, Campylobacter jejuni" ERY R "AZM, CLR" R Campylobacter coli/jejuni Breakpoints 12 -genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY S DOX S Campylobacter coli/jejuni Breakpoints 12 -genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY I DOX I Campylobacter coli/jejuni Breakpoints 12 -genus_species one_of "Campylobacter coli, Campylobacter jejuni" TCY R DOX R Campylobacter coli/jejuni Breakpoints 12 -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN S CTX S Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY I DOX I Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species one_of "Corynebacterium diphtheriae, Corynebacterium ulcerans" TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is "Aerococcus sanguinicola, Aerococcus urinae" NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 12 -genus_species is Kingella kingae BLA-S R "PEN, AMP, AMX" R Kingella kingae Breakpoints 12 -genus_species is Kingella kingae PEN S "AMP, AMX" S Kingella kingae Breakpoints 12 -genus_species is Kingella kingae PEN I "AMP, AMX" I Kingella kingae Breakpoints 12 -genus_species is Kingella kingae PEN R "AMP, AMX" R Kingella kingae Breakpoints 12 -genus_species is Kingella kingae ERY S "AZM, CLR" S Kingella kingae Breakpoints 12 -genus_species is Kingella kingae ERY I "AZM, CLR" I Kingella kingae Breakpoints 12 -genus_species is Kingella kingae ERY R "AZM, CLR" R Kingella kingae Breakpoints 12 -genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 12 -genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 12 -genus is Vibrio PEF-S S "CIP, LVX" S Vibrio spp. Breakpoints 12 -genus is Vibrio PEF-S I "CIP, LVX" I Vibrio spp. Breakpoints 12 -genus is Vibrio PEF-S R "CIP, LVX" R Vibrio spp. Breakpoints 12 -genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 12 -genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 12 -genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 12 -genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 12 -genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 12 -genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 12 -genus is Bacillus NOR-S S "CIP, LVX" I Bacillus Breakpoints 12 -genus is Bacillus NOR-S R "CIP, LVX" R Bacillus Breakpoints 12 -genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 12 -genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 12 -order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 13.1 -order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 13.1 -order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 13.1 -order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 13.1 -order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 13.1 -genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 13.1 -genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 13.1 -genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 13.1 -genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 13.1 -genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 13.1 -genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 13.1 -genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 13.1 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins -genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 13.1 -genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 13.1 -genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 13.1 -genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 13.1 -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 Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 13.1 -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 Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 13.1 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 13.1 -genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 13.1 -genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 13.1 -genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 13.1 -genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 13.1 -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 13.1 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 13.1 -genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 13.1 -genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 13.1 -genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 13.1 MRSA isolates are in this file safely denoted as FOX resistant -genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 13.1 -genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 13.1 -genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 13.1 -genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 13.1 -genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 13.1 -genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 13.1 -genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 13.1 -genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 13.1 -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 Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -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 Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -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 Streptococcus groups A, B, C, G Breakpoints 13.1 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 13.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 13.1 -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 Streptococcus pneumoniae Breakpoints 13.1 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) -genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 13.1 x <- unique(clinical_breakpoints$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")) -genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 13.1 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 13.1 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 13.1 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 13.1 -genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 13.1 -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 Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules() -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 Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules() -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 Haemophilus influenzae Breakpoints 13.1 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()]) -genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 13.1 -genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 13.1 -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 Moraxella catarrhalis Breakpoints 13.1 penicillins()[!penicillins() %in% betalactams_with_inhibitor()] -genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 13.1 -genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 13.1 -genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 13.1 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 13.1 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 13.1 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 13.1 -genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 13.1 -genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 13.1 -genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 13.1 -genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) -genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 13.1 -genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 13.1 -genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 13.1 -genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$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()]) -genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 13.1 -genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 13.1 -genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 13.1 -genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) -genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 13.1 -genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 13.1 -genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 13.1 -genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 13.1 x <- c(unique(clinical_breakpoints$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()]) -genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 13.1 -genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 13.1 -genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 13.1 -genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 13.1 -genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 13.1 -genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 13.1 -genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 13.1 -genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 13.1 -genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 13.1 -genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 13.1 -genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 13.1 -genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 13.1 -genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 13.1 -genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 13.1 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 13.1 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 13.1 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 13.1 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 13.1 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 13.1 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 13.1 -genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 13.1 -genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 13.1 -genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 13.1 -genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 13.1 -genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 13.1 -genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 13.1 -genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 13.1 -genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 13.1 -genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 13.1 -genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 13.1 -genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 13.1 -genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 13.1 -genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 13.1 -genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 13.1 -genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 13.1 -order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 14 -order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 14 -order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 14 -order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 14 -order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 14 -genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 14 -genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 14 -genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 14 -genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 14 -genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 14 -genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 14 -genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 14 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins -genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 14 -genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 14 -genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 14 -genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 14 -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 Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 14 -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 Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 14 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 14 -genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 14 -genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 14 -genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 14 -genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 14 -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 14 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 14 -genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 14 -genus_species is Staphylococcus coagulase-negative VAN, TEC S, S DAL S Staphylococcus Breakpoints 14 -genus_species is Staphylococcus aureus VAN S DAL, ORI S Staphylococcus Breakpoints 14 -genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S Staphylococcus Breakpoints 14 MRSA isolates are in this file safely denoted as FOX resistant -genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 14 -genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 14 -genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Enterococcus Breakpoints 14 -genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I Enterococcus Breakpoints 14 -genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R Enterococcus Breakpoints 14 -genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 14 -genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 14 -genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 14 -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 Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -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 Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -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 Streptococcus groups A, B, C, G Breakpoints 14 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 14 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 14 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 14 -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 Streptococcus pneumoniae Breakpoints 14 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")) -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 Streptococcus pneumoniae Breakpoints 14 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")) -genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 14 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 14 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 14 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 14 -genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 14 -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 Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules() -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 Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules() -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 Haemophilus influenzae Breakpoints 14 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()]) -genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 14 -genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 14 -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 Moraxella catarrhalis Breakpoints 14 penicillins()[!penicillins() %in% betalactams_with_inhibitor()] -genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 14 -genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 14 -genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 14 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 14 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 14 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 14 -genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 14 -genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 14 -genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 14 -genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 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()]) -genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 14 -genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 14 -genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 14 -genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) -genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 14 -genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 14 -genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 14 -genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 x <- c(unique(clinical_breakpoints$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()]) -genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 14 -genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 14 -genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 14 -genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 14 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()]) -genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 14 -genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 14 -genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 14 -genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 14 -genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 14 -genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 14 -genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 14 -genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 14 -genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 14 -genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 14 -genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 14 -genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 14 -genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 14 -genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 14 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 14 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 14 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 14 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 14 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 14 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 14 -genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R Kingella kingae Breakpoints 14 -genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 14 -genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 14 -genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 14 -genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 14 -genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 14 -genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 14 -genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 14 -genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 14 -genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 14 -genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 14 -genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 14 -genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 14 -genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 14 -genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 14 -genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 14 -genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 14 -genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 14 -genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 14 -genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 14 -genus_species is Bacillus anthracis PEN I AMX S Bacillus anthracis Breakpoints 14 -genus_species is Bacillus anthracis PEN R AMX R Bacillus anthracis Breakpoints 14 -genus_species is Bacillus anthracis TCY-S S DOX S Bacillus anthracis Breakpoints 14 -genus_species is Bacillus anthracis TCY-S R DOX R Bacillus anthracis Breakpoints 14 -genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoints 14 -genus_species is Brucella melitensis TCY-S R DOX R Brucella melitensis Breakpoints 14 -genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 14 -genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 14 -order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 15 -order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 15 -order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 15 -order is Enterobacterales LEX S CZO I Enterobacterales (Order) Breakpoints 15 -order is Enterobacterales CFR S CZO I Enterobacterales (Order) Breakpoints 15 -genus is Salmonella PEF-S S CIP S Enterobacterales (Order) Breakpoints 15 -genus is Salmonella PEF-S I CIP I Enterobacterales (Order) Breakpoints 15 -genus is Salmonella PEF-S R CIP R Enterobacterales (Order) Breakpoints 15 -genus_species is Yersinia enterocolitica TCY S DOX S Enterobacterales (Order) Breakpoints 15 -genus_species is Yersinia enterocolitica TCY I DOX I Enterobacterales (Order) Breakpoints 15 -genus_species is Yersinia enterocolitica TCY R DOX R Enterobacterales (Order) Breakpoints 15 -genus_species is Staphylococcus aureus FOX-S R penicillins R Staphylococcus Breakpoints 15 See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins -genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S Staphylococcus Breakpoints 15 -genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S Staphylococcus Breakpoints 15 -genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 15 -genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 15 -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 Staphylococcus Breakpoints 15 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 15 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 15 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R Staphylococcus Breakpoints 15 -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 Staphylococcus Breakpoints 15 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 15 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -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 Staphylococcus Breakpoints 15 sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c("cefalexin", "ceftazidim", "ceftazidim/avibactam", "ceftibuten", "ceftolozan/tazobactam"))])) -genus_species is Staphylococcus aureus FOX-S S CPT S Staphylococcus Breakpoints 15 -genus_species is Staphylococcus aureus FOX-S S BPR S Staphylococcus Breakpoints 15 -genus is Staphylococcus FOX-S S carbapenems S Staphylococcus Breakpoints 15 -genus is Staphylococcus FOX-S I carbapenems I Staphylococcus Breakpoints 15 -genus is Staphylococcus FOX-S R carbapenems R Staphylococcus Breakpoints 15 -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S S carbapenems S Staphylococcus Breakpoints 15 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Staphylococcus Breakpoints 15 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Staphylococcus Breakpoints 15 Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method -genus is Staphylococcus NOR-S S MFX S Staphylococcus Breakpoints 15 -genus is Staphylococcus NOR-S S CIP, LVX I Staphylococcus Breakpoints 15 -genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 15 -genus is Staphylococcus TCY-S S DOX, MNO S Staphylococcus Breakpoints 15 -genus is Enterococcus AMP S AMP, SAM, AMX S Enterococcus Breakpoints 15 -genus is Enterococcus AMP I AMP, SAM, AMX I Enterococcus Breakpoints 15 -genus is Enterococcus AMP R AMP, SAM, AMX R Enterococcus Breakpoints 15 -genus is Enterococcus AMP R AMX, AMC R Enterococcus Breakpoints 15 -genus is Enterococcus NOR-S S CIP, LVX S Enterococcus Breakpoints 15 -genus is Enterococcus NOR-S I CIP, LVX I Enterococcus Breakpoints 15 -genus is Enterococcus NOR-S R CIP, LVX R Enterococcus Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R Streptococcus groups A, B, C, G Breakpoints 15 -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 Streptococcus groups A, B, C, G Breakpoints 15 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -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 Streptococcus groups A, B, C, G Breakpoints 15 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -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 Streptococcus groups A, B, C, G Breakpoints 15 penicillins()[!penicillins() %in% c("PHN", isoxazolylpenicillins())] -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S cephalosporins S Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I cephalosporins I Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R cephalosporins R Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S carbapenems S Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I carbapenems I Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R carbapenems R Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S MFX S Streptococcus groups A, B, C, G Breakpoints 15 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S S LVX I Streptococcus groups A, B, C, G Breakpoints 15 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR-S R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 15 does not explicitly state that it is for other fluoroquinolones -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G VAN S DAL, ORI S Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 15 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 15 -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 Streptococcus pneumoniae Breakpoints 15 x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) -genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S Streptococcus pneumoniae Breakpoints 15 x <- unique(clinical_breakpoints$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")) -genus_species is Streptococcus pneumoniae OXA-S S CEC I Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae PEN S CEC I Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R Streptococcus pneumoniae Breakpoints 15 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae PEN R PHN R Streptococcus pneumoniae Breakpoints 15 from flowchart: when OXA < 20 or PEN > 0.06 -genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae NOR-S S MFX S Streptococcus pneumoniae Breakpoints 15 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S S LVX I Streptococcus pneumoniae Breakpoints 15 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae NOR-S R MFX, LVX R Streptococcus pneumoniae Breakpoints 15 does not explicitly state that it is for other fluoroquinolones -genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 15 -genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 15 -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 Viridans group streptococci Breakpoints 15 MO group name will be expanded in eucast_rules() -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 Viridans group streptococci Breakpoints 15 MO group name will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 15 MO group name will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 15 MO group name will be expanded in eucast_rules() -genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 15 MO group name will be expanded in eucast_rules() -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 Haemophilus influenzae Breakpoints 15 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()]) -genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae AMC I SAM I Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae AMC R SAM R Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 15 -genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 15 -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 Moraxella catarrhalis Breakpoints 15 penicillins()[!penicillins() %in% betalactams_with_inhibitor()] -genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 15 -genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 15 -genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R Neisseria gonorrhoeae Breakpoints 15 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S Neisseria gonorrhoeae Breakpoints 15 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I Neisseria gonorrhoeae Breakpoints 15 -genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R Neisseria gonorrhoeae Breakpoints 15 -genus_species is Neisseria meningitidis TCY-S S MNO S Neisseria meningitidis Breakpoints 15 -genus_species is Neisseria meningitidis TCY-S I MNO I Neisseria meningitidis Breakpoints 15 -genus_species is Neisseria meningitidis TCY-S R MNO R Neisseria meningitidis Breakpoints 15 -genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 15 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) -genus is Prevotella AMP S AMX S Anaerobic bacteria Breakpoints 15 -genus is Prevotella AMP I AMX I Anaerobic bacteria Breakpoints 15 -genus is Prevotella AMP R AMX R Anaerobic bacteria Breakpoints 15 -genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 15 x <- c(unique(clinical_breakpoints$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()]) -genus_species is Fusobacterium necrophorum AMP S AMX S Anaerobic bacteria Breakpoints 15 -genus_species is Fusobacterium necrophorum AMP I AMX I Anaerobic bacteria Breakpoints 15 -genus_species is Fusobacterium necrophorum AMP R AMX R Anaerobic bacteria Breakpoints 15 -genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 15 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) -genus_species is Clostridium perfringens AMP S AMX S Anaerobic bacteria Breakpoints 15 -genus_species is Clostridium perfringens AMP I AMX I Anaerobic bacteria Breakpoints 15 -genus_species is Clostridium perfringens AMP R AMX R Anaerobic bacteria Breakpoints 15 -genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S Anaerobic bacteria Breakpoints 15 x <- c(unique(clinical_breakpoints$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()]) -genus_species is Cutibacterium acnes AMP S AMX S Anaerobic bacteria Breakpoints 15 -genus_species is Cutibacterium acnes AMP I AMX I Anaerobic bacteria Breakpoints 15 -genus_species is Cutibacterium acnes AMP R AMX R Anaerobic bacteria Breakpoints 15 -genus_species is Cutibacterium acnes CTX S CRO S Anaerobic bacteria Breakpoints 15 -genus_species is Cutibacterium acnes CTX I CRO I Anaerobic bacteria Breakpoints 15 -genus_species is Cutibacterium acnes CTX R CRO R Anaerobic bacteria Breakpoints 15 -genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 15 -genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 15 -genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 15 -genus_species is Pasteurella multocida NAL-S S CIP, LVX S Pasteurella multocida Breakpoints 15 -genus_species is Pasteurella multocida NAL-S R CIP, LVX R Pasteurella multocida Breakpoints 15 -genus_species is Pasteurella multocida TCY-S S DOX S Neisseria meningitidis Breakpoints 15 -genus_species is Pasteurella multocida TCY-S I DOX I Neisseria meningitidis Breakpoints 15 -genus_species is Pasteurella multocida TCY-S R DOX R Neisseria meningitidis Breakpoints 15 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S Campylobacter coli/jejuni Breakpoints 15 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I Campylobacter coli/jejuni Breakpoints 15 -genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R Campylobacter coli/jejuni Breakpoints 15 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S Campylobacter coli/jejuni Breakpoints 15 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I Campylobacter coli/jejuni Breakpoints 15 -genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R Campylobacter coli/jejuni Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R Corynebacterium diphtheriae/ulcerans Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R Aerococcus sanguinicola/urinae Breakpoints 15 -genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R Kingella kingae Breakpoints 15 -genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 15 -genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 15 -genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 15 -genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 15 -genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 15 -genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 15 -genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 15 -genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 15 -genus is Vibrio PEF-S S CIP, LVX S Vibrio spp. Breakpoints 15 -genus is Vibrio PEF-S I CIP, LVX I Vibrio spp. Breakpoints 15 -genus is Vibrio PEF-S R CIP, LVX R Vibrio spp. Breakpoints 15 -genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 15 -genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 15 -genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 15 -genus is Vibrio TCY-S S DOX S Vibrio spp. Breakpoints 15 -genus is Vibrio TCY-S I DOX I Vibrio spp. Breakpoints 15 -genus is Vibrio TCY-S R DOX R Vibrio spp. Breakpoints 15 -genus is Bacillus NOR-S S CIP, LVX I Bacillus Breakpoints 15 -genus is Bacillus NOR-S R CIP, LVX R Bacillus Breakpoints 15 -genus_species is Bacillus anthracis PEN I AMX S Bacillus anthracis Breakpoints 15 -genus_species is Bacillus anthracis PEN R AMX R Bacillus anthracis Breakpoints 15 -genus_species is Bacillus anthracis TCY-S S DOX S Bacillus anthracis Breakpoints 15 -genus_species is Bacillus anthracis TCY-S R DOX R Bacillus anthracis Breakpoints 15 -genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoints 15 -genus_species is Brucella melitensis TCY-S R DOX R Brucella melitensis Breakpoints 15 -genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 15 -genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 15 -order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species one_of Citrobacter koseri, Citrobacter amalonaticus AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Citrobacter freundii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species one_of Enterobacter cloacae complex AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Escherichia hermannii AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Hafnia alvei AMP, AMX, PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Klebsiella aerogenes AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species one_of Klebsiella pneumoniae complex AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Klebsiella oxytoca AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Leclercia adecarboxylata FOS R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Morganella morganii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Plesiomonas shigelloides AMX, AMP, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Proteus mirabilis tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Proteus penneri AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Proteus vulgaris AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Providencia rettgeri AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Providencia stuartii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus is Raoultella AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Serratia marcescens AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Yersinia enterocolitica AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Yersinia pseudotuberculosis PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Aeromonas hydrophila AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Aeromonas veronii AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Aeromonas dhakensis AMP, AMX, SAM, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Aeromonas caviae AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -genus_species is Aeromonas jandaei AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2 -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 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species one_of Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter nosocomialis AMP, AMX, AMC, CTX, CRO, ATM, ETP, TMP, FOS, TCY, DOX R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species is Achromobacter xylosoxidans AMP, AMX, CTX, CRO, ATM, ETP R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -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 Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species is Elizabethkingia meningoseptica AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, PLB, COL R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species is Elizabethkingia anophelis AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species is Ochrobactrum anthropi AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species is Pseudomonas aeruginosa AMP, AMX, AMC, SAM, CTX, CRO, ETP, CHL, TMP, KAN, NEO, tetracyclines, TGC R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus_species is Stenotrophomonas maltophilia AMP, AMX, AMC, SAM, TIC, PIP, TZP, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus is Chryseobacterium AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, PLB, COL R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2 -genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Expected resistant phenotype in other gram-negative bacteria Expected phenotypes 1.2 -genus_species is Haemophilus influenzae FUS, streptogramins R Table 3: Expected resistant phenotype in other gram-negative bacteria Expected phenotypes 1.2 -genus_species is Moraxella catarrhalis TMP R Table 3: Expected resistant phenotype in other gram-negative bacteria Expected phenotypes 1.2 -genus is Neisseria TMP R Table 3: Expected resistant phenotype in other gram-negative bacteria Expected phenotypes 1.2 -genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 3: Expected resistant phenotype in other gram-negative bacteria Expected phenotypes 1.2 -genus_species one_of Campylobacter jejuni, Campylobacter coli FUS, streptogramins, TMP R Table 3: Expected resistant phenotype in other gram-negative bacteria Expected phenotypes 1.2 -gramstain is Gram-positive ATM, TEM, PLB, COL, NAL R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species one_of Coagulase-negative Staphylococcus (CoNS), Staphylococcus aureus CAZ R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, sulfonamides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species one_of Enterococcus gallinarum, Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, sulfonamides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, sulfonamides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus is Corynebacterium FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus one_of Leuconostoc, Pediococcus VAN, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species is Lactobacillus casei VAN, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -fullname is Lactobacillus casei rhamnosus VAN, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2 -genus_species one_of Clostridium ramosum, Clostridium innocuum VAN R Table 5: Expected resistant phenotype in anaerobes Expected phenotypes 1.2 -order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes -genus_species is Escherichia hermannii aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Morganella morganii aminopenicillins, AMC, CZO, DOX, MNO, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Proteus penneri aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Brucella anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, DOX, MNO, TCY, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1 -genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides_except_lipo, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1 -gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus capitis CAZ, FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus aureus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus epidermidis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus coagulase-negative CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus hominis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus is Lactobacillus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1 -genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1 -genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1 -order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules 3.1 -genus like .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1 -genus like .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1 -genus like .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules 3.1 -genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1 -genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1 -order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1 -order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules 3.1 -genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1 -genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1 -order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1 -genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1 -order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Yersinia pseudotuberculosis polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Aeromonas hydrophila aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2 -genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 -fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…) -genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2 -genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2 -genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2 -genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2 -fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2 -gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Staphylococcus aureus CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Staphylococcus coagulase-negative CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides -genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -fullname like ^Enterococcus (gallinarum|casseliflavus) FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides -fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 These last ones are all true sulfonamides -genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 Since R to sulfonamides - TMP result is equal with combinations -genus is Corynebacterium FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus one_of Leuconostoc, Pediococcus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus is Lactobacillus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -fullname like ^Clostridium (ramosum|innocuum) VAN R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2 -genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rules on Enterobacterales Expert Rules 3.2 -genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.2 -fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.2 -fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.2 -genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.2 This is Enterobacterales except Salmonella spp. -fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.2 -genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2 -genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2 -genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.2 -genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2 -genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.2 -genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.2 all penicillins without beta-lactamse inhibitor -genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus LVX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus MFX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus TCY S DOX, MNO, TGC S Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus TCY R DOX, MNO R Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus VAN S lipoglycopeptides S Expert Rules on Staphylococcus Expert Rules 3.2 -genus is Staphylococcus LNZ S TZD S Expert Rules on Staphylococcus Expert Rules 3.2 -fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.2 -fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.2 -genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.2 -genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.2 -genus_species is Enterococcus faecium CLI R Expert Rules on Enterococcus Expert Rules 3.2 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2 -genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2 -genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2 -genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2 -genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2 -genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2 -genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.2 -genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.2 -genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.2 -genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.2 -genus_species is Campylobacter ERY R CLR, AZM R Expert Rules on Campylobacter Expert Rules 3.2 -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Hafnia alvei aminopenicillins, AMC, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Yersinia pseudotuberculosis polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Aeromonas hydrophila aminopenicillins, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Aeromonas veronii aminopenicillins, SAM, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Aeromonas dhakensis aminopenicillins, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -genus_species is Aeromonas caviae aminopenicillins, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3 -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 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 -fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP, ATM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Elizabethkingia anophelis aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus is Chryseobacterium aminopenicillins, AMC, SAM, TIC, TCC, CRO, CTX, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…) -genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3 -genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3 -genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3 -genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3 -fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3 -gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Staphylococcus aureus CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Staphylococcus coagulase-negative CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides -genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -fullname like ^Enterococcus (gallinarum|casseliflavus) FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides -fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides -genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations -genus is Corynebacterium FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus one_of Leuconostoc, Pediococcus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus is Lactobacillus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -fullname like ^Clostridium (ramosum|innocuum) VAN R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 -genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rules on Enterobacterales Expert Rules 3.3 -genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.3 -fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.3 -fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.3 -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 Expert Rules on Enterobacterales Expert Rules 3.3 This is Enterobacterales except Salmonella spp. -fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.3 -genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.3 -genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.3 -genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.3 -genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3 -genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.3 -genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.3 all penicillins without beta-lactamse inhibitor -genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus LVX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus MFX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus TCY S DOX, MNO, TGC S Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus TCY R DOX, MNO R Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus VAN S lipoglycopeptides S Expert Rules on Staphylococcus Expert Rules 3.3 -genus is Staphylococcus LNZ S TZD S Expert Rules on Staphylococcus Expert Rules 3.3 -fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.3 -fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.3 -genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.3 -genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.3 -genus_species is Enterococcus faecium CLI R Expert Rules on Enterococcus Expert Rules 3.3 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3 -genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3 -genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3 -genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.3 -genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.3 -genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.3 -genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.3 -genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.3 -genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.3 -genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.3 -genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.3 -genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.3 -genus_species is Campylobacter ERY R CLR, AZM R Expert Rules on Campylobacter Expert Rules 3.3 -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument -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 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument +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 +Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S +Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I +Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R +Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP S LVX S +Breakpoints 10 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP I LVX I +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus sanguinicola CIP R LVX R +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae NOR S fluoroquinolones S +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae NOR I fluoroquinolones I +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae NOR R fluoroquinolones R +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae CIP S LVX S +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae CIP I LVX I +Breakpoints 10 Aerococcus urinae genus_species is Aerococcus urinae CIP R LVX R +Breakpoints 10 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S +Breakpoints 10 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I +Breakpoints 10 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R +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 +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 +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 +Breakpoints 10 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY S DOX S +Breakpoints 10 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY I DOX I +Breakpoints 10 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY R DOX R +Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli ERY S AZM, CLR S +Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli ERY I AZM, CLR I +Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli ERY R AZM, CLR R +Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli TCY S DOX S +Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli TCY I DOX I +Breakpoints 10 Campylobacter coli genus_species is Campylobacter coli TCY R DOX R +Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni TCY S DOX S +Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni TCY I DOX I +Breakpoints 10 Campylobacter jejuni genus_species is Campylobacter jejuni TCY R DOX R +Breakpoints 10 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 10 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 10 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 10 Enterococcus genus is Enterococcus AMP S AMX, AMC, PIP, TZP S +Breakpoints 10 Enterococcus genus is Enterococcus AMP I AMX, AMC, PIP, TZP I +Breakpoints 10 Enterococcus genus is Enterococcus AMP R AMX, AMC, PIP, TZP R +Breakpoints 10 Enterococcus genus is Enterococcus NOR S CIP, LVX S +Breakpoints 10 Enterococcus genus is Enterococcus NOR I CIP, LVX I +Breakpoints 10 Enterococcus genus is Enterococcus NOR R CIP, LVX R +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMP S AMX, PIP S +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMP I AMX, PIP I +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMP R AMX, PIP R +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S TZP S +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I TZP I +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R TZP R +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S +Breakpoints 10 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 10 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 10 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 10 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 10 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 10 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 10 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 10 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 10 Kingella kingae genus_species is Kingella kingae TCY I DOX I +Breakpoints 10 Kingella kingae genus_species is Kingella kingae TCY R DOX R +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 10 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 10 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 10 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 10 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 10 Staphylococcus genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S +Breakpoints 10 Staphylococcus genus is Staphylococcus PEN, FOX R, S OXA, FLC S +Breakpoints 10 Staphylococcus genus is Staphylococcus FOX R betalactams R +Breakpoints 10 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S +Breakpoints 10 Staphylococcus genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S +Breakpoints 10 Staphylococcus genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I +Breakpoints 10 Staphylococcus genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R +Breakpoints 10 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +Breakpoints 10 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 10 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I +Breakpoints 10 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R +Breakpoints 10 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S +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 +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 +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 +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 +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 +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 +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 +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 +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 +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S MFX S +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX I +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 10 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +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 +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 +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 +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 +Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S +Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I +Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R +Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP S LVX S +Breakpoints 11 Aerococcus sanguinicola genus_species is Aerococcus sanguinicola CIP I LVX I +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus sanguinicola CIP R LVX R +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae NOR S fluoroquinolones S +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae NOR I fluoroquinolones I +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae NOR R fluoroquinolones R +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae CIP S LVX S +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae CIP I LVX I +Breakpoints 11 Aerococcus urinae genus_species is Aerococcus urinae CIP R LVX R +Breakpoints 11 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TIC S +Breakpoints 11 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TIC I +Breakpoints 11 Anaerobic Gram-negatives genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TIC R +Breakpoints 11 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TIC S +Breakpoints 11 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TIC I +Breakpoints 11 Anaerobic Gram-positives genus one_of Actinomyces, Bifidobacterium, Clostridium, Clostridioides, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TIC R +Breakpoints 11 Bacillus genus is Bacillus NOR S fluoroquinolones S added in 11 +Breakpoints 11 Bacillus genus is Bacillus NOR I fluoroquinolones I added in 11 +Breakpoints 11 Bacillus genus is Bacillus NOR R fluoroquinolones R added in 11 +Breakpoints 11 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY S DOX S +Breakpoints 11 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY I DOX I +Breakpoints 11 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY R DOX R +Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli ERY S AZM, CLR S +Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli ERY I AZM, CLR I +Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli ERY R AZM, CLR R +Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli TCY S DOX S +Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli TCY I DOX I +Breakpoints 11 Campylobacter coli genus_species is Campylobacter coli TCY R DOX R +Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni TCY S DOX S +Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni TCY I DOX I +Breakpoints 11 Campylobacter jejuni genus_species is Campylobacter jejuni TCY R DOX R +Breakpoints 11 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 11 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 11 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 11 Enterococcus genus is Enterococcus AMP S AMX, AMC, PIP, TZP S +Breakpoints 11 Enterococcus genus is Enterococcus AMP I AMX, AMC, PIP, TZP I +Breakpoints 11 Enterococcus genus is Enterococcus AMP R AMX, AMC, PIP, TZP R +Breakpoints 11 Enterococcus genus is Enterococcus NOR S CIP, LVX S +Breakpoints 11 Enterococcus genus is Enterococcus NOR I CIP, LVX I +Breakpoints 11 Enterococcus genus is Enterococcus NOR R CIP, LVX R +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMP S AMX, PIP S +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMP I AMX, PIP I +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMP R AMX, PIP R +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S TZP S +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I TZP I +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R TZP R +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S +Breakpoints 11 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 11 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 11 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 11 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 11 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 11 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 11 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 11 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 11 Kingella kingae genus_species is Kingella kingae TCY I DOX I +Breakpoints 11 Kingella kingae genus_species is Kingella kingae TCY R DOX R +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 11 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 11 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 11 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 11 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 11 Staphylococcus genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S +Breakpoints 11 Staphylococcus genus is Staphylococcus PEN, FOX R, S OXA, FLC S +Breakpoints 11 Staphylococcus genus is Staphylococcus FOX R betalactams R +Breakpoints 11 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S +Breakpoints 11 Staphylococcus genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S +Breakpoints 11 Staphylococcus genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I +Breakpoints 11 Staphylococcus genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R +Breakpoints 11 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +Breakpoints 11 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 11 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I +Breakpoints 11 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R +Breakpoints 11 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S +Breakpoints 11 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +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 +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 +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 +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 +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 +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 +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 +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 +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 +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S MFX S +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX I +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 11 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +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 +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 +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 +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 +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +Breakpoints 12 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +Breakpoints 12 Bacillus genus is Bacillus NOR-S S CIP, LVX I +Breakpoints 12 Bacillus genus is Bacillus NOR-S R CIP, LVX R +Breakpoints 12 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +Breakpoints 12 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +Breakpoints 12 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +Breakpoints 12 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 12 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 12 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 12 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +Breakpoints 12 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +Breakpoints 12 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +Breakpoints 12 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +Breakpoints 12 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +Breakpoints 12 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +Breakpoints 12 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +Breakpoints 12 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +Breakpoints 12 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +Breakpoints 12 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I +Breakpoints 12 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R +Breakpoints 12 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +Breakpoints 12 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +Breakpoints 12 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +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()]) +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Breakpoints 12 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +Breakpoints 12 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 12 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 12 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 12 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 12 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 12 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 12 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 12 Kingella kingae genus_species is Kingella kingae TCY R DOX R +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()] +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 12 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +Breakpoints 12 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +Breakpoints 12 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +Breakpoints 12 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +Breakpoints 12 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +Breakpoints 12 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +Breakpoints 12 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +Breakpoints 12 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +Breakpoints 12 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +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 +Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +Breakpoints 12 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +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"))])) +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"))])) +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"))])) +Breakpoints 12 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +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"))])) +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"))])) +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"))])) +Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +Breakpoints 12 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +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 +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 +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 +Breakpoints 12 Staphylococcus genus is Staphylococcus NOR-S S MFX S +Breakpoints 12 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S +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 +Breakpoints 12 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 12 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +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 +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 +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 +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())] +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())] +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())] +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$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")) +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +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 +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +Breakpoints 12 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +Breakpoints 12 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +Breakpoints 12 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +Breakpoints 12 Vibrio spp. genus is Vibrio ERY S AZM S +Breakpoints 12 Vibrio spp. genus is Vibrio ERY I AZM I +Breakpoints 12 Vibrio spp. genus is Vibrio ERY R AZM R +Breakpoints 12 Vibrio spp. genus is Vibrio TCY-S S DOX S +Breakpoints 12 Vibrio spp. genus is Vibrio TCY-S I DOX I +Breakpoints 12 Vibrio spp. genus is Vibrio TCY-S R DOX R +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$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ") +Breakpoints 13 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +Breakpoints 14 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP S AMX S +Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP I AMX I +Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP R AMX R +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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +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()]) +Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +Breakpoints 14 Bacillus genus is Bacillus NOR-S S CIP, LVX I +Breakpoints 14 Bacillus genus is Bacillus NOR-S R CIP, LVX R +Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis PEN I AMX S +Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis PEN R AMX R +Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis TCY-S S DOX S +Breakpoints 14 Bacillus anthracis genus_species is Bacillus anthracis TCY-S R DOX R +Breakpoints 14 Brucella melitensis genus_species is Brucella melitensis TCY-S S DOX S +Breakpoints 14 Brucella melitensis genus_species is Brucella melitensis TCY-S R DOX R +Breakpoints 14 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +Breakpoints 14 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +Breakpoints 14 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +Breakpoints 14 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +Breakpoints 14 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 14 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 14 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 14 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +Breakpoints 14 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +Breakpoints 14 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +Breakpoints 14 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +Breakpoints 14 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +Breakpoints 14 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +Breakpoints 14 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +Breakpoints 14 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +Breakpoints 14 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +Breakpoints 14 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I +Breakpoints 14 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R +Breakpoints 14 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +Breakpoints 14 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +Breakpoints 14 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +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()]) +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Breakpoints 14 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +Breakpoints 14 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 14 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 14 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 14 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 14 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 14 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 14 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 14 Kingella kingae genus_species is Kingella kingae TCY R DOX R +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()] +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 14 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +Breakpoints 14 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +Breakpoints 14 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +Breakpoints 14 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +Breakpoints 14 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +Breakpoints 14 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +Breakpoints 14 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +Breakpoints 14 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +Breakpoints 14 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +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 +Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +Breakpoints 14 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +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"))])) +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"))])) +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"))])) +Breakpoints 14 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +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"))])) +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"))])) +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"))])) +Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +Breakpoints 14 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +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 +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 +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 +Breakpoints 14 Staphylococcus genus is Staphylococcus NOR-S S MFX S +Breakpoints 14 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +Breakpoints 14 Staphylococcus genus_species is Staphylococcus coagulase-negative VAN, TEC S, S DAL S +Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S +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 +Breakpoints 14 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 14 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +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 +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 +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 +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())] +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())] +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())] +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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")) +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")) +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +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 +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +Breakpoints 14 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +Breakpoints 14 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +Breakpoints 14 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +Breakpoints 14 Vibrio spp. genus is Vibrio ERY S AZM S +Breakpoints 14 Vibrio spp. genus is Vibrio ERY I AZM I +Breakpoints 14 Vibrio spp. genus is Vibrio ERY R AZM R +Breakpoints 14 Vibrio spp. genus is Vibrio TCY-S S DOX S +Breakpoints 14 Vibrio spp. genus is Vibrio TCY-S I DOX I +Breakpoints 14 Vibrio spp. genus is Vibrio TCY-S R DOX R +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() +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() +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() +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() +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() +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +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$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP S AMX S +Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP I AMX I +Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP R AMX R +Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +Breakpoints 15 Bacillus genus is Bacillus NOR-S S CIP, LVX I +Breakpoints 15 Bacillus genus is Bacillus NOR-S R CIP, LVX R +Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis PEN I AMX S +Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis PEN R AMX R +Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis TCY-S S DOX S +Breakpoints 15 Bacillus anthracis genus_species is Bacillus anthracis TCY-S R DOX R +Breakpoints 15 Brucella melitensis genus_species is Brucella melitensis TCY-S S DOX S +Breakpoints 15 Brucella melitensis genus_species is Brucella melitensis TCY-S R DOX R +Breakpoints 15 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +Breakpoints 15 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +Breakpoints 15 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +Breakpoints 15 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +Breakpoints 15 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 15 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 15 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 15 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +Breakpoints 15 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +Breakpoints 15 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +Breakpoints 15 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +Breakpoints 15 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +Breakpoints 15 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +Breakpoints 15 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +Breakpoints 15 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +Breakpoints 15 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX S +Breakpoints 15 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX I +Breakpoints 15 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX R +Breakpoints 15 Enterococcus genus is Enterococcus AMP R AMX, AMC R +Breakpoints 15 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +Breakpoints 15 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +Breakpoints 15 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +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()]) +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Breakpoints 15 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +Breakpoints 15 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 15 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 15 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 15 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 15 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 15 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 15 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 15 Kingella kingae genus_species is Kingella kingae TCY R DOX R +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()] +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 15 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +Breakpoints 15 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +Breakpoints 15 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +Breakpoints 15 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +Breakpoints 15 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +Breakpoints 15 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +Breakpoints 15 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +Breakpoints 15 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +Breakpoints 15 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +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 +Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +Breakpoints 15 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +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"))])) +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"))])) +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"))])) +Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +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"))])) +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"))])) +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"))])) +Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +Breakpoints 15 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +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 +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 +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 +Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S S MFX S +Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +Breakpoints 15 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 15 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I +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 +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 +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 +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())] +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())] +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())] +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$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")) +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +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 +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +Breakpoints 15 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +Breakpoints 15 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +Breakpoints 15 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +Breakpoints 15 Vibrio spp. genus is Vibrio ERY S AZM S +Breakpoints 15 Vibrio spp. genus is Vibrio ERY I AZM I +Breakpoints 15 Vibrio spp. genus is Vibrio ERY R AZM R +Breakpoints 15 Vibrio spp. genus is Vibrio TCY-S S DOX S +Breakpoints 15 Vibrio spp. genus is Vibrio TCY-S I DOX I +Breakpoints 15 Vibrio spp. genus is Vibrio TCY-S R DOX R +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() +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() +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() +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() +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() +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +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()]) +Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP S AMX S +Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP I AMX I +Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP R AMX R +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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +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()]) +Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +Breakpoints 16 Bacillus genus is Bacillus NOR-S S CIP, LVX I +Breakpoints 16 Bacillus genus is Bacillus NOR-S R CIP, LVX R +Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis PEN I AMX S +Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis PEN R AMX R +Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis TCY-S S DOX S +Breakpoints 16 Bacillus anthracis genus_species is Bacillus anthracis TCY-S R DOX R +Breakpoints 16 Brucella melitensis genus_species is Brucella melitensis TCY-S S DOX S +Breakpoints 16 Brucella melitensis genus_species is Brucella melitensis TCY-S R DOX R +Breakpoints 16 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +Breakpoints 16 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +Breakpoints 16 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +Breakpoints 16 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +Breakpoints 16 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 16 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 16 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 16 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +Breakpoints 16 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +Breakpoints 16 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +Breakpoints 16 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +Breakpoints 16 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +Breakpoints 16 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +Breakpoints 16 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +Breakpoints 16 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +Breakpoints 16 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX S +Breakpoints 16 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX I +Breakpoints 16 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX R +Breakpoints 16 Enterococcus genus is Enterococcus AMP R AMX, AMC R +Breakpoints 16 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +Breakpoints 16 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +Breakpoints 16 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +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()]) +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Breakpoints 16 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +Breakpoints 16 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 16 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 16 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 16 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 16 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 16 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 16 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 16 Kingella kingae genus_species is Kingella kingae TCY R DOX R +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()] +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 16 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +Breakpoints 16 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +Breakpoints 16 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +Breakpoints 16 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +Breakpoints 16 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +Breakpoints 16 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +Breakpoints 16 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +Breakpoints 16 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +Breakpoints 16 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +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 +Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +Breakpoints 16 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S S CZO, FEP, CTX, CRO, CXM I +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() +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() +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() +Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +Breakpoints 16 Staphylococcus genus is Staphylococcus OXA-S S CZO, FEP, CTX, CRO, CXM I +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() +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() +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() +Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +Breakpoints 16 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +Breakpoints 16 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +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 +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 +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 +Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S S MFX S +Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +Breakpoints 16 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 16 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +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 +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 +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 +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())] +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())] +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())] +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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")) +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")) +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S MFX S does not explicitly state that it is for other fluoroquinolones +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR-S S LVX I does not explicitly state that it is for other fluoroquinolones +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 +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +Breakpoints 16 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +Breakpoints 16 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +Breakpoints 16 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +Breakpoints 16 Vibrio spp. genus is Vibrio ERY S AZM S +Breakpoints 16 Vibrio spp. genus is Vibrio ERY I AZM I +Breakpoints 16 Vibrio spp. genus is Vibrio ERY R AZM R +Breakpoints 16 Vibrio spp. genus is Vibrio TCY-S S DOX S +Breakpoints 16 Vibrio spp. genus is Vibrio TCY-S I DOX I +Breakpoints 16 Vibrio spp. genus is Vibrio TCY-S R DOX R +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() +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() +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() +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() +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() +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP S LVX S +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP I LVX I +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae CIP R LVX R +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I +Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R +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$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP S AMX S +Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP I AMX I +Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP R AMX R +Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +Breakpoints 13.1 Bacillus genus is Bacillus NOR-S S CIP, LVX I +Breakpoints 13.1 Bacillus genus is Bacillus NOR-S R CIP, LVX R +Breakpoints 13.1 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S S DOX I +Breakpoints 13.1 Burkholderia pseudomallei genus_species is Burkholderia pseudomallei TCY-S R DOX R +Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY S AZM, CLR S +Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY I AZM, CLR I +Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni ERY R AZM, CLR R +Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY S DOX S +Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY I DOX I +Breakpoints 13.1 Campylobacter coli/jejuni genus_species one_of Campylobacter coli, Campylobacter jejuni TCY R DOX R +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I +Breakpoints 13.1 Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales AMP S AMX S +Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales AMP I AMX I +Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales AMP R AMX R +Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales LEX S CZO I +Breakpoints 13.1 Enterobacterales (Order) order is Enterobacterales CFR S CZO I +Breakpoints 13.1 Enterobacterales (Order) genus is Salmonella PEF-S S CIP S +Breakpoints 13.1 Enterobacterales (Order) genus is Salmonella PEF-S I CIP I +Breakpoints 13.1 Enterobacterales (Order) genus is Salmonella PEF-S R CIP R +Breakpoints 13.1 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY S DOX S +Breakpoints 13.1 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY I DOX I +Breakpoints 13.1 Enterobacterales (Order) genus_species is Yersinia enterocolitica TCY R DOX R +Breakpoints 13.1 Enterococcus genus is Enterococcus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +Breakpoints 13.1 Enterococcus genus is Enterococcus AMP I AMP, SAM, AMX, AMC, PIP, TZP I +Breakpoints 13.1 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AMC, PIP, TZP R +Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S +Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I +Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R +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()]) +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC R SAM R +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S I CIP, LVX, MFX, OFX I +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae BLA-S R PEN, AMP, AMX R +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae PEN S AMP, AMX S +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae PEN I AMP, AMX I +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae PEN R AMP, AMX R +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae ERY S AZM, CLR S +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae ERY I AZM, CLR I +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae ERY R AZM, CLR R +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae TCY S DOX S +Breakpoints 13.1 Kingella kingae genus_species is Kingella kingae TCY R DOX R +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()] +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC S TZP S +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC I TZP I +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis AMC R TZP R +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S S CIP, LVX, MFX, OFX S +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL-S R CIP, LVX, MFX, OFX R +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY S DOX, MNO S +Breakpoints 13.1 Moraxella catarrhalis genus_species is Moraxella catarrhalis TCY R DOX, MNO R +Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S R AMP, AMX R +Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, S AMP, AMX S +Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, I AMP, AMX I +Breakpoints 13.1 Neisseria gonorrhoeae genus_species is Neisseria gonorrhoeae BLA-S, PEN S, R AMP, AMX R +Breakpoints 13.1 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S S MNO S +Breakpoints 13.1 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S I MNO I +Breakpoints 13.1 Neisseria meningitidis genus_species is Neisseria meningitidis TCY-S R MNO R +Breakpoints 13.1 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S S DOX S +Breakpoints 13.1 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S I DOX I +Breakpoints 13.1 Neisseria meningitidis genus_species is Pasteurella multocida TCY-S R DOX R +Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida PEN S AMP, AMX S +Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida PEN I AMP, AMX I +Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida PEN R AMP, AMX R +Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida NAL-S S CIP, LVX S +Breakpoints 13.1 Pasteurella multocida genus_species is Pasteurella multocida NAL-S R CIP, LVX R +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 +Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S S, S penicillins S +Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus PEN, FOX-S R, S betalactams_with_inhibitor, isoxazolylpenicillins, NAF S +Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S R PEN, PHN, AMP, AMX, PIP, TIC R +Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus saprophyticus AMP S AMP, SAM, AMX, AMC, PIP, TZP S +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"))])) +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"))])) +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"))])) +Breakpoints 13.1 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R PEN, PHN, AMP, AMX, PIP, TIC R +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"))])) +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"))])) +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"))])) +Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CPT S +Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S S BPR S +Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S S carbapenems S +Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S I carbapenems I +Breakpoints 13.1 Staphylococcus genus is Staphylococcus FOX-S R carbapenems R +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 +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 +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 +Breakpoints 13.1 Staphylococcus genus is Staphylococcus NOR-S S MFX S +Breakpoints 13.1 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I +Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S +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 +Breakpoints 13.1 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S +Breakpoints 13.1 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S +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 +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 +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 +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())] +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())] +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())] +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$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")) +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I +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 +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN R PHN R from flowchart: when OXA < 20 or PEN > 0.06 +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP S AMX, AMC, SAM, PIP, TZP S +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP I AMX, AMC, SAM, PIP, TZP I +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae AMP R AMX, AMC, SAM, PIP, TZP R +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 +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 +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 +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S +Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R +Breakpoints 13.1 Vibrio spp. genus is Vibrio PEF-S S CIP, LVX S +Breakpoints 13.1 Vibrio spp. genus is Vibrio PEF-S I CIP, LVX I +Breakpoints 13.1 Vibrio spp. genus is Vibrio PEF-S R CIP, LVX R +Breakpoints 13.1 Vibrio spp. genus is Vibrio ERY S AZM S +Breakpoints 13.1 Vibrio spp. genus is Vibrio ERY I AZM I +Breakpoints 13.1 Vibrio spp. genus is Vibrio ERY R AZM R +Breakpoints 13.1 Vibrio spp. genus is Vibrio TCY-S S DOX S +Breakpoints 13.1 Vibrio spp. genus is Vibrio TCY-S I DOX I +Breakpoints 13.1 Vibrio spp. genus is Vibrio TCY-S R DOX R +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() +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() +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() +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() +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() +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()]) +Breakpoints Anaerobic bacteria genus is Prevotella AMP S AMX S +Breakpoints Anaerobic bacteria genus is Prevotella AMP I AMX I +Breakpoints Anaerobic bacteria genus is Prevotella AMP R AMX R +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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) +Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S +Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I +Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R +Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()]) +Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S +Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I +Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R +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()]) +Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S +Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I +Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R +Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S +Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I +Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I CTX I +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R CTX R +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I MEM S +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R MEM R +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY S DOX S +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY I DOX I +Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans TCY R DOX R +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 +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 +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 +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 +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii AMP, AMX, TIC R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Hafnia alvei AMP, AMX, PLB, COL R +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 +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 +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca AMX, AMP, TIC R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R +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 +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides AMX, AMP, SAM R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Proteus mirabilis tetracyclines, PLB, COL, NIT R +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 +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 +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 +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 +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus is Raoultella AMP, AMX, TIC R +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 +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 +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis PLB, COL R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila AMP, AMX, SAM R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii AMP, AMX, SAM, TIC R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis AMP, AMX, SAM, FOX R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae AMP, AMX, SAM R +Expected phenotypes 1.2 Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. genus_species is Aeromonas jandaei AMP, AMX, SAM, TIC R +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins R +Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species is Moraxella catarrhalis TMP R +Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus is Neisseria TMP R +Expected phenotypes 1.2 Table 3: Expected resistant phenotype in other gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R +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 +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria gramstain is Gram-positive ATM, TEM, PLB, COL, NAL R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +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 +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +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 +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 +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 +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus is Corynebacterium FOS R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, FOS R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Lactobacillus casei VAN, FOS R +Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria fullname is Lactobacillus casei rhamnosus VAN, FOS R +Expected phenotypes 1.2 Table 5: Expected resistant phenotype in anaerobes genus_species one_of Clostridium ramosum, Clostridium innocuum VAN R +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 +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 +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 +Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R +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 +Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Escherichia hermannii aminopenicillins, TIC R +Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R +Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus is Klebsiella aminopenicillins, TIC R +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 +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 +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 +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 +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 +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 +Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus is Raoultella aminopenicillins, TIC R +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 +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 +Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Yersinia pseudotuberculosis PLB, COL R +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins R +Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Moraxella catarrhalis TMP R +Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus is Neisseria TMP R +Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R +Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter jejuni FUS, streptogramins, TMP R +Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter coli FUS, streptogramins, TMP R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria gramstain is Gram-positive ATM, polymyxins, NAL R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus aureus CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus epidermidis CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus hominis CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus haemolyticus CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus intermedius CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus pseudintermedius CAZ R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +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 +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 +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 +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 +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Corynebacterium FOS R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Listeria monocytogenes cephalosporins R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Lactobacillus glycopeptides_except_lipo R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Clostridium ramosum VAN R +Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Clostridium innocuum VAN R +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 +Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus is Enterococcus AMP R ureidopenicillins, carbapenems R +Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus is Enterococcus AMX R ureidopenicillins, carbapenems R +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 +Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY S AZM, CLR S +Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY I AZM, CLR I +Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY R AZM, CLR R +Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides genus is Staphylococcus TOB R KAN, AMK R +Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides genus is Staphylococcus GEN R aminoglycosides R +Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides order is Enterobacterales GEN, TOB I, S GEN R +Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides order is Enterobacterales GEN, TOB R, I TOB R +Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus is Staphylococcus MFX R fluoroquinolones R +Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R +Expert Rules 3.1 Table 13: Interpretive rules for quinolones order is Enterobacterales CIP R fluoroquinolones R +Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R +Expert Rules 3.2 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S +Expert Rules 3.2 Expert Rules on Campylobacter genus_species is Campylobacter ERY R CLR, AZM R +Expert Rules 3.2 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R +Expert Rules 3.2 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S +Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R +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 +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. +Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Morganella morganii) TGC R +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 +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 +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 +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 +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 +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 +Expert Rules 3.2 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R +Expert Rules 3.2 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R +Expert Rules 3.2 Expert Rules on Enterococcus genus is Enterococcus NOR S CIP, LVX S +Expert Rules 3.2 Expert Rules on Enterococcus genus is Enterococcus VAN S lipoglycopeptides S +Expert Rules 3.2 Expert Rules on Enterococcus genus_species is Enterococcus faecium CLI R +Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae PEN S betalactams S +Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL S fluoroquinolones S +Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R +Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Expert Rules 3.2 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S fluoroquinolones S +Expert Rules 3.2 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL R fluoroquinolones R +Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella cephalosporins_2nd R +Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella aminoglycosides R +Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella PEF R CIP R +Expert Rules 3.2 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R betalactams R +Expert Rules 3.2 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S +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 +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus ERY, CLI S macrolides, lincosamides S +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus LVX R fluoroquinolones R +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus MFX R fluoroquinolones R +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus TCY S DOX, MNO, TGC S +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus TCY R DOX, MNO R +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus VAN S lipoglycopeptides S +Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus LNZ S TZD S +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 +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 +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 +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX, MFX S +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR R LVX, MFX R +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY R DOX, MNO R +Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S +Expert Rules 3.2 Expert Rules on Viridans Group Streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S +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 +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R +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 +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 +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii aminopenicillins, TIC R +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 +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 +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca aminopenicillins, TIC R +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R +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 +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R +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 +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 +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 +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 +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 +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus is Raoultella aminopenicillins, TIC R +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 +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 +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis polymyxins R +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila aminopenicillins, AMC, SAM, FOX R +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R +Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R +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 +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 +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…) +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…) +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…) +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…) +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…) +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…) +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…) +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…) +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 +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 +Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +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 +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 +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria gramstain is Gram-positive ATM, TEM, polymyxins, NAL R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus aureus CAZ R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Corynebacterium FOS R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, TEC R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Lactobacillus VAN, TEC R +Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Clostridium (ramosum|innocuum) VAN R +Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S +Expert Rules 3.3 Expert Rules on Campylobacter genus_species is Campylobacter ERY R CLR, AZM R +Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R +Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S +Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R +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 +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. +Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Morganella morganii) TGC R +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 +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 +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 +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 +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 +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 +Expert Rules 3.3 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R +Expert Rules 3.3 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R +Expert Rules 3.3 Expert Rules on Enterococcus genus is Enterococcus NOR S CIP, LVX S +Expert Rules 3.3 Expert Rules on Enterococcus genus is Enterococcus VAN S lipoglycopeptides S +Expert Rules 3.3 Expert Rules on Enterococcus genus_species is Enterococcus faecium CLI R +Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae PEN S betalactams S +Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL S fluoroquinolones S +Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R +Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S +Expert Rules 3.3 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R +Expert Rules 3.3 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S fluoroquinolones S +Expert Rules 3.3 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL R fluoroquinolones R +Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella cephalosporins_2nd R +Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella aminoglycosides R +Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella PEF R CIP R +Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R betalactams R +Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S +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 +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus ERY, CLI S macrolides, lincosamides S +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus LVX R fluoroquinolones R +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus MFX R fluoroquinolones R +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus TCY S DOX, MNO, TGC S +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus TCY R DOX, MNO R +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus VAN S lipoglycopeptides S +Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus LNZ S TZD S +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 +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 +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 +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX, MFX S +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR R LVX, MFX R +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY R DOX, MNO R +Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S +Expert Rules 3.3 Expert Rules on Viridans Group Streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S +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 +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R +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 +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 +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii aminopenicillins, TIC R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Hafnia alvei aminopenicillins, AMC, polymyxins R +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 +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca aminopenicillins, TIC R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R +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 +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R +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 +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 +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 +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 +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 +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus is Raoultella aminopenicillins, TIC R +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 +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 +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis polymyxins R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila aminopenicillins, SAM R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii aminopenicillins, SAM, TIC R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis aminopenicillins, SAM, FOX R +Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae aminopenicillins, SAM R +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 +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…) +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…) +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…) +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…) +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…) +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…) +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…) +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…) +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…) +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…) +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 +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 +Expert Rules 3.3 Table 3: Intrinsic resistance in other gram-negative bacteria genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R +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 +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 +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria gramstain is Gram-positive ATM, TEM, polymyxins, NAL R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus aureus CAZ R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus is Corynebacterium FOS R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, TEC R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria genus is Lactobacillus VAN, TEC R +Expert Rules 3.3 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Clostridium (ramosum|innocuum) VAN R diff --git a/data/clinical_breakpoints.rda b/data/clinical_breakpoints.rda index d9769832f..829385a46 100644 Binary files a/data/clinical_breakpoints.rda and b/data/clinical_breakpoints.rda differ diff --git a/man/AMR-options.Rd b/man/AMR-options.Rd index cc70d7b81..2b7abae75 100644 --- a/man/AMR-options.Rd +++ b/man/AMR-options.Rd @@ -12,7 +12,7 @@ This is an overview of all the package-specific options you can set in the \code \itemize{ \item \code{AMR_antibiogram_formatting_type} \cr A \link{numeric} (1-22) to use in \code{\link[=antibiogram]{antibiogram()}}, to indicate which formatting type to use. -\item \code{AMR_breakpoint_type} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human". +\item \code{AMR_breakpoint_type} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate which breakpoint type to use. This must be either {.val ECOFF}, {.val animal}, or {.val human}. \item \code{AMR_capped_mic_handling} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate how capped MIC values (\code{<}, \code{<=}, \code{>}, \code{>=}) should be interpreted. Must be one of \code{"none"}, \code{"conservative"}, \code{"standard"}, or \code{"lenient"} - the default is \code{"conservative"}. \item \code{AMR_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar". \item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}. diff --git a/man/antibiogram.Rd b/man/antibiogram.Rd index de84c48b8..83d1fe651 100644 --- a/man/antibiogram.Rd +++ b/man/antibiogram.Rd @@ -68,9 +68,9 @@ retrieve_wisca_parameters(wisca_model, ...) } }} -\item{mo_transform}{A character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.} +\item{mo_transform}{A character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: {.val mo}, {.val fullname}, {.val status}, {.val kingdom}, {.val phylum}, {.val class}, {.val order}, {.val family}, {.val genus}, {.val species}, {.val subspecies}, {.val rank}, {.val ref}, {.val oxygen_tolerance}, {.val source}, {.val lpsn}, {.val lpsn_parent}, {.val lpsn_renamed_to}, {.val mycobank}, {.val mycobank_parent}, {.val mycobank_renamed_to}, {.val gbif}, {.val gbif_parent}, {.val gbif_renamed_to}, {.val prevalence}, or {.val snomed}. Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.} -\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.} +\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): {.val ab}, {.val cid}, {.val name}, {.val group}, {.val atc}, {.val atc_group1}, {.val atc_group2}, {.val abbreviations}, {.val synonyms}, {.val oral_ddd}, {.val oral_units}, {.val iv_ddd}, {.val iv_units}, or {.val loinc}. Can also be \code{NULL} to not transform the input.} \item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.} diff --git a/man/antimicrobial_selectors.Rd b/man/antimicrobial_selectors.Rd index 68b567102..ea5de7a5f 100644 --- a/man/antimicrobial_selectors.Rd +++ b/man/antimicrobial_selectors.Rd @@ -157,7 +157,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL, \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} -\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".} +\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be {.val 1.2}.} } \value{ When used inside selecting or filtering, this returns a \link{character} vector of column names, with additional class \code{"amr_selector"}. When used individually, this returns an \link[=as.ab]{'ab' vector} with all possible antimicrobials that the function would be able to select or filter. diff --git a/man/as.sir.Rd b/man/as.sir.Rd index 95881beca..7439fe84d 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -138,7 +138,7 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain \item{include_PKPD}{A \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.} -\item{breakpoint_type}{The type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.} +\item{breakpoint_type}{The type of breakpoints to use, either {.val ECOFF}, {.val animal}, or {.val human}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.} \item{host}{A vector (or column name) with \link{character}s to indicate the host. Only useful for veterinary breakpoints, as it requires \code{breakpoint_type = "animal"}. The values can be any text resembling the animal species, even in any of the 28 supported languages of this package. For foreign languages, be sure to set the language with \code{\link[=set_AMR_locale]{set_AMR_locale()}} (though it will be automatically guessed based on the system language).} diff --git a/man/clinical_breakpoints.Rd b/man/clinical_breakpoints.Rd index 2207bfd7f..7138abec3 100644 --- a/man/clinical_breakpoints.Rd +++ b/man/clinical_breakpoints.Rd @@ -5,12 +5,12 @@ \alias{clinical_breakpoints} \title{Data Set with Clinical Breakpoints for SIR Interpretation} \format{ -A \link[tibble:tibble]{tibble} with 45 797 observations and 14 variables: +A \link[tibble:tibble]{tibble} with 45 730 observations and 14 variables: \itemize{ \item \code{guideline}\cr Name of the guideline -\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human" -\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine" -\item \code{method}\cr Testing method, either "DISK" or "MIC" +\item \code{type}\cr Breakpoint type, either {.val ECOFF}, {.val animal}, or {.val human} +\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either {.val ECOFF}, {.val aquatic}, {.val cats}, {.val cattle}, {.val dogs}, {.val horse}, {.val human}, {.val poultry}, or {.val swine} +\item \code{method}\cr Testing method, either {.val DISK} or {.val MIC} \item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory" \item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}} \item \code{rank_index}\cr Taxonomic rank index of \code{mo} from 1 (subspecies/infraspecies) to 5 (unknown microorganism) diff --git a/man/dosage.Rd b/man/dosage.Rd index 491d62d23..8e2ba35be 100644 --- a/man/dosage.Rd +++ b/man/dosage.Rd @@ -9,10 +9,10 @@ A \link[tibble:tibble]{tibble} with 759 observations and 9 variables: \itemize{ \item \code{ab}\cr Antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available \item \code{name}\cr Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO -\item \code{type}\cr Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti" +\item \code{type}\cr Type of the dosage, either {.val high_dosage}, {.val standard_dosage}, or {.val uncomplicated_uti} \item \code{dose}\cr Dose, such as "2 g" or "25 mg/kg" \item \code{dose_times}\cr Number of times a dose must be administered -\item \code{administration}\cr Route of administration, either "", "im", "iv", "oral", or NA +\item \code{administration}\cr Route of administration, either {.val }, {.val im}, {.val iv}, {.val oral}, or NA \item \code{notes}\cr Additional dosage notes \item \code{original_txt}\cr Original text in the PDF file of EUCAST \item \code{eucast_version}\cr Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 15, 14, 13.1, 12, or 11 diff --git a/man/example_isolates.Rd b/man/example_isolates.Rd index c77a4cee8..e52d4de22 100644 --- a/man/example_isolates.Rd +++ b/man/example_isolates.Rd @@ -10,8 +10,8 @@ A \link[tibble:tibble]{tibble} with 2 000 observations and 46 variables: \item \code{date}\cr Date of receipt at the laboratory \item \code{patient}\cr ID of the patient \item \code{age}\cr Age of the patient -\item \code{gender}\cr Gender of the patient, either "F" or "M" -\item \code{ward}\cr Ward type where the patient was admitted, either "Clinical", "ICU", or "Outpatient" +\item \code{gender}\cr Gender of the patient, either {.val F} or {.val M} +\item \code{ward}\cr Ward type where the patient was admitted, either {.val Clinical}, {.val ICU}, or {.val Outpatient} \item \code{mo}\cr ID of microorganism created with \code{\link[=as.mo]{as.mo()}}, see also the \link{microorganisms} data set \item \code{PEN:RIF}\cr 40 different antimicrobials with class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}}); these column names occur in the \link{antimicrobials} data set and can be translated with \code{\link[=set_ab_names]{set_ab_names()}} or \code{\link[=ab_name]{ab_name()}} } diff --git a/man/interpretive_rules.Rd b/man/interpretive_rules.Rd index e08412fcf..7ec09fc93 100644 --- a/man/interpretive_rules.Rd +++ b/man/interpretive_rules.Rd @@ -24,7 +24,7 @@ Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility test interpretive_rules(x, col_mo = NULL, info = interactive(), rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"), - verbose = FALSE, version_breakpoints = 15, + verbose = FALSE, version_breakpoints = 16, version_expected_phenotypes = 1.2, version_expertrules = 3.3, ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)), custom_rules = NULL, overwrite = FALSE, ...) @@ -52,11 +52,11 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15) \item{verbose}{A \link{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.} -\item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".} +\item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be {.val 16.0}, {.val 15.0}, {.val 14.0}, {.val 13.1}, {.val 12.0}, {.val 11.0}, or {.val 10.0}.} -\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".} +\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be {.val 1.2}.} -\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".} +\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be {.val 3.3}, {.val 3.2}, or {.val 3.1}.} \item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{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 \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.} @@ -70,7 +70,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15) \item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.} -\item{administration}{Route of administration, either "", "im", "iv", "oral", or NA.} +\item{administration}{Route of administration, either {.val }, {.val im}, {.val iv}, {.val oral}, or NA.} } \value{ The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations. @@ -81,7 +81,7 @@ Apply rules from clinical breakpoints notes and expected resistant phenotypes as To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see \emph{Details}. } \details{ -\strong{Note:} This function does not translate MIC values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr +\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}. diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 07028388f..d8d211178 100644 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -9,12 +9,12 @@ A \link[tibble:tibble]{tibble} with 78 679 observations and 26 variables: \itemize{ \item \code{mo}\cr ID of microorganism as used by this package. \emph{\strong{This is a unique identifier.}} \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. \emph{\strong{This is a unique identifier.}} -\item \code{status} \cr Status of the taxon, either "accepted", "not validly published", "synonym", or "unknown" +\item \code{status} \cr Status of the taxon, either {.val accepted}, {.val not validly published}, {.val synonym}, or {.val unknown} \item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism. Note that for fungi, \emph{phylum} is equal to their taxonomic \emph{division}. Also, for fungi, \emph{subkingdom} and \emph{subdivision} were left out since they do not occur in the bacterial taxonomy. \item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"} \item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters. -\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", "microaerophile", or NA. These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3\% of all ~39 000 bacteria in the data set contain an oxygen tolerance. -\item \code{source}\cr Either "GBIF", "LPSN", "Manually added", "MycoBank", or "manually added" (see \emph{Source}) +\item \code{oxygen_tolerance} \cr Oxygen tolerance, either {.val aerobe}, {.val anaerobe}, {.val anaerobe/microaerophile}, {.val facultative anaerobe}, {.val likely facultative anaerobe}, {.val microaerophile}, or NA. These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3\% of all ~39 000 bacteria in the data set contain an oxygen tolerance. +\item \code{source}\cr Either {.val GBIF}, {.val LPSN}, {.val Manually added}, {.val MycoBank}, or {.val manually added} (see \emph{Source}) \item \code{lpsn}\cr Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, \emph{Acetobacter ascendens} has LPSN Record number 7864 and 11011. Only the first is available in the \code{microorganisms} data set. \emph{\strong{This is a unique identifier}}, though available for only ~33 000 records. \item \code{lpsn_parent}\cr LPSN identifier of the parent taxon \item \code{lpsn_renamed_to}\cr LPSN identifier of the currently valid taxon diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 676e66343..1655c258a 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -165,7 +165,7 @@ The default is \code{FALSE}, which will return a note if outdated taxonomic name \item{open}{Browse the URL using \code{\link[utils:browseURL]{browseURL()}}.} -\item{property}{One of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be \code{"shortname"}.} +\item{property}{One of the column names of the \link{microorganisms} data set: {.val mo}, {.val fullname}, {.val status}, {.val kingdom}, {.val phylum}, {.val class}, {.val order}, {.val family}, {.val genus}, {.val species}, {.val subspecies}, {.val rank}, {.val ref}, {.val oxygen_tolerance}, {.val source}, {.val lpsn}, {.val lpsn_parent}, {.val lpsn_renamed_to}, {.val mycobank}, {.val mycobank_parent}, {.val mycobank_renamed_to}, {.val gbif}, {.val gbif_parent}, {.val gbif_renamed_to}, {.val prevalence}, or {.val snomed}, or must be \code{"shortname"}.} } \value{ \itemize{ diff --git a/man/plot.Rd b/man/plot.Rd index 6584cacf5..2b9813c18 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -137,7 +137,7 @@ labels_sir_count(position = NULL, x = "antibiotic", \item{include_PKPD}{A \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.} -\item{breakpoint_type}{The type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.} +\item{breakpoint_type}{The type of breakpoints to use, either {.val ECOFF}, {.val animal}, or {.val human}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.} \item{facet}{Variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable.} diff --git a/man/top_n_microorganisms.Rd b/man/top_n_microorganisms.Rd index 039047f87..fe9adccac 100644 --- a/man/top_n_microorganisms.Rd +++ b/man/top_n_microorganisms.Rd @@ -12,7 +12,7 @@ top_n_microorganisms(x, n, property = "species", n_for_each = NULL, \item{n}{An integer specifying the maximum number of unique values of the \code{property} to include in the output.} -\item{property}{A character string indicating the microorganism property to use for filtering. Must be one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". If \code{NULL}, the raw values from \code{col_mo} will be used without transformation. When using \code{"species"} (default) or \code{"subpecies"}, the genus will be added to make sure each (sub)species still belongs to the right genus.} +\item{property}{A character string indicating the microorganism property to use for filtering. Must be one of the column names of the \link{microorganisms} data set: {.val mo}, {.val fullname}, {.val status}, {.val kingdom}, {.val phylum}, {.val class}, {.val order}, {.val family}, {.val genus}, {.val species}, {.val subspecies}, {.val rank}, {.val ref}, {.val oxygen_tolerance}, {.val source}, {.val lpsn}, {.val lpsn_parent}, {.val lpsn_renamed_to}, {.val mycobank}, {.val mycobank_parent}, {.val mycobank_renamed_to}, {.val gbif}, {.val gbif_parent}, {.val gbif_renamed_to}, {.val prevalence}, or {.val snomed}. If \code{NULL}, the raw values from \code{col_mo} will be used without transformation. When using \code{"species"} (default) or \code{"subpecies"}, the genus will be added to make sure each (sub)species still belongs to the right genus.} \item{n_for_each}{An optional integer specifying the maximum number of rows to retain for each value of the selected property. If \code{NULL}, all rows within the top \emph{n} groups will be included.}