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(v2.1.1.9247) CLSI/EUCAST 2025!
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 2.1.1.9246
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Date: 2025-04-19
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Version: 2.1.1.9247
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Date: 2025-04-20
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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12
NEWS.md
12
NEWS.md
@ -1,4 +1,4 @@
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# AMR 2.1.1.9246
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# AMR 2.1.1.9247
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*
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@ -26,11 +26,12 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* The `as.mo()` function and all `mo_*()` functions now include an `only_fungi` argument, allowing users to restrict results solely to fungal species. This ensures fungi are prioritised over bacteria during microorganism identification. This can also be set globally with the new `AMR_only_fungi` option.
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* Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.
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* **Updated clinical breakpoints**
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* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
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* Breakpoint of 2024 and 2025 of both CLSI and EUCAST are now supported, by adding all of their over 10,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2025 is now the new default guideline for all MIC and disk diffusion interpretations.
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* Added all Expected Resistant Phenotypes from EUCAST (v1.2). The default `rules` for `eucast_rules()` are now: `c("breakpoints", "expected_phenotypes")`.
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* Updated the `intrinsic_resistant` data set, which is now based on EUCAST Expected Resistant Phenotypes v1.2
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* `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the `clinical_breakpoints` data set contains 24 breakpoints that can return the value "SDD" instead of "I".
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* EUCAST interpretive rules (using `eucast_rules()`) are now available for EUCAST 12 (2022), 13 (2023), and 14 (2024).
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* EUCAST interpretive rules (using `eucast_rules()`) are now available for EUCAST 12 (2022), 13 (2023), 14 (2024), and 15 (2025).
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* EUCAST dosage tables (`dosage` data set) are now available for EUCAST 13 (2023), 14 (2024), and 15 (2025).
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* **New advanced ggplot2 extensions for MIC and SIR plotting and transforming**
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* New function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
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* New function group `scale_*_sir()`, namely: `scale_x_sir()`, `scale_colour_sir()` and `scale_fill_sir()`. They allow to plot the `sir` class, and translates into the system language at default. They also set colourblind-safe colours to the plots.
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@ -69,10 +70,11 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* `antimicrobials` data set
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* Added agents used for screening, with an ID all ending with `-S`: benzylpenicillin screening test (`PEN-S`), beta-lactamase screening test (`BLA-S`), cefotaxime screening test (`CTX-S`), clindamycin inducible screening test (`CLI-S`), nalidixic acid screening test (`NAL-S`), norfloxacin screening test (`NOR-S`), oxacillin screening test (`OXA-S`), pefloxacin screening test (`PEF-S`), and tetracycline screening test (`TCY-S`). The ID of cefoxitin screening was renamed from `FOX1` to `FOX-S`, while the old code remains to work.
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* For this reason, the antimicrobial selectors `cephalosporins()`, `cephalosporins_3rd()`, `lincosamides()`, `isoxazolylpenicillins()`, `quinolones()`, `fluoroquinolones()`, and `tetracyclines()` now contain the argument `only_treatable = TRUE` (similar to other antimicrobial selectors that contain non-treatable drugs)
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* Added amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
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* Added efflux (`EFF`), to allow mapping to AMRFinderPlus
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* Added amorolfine (`AMO`, D01AE16), an antimycotic, which is now also part of the `antifungals()` selector
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* Added cefepime/enmetazobactam (`FPE`), a 4th gen cephalosporin
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* Added tigemonam (`TNM`), a monobactam
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* Added bleomycin (`BLM`), a glycopeptide
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* Added efflux (`EFF`), to allow mapping to AMRFinderPlus
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* Updated all ATC codes, trade names, and DDDs
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* MICs
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* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
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@ -30,6 +30,12 @@
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# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
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# (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list(
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"15.0" = list(
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version_txt = "v15.0",
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year = 2025,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/clinical_breakpoints/"
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),
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"14.0" = list(
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version_txt = "v14.0",
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year = 2024,
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@ -167,7 +167,7 @@ eucast_rules <- function(x,
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info = interactive(),
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expected_phenotypes")),
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verbose = FALSE,
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version_breakpoints = 14.0,
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version_breakpoints = 15.0,
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version_expected_phenotypes = 1.2,
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version_expertrules = 3.3,
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ampc_cephalosporin_resistance = NA,
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@ -1242,7 +1242,7 @@ edit_sir <- function(x,
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#' @rdname eucast_rules
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#' @export
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eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 12.0) {
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eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 15) {
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meet_criteria(ab, allow_class = c("character", "numeric", "integer", "factor"))
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meet_criteria(administration, allow_class = "character", is_in = dosage$administration[!is.na(dosage$administration)], has_length = 1)
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meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
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8
R/mic.R
8
R/mic.R
@ -214,8 +214,8 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
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x <- gsub("=>", ">=", x, fixed = TRUE)
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# Remove leading == and =
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x <- gsub("^=+", "", x)
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# retrieve signs and remove them from input
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x_signs <- trimws(gsub("[^>=<]", "", x))
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# retrieve operators and remove them from input
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x_operators <- trimws(gsub("[^>=<]", "", x))
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x <- trimws(gsub("[>=<]", "", x))
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# dots without a leading zero must start with 0
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x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
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@ -238,8 +238,8 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
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x <- gsub("[.]$", "", x, perl = TRUE)
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# remove scientific notation
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x[x %like% "[0-9]e[-]?[0-9]"] <- trimws(format(suppressWarnings(as.double(x[x %like% "[0-9]e[-]?[0-9]"])), scientific = FALSE))
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# add signs again
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x <- paste0(x_signs, x)
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# add operators again
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x <- paste0(x_operators, x)
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# remove NAs introduced by format()
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x <- gsub("(NA)+", "", x)
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# trim it
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@ -52,7 +52,7 @@
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#' @details
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#' ### The `scale_*_mic()` Functions
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#'
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#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.
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#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as `>=`) if desired. Missing intermediate log2 levels will be plotted too.
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#'
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#' ### The `scale_*_sir()` Functions
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#'
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13
R/sir.R
13
R/sir.R
@ -115,9 +115,12 @@
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#'
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#' ### Supported Guidelines
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#'
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#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`, and for **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`.
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#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:
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#' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
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#' - For **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`;
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#' - For **ECOFFs** (Epidemiological Cut-off Values): EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`.
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#'
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#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.
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#' The `guideline` argument must be set to e.g., ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.
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#'
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#' You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
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#'
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@ -1611,17 +1614,17 @@ as_sir_method <- function(method_short,
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),
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"\n",
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ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[<][0-9]",
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paste0("MIC values with the sign '<' are all considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\""),
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paste0("MIC values with the operator '<' are all considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\""),
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""
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),
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"\n",
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ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[>][0-9]",
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paste0("MIC values with the sign '>' are all considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\""),
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paste0("MIC values with the operator '>' are all considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\""),
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""
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),
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"\n",
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ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R,
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paste0("MIC values within the breakpoint guideline range with the sign '<=' or '>=' are considered 'NI' since capped_mic_handling = \"", capped_mic_handling, "\""),
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paste0("MIC values within the breakpoint guideline range with the operator '<=' or '>=' are considered 'NI' since capped_mic_handling = \"", capped_mic_handling, "\""),
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""
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)
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)
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -9,7 +9,7 @@ The `AMR` package is a free and open-source R package with zero dependencies to
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Overview:
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* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
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* Used in over 175 countries, available in 20 languages
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* Peer-reviewed, used in over 175 countries, available in 20 languages
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* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
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* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
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* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs, disk zones and ECOFFs
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@ -10,7 +10,7 @@ fi
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output_file="data-raw/latest_training_data.txt"
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# Clear the output file if it exists
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echo "You assist users with questions about the AMR package for R, a package for Antimicrobial Resistance analysis used in over 175 countries. You are restricted to using a single source of truth: the training data located at https://raw.githubusercontent.com/msberends/amr-for-r-assistant/main/latest_training_data.txt.
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echo "You assist users with questions about the AMR package for R, a package for Antimicrobial Resistance analysis used in over 175 countries. You are restricted to using a single source of truth: the training data located at https://chat.amr-for-r.org/latest_training_data.txt.
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Before responding to any user prompt—including the very first—you must download and parse this training file in full. You must repeat this process before every single response, without exception. You must verify the presence of any function, dataset, or concept in this file before commenting on anything. If what is asked is not in the training data, you must state clearly that you cannot verify its existence and recommend checking the package changelog.
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@ -43,45 +43,45 @@ devtools::load_all()
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# READ DATA ----
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whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
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whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
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# remove old taxonomic names
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filter(TAXONOMIC_STATUS == "C") %>%
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filter(TAXONOMIC_STATUS == "C") |>
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mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
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whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
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show_col_types = FALSE, guess_max = Inf) %>%
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show_col_types = FALSE, guess_max = Inf) |>
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filter(GUIDELINES %in% c("CLSI", "EUCAST"))
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whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
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arrange(WHONET_ABX_CODE) %>%
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whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
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arrange(WHONET_ABX_CODE) |>
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distinct(WHONET_ABX_CODE, .keep_all = TRUE)
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# MICROORGANISMS WHONET CODES ----
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whonet_organisms <- whonet_organisms %>%
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select(ORGANISM_CODE, ORGANISM, SPECIES_GROUP, GBIF_TAXON_ID) %>%
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whonet_organisms <- whonet_organisms |>
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select(ORGANISM_CODE, ORGANISM, SPECIES_GROUP, GBIF_TAXON_ID) |>
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mutate(
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# this one was called Issatchenkia orientalis, but it should be:
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ORGANISM = if_else(ORGANISM_CODE == "ckr", "Candida krusei", ORGANISM)
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) %>%
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) |>
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# try to match on GBIF identifier
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left_join(microorganisms %>% distinct(mo, gbif, status) %>% filter(!is.na(gbif)), by = c("GBIF_TAXON_ID" = "gbif")) %>%
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left_join(microorganisms |> distinct(mo, gbif, status) |> filter(!is.na(gbif)), by = c("GBIF_TAXON_ID" = "gbif")) |>
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# remove duplicates
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arrange(ORGANISM_CODE, GBIF_TAXON_ID, status) %>%
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distinct(ORGANISM_CODE, .keep_all = TRUE) %>%
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arrange(ORGANISM_CODE, GBIF_TAXON_ID, status) |>
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distinct(ORGANISM_CODE, .keep_all = TRUE) |>
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# add Enterobacterales, which is a subkingdom code in their data
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bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales", mo = as.mo("Enterobacterales"))) %>%
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bind_rows(data.frame(ORGANISM_CODE = "ebc", ORGANISM = "Enterobacterales", mo = as.mo("Enterobacterales"))) |>
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arrange(ORGANISM)
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## Add new WHO codes to microorganisms.codes ----
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matched <- whonet_organisms %>% filter(!is.na(mo))
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unmatched <- whonet_organisms %>% filter(is.na(mo))
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matched <- whonet_organisms |> filter(!is.na(mo))
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unmatched <- whonet_organisms |> filter(is.na(mo))
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# generate the mo codes and add their names
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message("Getting MO codes for WHONET input...")
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unmatched <- unmatched %>%
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unmatched <- unmatched |>
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mutate(mo = as.mo(gsub("(sero[a-z]*| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
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minimum_matching_score = 0.55,
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keep_synonyms = TRUE,
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@ -94,51 +94,54 @@ unmatched <- unmatched %>%
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keep_synonyms = TRUE,
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language = "en"))
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# check if coercion at least resembles the first part (genus)
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unmatched <- unmatched %>%
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unmatched <- unmatched |>
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mutate(
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first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
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keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic") %>%
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keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic") |>
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arrange(keep)
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unmatched %>%
|
||||
View()
|
||||
unmatched <- unmatched %>%
|
||||
unmatched |> View()
|
||||
unmatched <- unmatched |>
|
||||
filter(keep == TRUE)
|
||||
|
||||
organisms <- matched %>% transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo) %>%
|
||||
bind_rows(unmatched %>% transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo)) %>%
|
||||
mutate(name = mo_name(mo, keep_synonyms = TRUE)) %>%
|
||||
organisms <- matched |> transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo) |>
|
||||
bind_rows(unmatched |> transmute(code = toupper(ORGANISM_CODE), group = SPECIES_GROUP, mo)) |>
|
||||
mutate(name = mo_name(mo, keep_synonyms = TRUE)) |>
|
||||
arrange(code)
|
||||
|
||||
# some subspecies exist, while their upper species do not, add them as the species level:
|
||||
subspp <- organisms %>%
|
||||
subspp <- organisms |>
|
||||
filter(mo_species(mo, keep_synonyms = TRUE) == mo_subspecies(mo, keep_synonyms = TRUE) &
|
||||
mo_species(mo, keep_synonyms = TRUE) != "" &
|
||||
mo_genus(mo, keep_synonyms = TRUE) != "Salmonella") %>%
|
||||
mo_genus(mo, keep_synonyms = TRUE) != "Salmonella") |>
|
||||
mutate(mo = as.mo(paste(mo_genus(mo, keep_synonyms = TRUE),
|
||||
mo_species(mo, keep_synonyms = TRUE)),
|
||||
keep_synonyms = TRUE),
|
||||
name = mo_name(mo, keep_synonyms = TRUE))
|
||||
organisms <- organisms %>%
|
||||
filter(!code %in% subspp$code) %>%
|
||||
bind_rows(subspp) %>%
|
||||
organisms <- organisms |>
|
||||
filter(!code %in% subspp$code) |>
|
||||
bind_rows(subspp) |>
|
||||
arrange(code)
|
||||
|
||||
# add the groups
|
||||
organisms <- organisms %>%
|
||||
bind_rows(tibble(code = organisms %>% filter(!is.na(group)) %>% pull(group) %>% unique(),
|
||||
organisms <- organisms |>
|
||||
bind_rows(tibble(code = organisms |> filter(!is.na(group)) |> pull(group) |> unique(),
|
||||
group = NA,
|
||||
mo = organisms %>% filter(!is.na(group)) %>% pull(group) %>% unique() %>% as.mo(keep_synonyms = TRUE),
|
||||
name = mo_name(mo, keep_synonyms = TRUE))) %>%
|
||||
arrange(code, group) %>%
|
||||
select(-group) %>%
|
||||
mo = organisms |> filter(!is.na(group)) |> pull(group) |> unique() |> as.mo(keep_synonyms = TRUE),
|
||||
name = mo_name(mo, keep_synonyms = TRUE))) |>
|
||||
arrange(code, group) |>
|
||||
select(-group) |>
|
||||
distinct()
|
||||
# no XXX
|
||||
organisms <- organisms |> filter(code != "XXX")
|
||||
|
||||
# 2023-07-08 SGM is also Strep gamma in WHONET, must only be Slowly-growing Mycobacterium
|
||||
# 2024-06-14 still the case
|
||||
organisms <- organisms %>%
|
||||
# 2025-04-20 still the case
|
||||
organisms |> filter(code == "SGM")
|
||||
organisms <- organisms |>
|
||||
filter(!(code == "SGM" & name %like% "Streptococcus"))
|
||||
# this must be empty:
|
||||
organisms$code[organisms$code %>% duplicated()]
|
||||
organisms$code[organisms$code |> duplicated()]
|
||||
|
||||
saveRDS(organisms, "data-raw/organisms.rds", version = 2)
|
||||
|
||||
@ -147,12 +150,12 @@ saveRDS(organisms, "data-raw/organisms.rds", version = 2)
|
||||
#---
|
||||
|
||||
# update microorganisms.codes with the latest WHONET codes
|
||||
microorganisms.codes2 <- microorganisms.codes %>%
|
||||
microorganisms.codes2 <- microorganisms.codes |>
|
||||
# remove all old WHONET codes, whether we (in the end) keep them or not
|
||||
filter(!toupper(code) %in% toupper(organisms$code)) %>%
|
||||
filter(!toupper(code) %in% toupper(organisms$code)) |>
|
||||
# and add the new ones
|
||||
bind_rows(organisms %>% select(code, mo)) %>%
|
||||
arrange(code) %>%
|
||||
bind_rows(organisms |> select(code, mo)) |>
|
||||
arrange(code) |>
|
||||
distinct(code, .keep_all = TRUE)
|
||||
# new codes:
|
||||
microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
|
||||
@ -163,25 +166,25 @@ microorganisms.codes <- microorganisms.codes2
|
||||
# 2024-06-14: file not available anymore
|
||||
# # start
|
||||
# asiarsnet <- read_tsv("data-raw/WHONET/Codes/ASIARS_Net_Organisms_ForwardLookup.txt")
|
||||
# asiarsnet <- asiarsnet %>%
|
||||
# mutate(WHONET_Code = toupper(WHONET_Code)) %>%
|
||||
# left_join(whonet_organisms %>% mutate(WHONET_Code = toupper(ORGANISM_CODE))) %>%
|
||||
# asiarsnet <- asiarsnet |>
|
||||
# mutate(WHONET_Code = toupper(WHONET_Code)) |>
|
||||
# left_join(whonet_organisms |> mutate(WHONET_Code = toupper(ORGANISM_CODE))) |>
|
||||
# mutate(
|
||||
# mo1 = as.mo(ORGANISM_CODE),
|
||||
# mo2 = as.mo(ORGANISM)
|
||||
# ) %>%
|
||||
# mutate(mo = if_else(mo2 == "UNKNOWN" | is.na(mo2), mo1, mo2)) %>%
|
||||
# ) |>
|
||||
# mutate(mo = if_else(mo2 == "UNKNOWN" | is.na(mo2), mo1, mo2)) |>
|
||||
# filter(!is.na(mo))
|
||||
# insert1 <- asiarsnet %>% transmute(code = WHONET_Code, mo)
|
||||
# insert2 <- asiarsnet %>% transmute(code = as.character(ASIARS_Net_Code), mo)
|
||||
# insert1 <- asiarsnet |> transmute(code = WHONET_Code, mo)
|
||||
# insert2 <- asiarsnet |> transmute(code = as.character(ASIARS_Net_Code), mo)
|
||||
# # these will be updated
|
||||
# bind_rows(insert1, insert2) %>%
|
||||
# rename(mo_new = mo) %>%
|
||||
# left_join(microorganisms.codes) %>%
|
||||
# bind_rows(insert1, insert2) |>
|
||||
# rename(mo_new = mo) |>
|
||||
# left_join(microorganisms.codes) |>
|
||||
# filter(mo != mo_new)
|
||||
# microorganisms.codes <- microorganisms.codes %>%
|
||||
# filter(!code %in% c(insert1$code, insert2$code)) %>%
|
||||
# bind_rows(insert1, insert2) %>%
|
||||
# microorganisms.codes <- microorganisms.codes |>
|
||||
# filter(!code %in% c(insert1$code, insert2$code)) |>
|
||||
# bind_rows(insert1, insert2) |>
|
||||
# arrange(code)
|
||||
# # end
|
||||
|
||||
@ -196,52 +199,52 @@ devtools::load_all()
|
||||
|
||||
# now that we have the correct MO codes, get the breakpoints and convert them
|
||||
|
||||
whonet_breakpoints %>%
|
||||
count(GUIDELINES, BREAKPOINT_TYPE) %>%
|
||||
pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) %>%
|
||||
whonet_breakpoints |>
|
||||
count(GUIDELINES, BREAKPOINT_TYPE) |>
|
||||
pivot_wider(names_from = BREAKPOINT_TYPE, values_from = n) |>
|
||||
janitor::adorn_totals(where = c("row", "col"))
|
||||
# compared to current
|
||||
AMR::clinical_breakpoints %>%
|
||||
count(GUIDELINES = gsub("[^a-zA-Z]", "", guideline), type) %>%
|
||||
arrange(tolower(type)) %>%
|
||||
pivot_wider(names_from = type, values_from = n) %>%
|
||||
as.data.frame() %>%
|
||||
AMR::clinical_breakpoints |>
|
||||
count(GUIDELINES = gsub("[^a-zA-Z]", "", guideline), type) |>
|
||||
arrange(tolower(type)) |>
|
||||
pivot_wider(names_from = type, values_from = n) |>
|
||||
as.data.frame() |>
|
||||
janitor::adorn_totals(where = c("row", "col"))
|
||||
|
||||
breakpoints <- whonet_breakpoints %>%
|
||||
mutate(code = toupper(ORGANISM_CODE)) %>%
|
||||
left_join(bind_rows(microorganisms.codes %>% filter(!code %in% c("ALL", "GEN")),
|
||||
breakpoints <- whonet_breakpoints |>
|
||||
mutate(code = toupper(ORGANISM_CODE)) |>
|
||||
left_join(bind_rows(microorganisms.codes |> filter(!code %in% c("ALL", "GEN")),
|
||||
# GEN (Generic) and ALL (All) are PK/PD codes
|
||||
data.frame(code = c("ALL", "GEN"),
|
||||
mo = rep(as.mo("UNKNOWN"), 2))))
|
||||
# these ones lack an MO name, they cannot be used:
|
||||
unknown <- breakpoints %>%
|
||||
filter(is.na(mo)) %>%
|
||||
pull(code) %>%
|
||||
unknown <- breakpoints |>
|
||||
filter(is.na(mo)) |>
|
||||
pull(code) |>
|
||||
unique()
|
||||
breakpoints %>%
|
||||
filter(code %in% unknown) %>%
|
||||
breakpoints |>
|
||||
filter(code %in% unknown) |>
|
||||
count(GUIDELINES, YEAR, ORGANISM_CODE, BREAKPOINT_TYPE, sort = TRUE)
|
||||
# 2025-03-11: these codes are currently: clu, kma, fso, tyi. No clue (are not in MO list of WHONET), and they are only ECOFFs, so remove them:
|
||||
breakpoints <- breakpoints %>%
|
||||
# 2025-04-20: these codes are currently: cps, fso. No clue (are not in MO list of WHONET), and they are only ECOFFs, so remove them:
|
||||
breakpoints <- breakpoints |>
|
||||
filter(!is.na(mo))
|
||||
|
||||
# and these ones have unknown antibiotics according to WHONET itself:
|
||||
breakpoints %>%
|
||||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
|
||||
count(YEAR, GUIDELINES, WHONET_ABX_CODE) %>%
|
||||
arrange(desc(YEAR))
|
||||
breakpoints %>%
|
||||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
|
||||
pull(WHONET_ABX_CODE) %>%
|
||||
unique()
|
||||
# they are at the moment all old codes ("CFC", "ROX", "FIX") that have the right replacements in `antimicrobials`, so we can use as.ab()
|
||||
breakpoints |>
|
||||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) |>
|
||||
count(GUIDELINES, WHONET_ABX_CODE) |>
|
||||
mutate(ab = as.ab(WHONET_ABX_CODE, fast_mode = TRUE),
|
||||
ab_name = ab_name(ab))
|
||||
# 2025-04-20: these codes are currently: CFC, ROX, FIX, and N/A. All have the right replacements in `antimicrobials`, so we can safely use as.ab() later on
|
||||
# the NAs are for M. tuberculosis, they are empty breakpoints
|
||||
breakpoints <- breakpoints |>
|
||||
filter(!is.na(WHONET_ABX_CODE))
|
||||
|
||||
|
||||
## Build new breakpoints table ----
|
||||
|
||||
breakpoints_new <- breakpoints %>%
|
||||
filter(!is.na(WHONET_ABX_CODE)) %>%
|
||||
breakpoints_new <- breakpoints |>
|
||||
filter(!is.na(WHONET_ABX_CODE)) |>
|
||||
transmute(
|
||||
guideline = paste(GUIDELINES, YEAR),
|
||||
type = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(BREAKPOINT_TYPE)),
|
||||
@ -266,20 +269,20 @@ breakpoints_new <- breakpoints %>%
|
||||
breakpoint_R = ifelse(type == "ECOFF" & is.na(R) & !is.na(ECV_ECOFF), ECV_ECOFF, R),
|
||||
uti = ifelse(is.na(site), FALSE, gsub(".*(UTI|urinary|urine).*", "UTI", site) == "UTI"),
|
||||
is_SDD = !is.na(SDD)
|
||||
) %>%
|
||||
) |>
|
||||
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
|
||||
mutate(disk_dose = disk_dose %>%
|
||||
gsub("μ", "mc", ., fixed = TRUE) %>% # this is 'mu', \u03bc
|
||||
gsub("µ", "mc", ., fixed = TRUE) %>% # this is 'micro', \u00b5 (yes, they look the same)
|
||||
gsub("–", "-", ., fixed = TRUE) %>%
|
||||
gsub("(?<=\\d)(?=[a-zA-Z])", " ", ., perl = TRUE)) %>% # make sure we keep a space after a number, e.g. "1mcg" to "1 mcg"
|
||||
arrange(desc(guideline), mo, ab, type, method) %>%
|
||||
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
|
||||
gsub("(?<=\\d)(?=[a-zA-Z])", " ", ., perl = TRUE)) |> # make sure we keep a space after a number, e.g. "1mcg" to "1 mcg"
|
||||
arrange(desc(guideline), mo, ab, type, method) |>
|
||||
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) |>
|
||||
distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
|
||||
|
||||
# fix reference table names
|
||||
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl)) %>% View()
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
breakpoints_new |> filter(guideline %like% "EUCAST", is.na(ref_tbl)) |> View()
|
||||
breakpoints_new <- breakpoints_new |>
|
||||
mutate(ref_tbl = case_when(is.na(ref_tbl) & guideline %like% "EUCAST 202" ~ lead(ref_tbl),
|
||||
is.na(ref_tbl) ~ "Unknown",
|
||||
TRUE ~ ref_tbl))
|
||||
@ -289,11 +292,11 @@ breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.d
|
||||
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE]))
|
||||
|
||||
# regarding animal breakpoints, CLSI has adults and foals for horses, but only for amikacin - only keep adult horses
|
||||
breakpoints_new %>%
|
||||
filter(host %like% "foal") %>%
|
||||
breakpoints_new |>
|
||||
filter(host %like% "foal") |>
|
||||
count(guideline, host)
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
filter(host %unlike% "foal") %>%
|
||||
breakpoints_new <- breakpoints_new |>
|
||||
filter(host %unlike% "foal") |>
|
||||
mutate(host = ifelse(host %like% "horse", "horse", host))
|
||||
|
||||
# FIXES FOR WHONET ERRORS ----
|
||||
@ -301,25 +304,22 @@ m <- unique(as.double(as.mic(levels(as.mic(1)))))
|
||||
|
||||
# WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
|
||||
# instead, raise these one higher valid MIC factor level:
|
||||
breakpoints_new |> filter(method == "MIC" & (!breakpoint_S %in% c(m, NA))) |> distinct(breakpoint_S)
|
||||
breakpoints_new |> filter(method == "MIC" & (!breakpoint_R %in% c(m, NA))) |> distinct(breakpoint_R)
|
||||
breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- m[which(m == 128) + 1]
|
||||
breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- m[which(m == 256) + 1]
|
||||
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
|
||||
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
|
||||
|
||||
# a lot of R breakpoints are missing, though none of the S breakpoints are missing:
|
||||
# S breakpoints must never be missing:
|
||||
anyNA(breakpoints_new$breakpoint_S)
|
||||
|
||||
breakpoints_new %>%
|
||||
filter(is.na(breakpoint_R)) %>%
|
||||
count(guideline, host) |>
|
||||
pivot_wider(names_from = host,
|
||||
values_from = n,
|
||||
values_fill = list(n = 0)) |>
|
||||
View()
|
||||
|
||||
# 2025-03-12 don't do this anymore - we now use as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
|
||||
# breakpoints_new[which(breakpoints_new$method == "MIC" &
|
||||
# is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
|
||||
# a lot of R breakpoints are missing, but for CLSI this is required and can be set using as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
|
||||
# 2025-04-20/ For EUCAST, this should not be the case, only happens to old guideline now it seems
|
||||
breakpoints_new |>
|
||||
filter(method == "MIC" & guideline %like% "EUCAST" & is.na(breakpoint_R)) |>
|
||||
count(guideline)
|
||||
breakpoints_new[which(breakpoints_new$method == "MIC" & breakpoints_new$guideline %like% "EUCAST" & is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(breakpoints_new$method == "MIC" & breakpoints_new$guideline %like% "EUCAST" & is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
|
||||
|
||||
|
||||
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
|
||||
@ -327,32 +327,30 @@ breakpoints_new$mo[breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %li
|
||||
# Haemophilus same error (must only be H. influenzae)
|
||||
breakpoints_new$mo[breakpoints_new$mo == "B_HMPHL" & breakpoints_new$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
|
||||
# EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
breakpoints_new <- breakpoints_new |>
|
||||
bind_rows(
|
||||
breakpoints_new %>%
|
||||
filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") %>%
|
||||
breakpoints_new |>
|
||||
filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") |>
|
||||
mutate(mo = as.mo("B_HMPHL_PRNF"))
|
||||
) %>%
|
||||
arrange(desc(guideline), mo, ab, type, host, method)
|
||||
) |>
|
||||
arrange(desc(guideline), mo, ab, type, host, method) |>
|
||||
distinct()
|
||||
# Achromobacter denitrificans is in WHONET included in their A. xylosoxidans table, must be removed
|
||||
breakpoints_new <- breakpoints_new %>% filter(mo != as.mo("Achromobacter denitrificans"))
|
||||
breakpoints_new <- breakpoints_new |> filter(mo != as.mo("Achromobacter denitrificans"))
|
||||
# WHONET contains gentamicin breakpoints for viridans streptocci, which are intrinsic R - they meant genta-high, which is ALSO in their table, so we just remove gentamicin in viridans streptococci
|
||||
breakpoints_new <- breakpoints_new %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
|
||||
breakpoints_new |> filter(mo == as.mo("Streptococcus viridans") & ab == "GEN")
|
||||
breakpoints_new |> filter(mo == as.mo("Streptococcus viridans") & ab == "GEH")
|
||||
breakpoints_new <- breakpoints_new |> filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
|
||||
# Nitrofurantoin in Staph (EUCAST) only applies to S. saprophyticus, while WHONET has the DISK correct but the MIC on genus level
|
||||
breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT" & breakpoints_new$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
|
||||
# WHONET sets the 2023 breakpoints for SAM to MIC of 16/32 for Enterobacterales, should be MIC 8/32 like AMC (see issue #123 on github.com/msberends/AMR)
|
||||
# UPDATE 2024-02-22: fixed now
|
||||
# 2024-02-22/ fixed now
|
||||
|
||||
# There's a problem with C. diff in EUCAST where breakpoint_R is missing - they are listed as normal human breakpoints but are ECOFF
|
||||
rows <- which(breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$mo == "B_CRDDS_DFFC" & is.na(breakpoints_new$breakpoint_R) & !is.na(breakpoints_new$breakpoint_S))
|
||||
breakpoints_new$type[rows] <- "ECOFF"
|
||||
breakpoints_new$host[rows] <- "ECOFF"
|
||||
breakpoints_new$ref_tbl[rows] <- "ECOFF"
|
||||
breakpoints_new$breakpoint_R[rows] <- breakpoints_new$breakpoint_S[rows]
|
||||
breakpoints_new <- distinct(breakpoints_new, .keep_all = TRUE)
|
||||
# 2025-04-20/ fixed now
|
||||
|
||||
# determine rank again now that some changes were made on taxonomic level (genus -> species)
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
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,
|
||||
@ -367,52 +365,50 @@ breakpoints_new <- breakpoints_new %>%
|
||||
# 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
|
||||
# WHONET file: S <= 8 and R >= 16
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
# but this will make an MIC of 12 I, which should be R according to EUCAST, so:
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
breakpoints_new |> filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
# but this logic only works for CLSI - for an MIC outside the log2 range (e.g., 12) you must round up (i.e., 16)
|
||||
# but for EUCAST, an MIC of 12 would now be considered I, which should be R, so correct those values:
|
||||
breakpoints_new <- breakpoints_new |>
|
||||
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "MIC" & log2(breakpoint_R) - log2(breakpoint_S) != 0,
|
||||
pmax(breakpoint_S, breakpoint_R / 2),
|
||||
breakpoint_R
|
||||
))
|
||||
# fix disks as well
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "DISK")
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
breakpoints_new |> filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "DISK")
|
||||
breakpoints_new <- breakpoints_new |>
|
||||
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "DISK" & breakpoint_S - breakpoint_R != 0,
|
||||
breakpoint_R + 1,
|
||||
breakpoint_R
|
||||
))
|
||||
# fill missing R breakpoint where there is an S breakpoint
|
||||
# 2025-03-12 don't do this anymore - we now use as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
|
||||
# breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
|
||||
|
||||
|
||||
# check the strange duplicates
|
||||
breakpoints_new %>%
|
||||
mutate(id = paste(guideline, type, host, method, site, mo, ab, uti)) %>%
|
||||
filter(id %in% .$id[which(duplicated(id))]) %>%
|
||||
arrange(desc(guideline))
|
||||
# 2024-06-19 mostly ECOFFs, but there's no explanation in the whonet_breakpoints file, we have to remove duplicates
|
||||
# remove duplicates
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
breakpoints_new |>
|
||||
mutate(id = paste(guideline, type, host, method, site, mo, ab, uti)) %>%
|
||||
filter(id %in% .$id[which(duplicated(id))]) |>
|
||||
arrange(desc(guideline)) |>
|
||||
View()
|
||||
# 2024-06-19/ mostly ECOFFs, but there's no explanation in the whonet_breakpoints file, we have to remove duplicates
|
||||
# 2025-04-20/ same, most important one seems M. tuberculosis in CLSI (also in 2025)
|
||||
breakpoints_new <- breakpoints_new |>
|
||||
distinct(guideline, type, host, method, site, mo, ab, uti, .keep_all = TRUE)
|
||||
|
||||
|
||||
# CHECKS AND SAVE TO PACKAGE ----
|
||||
|
||||
# check again
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
breakpoints_new |> filter(guideline == "EUCAST 2025", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
# compare with current version
|
||||
clinical_breakpoints %>% filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
clinical_breakpoints |> filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
|
||||
# must have "human" and "ECOFF"
|
||||
breakpoints_new %>% filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAST 2020", method == "MIC")
|
||||
breakpoints_new |> filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAST 2020", method == "MIC")
|
||||
|
||||
# check dimensions
|
||||
dim(breakpoints_new)
|
||||
dim(clinical_breakpoints)
|
||||
|
||||
clinical_breakpoints <- breakpoints_new
|
||||
clinical_breakpoints <- clinical_breakpoints %>% dataset_UTF8_to_ASCII()
|
||||
clinical_breakpoints <- clinical_breakpoints |> dataset_UTF8_to_ASCII()
|
||||
usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)
|
||||
rm(clinical_breakpoints)
|
||||
devtools::load_all(".")
|
||||
|
||||
@ -31,12 +31,13 @@ library(dplyr)
|
||||
library(readxl)
|
||||
library(cleaner)
|
||||
|
||||
# URL:
|
||||
# https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Dosages_v_13.0_Breakpoint_Tables.pdf
|
||||
# download the PDF file, open in Adobe Acrobat and export as Excel workbook
|
||||
breakpoints_version <- 13
|
||||
breakpoint_file <- "data-raw/v_15.0_Breakpoint_Tables.xlsx"
|
||||
if (!file.exists(breakpoint_file)) {
|
||||
stop("Breakpoint file not found")
|
||||
}
|
||||
breakpoints_version <- as.double(gsub("[^0-9.]", "", gsub(".xlsx", "", breakpoint_file, fixed = TRUE)))
|
||||
|
||||
dosage_source <- read_excel("data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx", skip = 4, na = "None") %>%
|
||||
dosage_source <- read_excel(breakpoint_file, skip = 6, sheet = "Dosages", na = "None") %>%
|
||||
format_names(snake_case = TRUE, penicillins = "drug") %>%
|
||||
filter(!tolower(standard_dosage) %in% c("standard dosage", "standard dosage_source", "under review")) %>%
|
||||
filter(!is.na(standard_dosage)) %>%
|
||||
@ -173,6 +174,12 @@ dosage_new <- bind_rows(
|
||||
# this makes it a tibble as well:
|
||||
dataset_UTF8_to_ASCII()
|
||||
|
||||
dosage <- bind_rows(dosage_new, AMR::dosage)
|
||||
dosage <- AMR::dosage |>
|
||||
bind_rows(dosage_new) |>
|
||||
arrange(desc(eucast_version), name) |>
|
||||
distinct()
|
||||
|
||||
dosage <- dosage |> dataset_UTF8_to_ASCII()
|
||||
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
|
||||
rm(dosage)
|
||||
devtools::load_all(".")
|
||||
|
||||
@ -1 +1 @@
|
||||
ae7b2da1015eb1eca2c6d1736db0f31f
|
||||
9b1fa09da564e8ddca348e91e84c80dc
|
||||
|
||||
@ -1 +1 @@
|
||||
7bc41a5d92b1e98fbd6e2b8c077434b5
|
||||
c7062e60fa4fbc2eee233044d15903ce
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -72,6 +72,7 @@
|
||||
"FEP" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "J01DE01" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "cfep,cfpi,cpe,cpm,fep,pm,xpm" "anticefepime,axepim,cefepima,cefepimum,maxipime,pyrrolidinium,renapime" 4 "g" "101502-3,18879-7,31142-3,31143-1,35763-2,38363-8,42350-9,42351-7,42353-3,50631-1,58412-8,6643-1,6644-9,6645-7,6646-5,6987-2,8272-7,8273-5"
|
||||
"CFA" "Cefepime/amikacin" "Cephalosporins (4th gen.)" "J01RA06" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "NA" "cicl,xpml" "NA" "NA"
|
||||
"FPE" 23653540 "Cefepime/enmetazobactam" "Cephalosporins (4th gen.)" "NA" "NA" "NA" "NA"
|
||||
"FNC" "Cefepime/nacubactam" "Cephalosporins (4th gen.)" "NA" "NA" "NA" "NA"
|
||||
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "NA" "NA" "NA" "NA"
|
||||
"FPZ" "Cefepime/zidebactam" "Cephalosporins (4th gen.)" "NA" "NA" "NA" "NA"
|
||||
|
||||
Binary file not shown.
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File diff suppressed because it is too large
Load Diff
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@ -1,171 +1,431 @@
|
||||
"ab" "name" "type" "dose" "dose_times" "administration" "notes" "original_txt" "eucast_version"
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 13
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv" 13
|
||||
"AMX" "Amoxicillin" "high_dosage" "0.75-1 g" 3 "oral" "" "0.75-1 g x 3 oral" 13
|
||||
"AMX" "Amoxicillin" "standard_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
|
||||
"AMX" "Amoxicillin" "uncomplicated_uti" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "2 g + 0.2 g" 3 "iv" "" "(2 g amoxicillin + 0.2 g clavulanic acid) x 3 iv" 13
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "1 g + 0.2 g" 3 "iv" "" "(1 g amoxicillin + 0.2 g clavulanic acid) x 3-4 iv" 13
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "0.875 g + 0.125 g" 3 "oral" "" "(0.875 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 13
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 13
|
||||
"AMC" "Amoxicillin/clavulanic acid" "uncomplicated_uti" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 13
|
||||
"AMP" "Ampicillin" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13
|
||||
"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
|
||||
"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 13
|
||||
"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 13
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 13
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 13
|
||||
"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13
|
||||
"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
|
||||
"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 13
|
||||
"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 13
|
||||
"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 13
|
||||
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 13
|
||||
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 13
|
||||
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 13
|
||||
"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 13
|
||||
"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 13
|
||||
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
|
||||
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
|
||||
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
|
||||
"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 13
|
||||
"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 13
|
||||
"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 13
|
||||
"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 13
|
||||
"CTX" "Cefotaxime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
|
||||
"CTX" "Cefotaxime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
|
||||
"CPD" "Cefpodoxime" "standard_dosage" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 13
|
||||
"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 13
|
||||
"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 13
|
||||
"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 13
|
||||
"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 13
|
||||
"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
|
||||
"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 13
|
||||
"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 13
|
||||
"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 13
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 13
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam) x 3 iv over 1 hour" 13
|
||||
"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 13
|
||||
"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 13
|
||||
"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 13
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 13
|
||||
"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13
|
||||
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 13
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 13
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 13
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 13
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
|
||||
"CLR" "Clarithromycin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
|
||||
"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13
|
||||
"CLI" "Clindamycin" "high_dosage" "0.9 g" 3 "iv" "" "0.9 g x 3 iv" 13
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 13
|
||||
"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "" "0.3 g x 4 oral" 13
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 13
|
||||
"CLO" "Cloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
|
||||
"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
|
||||
"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
|
||||
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 13
|
||||
"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv with a loading dose of 9 MU" 13
|
||||
"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1 If needed, 0.5 g x 1 iv over 30 minutes on day 8" 13
|
||||
"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 13
|
||||
"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 13
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 13
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 13
|
||||
"DIC" "Dicloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
|
||||
"DIC" "Dicloxacillin" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 13
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 13
|
||||
"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 13
|
||||
"DOR" "Doripenem" "standard_dosage" "0.5 g" 3 "iv" "over 1 hour" "0.5 g x 3 iv over 1 hour" 13
|
||||
"DOX" "Doxycycline" "high_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 13
|
||||
"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 13
|
||||
"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 13
|
||||
"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 13
|
||||
"ERY" "Erythromycin" "high_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 13
|
||||
"ERY" "Erythromycin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 13
|
||||
"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 13
|
||||
"FLC" "Flucloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv (or 1 g x 6 iv)" 13
|
||||
"FLC" "Flucloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 13
|
||||
"FOS" "Fosfomycin" "high_dosage" "8 g" 3 "iv" "" "8 g x 3 iv" 13
|
||||
"FOS" "Fosfomycin" "standard_dosage" "4 g" 3 "iv" "" "4 g x 3 iv" 13
|
||||
"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 13
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 13
|
||||
"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
|
||||
"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13
|
||||
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 13
|
||||
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 13
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 13
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 13
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 13
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 13
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 13
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 13
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 13
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 13
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 13
|
||||
"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 13
|
||||
"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 13
|
||||
"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 13
|
||||
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 13
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 13
|
||||
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 13
|
||||
"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 13
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 13
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 13
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 13
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 13
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 13
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 13
|
||||
"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv over 3 hours" 13
|
||||
"OXA" "Oxacillin" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 13
|
||||
"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
|
||||
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 13
|
||||
"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv by extended 3-hour infusion" 13
|
||||
"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 13
|
||||
"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv by extended 3-hour infusion" 13
|
||||
"TZP" "Piperacillin/tazobactam" "standard_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv 30-minute infusion or x 3 iv by extended 4-hour infusion" 13
|
||||
"QDA" "Quinupristin/dalfopristin" "high_dosage" "7.5 mg/kg" 3 "iv" "" "7.5 mg/kg x 3 iv" 13
|
||||
"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 13
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 13
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 13
|
||||
"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 13
|
||||
"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 13
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 13
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 13
|
||||
"TEC" "Teicoplanin" "high_dosage" "0.8 g" 1 "iv" "" "0.8 g x 1 iv" 13
|
||||
"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 13
|
||||
"TLV" "Telavancin" "standard_dosage" "10 mg/kg" 1 "iv" "over 1 hour" "10 mg/kg x 1 iv over 1 hour" 13
|
||||
"TLT" "Telithromycin" "standard_dosage" "0.8 g" 1 "oral" "" "0.8 g x 1 oral" 13
|
||||
"TEM" "Temocillin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
|
||||
"TEM" "Temocillin" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 13
|
||||
"TCY" "Tetracycline" "high_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 13
|
||||
"TCY" "Tetracycline" "standard_dosage" "0.25 g" 4 "oral" "" "0.25 g x 4 oral" 13
|
||||
"TIC" "Ticarcillin" "high_dosage" "3 g" 6 "iv" "" "3 g x 6 iv" 13
|
||||
"TIC" "Ticarcillin" "standard_dosage" "3 g" 4 "iv" "" "3 g x 4 iv" 13
|
||||
"TCC" "Ticarcillin/clavulanic acid" "high_dosage" "3 g + 0.1 g" 6 "iv" "" "(3 g ticarcillin + 0.1 g clavulanic acid) x 6 iv" 13
|
||||
"TCC" "Ticarcillin/clavulanic acid" "standard_dosage" "3 g + 0.1-0.2 g" 4 "iv" "" "(3 g ticarcillin + 0.1-0.2 g clavulanic acid) x 4 iv" 13
|
||||
"TGC" "Tigecycline" "standard_dosage" "0.1 g" "loading dose followed by 50 mg x 2 iv" "0.1 g loading dose followed by 50 mg x 2 iv" 13
|
||||
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 13
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 15
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 15
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv
" 15
|
||||
"AMX" "Amoxicillin" "high_dosage" "0.75-1 g" 3 "oral" "" "0.75-1 g x 3 oral" 15
|
||||
"AMX" "Amoxicillin" "standard_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 15
|
||||
"AMX" "Amoxicillin" "uncomplicated_uti" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 15
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "2 g + 0.2 g" 3 "iv" "" "(2 g amoxicillin + 0.2 g clavulanic acid) x 3 iv" 15
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "1 g + 0.2 g" 3 "iv" "" "(1 g amoxicillin + 0.2 g clavulanic acid) x 3-4 iv" 15
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "0.875 g + 0.125 g" 3 "oral" "" "(0.875 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 15
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g
clavulanic acid) x 3 oral" 15
|
||||
"AMC" "Amoxicillin/clavulanic acid" "uncomplicated_uti" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g
clavulanic acid) x 3 oral" 15
|
||||
"AMP" "Ampicillin" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv
" 15
|
||||
"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 15
|
||||
"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 15
|
||||
"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 15
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 15
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 15
|
||||
"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 15
|
||||
"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 15
|
||||
"AZA" "Aztreonam/avibactam" "standard_dosage" "2 g + 0.67 g" 1 "" "over 3 hours" "(2 g aztreonam + 0.67 g avibactam) x 1
followed by (1.5 g aztreonam + 0.5 g avibactam) x 4 iv over 3 hours" 15
|
||||
"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 6 "iv" "" "1.2 g (2 MU) x 6 iv" 15
|
||||
"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 15
|
||||
"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" 15
|
||||
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 15
|
||||
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 15
|
||||
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 15
|
||||
"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 15
|
||||
"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 15
|
||||
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 15
|
||||
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 15
|
||||
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 15
|
||||
"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 15
|
||||
"FPE" "Cefepime/enmetazobactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 4 hours" "(2 g cefepime + 0.5 g enmetazobactam) x 3 iv over 4 hours" 15
|
||||
"FPE" "Cefepime/enmetazobactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g cefepime + 0.5 g enmetazobactam) x 3 iv over 2 hours" 15
|
||||
"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 15
|
||||
"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 15
|
||||
"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 15
|
||||
"CTX" "Cefotaxime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 15
|
||||
"CTX" "Cefotaxime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 15
|
||||
"CPD" "Cefpodoxime" "standard_dosage" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 15
|
||||
"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 15
|
||||
"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 15
|
||||
"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 15
|
||||
"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 15
|
||||
"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 15
|
||||
"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 15
|
||||
"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 15
|
||||
"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 15
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 15
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam)
x 3 iv over 1 hour" 15
|
||||
"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 15
|
||||
"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 15
|
||||
"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 15
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 15
|
||||
"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 15
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 15
|
||||
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 15
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 15
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 15
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 15
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 15
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 15
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 15
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 15
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 15
|
||||
"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 15
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 15
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 15
|
||||
"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 15
|
||||
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 15
|
||||
"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv
with a loading dose of 9 MU" 15
|
||||
"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1
If needed, 0.5 g x 1 iv over 30 minutes on day 8" 15
|
||||
"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 15
|
||||
"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 15
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 15
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 15
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 15
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 15
|
||||
"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 15
|
||||
"DOR" "Doripenem" "standard_dosage" "0.5 g" 3 "iv" "over 1 hour" "0.5 g x 3 iv over 1 hour" 15
|
||||
"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 15
|
||||
"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 15
|
||||
"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 15
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 15
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 15
|
||||
"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 15
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv
(or 1 g x 6 iv)" 15
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 15
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 15
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 15
|
||||
"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 15
|
||||
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 15
|
||||
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 15
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam)
x 4 iv over 30 minutes" 15
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 15
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 15
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 15
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 15
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 15
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 15
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 15
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 15
|
||||
"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 15
|
||||
"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 15
|
||||
"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 15
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 15
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 15
|
||||
"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 15
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 15
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 15
|
||||
"NET" "Netilmicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 15
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 15
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 15
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 15
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 15
|
||||
"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv
over 3 hours" 15
|
||||
"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 15
|
||||
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 15
|
||||
"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv
by extended 3-hour infusion" 15
|
||||
"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 15
|
||||
"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam)
x 4 iv by extended 3-hour infusion" 15
|
||||
"TZP" "Piperacillin/tazobactam" "standard_dosage" "" 3 "iv" "" "
x 3 iv by extended 4-hour infusion" 15
|
||||
"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 15
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 15
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 15
|
||||
"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 15
|
||||
"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 15
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 15
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 15
|
||||
"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 15
|
||||
"TLV" "Telavancin" "standard_dosage" "10 mg/kg" 1 "iv" "over 1 hour" "10 mg/kg x 1 iv over 1 hour" 15
|
||||
"TEM" "Temocillin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 15
|
||||
"TEM" "Temocillin" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 15
|
||||
"TCY" "Tetracycline" "standard_dosage" "0.25 g" 4 "oral" "" "0.25 g x 4 oral" 15
|
||||
"TCC" "Ticarcillin/clavulanic acid" "high_dosage" "3 g + 0.1 g" 6 "iv" "" "(3 g ticarcillin + 0.1 g clavulanic acid) x 6 iv" 15
|
||||
"TCC" "Ticarcillin/clavulanic acid" "standard_dosage" "3 g + 0.1-0.2 g" 4 "iv" "" "(3 g ticarcillin + 0.1-0.2 g clavulanic acid) x 4 iv" 15
|
||||
"TGC" "Tigecycline" "standard_dosage" "0.1 g" "loading dose
followed by 50 mg x 2 iv" "0.1 g loading dose
followed by 50 mg x 2 iv" 15
|
||||
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 15
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 15
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral
or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 15
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 15
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral
or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 15
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 15
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv
or 2 g x 1 by continuous infusion" 15
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 14
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 14
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv
" 14
|
||||
"AMX" "Amoxicillin" "high_dosage" "0.75-1 g" 3 "oral" "" "0.75-1 g x 3 oral" 14
|
||||
"AMX" "Amoxicillin" "standard_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 14
|
||||
"AMX" "Amoxicillin" "uncomplicated_uti" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 14
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "2 g + 0.2 g" 3 "iv" "" "(2 g amoxicillin + 0.2 g clavulanic acid) x 3 iv" 14
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "1 g + 0.2 g" 3 "iv" "" "(1 g amoxicillin + 0.2 g clavulanic acid) x 3-4 iv" 14
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "0.875 g + 0.125 g" 3 "oral" "" "(0.875 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 14
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g
clavulanic acid) x 3 oral" 14
|
||||
"AMC" "Amoxicillin/clavulanic acid" "uncomplicated_uti" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g
clavulanic acid) x 3 oral" 14
|
||||
"AMP" "Ampicillin" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv
" 14
|
||||
"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 14
|
||||
"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 14
|
||||
"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 14
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 14
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 14
|
||||
"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 14
|
||||
"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 14
|
||||
"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 14
|
||||
"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 14
|
||||
"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" 14
|
||||
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 14
|
||||
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 14
|
||||
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 14
|
||||
"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 14
|
||||
"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 14
|
||||
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 14
|
||||
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 14
|
||||
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 14
|
||||
"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 14
|
||||
"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 14
|
||||
"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 14
|
||||
"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 14
|
||||
"CTX" "Cefotaxime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 14
|
||||
"CTX" "Cefotaxime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 14
|
||||
"CPD" "Cefpodoxime" "standard_dosage" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 14
|
||||
"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 14
|
||||
"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 14
|
||||
"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 14
|
||||
"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 14
|
||||
"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 14
|
||||
"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 14
|
||||
"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 14
|
||||
"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 14
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 14
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam)
x 3 iv over 1 hour" 14
|
||||
"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 14
|
||||
"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 14
|
||||
"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 14
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 14
|
||||
"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 14
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 14
|
||||
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 14
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 14
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 14
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 14
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 14
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 14
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 14
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 14
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 14
|
||||
"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 14
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 14
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 14
|
||||
"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 14
|
||||
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 14
|
||||
"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv
with a loading dose of 9 MU" 14
|
||||
"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1
If needed, 0.5 g x 1 iv over 30 minutes on day 8" 14
|
||||
"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 14
|
||||
"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 14
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 14
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 14
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 14
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 14
|
||||
"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 14
|
||||
"DOR" "Doripenem" "standard_dosage" "0.5 g" 3 "iv" "over 1 hour" "0.5 g x 3 iv over 1 hour" 14
|
||||
"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 14
|
||||
"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 14
|
||||
"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 14
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 14
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 14
|
||||
"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 14
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv
(or 1 g x 6 iv)" 14
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 14
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 14
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 14
|
||||
"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 14
|
||||
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 14
|
||||
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 14
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam)
x 4 iv over 30 minutes" 14
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 14
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 14
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 14
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 14
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 14
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 14
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 14
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 14
|
||||
"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 14
|
||||
"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 14
|
||||
"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 14
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 14
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 14
|
||||
"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 14
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 14
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 14
|
||||
"NET" "Netilmicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 14
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 14
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 14
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 14
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 14
|
||||
"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv
over 3 hours" 14
|
||||
"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 14
|
||||
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 14
|
||||
"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv
by extended 3-hour infusion" 14
|
||||
"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 14
|
||||
"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam)
x 4 iv by extended 3-hour infusion" 14
|
||||
"TZP" "Piperacillin/tazobactam" "standard_dosage" "" 3 "iv" "" "
x 3 iv by extended 4-hour infusion" 14
|
||||
"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 14
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 14
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 14
|
||||
"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 14
|
||||
"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 14
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 14
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 14
|
||||
"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 14
|
||||
"TLV" "Telavancin" "standard_dosage" "10 mg/kg" 1 "iv" "over 1 hour" "10 mg/kg x 1 iv over 1 hour" 14
|
||||
"TEM" "Temocillin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 14
|
||||
"TEM" "Temocillin" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 14
|
||||
"TCY" "Tetracycline" "standard_dosage" "0.25 g" 4 "oral" "" "0.25 g x 4 oral" 14
|
||||
"TCC" "Ticarcillin/clavulanic acid" "high_dosage" "3 g + 0.1 g" 6 "iv" "" "(3 g ticarcillin + 0.1 g clavulanic acid) x 6 iv" 14
|
||||
"TCC" "Ticarcillin/clavulanic acid" "standard_dosage" "3 g + 0.1-0.2 g" 4 "iv" "" "(3 g ticarcillin + 0.1-0.2 g clavulanic acid) x 4 iv" 14
|
||||
"TGC" "Tigecycline" "standard_dosage" "0.1 g" "loading dose
followed by 50 mg x 2 iv" "0.1 g loading dose
followed by 50 mg x 2 iv" 14
|
||||
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 14
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 14
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral
or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 14
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 14
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral
or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 14
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 14
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv
or 2 g x 1 by continuous infusion" 14
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 13.1
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13.1
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv
" 13.1
|
||||
"AMX" "Amoxicillin" "high_dosage" "0.75-1 g" 3 "oral" "" "0.75-1 g x 3 oral" 13.1
|
||||
"AMX" "Amoxicillin" "standard_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13.1
|
||||
"AMX" "Amoxicillin" "uncomplicated_uti" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13.1
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "2 g + 0.2 g" 3 "iv" "" "(2 g amoxicillin + 0.2 g clavulanic acid) x 3 iv" 13.1
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "1 g + 0.2 g" 3 "iv" "" "(1 g amoxicillin + 0.2 g clavulanic acid) x 3-4 iv" 13.1
|
||||
"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "0.875 g + 0.125 g" 3 "oral" "" "(0.875 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 13.1
|
||||
"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g
clavulanic acid) x 3 oral" 13.1
|
||||
"AMC" "Amoxicillin/clavulanic acid" "uncomplicated_uti" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g
clavulanic acid) x 3 oral" 13.1
|
||||
"AMP" "Ampicillin" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv
" 13.1
|
||||
"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13.1
|
||||
"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 13.1
|
||||
"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 13.1
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 13.1
|
||||
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 13.1
|
||||
"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13.1
|
||||
"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13.1
|
||||
"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 13.1
|
||||
"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 13.1
|
||||
"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" 13.1
|
||||
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 13.1
|
||||
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 13.1
|
||||
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 13.1
|
||||
"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 13.1
|
||||
"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 13.1
|
||||
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13.1
|
||||
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13.1
|
||||
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13.1
|
||||
"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 13.1
|
||||
"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 13.1
|
||||
"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 13.1
|
||||
"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 13.1
|
||||
"CTX" "Cefotaxime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13.1
|
||||
"CTX" "Cefotaxime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13.1
|
||||
"CPD" "Cefpodoxime" "standard_dosage" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 13.1
|
||||
"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 13.1
|
||||
"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 13.1
|
||||
"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 13.1
|
||||
"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 13.1
|
||||
"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13.1
|
||||
"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 13.1
|
||||
"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 13.1
|
||||
"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 13.1
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 13.1
|
||||
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam)
x 3 iv over 1 hour" 13.1
|
||||
"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 13.1
|
||||
"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 13.1
|
||||
"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 13.1
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 13.1
|
||||
"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13.1
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13.1
|
||||
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13.1
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13.1
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13.1
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 13.1
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13.1
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 13.1
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 13.1
|
||||
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 13.1
|
||||
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13.1
|
||||
"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13.1
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 13.1
|
||||
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 13.1
|
||||
"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13.1
|
||||
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 13.1
|
||||
"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv
with a loading dose of 9 MU" 13.1
|
||||
"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1
If needed, 0.5 g x 1 iv over 30 minutes on day 8" 13.1
|
||||
"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 13.1
|
||||
"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 13.1
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 13.1
|
||||
"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 13.1
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13.1
|
||||
"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 13.1
|
||||
"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 13.1
|
||||
"DOR" "Doripenem" "standard_dosage" "0.5 g" 3 "iv" "over 1 hour" "0.5 g x 3 iv over 1 hour" 13.1
|
||||
"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 13.1
|
||||
"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 13.1
|
||||
"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 13.1
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 13.1
|
||||
"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 13.1
|
||||
"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 13.1
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv
(or 1 g x 6 iv)" 13.1
|
||||
"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 13.1
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 13.1
|
||||
"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13.1
|
||||
"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13.1
|
||||
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 13.1
|
||||
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 13.1
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam)
x 4 iv over 30 minutes" 13.1
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 13.1
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 13.1
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 13.1
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 13.1
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13.1
|
||||
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 13.1
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 13.1
|
||||
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 13.1
|
||||
"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 13.1
|
||||
"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 13.1
|
||||
"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 13.1
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 13.1
|
||||
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 13.1
|
||||
"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 13.1
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 13.1
|
||||
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 13.1
|
||||
"NET" "Netilmicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13.1
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 13.1
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 13.1
|
||||
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 13.1
|
||||
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 13.1
|
||||
"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv
over 3 hours" 13.1
|
||||
"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13.1
|
||||
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 13.1
|
||||
"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv
by extended 3-hour infusion" 13.1
|
||||
"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 13.1
|
||||
"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam)
x 4 iv by extended 3-hour infusion" 13.1
|
||||
"TZP" "Piperacillin/tazobactam" "standard_dosage" "" 3 "iv" "" "
x 3 iv by extended 4-hour infusion" 13.1
|
||||
"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 13.1
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 13.1
|
||||
"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 13.1
|
||||
"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 13.1
|
||||
"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 13.1
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 13.1
|
||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 13.1
|
||||
"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 13.1
|
||||
"TLV" "Telavancin" "standard_dosage" "10 mg/kg" 1 "iv" "over 1 hour" "10 mg/kg x 1 iv over 1 hour" 13.1
|
||||
"TLT" "Telithromycin" "standard_dosage" "0.8 g" 1 "oral" "" "0.8 g x 1 oral" 13.1
|
||||
"TEM" "Temocillin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13.1
|
||||
"TEM" "Temocillin" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 13.1
|
||||
"TCY" "Tetracycline" "standard_dosage" "0.25 g" 4 "oral" "" "0.25 g x 4 oral" 13.1
|
||||
"TCC" "Ticarcillin/clavulanic acid" "high_dosage" "3 g + 0.1 g" 6 "iv" "" "(3 g ticarcillin + 0.1 g clavulanic acid) x 6 iv" 13.1
|
||||
"TCC" "Ticarcillin/clavulanic acid" "standard_dosage" "3 g + 0.1-0.2 g" 4 "iv" "" "(3 g ticarcillin + 0.1-0.2 g clavulanic acid) x 4 iv" 13.1
|
||||
"TGC" "Tigecycline" "standard_dosage" "0.1 g" "loading dose
followed by 50 mg x 2 iv" "0.1 g loading dose
followed by 50 mg x 2 iv" 13.1
|
||||
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13.1
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 13.1
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral
or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 13.1
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13.1
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral
or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 13.1
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13.1
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv
or 2 g x 1 by continuous infusion" 13.1
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 12
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 12
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv" 12
|
||||
@ -273,7 +533,6 @@
|
||||
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 12
|
||||
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 12
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 12
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 12
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 12
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 12
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 12
|
||||
@ -331,7 +590,6 @@
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 12
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 12
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 11
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 11
|
||||
@ -358,6 +616,8 @@
|
||||
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 11
|
||||
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 11
|
||||
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 11
|
||||
"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
|
||||
"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
|
||||
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
|
||||
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
|
||||
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
|
||||
@ -385,8 +645,6 @@
|
||||
"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
|
||||
"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
|
||||
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
|
||||
"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
|
||||
"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
|
||||
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
|
||||
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11
|
||||
@ -440,7 +698,6 @@
|
||||
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 11
|
||||
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 11
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 11
|
||||
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 11
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 11
|
||||
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 11
|
||||
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 11
|
||||
@ -500,5 +757,4 @@
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 11
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 11
|
||||
|
||||
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@ -1 +1 @@
|
||||
cf0833ed69cfd2b6afb5b6d18cf2df26
|
||||
ac97b111185490535890ea6df22f9a4f
|
||||
|
||||
@ -783,6 +783,193 @@ genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoin
|
||||
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
|
||||
|
||||
|
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|
@ -1 +1 @@
|
||||
cbf15fce0784e20b87aaa33b88b97f3f
|
||||
4862699a91a23f2fe6a790ac277697d0
|
||||
|
||||
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data-raw/v_15.0_Breakpoint_Tables.xlsx
Normal file
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data-raw/v_15.0_Breakpoint_Tables.xlsx
Normal file
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data/dosage.rda
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data/dosage.rda
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2
index.md
2
index.md
@ -22,7 +22,7 @@
|
||||
|
||||
### Introduction
|
||||
|
||||
The `AMR` package is a peer-reviewed, [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](./authors.html) from around the globe are continually helping us to make this a successful and durable project!
|
||||
The `AMR` package is a peer-reviewed, [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of [many different researchers](./authors.html) from around the globe to make this a successful and durable project!
|
||||
|
||||
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
|
||||
|
||||
|
||||
@ -8,7 +8,7 @@
|
||||
\alias{ab_selector}
|
||||
\title{Deprecated Functions, Arguments, or Datasets}
|
||||
\format{
|
||||
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.
|
||||
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
|
||||
}
|
||||
\usage{
|
||||
ab_class(...)
|
||||
|
||||
@ -16,7 +16,7 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
|
||||
\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()}}.
|
||||
\item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
|
||||
\item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
|
||||
\item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2024"}. Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).
|
||||
\item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2025"}. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).
|
||||
\item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
|
||||
\item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
|
||||
\item \code{AMR_substitute_missing_r_breakpoint} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that missing R breakpoints must be substituted with \code{"R"} - the default is \code{FALSE}.
|
||||
|
||||
@ -182,14 +182,14 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
|
||||
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
|
||||
\item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
|
||||
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
|
||||
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
|
||||
\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
|
||||
\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
|
||||
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
|
||||
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
|
||||
\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)
|
||||
\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)
|
||||
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
|
||||
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
|
||||
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
|
||||
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
|
||||
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
|
||||
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)
|
||||
|
||||
@ -4,9 +4,9 @@
|
||||
\name{antimicrobials}
|
||||
\alias{antimicrobials}
|
||||
\alias{antivirals}
|
||||
\title{Data Sets with 616 Antimicrobial Drugs}
|
||||
\title{Data Sets with 617 Antimicrobial Drugs}
|
||||
\format{
|
||||
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 496 observations and 14 variables:}{
|
||||
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 497 observations and 14 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. \emph{\strong{This is a unique identifier.}}
|
||||
\item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
|
||||
|
||||
@ -46,7 +46,7 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati
|
||||
This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
|
||||
}
|
||||
\details{
|
||||
To interpret MIC values as SIR values, use \code{\link[=as.sir]{as.sir()}} on MIC values. It supports guidelines from EUCAST (2011-2024) and CLSI (2011-2024).
|
||||
To interpret MIC values as SIR values, use \code{\link[=as.sir]{as.sir()}} on MIC values. It supports guidelines from EUCAST (2011-2025) and CLSI (2011-2025).
|
||||
|
||||
This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
|
||||
|
||||
|
||||
@ -16,11 +16,11 @@
|
||||
\source{
|
||||
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
|
||||
\itemize{
|
||||
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
|
||||
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
|
||||
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
|
||||
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
|
||||
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
|
||||
\item \strong{CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
|
||||
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
|
||||
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2025, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
|
||||
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2025, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
|
||||
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2025, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
|
||||
}
|
||||
}
|
||||
\usage{
|
||||
@ -84,7 +84,7 @@ sir_interpretation_history(clean = FALSE)
|
||||
|
||||
\item{ab}{A vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
|
||||
|
||||
\item{guideline}{A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see \emph{Details}. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.}
|
||||
\item{guideline}{A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see \emph{Details}. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.}
|
||||
|
||||
\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
|
||||
|
||||
@ -146,9 +146,9 @@ Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC
|
||||
|
||||
These breakpoints are currently implemented:
|
||||
\itemize{
|
||||
\item For \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024;
|
||||
\item For \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024;
|
||||
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
|
||||
\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
|
||||
\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
|
||||
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
|
||||
}
|
||||
|
||||
All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
|
||||
@ -196,9 +196,14 @@ your_data \%>\% mutate_if(is.disk, as.sir, host = "column_with_animal_species",
|
||||
|
||||
\subsection{Supported Guidelines}{
|
||||
|
||||
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024, and for \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024.
|
||||
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:
|
||||
\itemize{
|
||||
\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
|
||||
\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
|
||||
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
|
||||
}
|
||||
|
||||
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2024"} or \code{"CLSI 2024"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.
|
||||
The \code{guideline} argument must be set to e.g., \code{"EUCAST 2025"} or \code{"CLSI 2025"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.
|
||||
|
||||
You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
|
||||
|
||||
|
||||
@ -5,7 +5,7 @@
|
||||
\alias{clinical_breakpoints}
|
||||
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
|
||||
\format{
|
||||
A \link[tibble:tibble]{tibble} with 34 376 observations and 14 variables:
|
||||
A \link[tibble:tibble]{tibble} with 40 217 observations and 14 variables:
|
||||
\itemize{
|
||||
\item \code{guideline}\cr Name of the guideline
|
||||
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
|
||||
@ -20,7 +20,7 @@ A \link[tibble:tibble]{tibble} with 34 376 observations and 14 variables:
|
||||
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
|
||||
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA}
|
||||
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
|
||||
\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 24 breakpoints.
|
||||
\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 48 breakpoints.
|
||||
}
|
||||
}
|
||||
\usage{
|
||||
@ -31,9 +31,9 @@ Data set containing clinical breakpoints to interpret MIC and disk diffusion to
|
||||
|
||||
These breakpoints are currently implemented:
|
||||
\itemize{
|
||||
\item For \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024;
|
||||
\item For \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024;
|
||||
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2012-2024 and CLSI 2022-2024.
|
||||
\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
|
||||
\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
|
||||
\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
|
||||
}
|
||||
|
||||
Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
|
||||
|
||||
@ -92,16 +92,16 @@ These 35 antimicrobial groups are allowed in the rules (case-insensitive) and ca
|
||||
\item aminopenicillins\cr(amoxicillin and ampicillin)
|
||||
\item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
|
||||
\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
|
||||
\item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
|
||||
\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
|
||||
\item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
|
||||
\item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
|
||||
\item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
|
||||
\item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
|
||||
\item cephalosporins\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
|
||||
\item cephalosporins_1st\cr(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)
|
||||
\item cephalosporins_2nd\cr(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)
|
||||
\item cephalosporins_3rd\cr(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)
|
||||
\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
|
||||
\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
|
||||
\item cephalosporins_5th\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)
|
||||
\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
|
||||
\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
|
||||
\item fluoroquinolones\cr(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
|
||||
\item glycopeptides\cr(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)
|
||||
\item glycopeptides_except_lipo\cr(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
|
||||
|
||||
@ -5,17 +5,17 @@
|
||||
\alias{dosage}
|
||||
\title{Data Set with Treatment Dosages as Defined by EUCAST}
|
||||
\format{
|
||||
A \link[tibble:tibble]{tibble} with 503 observations and 9 variables:
|
||||
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{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", or "oral"
|
||||
\item \code{administration}\cr Route of administration, either "", "im", "iv", or "oral"
|
||||
\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 13, 12, or 11
|
||||
\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
|
||||
}
|
||||
}
|
||||
\usage{
|
||||
|
||||
@ -21,12 +21,12 @@ Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility test
|
||||
\usage{
|
||||
eucast_rules(x, col_mo = NULL, info = interactive(),
|
||||
rules = getOption("AMR_eucastrules", default = c("breakpoints",
|
||||
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 14,
|
||||
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
|
||||
version_expected_phenotypes = 1.2, version_expertrules = 3.3,
|
||||
ampc_cephalosporin_resistance = NA, only_sir_columns = FALSE,
|
||||
custom_rules = NULL, overwrite = FALSE, ...)
|
||||
|
||||
eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
|
||||
eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{A data set with antimicrobials columns, such as \code{amox}, \code{AMX} and \code{AMC}.}
|
||||
@ -39,7 +39,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
|
||||
|
||||
\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 "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 "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".}
|
||||
|
||||
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".}
|
||||
|
||||
@ -57,7 +57,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
|
||||
|
||||
\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", or "oral".}
|
||||
\item{administration}{Route of administration, either "", "im", "iv", or "oral".}
|
||||
}
|
||||
\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.
|
||||
|
||||
@ -3,9 +3,9 @@
|
||||
\docType{data}
|
||||
\name{microorganisms.codes}
|
||||
\alias{microorganisms.codes}
|
||||
\title{Data Set with 4 971 Common Microorganism Codes}
|
||||
\title{Data Set with 5 063 Common Microorganism Codes}
|
||||
\format{
|
||||
A \link[tibble:tibble]{tibble} with 4 971 observations and 2 variables:
|
||||
A \link[tibble:tibble]{tibble} with 5 063 observations and 2 variables:
|
||||
\itemize{
|
||||
\item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}}
|
||||
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
|
||||
|
||||
@ -172,7 +172,7 @@ Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC
|
||||
\details{
|
||||
\subsection{The \verb{scale_*_mic()} Functions}{
|
||||
|
||||
The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.
|
||||
The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as \code{>=}) if desired. Missing intermediate log2 levels will be plotted too.
|
||||
}
|
||||
|
||||
\subsection{The \verb{scale_*_sir()} Functions}{
|
||||
@ -193,7 +193,7 @@ This package contains more functions that extend the \code{ggplot2} package, to
|
||||
|
||||
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
|
||||
|
||||
For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
|
||||
For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2025, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
|
||||
@ -33,7 +33,7 @@ These functions can be used for generating random MIC values and disk diffusion
|
||||
\details{
|
||||
The base \R function \code{\link[=sample]{sample()}} is used for generating values.
|
||||
|
||||
Generated values are based on the EUCAST 2024 guideline as implemented in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
|
||||
Generated values are based on the EUCAST 2025 guideline as implemented in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
|
||||
}
|
||||
\examples{
|
||||
random_mic(25)
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user