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Set the order of sites in as.sir(), and add the veterinary sites
Sites now go from systemic, IV, meningitis, endocarditis, pneumonia and mastitis to UTI, topical and screen. A breakpoint without a site takes the position of "other", as both mean any site that is not listed next to it. A second site breaks a tie on the first one. The veterinary sites are now fixed codes as well: mastitis (includes Mammary gland), respiratory, metritis, genital, soft tissue and wounds (includes Abscesses). Sites that are part of each other do not contradict. site = "other" now leaves out every breakpoint limited to an indication, and prefers a breakpoint without a site. A rebuild of clinical_breakpoints with this order gives the same data, so the same blocking rows stay.
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dr. M.S. (Matthijs) Berends committed
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@@ -9,11 +9,11 @@ It also adds a `site` argument to `as.sir()`, stores EUCAST MIC breakpoints exac
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* `include_screening` in `as.sir()` now defaults to `NULL`, using screening breakpoints for screening agents only. `include_screening = FALSE` now also returns `NA`, with a note, for a screening agent (#328)
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* EUCAST's breakpoints in brackets are no longer in `clinical_breakpoints`. They were blocking rows, so `as.sir()` can now use PK/PD breakpoints or the breakpoints of a broader taxon instead, e.g., for aminoglycosides in EUCAST 2020-2023. They stay available in [`data-raw/breakpoints_eucast_raw.csv`](https://github.com/msberends/AMR/blob/main/data-raw/breakpoints_eucast_raw.csv) (#327)
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* With unknown `uti`, a blocking row without UTI status no longer overrides a UTI breakpoint at the same taxonomic level, e.g., amikacin in *Acinetobacter* now gives S or R instead of `NA`, which is noted in `sir_interpretation_history()`. Use `uti = FALSE` to prevent this
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* If several breakpoints fit and no `site` is set, `as.sir()` now takes the one for the most systemic site, instead of the first one in the data set. Use `site` to choose another one
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* If several breakpoints fit and no `site` is set, `as.sir()` now takes the one for the most systemic site, instead of the first one in the data set. This means, e.g., that a meningitis breakpoint now precedes a non-meningitis breakpoint, such as for benzylpenicillin in *S. pneumoniae*. Use `site` to choose another one
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### New
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* **Site of infection**
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* `as.sir()` gained the argument `site`, in fixed codes such as `"meningitis"`, `"iv"` and `"uti"`, which can also be a column name. A breakpoint for a contradicting site is left out, a breakpoint without a site still applies, and the result is `NA` if only contradicting sites are available, without using PK/PD breakpoints. `uti = TRUE` stays available and equals `site = "uti"`
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* `as.sir()` gained the argument `site`, in fixed codes such as `"meningitis"`, `"iv"`, `"uti"` and, for animals, `"mastitis"` and `"respiratory"`, which can also be a column name. A breakpoint for a contradicting site is left out, a breakpoint without a site still applies, and the result is `NA` if only contradicting sites are available, without using PK/PD breakpoints. `"other"` takes a breakpoint for other infections or without a site, and leaves out those limited to an indication. `uti = TRUE` stays available and equals `site = "uti"`
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* `sir_interpretation_history()` now holds the site of the breakpoint used, and notes every assumption about sites
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* **Screening agents**
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* 13 screening agents in the `antimicrobials` data set: `CHL-S`, `CIP-S`, `COL-S`, `ERY-S`, `FUS-S`, `GEN-S`, `LVX-S`, `MUP-S`, `NEO-S`, `OFX-S`, `RTP-S`, `STR1-S` and `TOB-S` (#328)
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@@ -41,7 +41,7 @@ VALID_SIR_LEVELS <- c("S", "SDD", "I", "R", "NI", "WT", "NWT", "NS")
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#' @param uti (Urinary Tract Infection) a vector (or column name) with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.sir()] on a [data.frame], this can also be a column containing [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. If `uti` is `NA` (unknown), non-UTI breakpoints are preferred, and UTI breakpoints are only used if no non-UTI breakpoints exist for the drug-bug combination, which is noted in [sir_interpretation_history()]. With `uti = FALSE`, UTI breakpoints are never used. See *Examples*.
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#' @inheritParams first_isolate
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#' @param guideline A guideline name (or column name) to use for SIR interpretation. Defaults to `r AMR::clinical_breakpoints$guideline[1]` (the latest implemented EUCAST guideline in the [AMR::clinical_breakpoints] data set), but can be set with the package option [`AMR_guideline`][AMR-options]. Currently supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.
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#' @param site The site or route that the isolate is interpreted for: a [character] vector or a column name, in the fixed codes `"meningitis"`, `"non-meningitis"`, `"endocarditis"`, `"non-endocarditis"`, `"pneumonia"`, `"non-pneumonia"`, `"systemic"`, `"extraintestinal"`, `"other"`, `"intestinal"`, `"skin"`, `"inhaled"`, `"oral"`, `"prophylaxis"`, `"uti"`, `"iv"` and `"topical"`, which can be combined with a comma, e.g. `"iv, meningitis"`. If `site` is `NA` (default), any breakpoint matching all other criteria can apply, taken from most to least systemic site in the order just given, with `"iv"` directly after `"endocarditis"`; a breakpoint without a site is taken after `"other"`. If `site` is set, a breakpoint for a contradicting site is left out, e.g. `"meningitis"` leaves out `Non-meningitis`, while a breakpoint without a site still applies. The result is `NA` if only contradicting sites are available, also when PK/PD breakpoints exist. All choices are noted in [sir_interpretation_history()].
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#' @param site The site or route that the isolate is interpreted for: a [character] vector or a column name, in the fixed codes `"systemic"`, `"iv"`, `"meningitis"`, `"endocarditis"`, `"pneumonia"`, `"mastitis"`, `"respiratory"`, `"metritis"`, `"genital"`, `"intestinal"`, `"other"`, `"non-meningitis"`, `"non-endocarditis"`, `"non-pneumonia"`, `"extraintestinal"`, `"soft tissue"`, `"skin"`, `"wounds"`, `"inhaled"`, `"oral"`, `"prophylaxis"`, `"uti"` and `"topical"`, which can be combined with a comma, e.g. `"iv, meningitis"`. If `site` is `NA` (default), any breakpoint matching all other criteria can apply, taken from most to least systemic site in the order just given; a breakpoint without a site takes the position of `"other"`, as both mean any site that is not listed next to it. If `site` is set, a breakpoint for a contradicting site is left out, e.g. `"meningitis"` leaves out `Non-meningitis`, while a breakpoint without a site still applies. `"other"` leaves out every breakpoint limited to an indication, and prefers a breakpoint without a site. Related sites do not contradict each other: `"pneumonia"` and `"respiratory"`, `"metritis"` and `"genital"`, and `"soft tissue"`, `"skin"` and `"wounds"`. The code `"mastitis"` includes `Mammary gland`, and `"wounds"` includes `Abscesses`. The result is `NA` if only contradicting sites are available, also when PK/PD breakpoints exist. All choices are noted in [sir_interpretation_history()].
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#' @param capped_mic_handling A [character] string that controls how MIC values with a cap (i.e., starting with `<`, `<=`, `>`, or `>=`) are interpreted. Supports the following options:
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#'
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#' `"none"`
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@@ -1257,23 +1257,29 @@ convert_host <- function(x, lang = NULL) {
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x_out
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}
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# Sites in clinical_breakpoints and in the `site` argument, from most to least systemic. Every value in the `site` column consists of one or more of these, see sir_site_tokens(). A breakpoint without a site is taken right after "other".
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SIR_SITE_ORDER <- c("meningitis", "endocarditis", "iv", "pneumonia", "systemic", "non-meningitis", "non-endocarditis", "non-pneumonia", "extraintestinal", "other", NA, "intestinal", "skin", "inhaled", "oral", "prophylaxis", "uti", "topical", "screen")
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# Sites in clinical_breakpoints and in the `site` argument, from most to least systemic. Every value in the `site` column consists of one or more of these, see sir_site_tokens(). A breakpoint without a site takes the same position as "other": both mean any site that is not listed next to it. That single position gives both meanings: below "meningitis", as "other" then means non-meningitis, and above "uti", as "other" then means non-UTI.
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SIR_SITE_ORDER <- c("systemic", "iv", "meningitis", "endocarditis", "pneumonia", "mastitis", "respiratory", "metritis", "genital", "intestinal", "other", "non-meningitis", "non-endocarditis", "non-pneumonia", "extraintestinal", "soft tissue", "skin", "wounds", "inhaled", "oral", "prophylaxis", "uti", "topical", "screen")
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# all notations in the `site` column of clinical_breakpoints and of the `site` argument
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SIR_SITE_PATTERNS <- c(
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systemic = "systemic( infections)?",
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iv = "(iv|intravenous|parenteral)",
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meningitis = "meningitis",
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endocarditis = "endocarditis",
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iv = "(iv|intravenous|parenteral)",
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pneumonia = "((community-acquired )?pneumonia)",
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systemic = "systemic( infections)?",
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mastitis = "(mastitis|mammary gland)",
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respiratory = "respiratory",
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metritis = "metritis",
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genital = "genital",
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intestinal = "intestinal",
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other = "other( infections)?",
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`non-meningitis` = "non-meningitis",
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`non-endocarditis` = "non-endocarditis",
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`non-pneumonia` = "non-pneumonia",
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extraintestinal = "extraintestinal",
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other = "other( infections)?",
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intestinal = "intestinal",
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`soft tissue` = "soft tissue",
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skin = "skin",
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wounds = "(wounds?|abscess(es)?)",
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inhaled = "inhaled",
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oral = "oral",
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prophylaxis = "prophylaxis",
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@@ -1281,6 +1287,8 @@ SIR_SITE_PATTERNS <- c(
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topical = "topical",
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screen = "screen"
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)
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# sites of which one is part of the other, or which are hard to tell apart, and so do not contradict each other
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SIR_SITE_RELATED <- list(c("pneumonia", "respiratory"), c("metritis", "genital"), c("soft tissue", "skin", "wounds"))
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# parts of the `site` column that do not say anything about where a breakpoint applies
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SIR_SITE_NOT_A_SITE <- c("liposomal", "investigational agent")
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@@ -1315,6 +1323,11 @@ sir_site_normalise <- function(x) {
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normalised[match(x, unique_x)]
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}
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# the sites of the user, with the sites that are related to them
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sir_site_expand <- function(tokens) {
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unique(c(tokens, unlist(SIR_SITE_RELATED[vapply(SIR_SITE_RELATED, function(related) any(tokens %in% related), logical(1))])))
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}
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# whether a breakpoint with these sites does not contradict the sites set by the user
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sir_site_fits <- function(breakpoint_tokens, user_tokens) {
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negated <- function(tokens) sub("^non-", "", tokens[startsWith(tokens, "non-")])
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@@ -1325,10 +1338,13 @@ sir_site_fits <- function(breakpoint_tokens, user_tokens) {
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if (("systemic" %in% breakpoint_tokens && "uti" %in% user_tokens) || ("uti" %in% breakpoint_tokens && "systemic" %in% user_tokens)) {
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return(FALSE)
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}
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groups <- list(
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route = c("iv", "oral", "topical", "inhaled"),
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indication = c("meningitis", "endocarditis", "pneumonia", "uti", "intestinal", "extraintestinal", "skin", "prophylaxis")
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)
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indications <- c("meningitis", "endocarditis", "pneumonia", "mastitis", "respiratory", "metritis", "genital", "uti", "intestinal", "extraintestinal", "soft tissue", "skin", "wounds", "prophylaxis")
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# "other" is any site that is not listed, so it contradicts every breakpoint that is limited to an indication
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if ("other" %in% user_tokens && !any(user_tokens %in% indications) && any(breakpoint_tokens %in% indications)) {
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return(FALSE)
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}
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groups <- list(route = c("iv", "oral", "topical", "inhaled"), indication = indications)
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user_tokens <- sir_site_expand(user_tokens)
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for (group in groups) {
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from_user <- intersect(user_tokens, group)
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from_breakpoint <- intersect(breakpoint_tokens, group)
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@@ -1339,13 +1355,19 @@ sir_site_fits <- function(breakpoint_tokens, user_tokens) {
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TRUE
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}
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# the position in SIR_SITE_ORDER, of the most systemic site if there are more
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# whether a breakpoint holds one of the sites that the user set, where "other" is also a breakpoint without a site
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sir_site_given <- function(breakpoint_tokens, user_tokens) {
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any(breakpoint_tokens %in% sir_site_expand(user_tokens)) || ("other" %in% user_tokens && length(breakpoint_tokens) == 0)
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}
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# The position in SIR_SITE_ORDER, of the most systemic site if there are more. The other sites are the decimals, so that "Intravenous, Meningitis" comes before "Intravenous, Non-meningitis".
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sir_site_rank <- function(x) {
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tokens <- sir_site_tokens(x)
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if (length(tokens) == 0) {
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return(match(NA_character_, SIR_SITE_ORDER))
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return(as.double(match("other", SIR_SITE_ORDER)))
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}
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min(match(tokens, SIR_SITE_ORDER))
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ranks <- sort(match(tokens, SIR_SITE_ORDER))
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sum(ranks / 100^(seq_along(ranks) - 1))
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}
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# Whether a blocking row has any effect, which is the definition used for clinical_breakpoints (#326): as.sir() must give another result without it. This takes one row number and the rows of one guideline, agent and method.
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@@ -2081,7 +2103,7 @@ as_sir_method <- function(method_short,
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# sort on taxonomic rank first (this will e.g. prefer 'species' breakpoints over 'order' breakpoints), within a rank on the site that the user set, then on whether it is a blocking row, on most to least systemic site, and finally on UTI
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site_tokens_current <- if (is.na(site_current)) character(0) else strsplit(site_current, ",", fixed = TRUE)[[1]]
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site_not_given <- vapply(breakpoints_current$site, function(s) !any(sir_site_tokens(s) %in% site_tokens_current), logical(1), USE.NAMES = FALSE)
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site_not_given <- vapply(breakpoints_current$site, function(s) !sir_site_given(sir_site_tokens(s), site_tokens_current), logical(1), USE.NAMES = FALSE)
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if (length(site_tokens_current) == 0) {
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site_not_given[] <- FALSE
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}
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@@ -15,7 +15,7 @@ Overview:
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- Generates **antibiograms** - WISCA for empiric coverage estimates, or
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traditional/syndromic for AMR surveillance
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- Provides the **full microbiological taxonomy** of ~103 000 distinct
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species and extensive info of ~630 antimicrobial drugs
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species and extensive info of ~640 antimicrobial drugs
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- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
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veterinary breakpoints, and ECOFFs, for MIC and disk zone
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interpretation
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@@ -140,11 +140,13 @@
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"CED" 38103 "Cephradine" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "NA" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephra,cfra,cfrd" "anspor,cefradin,cefradina,cefradine,cefradinum,cekodin,cephradin,ecosporina,eskacef,infexin,megacef,sefril,velocef,velosef" "168-5,169-3,170-1,171-9,18902-7,55646-4"
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"CTO" 71402 "Cetocycline" "Tetracyclines" "NA" "NA" "cetocyline,cetotetrine,chelocardin" "NA"
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"CHL" 5959 "Chloramphenicol" "Phenicols" "D06AX02,D10AF03,G01AA05,J01BA01,QD06AX02,QD10AF03,QG01AA05,QJ01BA01,QJ51BA01,QS01AA01,QS02AA01,QS03AA08,S01AA01,S02AA01,S03AA08" "Amphenicols" "Amphenicols" "c,chl,chlo,chlora,cl" "alficetyn,ambofen,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocide,chlorocin,chlorocol,chlorofair,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chlorovules,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextramycin,dextromycetin,doctamicina,econochlor,embacetin,emetren,enteromycetin,erbaplast,ertilen,farmicetina,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,intramycetin,isicetin,ismicetina,isophenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromisan,loromisin,mastiphen,maybridge,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,petnamycetin,quemicetina,rivomycin,romphenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,viceton" 3 "g" 3 "g" "15101-9,16603-3,16604-1,172-7,173-5,174-3,175-0,18903-5,25247-8,29214-4,29346-4,29347-2,3455-3,7001-1"
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"CHL-S" "Chloramphenicol screening test" "Phenicols" "" "chl screen" "" ""
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"CTE" 54675777 "Chlortetracycline" "Tetracyclines" "A01AB21,D06AA02,J01AA03,QA01AB21,QD06AA02,QG51AA08,QJ01AA03,QJ51AA03,QS01AA02,S01AA02" "Tetracyclines" "Tetracyclines" "chltet" "acronize,alexomycin,aueromycin,aureocarmyl,aureociclina,aureocina,aureocycline,aureomycin,aureomykoin,aurofac,auxeomycin,biomitsin,biomycin,chlormax,chlorotetracycline,chlortetracyclinum,chrysomykine,clorocipan,clortetraciclina,clortetrin,declomycin,declostatin,deganol,demeclor,demeplus,demetraciclina,demetraclin,detracin,detravis,diuciclin,duomycin,elkamicina,flamycin,isphamycin,ledermicina,ledermycin,ledermycine,mexocine,novotriclina,pennchlor,perciclina,periciclina,sumaclina,uromycin,veraciclina" 1 "g" "176-8,177-6,178-4,179-2,18904-3,55655-5,87600-3"
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"CIC" 19003 "Ciclacillin" "Penicillins,Beta-lactams" "NA" "cyclac" "bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital" "NA"
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||||
"CIX" "Ciclopirox" "Antifungals" "D01AE14,G01AX12,QD01AE14,QG01AX12" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "NA" "NA"
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"CIN" 2762 "Cinoxacin" "Quinolones" "J01MB06,QJ01MB06" "Quinolone antibacterials" "Other quinolones" "cino,cinoxa,cnox" "cinobac,cinobactin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm" 1 "g" "180-0,181-8,182-6,183-4,18905-0,55656-3"
|
||||
"CIP" 2764 "Ciprofloxacin" "Fluoroquinolones,Quinolones" "J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07" "Quinolone antibacterials" "Fluoroquinolones" "ci,cip,cipr,ciprof,cp" "alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,zumaflox" 1 "g" 0.8 "g" "101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9"
|
||||
"CIP-S" "Ciprofloxacin screening test" "Fluoroquinolones,Quinolones" "" "cip screen" "" ""
|
||||
"CIM" "Ciprofloxacin/metronidazole" "Fluoroquinolones,Quinolones" "J01RA10,QJ01RA10" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
"CIO" "Ciprofloxacin/ornidazole" "Fluoroquinolones,Quinolones" "J01RA12,QJ01RA12" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
"CIT" "Ciprofloxacin/tinidazole" "Fluoroquinolones,Quinolones" "J01RA11,QJ01RA11" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
@@ -161,6 +163,7 @@
|
||||
"CTR" 2812 "Clotrimazole" "Antifungals" "A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90" "clot" "alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole" "10653-4,10654-2,18909-2,54177-1,55663-9"
|
||||
"CLO" 6098 "Cloxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF02,QJ01CF02,QJ51CF02,QS01AA90" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,cloxac" "ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen" 2 "g" 2 "g" "16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
|
||||
"COL" 5311054 "Colistin" "Polymyxins" "A07AA10,J01XB01,QA07AA10,QJ01XB01,QJ51XB01" "Other antibacterials" "Polymyxins" "cl,coli,colist,cs,cst,ct" "colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,totazina" 9 "MU" 9 "MU" "16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6"
|
||||
"COL-S" "Colistin screening test" "Polymyxins" "" "col screen" "" ""
|
||||
"COP" "Colistin/polysorbate" "Other" "NA" "NA" "NA" "NA"
|
||||
"CYC" 6234 "Cycloserine" "Oxazolidinones" "J04AB01,QJ04AB01" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl,cyclos" "cicloserina,closina,cyclorin,cycloserin,cycloserinum,farmiserina,levcicloserina,levcycloserine,levcycloserinum,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,wasserina" 0.75 "g" "16702-3,18914-2,212-1,213-9,214-7,215-4,23608-3,25207-2,25208-0,25209-8,25251-0,3519-6,55667-0"
|
||||
"DAL" 23724878 "Dalbavancin" "Lipoglycopeptides,Glycopeptides,Peptides" "J01XA04,QJ01XA04" "Other antibacterials" "Glycopeptide antibacterials" "dalb,dalbav" "dalbavancina,dalvance,xydalba,zeven" 1.5 "g" "41688-3,41689-1,41690-9,41734-5"
|
||||
@@ -187,6 +190,7 @@
|
||||
"ERV" 54726192 "Eravacycline" "Tetracyclines" "J01AA13,QJ01AA13" "Tetracyclines" "Tetracyclines" "erav" "xerava" 0.14 "g" "100049-6,85423-2,93767-2"
|
||||
"ETP" 150610 "Ertapenem" "Carbapenems,Beta-lactams" "J01DH03,QJ01DH03" "Other beta-lactam antibacterials" "Carbapenems" "erta,ertape,etp" "ertapenemsalt,invanz" 1 "g" "101486-9,35799-6,35800-2,35801-0,35802-8"
|
||||
"ERY" 12560 "Erythromycin" "Macrolides" "D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17" "Macrolides, lincosamides and streptogramins" "Macrolides" "e,em,ery,ery32,eryt,eryth" "abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid" 2 "g" 1 "g" "100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
|
||||
"ERY-S" "Erythromycin screening test" "Macrolides" "" "ery screen" "" ""
|
||||
"ETH" 14052 "Ethambutol" "Antimycobacterials" "J04AK02,QJ04AK02" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "emb,etha,ethamb" "aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol" 1.2 "g" 1.2 "g" "100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
|
||||
"ETI" 456476 "Ethambutol/isoniazid" "Antimycobacterials" "J04AM03,QJ04AM03" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
|
||||
"ETI1" 2761171 "Ethionamide" "Antimycobacterials" "J04AD03,QJ04AD03" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi,ethion" "aethionamidum,aetina,aetiva,amidazin,amidazine,atina,ethimide,ethina,ethinamide,ethionamidum,ethioniamide,ethylisothiamide,ethyonomide,etimid,etiocidan,etionamid,etionamida,etionamide,etioniamid,etionid,etionizin,etionizina,etionizine,fatoliamid,iridocin,iridozin,isothin,isotiamida,itiocide,nicotion,nisotin,nizotin,rigenicid,sertinon,teberus,thianid,thianide,thioamide,thiodine,thiomid,thioniden,tianid,tiomid,trecator,trekator,trescatyl,trescazide,tubenamide,tubermin,tuberoid,tuberoson" 0.75 "g" "16099-4,16845-0,18922-5,20382-8,23617-4,25183-5,25196-7,25198-3,25231-2,41693-3,42647-8,42648-6,7011-0,96110-2"
|
||||
@@ -211,11 +215,13 @@
|
||||
"FUR" 6870646 "Furazidin" "Nitrofurans" "J01XE03,QJ01XE03" "Other antibacterials" "Nitrofuran derivatives" "NA" "akritoin,furagin,furaginum,furamag,furazidine,hydantoin" 0.3 "g" "NA"
|
||||
"FRZ" 5323714 "Furazolidone" "Nitrofurans" "G01AX06,QG01AX06,QJ01XE90" "furazo" "bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furanzolidone,furaxon,furaxone,furazolidine,furazolidon,furazolidona,furazolidonum,furazolum,furidon,furmethoxadone,furovag,furoxal,furoxane,furoxon,furoxone,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofuradoxon,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn" "69574-2,87794-4"
|
||||
"FUS" 3000226 "Fusidic acid" "Fusidanes" "D06AX01,D09AA02,J01XC01,QD06AX01,QD09AA02,QJ01XC01,QS01AA13,S01AA13" "Other antibacterials" "Steroid antibacterials" "fa,fusaci,fusi" "flucidin,fucidate,fucidina,fucidine,fucithalmic,fusidate,fusidicacid,fusidin,fusidine,taksta" 1.5 "g" 1.5 "g" "NA"
|
||||
"FUS-S" "Fusidic acid screening test" "Fusidanes" "" "fus screen" "" ""
|
||||
"GAM" 59364992 "Gamithromycin" "Macrolides" "QJ01FA95" "NA" "zactran" "100054-6,88376-9,88378-5"
|
||||
"GRN" 124093 "Garenoxacin" "Fluoroquinolones,Quinolones" "J01MA19,QJ01MA19" "gareno" "ganefloxacin,garenfloxacin" 0.4 "g" "35811-9,35812-7,35813-5"
|
||||
"GAT" 5379 "Gatifloxacin" "Fluoroquinolones,Quinolones" "J01MA16,QJ01MA16,QS01AE06,S01AE06" "Quinolone antibacterials" "Fluoroquinolones" "gati,gatifl" "acorafloxacin,avarofloxacin,balofloxacin,balofox,bazucin,bilimin,bonoq,gaity,gatiflo,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,kinome,tequin,tymer,zymar,zymaxid,zymer" 0.4 "g" 0.4 "g" "31036-7,31038-3,31040-9,31042-5,41494-6"
|
||||
"GEM" 9571107 "Gemifloxacin" "Fluoroquinolones,Quinolones" "J01MA15,QJ01MA15" "Quinolone antibacterials" "Fluoroquinolones" "gemifl" "factiv,gemifioxacin,gemifloxacine,gemifloxacino,gemifloxacinum" 0.32 "g" 0.2 "g" "35814-3,35815-0,35816-8,41697-4"
|
||||
"GEN" 3467 "Gentamicin" "Aminoglycosides" "D06AX07,J01GB03,QA07AA91,QD06AX07,QG01AA91,QG51AA04,QJ01GB03,QJ51GB03,QS01AA11,QS02AA14,QS03AA06,S01AA11,S02AA14,S03AA06" "Aminoglycoside antibacterials" "Other aminoglycosides" "cn,ge1000,ge2000,gen,gen128,gen500,gent,genta1,gentam,gm" "centicin,cidomycin,garamicin,garamycin,gentacycol,gentamicina,gentamicine,gentamicins,gentamicinum,gentamycins,gentamycinum,gentocin,lyramycin,oksitselanim,septigen,septocin" 0.24 "g" "101494-3,13561-6,13562-4,15106-8,18928-2,18929-0,22746-2,22747-0,266-7,267-5,268-3,269-1,31091-2,31092-0,31093-8,35668-3,35817-6,3663-2,3664-0,3665-7,39082-3,47109-4,50630-3,59379-8,7016-9,7017-7,7018-5,80971-5,88111-0,89481-6"
|
||||
"GEN-S" "Gentamicin screening test" "Aminoglycosides" "" "gen screen" "" ""
|
||||
"GEH" "Gentamicin-high" "Aminoglycosides" "NA" "gehi,gehl,genta high,gentamicin high" "NA" "18929-0,35817-6,7017-7,7018-5"
|
||||
"GEP" 25101874 "Gepotidacin" "Other" "J01XX13,QJ01XX13" "NA" "gepotidacina,gepotidacine" "NA"
|
||||
"GRX" 72474 "Grepafloxacin" "Fluoroquinolones,Quinolones" "J01MA11,QJ01MA11" "Quinolone antibacterials" "Fluoroquinolones" "grep,grepaf" "grepafloxacine,grepafloxacino,lungaskin,raxar,vaxar" 0.4 "g" "21316-5,23638-0,23639-8,35818-4"
|
||||
@@ -248,6 +254,7 @@
|
||||
"LMU" 25185057 "Lefamulin" "Other" "J01XX12,QJ01XX12" "NA" "lefamulinacetate,xenleta" "85425-7,99281-8"
|
||||
"LEN" 65646 "Lenampicillin" "Penicillins,Beta-lactams" "NA" "NA" "lenampicilina,lenampicilline,lenampicillinum,takacillin,valacillin,varacillin" "NA"
|
||||
"LVX" 149096 "Levofloxacin" "Fluoroquinolones,Quinolones" "J01MA12,QJ01MA12,QS01AE05,S01AE05" "Quinolone antibacterials" "Fluoroquinolones" "le,lev,levo,levofl,lvx" "aeroquin,cravit,dextrofloxacin,dynaquin,elequine,iquix,levaquin,levofiexacin,levofloxacine,levofloxacino,levofloxacinum,loxof,ofloxcacin,oftaquix,quinsair,quixin,tavanic,unibiotic,venaxan" 0.5 "g" 0.5 "g" "101501-5,20396-8,20629-2,21367-8,21368-6,30532-6,30533-4,48173-9,53716-7,7026-8,76040-5,76041-3,76042-1"
|
||||
"LVX-S" "Levofloxacin screening test" "Fluoroquinolones,Quinolones" "" "lvx screen" "" ""
|
||||
"LEO" "Levofloxacin/ornidazole" "Fluoroquinolones,Quinolones" "J01RA05,QJ01RA05" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
"LND" 9850038 "Levonadifloxacin" "Fluoroquinolones,Quinolones" "J01MA24,QJ01MA24" "NA" "NA" "NA"
|
||||
"LSP" "Linco-spectin" "Other" "NA" "lincomycin/spectinomycin" "NA" "NA"
|
||||
@@ -286,6 +293,7 @@
|
||||
"MRN" 70374 "Morinamide" "Antimycobacterials" "J04AK04,QJ04AK04" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "morfazinamide,morfazinammide,morfgazinamide,morinamida,morinamidum,morphazinamid,morphazinamide,piazofolina,piazolin,piazolina" "NA"
|
||||
"MFX" 152946 "Moxifloxacin" "Fluoroquinolones,Quinolones" "J01MA14,QJ01MA14,QS01AE07,S01AE07" "Quinolone antibacterials" "Fluoroquinolones" "mox,moxi,moxifl,mxf" "actira,actura,avalox,avelox,avolex,izilox,moxeza,moxifloxacine,moxifloxacino,octegra,vegamox,vigamox,zimoxin" 0.4 "g" 0.4 "g" "31037-5,31039-1,31041-7,31043-3,41502-6,43751-7,45223-5,76043-9,76044-7,76045-4,80540-8,88707-5,93497-6,96112-8"
|
||||
"MUP" 446596 "Mupirocin" "Other" "D06AX09,QD06AX09,QR01AX06,R01AX06" "mup,mupi,mupiro" "bactoderm,bactroban,centany,mupirocina,mupirocine,mupirocinum,plasimine,turixin" "20389-3,35822-6,35823-4,60542-8,60543-6,7033-4"
|
||||
"MUP-S" "Mupirocin screening test" "Other" "" "mup screen" "" ""
|
||||
"NAC" 73386748 "Nacubactam" "Beta-lactamase inhibitors" "NA" "NA" "NA" "NA"
|
||||
"NAD" 4410 "Nadifloxacin" "Fluoroquinolones,Quinolones" "D10AF05,QD10AF05" "NA" "acuatim,nadifloxacine,nadifloxacino,nadifloxacinum,nadixa,nadoxin" "NA"
|
||||
"NAF" 8982 "Nafcillin" "Penicillins,Beta-lactams" "J01CF06,QJ01CF06" "nafcil" "nafcil,nafcilin,nafcilina,nafcillinanhydrous,nafcilline,nafcillinhydrate,nafcillinmonohydrate,nafcillinsalt,nafcillinum,naftopen,nallpen,naphcillin,naphthicillin,unipen" 3 "g" "10993-4,18951-4,25232-0,346-7,347-5,348-3,349-1,41704-8"
|
||||
@@ -295,6 +303,7 @@
|
||||
"NAR" 65452 "Narasin" "Ionophores" "QP51BB04" "narasi" "monteban,narasine,narasino,narasinum,skycis" "87570-8"
|
||||
"NEM" 11993740 "Nemonoxacin" "Fluoroquinolones,Quinolones" "J01MB08,QJ01MB08" "Quinolone antibacterials" "Other quinolones" "NA" "NA" "NA"
|
||||
"NEO" "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom,neomyc" "NA" 5 "g" 1 "g" "10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
|
||||
"NEO-S" "Neomycin screening test" "Aminoglycosides" "" "neo screen" "" ""
|
||||
"NET" 441306 "Netilmicin" "Aminoglycosides" "J01GB07,QJ01GB07,QS01AA23,S01AA23" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti,netilm" "netillin,netilmicina,netilmicine,netilmicinum,netilyn,netira,netromicine,netromycin,nettacin,ntromicine,ntromycin,vectacin,zetamicin" 0.35 "g" 0.35 "g" "18954-8,25263-5,358-2,359-0,360-8,361-6,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8,7035-9"
|
||||
"NIC" 9507 "Nicarbazin" "Other" "NA" "NA" "nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin" "NA"
|
||||
"NIF" 71946 "Nifuroquine" "Fluoroquinolones,Quinolones" "NA" "NA" "abimasten,nifuroquina,nifuroquinum,quinaldofur" "NA"
|
||||
@@ -311,6 +320,7 @@
|
||||
"NOV" 54675769 "Novobiocin" "Aminocoumarins" "QJ01XX95" "novo,novobi" "albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
|
||||
"NYS" 6433272 "Nystatin" "Ionophores,Antifungals" "A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01" "nyst,nystan" "biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex" 1.5 "MU" "10697-1,10698-9,18958-9,35824-2,55689-4"
|
||||
"OFX" 4583 "Ofloxacin" "Fluoroquinolones,Quinolones" "J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16" "Quinolone antibacterials" "Fluoroquinolones" "of,ofl,oflo,ofloxa,ofx" "exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin" 0.4 "g" 0.4 "g" "18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
|
||||
"OFX-S" "Ofloxacin screening test" "Fluoroquinolones,Quinolones" "" "ofx screen" "" ""
|
||||
"OOR" "Ofloxacin/ornidazole" "Fluoroquinolones,Quinolones" "J01RA09,QJ01RA09" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
"OLE" 72493 "Oleandomycin" "Macrolides" "J01FA05,QJ01FA05" "Macrolides, lincosamides and streptogramins" "Macrolides" "oleand" "amimycin,landomycin,matromycin,oleandomicina,oleandomycine,oleandomycinum,romicil" 1 "g" "18960-5,378-0,379-8,380-6,381-4,55690-2"
|
||||
"OMC" 54697325 "Omadacycline" "Tetracyclines" "J01AA15,QJ01AA15" "NA" "amadacycline" 0.3 "g" 0.1 "g" "73594-4,73616-5,73639-7"
|
||||
@@ -371,6 +381,7 @@
|
||||
"RAM" 16132338 "Ramoplanin" "Glycopeptides,Peptides" "NA" "ramopl" "NA" "41710-5,41711-3,41712-1,41737-8"
|
||||
"RZM" 10993211 "Razupenem" "Carbapenems,Beta-lactams" "NA" "razupe" "NA" "73590-2,73612-4,73635-5"
|
||||
"RTP" 6918462 "Retapamulin" "Pleuromutilins" "D06AX13,QD06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" "ret" "altabax,altargo,rebapamulin,retapamulina" "NA"
|
||||
"RTP-S" "Retapamulin screening test" "Pleuromutilins" "" "rtp screen" "" ""
|
||||
"RZF" "Rezafungin" "Antifungals" "NA" "NA" "NA" "NA"
|
||||
"RBC" 44631912 "Ribociclib" "Antifungals" "L01EF02,QL01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali" 0.45 "g" "NA"
|
||||
"RST" 33042 "Ribostamycin" "Aminoglycosides" "J01GB10,QJ01GB10" "Aminoglycoside antibacterials" "Other aminoglycosides" "NA" "exaluren,hetangmycin,ribastamin,ribostamicina,ribostamycine,ribostamycinum,vistamycin,xylostatin" 1 "g" "NA"
|
||||
@@ -406,6 +417,7 @@
|
||||
"SPM" "Spiramycin/metronidazole" "Other" "J01RA04,QJ01RA04" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
|
||||
"STR" "Streptoduocin" "Aminoglycosides" "J01GA02,QJ01GA02" "Aminoglycoside antibacterials" "Streptomycins" "NA" "NA" 1 "g" "NA"
|
||||
"STR1" 19649 "Streptomycin" "Aminoglycosides" "A07AA04,J01GA01,QA07AA04,QJ01GA01" "Aminoglycoside antibacterials" "Streptomycins" "s,st1000,st2000,stm,str,stre,strept" "agrept,agrimycin,chemform,estreptomicina,gerox,neodiestreptopab,strepcen,streptomicina,streptomycine,streptomycinum,streptomyzin" 1 "g" "18982-9,18983-7,20462-8,23626-5,25185-0,25205-6,25206-4,35841-6,4039-4,42658-5,42659-3,459-8,460-6,461-4,462-2,46719-1,48177-0,6933-6,7048-2,7049-0,96114-4"
|
||||
"STR1-S" "Streptomycin screening test" "Aminoglycosides" "" "str1 screen" "" ""
|
||||
"STH" "Streptomycin-high" "Aminoglycosides" "NA" "sthi,sthl,strepto high,streptomycin high" "NA" "18983-7,35841-6,6933-6,7049-0"
|
||||
"STI" "Streptomycin/isoniazid" "Antimycobacterials" "J04AM01,QJ04AM01" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
|
||||
"SUL" 130313 "Sulbactam" "Beta-lactamase inhibitors" "J01CG01,QJ01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "sulbac" "betamaze,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4"
|
||||
@@ -484,6 +496,7 @@
|
||||
"TXC" 65788 "Tioxacin" "Fluoroquinolones,Quinolones" "NA" "NA" "tioxacine,tioxacino,tioxacinum" "NA"
|
||||
"TIZ" 394397 "Tizoxanide" "Other" "NA" "NA" "NA" "73585-2,73607-4,73629-8"
|
||||
"TOB" 36294 "Tobramycin" "Aminoglycosides" "J01GB01,QJ01GB01,QS01AA12,S01AA12" "Aminoglycoside antibacterials" "Other aminoglycosides" "nn,tm,to,tob,tobr,tobram" "aktob,bethkis,distobram,gotabiotic,kitabis,nebcin,nebicin,nebramycin,tenebrimycin,tenemycin,tobacin,tobracin,tobradex,tobradistin,tobralex,tobramaxin,tobramicin,tobramicina,tobramitsetin,tobramycetin,tobramycine,tobramycinum,tobrased,tobrex" 0.24 "g" "101496-8,13584-8,17808-7,18996-9,22750-4,22751-2,22752-0,25227-0,25800-4,31094-6,31095-3,31096-1,35239-3,35670-9,4057-6,4058-4,4059-2,507-4,508-2,509-0,50927-3,510-8,52962-8,59380-6,7055-7,80966-5"
|
||||
"TOB-S" "Tobramycin screening test" "Aminoglycosides" "" "tob screen" "" ""
|
||||
"TOH" "Tobramycin-high" "Aminoglycosides" "NA" "tobra high,tobramycin high,tohl" "NA" "NA"
|
||||
"TFX" 5517 "Tosufloxacin" "Fluoroquinolones,Quinolones" "J01MA22,QJ01MA22,QS01AE09,S01AE09" "tosufl" "NA" 0.45 "g" "100061-1,76146-0"
|
||||
"TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01,QJ01EA01,QJ51EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacin,bacterial,bacticel,bactifor,bactoprim,bactramin,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,conprim,cotrimel,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,futin,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lastrim,lescot,monoprim,monotrim,monotrimin,novotrimel,omstat,pancidim,proloprim,protrin,purbal,resprim,roubac,roubal,salvatrim,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,trimethioprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexol,trimezol,trimogal,trimono,trimopan,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim" 0.4 "g" 0.4 "g" "101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1"
|
||||
|
||||
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+2810
-15999
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@@ -10,7 +10,7 @@
|
||||
- Generates **antibiograms** - WISCA for empiric coverage estimates, or
|
||||
traditional/syndromic for AMR surveillance
|
||||
- Provides the **full microbiological taxonomy** of ~103 000 distinct
|
||||
species and extensive info of ~630 antimicrobial drugs
|
||||
species and extensive info of ~640 antimicrobial drugs
|
||||
- Applies **CLSI 2011-2026** and **EUCAST 2011-2026** clinical and
|
||||
veterinary breakpoints, and ECOFFs, for MIC and disk zone
|
||||
interpretation
|
||||
@@ -60,7 +60,7 @@ in scientific research.
|
||||
|
||||
After installing this package, R knows [**~103 000 distinct microbial
|
||||
species**](./reference/microorganisms.html) (updated October 2026) and
|
||||
all [**~630 antimicrobial and antiviral
|
||||
all [**~640 antimicrobial and antiviral
|
||||
drugs**](./reference/antimicrobials.html) by name and code (including
|
||||
ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all
|
||||
about valid SIR and MIC values. The integral clinical breakpoint
|
||||
|
||||
@@ -247,7 +247,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
|
||||
\section{Full list of supported (antimicrobial) classes}{
|
||||
|
||||
\itemize{
|
||||
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), kasugamycin (KAS), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)
|
||||
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin screening test (GEN-S), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), kasugamycin (KAS), micronomicin (MCR), neomycin (NEO), neomycin screening test (NEO-S), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin screening test (STR1-S), streptomycin-high (STH), tobramycin (TOB), tobramycin screening test (TOB-S), and tobramycin-high (TOH)
|
||||
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), 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), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
|
||||
@@ -260,22 +260,22 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
|
||||
\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), ceftibuten/avibactam (CTA), 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/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), 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[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin screening test (CIP-S), 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 screening test (LVX-S), 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 screening test (OFX-S), 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), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
|
||||
\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)
|
||||
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)
|
||||
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)
|
||||
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)
|
||||
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), clindamycin inducible screening test (CLI-S), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)
|
||||
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), clindamycin inducible screening test (CLI-S), dirithromycin (DIR), erythromycin (ERY), erythromycin screening test (ERY-S), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)
|
||||
\item \code{\link[=monobactams]{monobactams()}} can select: \cr aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), carumonam (CAR), and tigemonam (TMN)
|
||||
\item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)
|
||||
\item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)
|
||||
\item \code{\link[=penicillins]{penicillins()}} 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), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), 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), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{\link[=peptides]{peptides()}} can select: \cr avoparcin (AVO), bacitracin (BAC), bleomycin (BLM), dalbavancin (DAL), daptomycin (DAP), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), thiostrepton (THS), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
|
||||
\item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)
|
||||
\item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol (CHL), chloramphenicol screening test (CHL-S), florfenicol (FLR), and thiamphenicol (THI)
|
||||
\item \code{\link[=phosphonics]{phosphonics()}} can select: \cr amikacin/fosfomycin (AKF) and fosfomycin (FOS)
|
||||
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)
|
||||
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), 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), flumequine (FLM), 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), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), 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), oxolinic acid (OXO), ozenoxacin (OZN), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
|
||||
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), colistin screening test (COL-S), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)
|
||||
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin screening test (CIP-S), 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), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin screening test (LVX-S), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin screening test (OFX-S), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), ozenoxacin (OZN), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
|
||||
\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)
|
||||
\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin (ZFD)
|
||||
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr ostreogrycin (OST), pristinamycin (PRI), quinupristin/dalfopristin (QDA), and virginiamycine (VIR)
|
||||
|
||||
@@ -50,7 +50,7 @@ LOINC:
|
||||
}
|
||||
}
|
||||
|
||||
An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 506 rows and 14 columns.
|
||||
An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 519 rows and 14 columns.
|
||||
|
||||
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
|
||||
}
|
||||
|
||||
+1
-1
@@ -182,7 +182,7 @@ The default \code{"standard"} setting ensures cautious handling of uncertain val
|
||||
|
||||
\item{conserve_capped_values}{Deprecated, use \code{capped_mic_handling} instead.}
|
||||
|
||||
\item{site}{The site or route that the isolate is interpreted for: a \link{character} vector or a column name, in the fixed codes \code{"meningitis"}, \code{"non-meningitis"}, \code{"endocarditis"}, \code{"non-endocarditis"}, \code{"pneumonia"}, \code{"non-pneumonia"}, \code{"systemic"}, \code{"extraintestinal"}, \code{"other"}, \code{"intestinal"}, \code{"skin"}, \code{"inhaled"}, \code{"oral"}, \code{"prophylaxis"}, \code{"uti"}, \code{"iv"} and \code{"topical"}, which can be combined with a comma, e.g. \code{"iv, meningitis"}. If \code{site} is \code{NA} (default), any breakpoint matching all other criteria can apply, taken from most to least systemic site in the order just given, with \code{"iv"} directly after \code{"endocarditis"}; a breakpoint without a site is taken after \code{"other"}. If \code{site} is set, a breakpoint for a contradicting site is left out, e.g. \code{"meningitis"} leaves out \code{Non-meningitis}, while a breakpoint without a site still applies. The result is \code{NA} if only contradicting sites are available, also when PK/PD breakpoints exist. All choices are noted in \code{\link[=sir_interpretation_history]{sir_interpretation_history()}}.}
|
||||
\item{site}{The site or route that the isolate is interpreted for: a \link{character} vector or a column name, in the fixed codes \code{"systemic"}, \code{"iv"}, \code{"meningitis"}, \code{"endocarditis"}, \code{"pneumonia"}, \code{"mastitis"}, \code{"respiratory"}, \code{"metritis"}, \code{"genital"}, \code{"intestinal"}, \code{"other"}, \code{"non-meningitis"}, \code{"non-endocarditis"}, \code{"non-pneumonia"}, \code{"extraintestinal"}, \code{"soft tissue"}, \code{"skin"}, \code{"wounds"}, \code{"inhaled"}, \code{"oral"}, \code{"prophylaxis"}, \code{"uti"} and \code{"topical"}, which can be combined with a comma, e.g. \code{"iv, meningitis"}. If \code{site} is \code{NA} (default), any breakpoint matching all other criteria can apply, taken from most to least systemic site in the order just given; a breakpoint without a site takes the position of \code{"other"}, as both mean any site that is not listed next to it. If \code{site} is set, a breakpoint for a contradicting site is left out, e.g. \code{"meningitis"} leaves out \code{Non-meningitis}, while a breakpoint without a site still applies. \code{"other"} leaves out every breakpoint limited to an indication, and prefers a breakpoint without a site. Related sites do not contradict each other: \code{"pneumonia"} and \code{"respiratory"}, \code{"metritis"} and \code{"genital"}, and \code{"soft tissue"}, \code{"skin"} and \code{"wounds"}. The code \code{"mastitis"} includes \verb{Mammary gland}, and \code{"wounds"} includes \code{Abscesses}. The result is \code{NA} if only contradicting sites are available, also when PK/PD breakpoints exist. All choices are noted in \code{\link[=sir_interpretation_history]{sir_interpretation_history()}}.}
|
||||
|
||||
\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
|
||||
|
||||
|
||||
@@ -101,7 +101,7 @@ x
|
||||
These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
|
||||
\itemize{
|
||||
\item aminocoumarins\cr(clorobiocin, novobiocin, and penicillin/novobiocin)
|
||||
\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
|
||||
\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin screening test, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, neomycin screening test, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin screening test, streptomycin-high, tobramycin, tobramycin screening test, and tobramycin-high)
|
||||
\item aminopenicillins\cr(amoxicillin, amoxicillin/clavulanic acid, 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, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
|
||||
@@ -116,25 +116,25 @@ These 43 antimicrobial groups are allowed in the rules (case-insensitive) and ca
|
||||
\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, 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/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, 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, ceftibuten/avibactam, 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 fusidanes\cr(fusidic acid)
|
||||
\item fluoroquinolones\cr(besifloxacin, ciprofloxacin, ciprofloxacin screening test, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin screening test, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin screening test, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
|
||||
\item fusidanes\cr(fusidic acid and fusidic acid screening test)
|
||||
\item glycopeptides\cr(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin)
|
||||
\item glycopeptides_except_lipo\cr(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod, and zorbamycin)
|
||||
\item ionophores\cr(lasalocid, monensin sodium, narasin, nystatin, and salinomycin)
|
||||
\item isoxazolylpenicillins\cr(cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test)
|
||||
\item lincosamides\cr(clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin)
|
||||
\item lipoglycopeptides\cr(dalbavancin, oritavancin, and telavancin)
|
||||
\item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)
|
||||
\item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, erythromycin screening test, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)
|
||||
\item monobactams\cr(aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam)
|
||||
\item nitrofurans\cr(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone)
|
||||
\item oxazolidinones\cr(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)
|
||||
\item penicillins\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid)
|
||||
\item peptides\cr(avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, thiostrepton, vancomycin, vancomycin-macromethod, and zorbamycin)
|
||||
\item phenicols\cr(chloramphenicol, florfenicol, and thiamphenicol)
|
||||
\item phenicols\cr(chloramphenicol, chloramphenicol screening test, florfenicol, and thiamphenicol)
|
||||
\item phosphonics\cr(amikacin/fosfomycin and fosfomycin)
|
||||
\item pleuromutilins\cr(retapamulin and tiamulin)
|
||||
\item polymyxins\cr(colistin, polymyxin B, and polymyxin B/polysorbate 80)
|
||||
\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
|
||||
\item pleuromutilins\cr(retapamulin, retapamulin screening test, and tiamulin)
|
||||
\item polymyxins\cr(colistin, colistin screening test, polymyxin B, and polymyxin B/polysorbate 80)
|
||||
\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin screening test, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin screening test, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin screening test, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
|
||||
\item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
|
||||
\item spiropyrimidinetriones\cr(zoliflodacin)
|
||||
\item streptogramins\cr(ostreogrycin, pristinamycin, quinupristin/dalfopristin, and virginiamycine)
|
||||
|
||||
@@ -96,7 +96,7 @@ You can define antimicrobial groups instead of single antimicrobials for the rul
|
||||
|
||||
All 43 antimicrobial selectors are supported for use in the rules:
|
||||
\itemize{
|
||||
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
|
||||
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin screening test, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, neomycin screening test, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin screening test, streptomycin-high, tobramycin, tobramycin screening test, and tobramycin-high
|
||||
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, and ampicillin
|
||||
\item \code{\link[=antifungals]{antifungals()}} can select: \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 \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \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, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
|
||||
@@ -109,22 +109,22 @@ All 43 antimicrobial selectors are supported for use in the rules:
|
||||
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \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, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef
|
||||
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome
|
||||
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam
|
||||
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \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 \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin, ciprofloxacin, ciprofloxacin screening test, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin screening test, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin screening test, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
|
||||
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin
|
||||
\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid, monensin sodium, narasin, nystatin, and salinomycin
|
||||
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test
|
||||
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin
|
||||
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin
|
||||
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin
|
||||
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, clindamycin inducible screening test, dirithromycin, erythromycin, erythromycin screening test, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin
|
||||
\item \code{\link[=monobactams]{monobactams()}} can select: \cr aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and tigemonam
|
||||
\item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone
|
||||
\item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone
|
||||
\item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, carbenicillin, carindacillin, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic acid
|
||||
\item \code{\link[=peptides]{peptides()}} can select: \cr avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, thiostrepton, vancomycin, vancomycin-macromethod, and zorbamycin
|
||||
\item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol, florfenicol, and thiamphenicol
|
||||
\item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol, chloramphenicol screening test, florfenicol, and thiamphenicol
|
||||
\item \code{\link[=phosphonics]{phosphonics()}} can select: \cr amikacin/fosfomycin and fosfomycin
|
||||
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin, polymyxin B, and polymyxin B/polysorbate 80
|
||||
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
|
||||
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin, colistin screening test, polymyxin B, and polymyxin B/polysorbate 80
|
||||
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin screening test, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin screening test, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nalidixic acid screening test, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin screening test, ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
|
||||
\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine
|
||||
\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin
|
||||
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr ostreogrycin, pristinamycin, quinupristin/dalfopristin, and virginiamycine
|
||||
|
||||
@@ -663,15 +663,20 @@ test_that("as.sir() takes the site of a breakpoint into account", {
|
||||
sir <- function(x, mo, ab, ..., guideline = "EUCAST 2026") {
|
||||
as.character(suppressMessages(suppressWarnings(as.sir(x, mo = mo, ab = ab, guideline = guideline, info = FALSE, ...))))
|
||||
}
|
||||
# every site for humans in the data set must be known, so that none can be overlooked
|
||||
sites <- unique(clinical_breakpoints$site[!is.na(clinical_breakpoints$site) & clinical_breakpoints$type == "human"])
|
||||
# every site in the data set, for humans and for animals, must be known, so that none can be overlooked
|
||||
sites <- unique(clinical_breakpoints$site[!is.na(clinical_breakpoints$site)])
|
||||
for (s in sites) {
|
||||
expect_true(length(setdiff(sir_site_parts(s), SIR_SITE_NOT_A_SITE)) == length(sir_site_tokens(s)), info = s)
|
||||
known <- vapply(setdiff(sir_site_parts(s), SIR_SITE_NOT_A_SITE), function(part) length(sir_site_tokens(part)) == 1, logical(1))
|
||||
expect_true(all(known), info = s)
|
||||
}
|
||||
expect_identical(sort(c(names(SIR_SITE_PATTERNS), NA), na.last = TRUE), sort(SIR_SITE_ORDER, na.last = TRUE))
|
||||
expect_identical(sort(names(SIR_SITE_PATTERNS)), sort(SIR_SITE_ORDER))
|
||||
expect_identical(
|
||||
SIR_SITE_ORDER,
|
||||
c("systemic", "iv", "meningitis", "endocarditis", "pneumonia", "mastitis", "respiratory", "metritis", "genital", "intestinal", "other", "non-meningitis", "non-endocarditis", "non-pneumonia", "extraintestinal", "soft tissue", "skin", "wounds", "inhaled", "oral", "prophylaxis", "uti", "topical", "screen")
|
||||
)
|
||||
|
||||
# the fixed codes, all other values give an error
|
||||
expect_identical(sir_site_normalise(c("Meningitis", "iv, meningitis", NA)), c("meningitis", "meningitis,iv", NA))
|
||||
expect_identical(sir_site_normalise(c("Meningitis", "iv, meningitis", NA)), c("meningitis", "iv,meningitis", NA))
|
||||
expect_error(as.sir(as.mic(1), mo = "E. coli", ab = "AMC", site = "brain", info = FALSE))
|
||||
expect_error(as.sir(as.mic(1), mo = "E. coli", ab = "AMC", site = "uti", uti = FALSE, info = FALSE))
|
||||
|
||||
@@ -687,12 +692,56 @@ test_that("as.sir() takes the site of a breakpoint into account", {
|
||||
expect_true(sir_site_fits("systemic", "meningitis"))
|
||||
expect_false(sir_site_fits("systemic", "uti"))
|
||||
|
||||
# veterinary sites: the same rules, where sites that are part of each other do not contradict
|
||||
expect_identical(sir_site_tokens("Mammary gland"), "mastitis")
|
||||
expect_identical(sir_site_tokens("Wounds, abscesses"), "wounds")
|
||||
expect_false(sir_site_fits("mastitis", "respiratory"))
|
||||
expect_false(sir_site_fits("respiratory", "uti"))
|
||||
expect_true(sir_site_fits("respiratory", "pneumonia"))
|
||||
expect_true(sir_site_fits("pneumonia", "respiratory"))
|
||||
expect_true(sir_site_fits("metritis", "genital"))
|
||||
expect_true(sir_site_fits(c("skin", "soft tissue"), "wounds"))
|
||||
|
||||
# "other" means any site not listed: it fits no breakpoint limited to an indication, but it does fit the rest
|
||||
expect_false(sir_site_fits("meningitis", "other"))
|
||||
expect_false(sir_site_fits("uti", "other"))
|
||||
expect_false(sir_site_fits("mastitis", "other"))
|
||||
expect_true(sir_site_fits(character(0), "other"))
|
||||
expect_true(sir_site_fits("other", "other"))
|
||||
expect_true(sir_site_fits("non-meningitis", "other"))
|
||||
expect_true(sir_site_fits("iv", "other"))
|
||||
expect_true(sir_site_given(character(0), "other"))
|
||||
expect_false(sir_site_given(character(0), "uti"))
|
||||
|
||||
# site = NA takes the most systemic site, also compared to a breakpoint without a site
|
||||
expect_true(sir_site_rank("Meningitis") < sir_site_rank("Non-meningitis"))
|
||||
expect_true(sir_site_rank("Intravenous") < sir_site_rank(NA))
|
||||
expect_true(sir_site_rank(NA) < sir_site_rank("Oral"))
|
||||
expect_true(sir_site_rank("Systemic infections") < sir_site_rank("Intravenous"))
|
||||
expect_true(sir_site_rank("Intravenous") < sir_site_rank("Meningitis"))
|
||||
expect_true(sir_site_rank("Pneumonia") < sir_site_rank("Mastitis"))
|
||||
expect_identical(sir_site_rank("Mastitis"), sir_site_rank("Mammary gland"))
|
||||
expect_true(sir_site_rank("Mastitis") < sir_site_rank("Intestinal"))
|
||||
# "other" and no site are one position: below meningitis, and above UTI
|
||||
expect_identical(sir_site_rank(NA), sir_site_rank("Other infections"))
|
||||
expect_true(sir_site_rank("Meningitis") < sir_site_rank("Other infections"))
|
||||
expect_true(sir_site_rank("Other infections") < sir_site_rank("Uncomplicated urinary tract infection"))
|
||||
expect_true(sir_site_rank("Intestinal") < sir_site_rank(NA))
|
||||
expect_true(sir_site_rank(NA) < sir_site_rank("Non-meningitis"))
|
||||
expect_true(sir_site_rank("Oral") < sir_site_rank("Uncomplicated urinary tract infection"))
|
||||
expect_identical(sir_site_rank("Intravenous, Meningitis"), sir_site_rank("Meningitis"))
|
||||
# a second site breaks a tie on the first one
|
||||
expect_true(sir_site_rank("Intravenous, Meningitis") < sir_site_rank("Intravenous, Non-meningitis"))
|
||||
expect_true(sir_site_rank("Intravenous, Non-meningitis") < sir_site_rank("Meningitis"))
|
||||
|
||||
# "other" in as.sir(): takes the breakpoint for other infections, or without a site
|
||||
expect_identical(sir(as.mic(0.25), "Streptococcus pneumoniae", "PEN", site = "other", guideline = "EUCAST 2012"), "I")
|
||||
expect_identical(sir(as.mic(0.25), "Streptococcus pneumoniae", "PEN", site = "meningitis", guideline = "EUCAST 2012"), "R")
|
||||
# only breakpoints limited to an indication: no result
|
||||
expect_identical(sir(as.mic(1), "Escherichia coli", "NTR", site = "other"), NA_character_)
|
||||
# veterinary: per site for the host, and no result for another site
|
||||
vet <- function(x, mo, ab, ...) {
|
||||
sir(x, mo, ab, guideline = "CLSI 2026", breakpoint_type = "animal", host = "cattle", ...)
|
||||
}
|
||||
expect_identical(vet(as.mic(2), "Staphylococcus aureus", "KAC", site = "mastitis"), "S")
|
||||
expect_identical(vet(as.mic(32), "Staphylococcus aureus", "KAC", site = "mastitis"), "R")
|
||||
expect_identical(vet(as.mic(2), "Staphylococcus aureus", "KAC", site = "meningitis"), NA_character_)
|
||||
|
||||
# S. pneumoniae and benzylpenicillin, with breakpoints for meningitis and for other infections
|
||||
pen <- as.mic(0.25)
|
||||
|
||||
Reference in new issue
Block a user