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(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 2.1.1.9224
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Date: 2025-03-20
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Version: 2.1.1.9225
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Date: 2025-03-26
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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@ -20,12 +20,15 @@ Authors@R: c(
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person(given = c("Dmytro"), family = "Mykhailenko", role = "ctb"),
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person(given = c("Eric", "H.", "L.", "C.", "M."), family = "Hazenberg", role = "ctb"),
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person(given = c("Gwen"), family = "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
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person(given = c("Jane"), family = "Hawkey", role = "ctb", comment = c(ORCID = "0000-0001-9661-5293")),
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person(given = c("Jason"), family = "Stull", role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
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person(given = c("Javier"), family = "Sanchez", role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
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person(given = c("Jonas"), family = "Salm", role = "ctb"),
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person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
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person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
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person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
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person(given = c("Matthew"), family = "Saab", role = "ctb"),
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person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
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person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
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person(given = c("Rogier", "P."), family = "Schade", role = "ctb"),
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person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
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@ -349,6 +349,7 @@ export(sir_interpretation_history)
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export(sir_predict)
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export(skewness)
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export(streptogramins)
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export(sulfonamides)
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export(susceptibility)
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export(tetracyclines)
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export(theme_sir)
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7
NEWS.md
7
NEWS.md
@ -1,4 +1,4 @@
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# AMR 2.1.1.9224
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# AMR 2.1.1.9225
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
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@ -26,6 +26,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.
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* **Updated clinical breakpoints**
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* EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
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* Added all Expected Resistant Phenotypes from EUCAST (v1.2). The default `rules` for `eucast_rules()` are now: `c("breakpoints", "expected_phenotypes")`.
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* `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the `clinical_breakpoints` data set contains 24 breakpoints that can return the value "SDD" instead of "I".
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* EUCAST interpretive rules (using `eucast_rules()`) are now available for EUCAST 12 (2022), 13 (2023), and 14 (2024).
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* **New advanced ggplot2 extensions for MIC and SIR plotting and transforming**
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@ -48,6 +49,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* To get quantitative values, `as.double()` on a `sir` object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become `NA`). Other functions using `sir` classes (e.g., `summary()`) are updated to reflect the change to contain NI and SDD.
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* Combined MIC values (e.g., from CLSI) are now supported
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* The argument `conserve_capped_values` in `as.sir()` has been replaced with `capped_mic_handling`, which allows greater flexibility in handling capped MIC values (`<`, `<=`, `>`, `>=`). The four available options (`"standard"`, `"strict"`, `"relaxed"`, `"inverse"`) provide full control over whether these values should be interpreted conservatively or ignored. Using `conserve_capped_values` is now deprecated and returns a warning.
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* Added argument `info` so silence all console messages
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* `antibiogram()` function
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* Argument `antibiotics` has been renamed to `antimicrobials`. Using `antibiotics` will still work, but now returns a warning.
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* Added argument `formatting_type` to set any of the 22 options for the formatting of all 'cells'. This defaults to `18` for non-WISCA and `14` for WISCA, changing the output of antibiograms to cells with more info.
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@ -55,7 +57,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
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* The `ab_transform` argument now defaults to `"name"`, displaying antibiotic column names instead of codes
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* Antimicrobial selectors (previously: *antibiotic selectors*)
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* 'Antibiotic selectors' are now called 'antimicrobial selectors' since their scope is broader than just antibiotics. All documentation have been updated, and `ab_class()` and `ab_selector()` have been replaced with `amr_class()` and `amr_selector()`. The old functions are now deprecated and will be removed in a future version.
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* Added selectors `isoxazolylpenicillins()`, `monobactams()`, `nitrofurans()`, `phenicols()`, and `rifamycins()`
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* Added selectors `isoxazolylpenicillins()`, `monobactams()`, `nitrofurans()`, `phenicols()`, `rifamycins()`, and `sulfonamides()`
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* When using antimicrobial selectors that exclude non-treatable drugs (such as gentamicin-high when using `aminoglycosides()`), the function now always returns a warning that these can be included using `only_treatable = FALSE`
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* Added a new argument `return_all` to all selectors, which defaults to `TRUE` to include any match. With `FALSE`, the old behaviour, only the first hit for each unique antimicrobial is returned.
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* All selectors can now be run as a separate command to retrieve a vector of all possible antimicrobials that the selector can select
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@ -102,6 +104,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
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## Other
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* Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
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* Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
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* Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes
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* Greatly improved `vctrs` integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as `dplyr`'s `bind_rows()`, `rowwise()` and `c_across()` are now supported for e.g. columns of class `mic`. Despite this, this `AMR` package is still zero-dependent on any other package, including `dplyr` and `vctrs`.
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* Greatly updated and expanded documentation
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* Stopped support for SAS (`.xpt`) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
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@ -81,14 +81,14 @@ EUCAST_VERSION_EXPERT_RULES <- list(
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
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)
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)
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# EUCAST_VERSION_RESISTANTPHENOTYPES <- list(
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# "1.2" = list(
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# version_txt = "v1.2",
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# year = 2023,
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# title = "'Expected Resistant Phenotypes'",
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# url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
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# )
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# )
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EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
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"1.2" = list(
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version_txt = "v1.2",
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year = 2023,
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title = "'EUCAST Expected Resistant Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
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)
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)
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TAXONOMY_VERSION <- list(
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GBIF = list(
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@ -458,6 +458,14 @@ streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("streptogramins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_selectors
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#' @export
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sulfonamides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(return_all, allow_class = "logical", has_length = 1)
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amr_select_exec("sulfonamides", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_selectors
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#' @export
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tetracyclines <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
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@ -69,7 +69,7 @@
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#' #> 1 Escherichia coli R S S
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#' #> 2 Klebsiella pneumoniae R S S
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#'
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#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
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#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
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#' #> mo TZP ampi cipro
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#' #> 1 Escherichia coli R R S
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#' #> 2 Klebsiella pneumoniae R R S
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@ -83,7 +83,7 @@
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#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
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#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
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#'
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#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
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#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
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#' #> mo TZP ampi cipro
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#' #> 1 Escherichia coli R S S
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#' #> 2 Klebsiella pneumoniae R R S
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@ -121,6 +121,7 @@
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#' rules = "custom",
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#' custom_rules = x,
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#' info = FALSE,
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#' overwrite = TRUE,
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#' verbose = TRUE
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#' )
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#'
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204
R/eucast_rules.R
204
R/eucast_rules.R
@ -61,11 +61,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
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#' @param x a data set with antimicrobials columns, such as `amox`, `AMX` and `AMC`
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#' @param info a [logical] to indicate whether progress should be printed to the console - the default is only print while in interactive sessions
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#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using the package option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
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#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
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#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
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#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
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#' @param version_expected_phenotypes the version number to use for the EUCAST Expected Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_EXPECTED_PHENOTYPES), reverse = TRUE)`.
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#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
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# @param version_resistant_phenotypes the version number to use for the EUCAST Expected Resistant Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_RESISTANTPHENOTYPES), reverse = TRUE)`.
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#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these version of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
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#' @param ... column name of an antimicrobial, see section *Antimicrobials* below
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#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
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@ -146,14 +146,14 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#'
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#'
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#' # apply EUCAST rules: some results wil be changed
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#' b <- eucast_rules(a)
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#' b <- eucast_rules(a, overwrite = TRUE)
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#'
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#' head(b)
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#'
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#'
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#' # do not apply EUCAST rules, but rather get a data.frame
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#' # containing all details about the transformations:
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#' c <- eucast_rules(a, verbose = TRUE)
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#' c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
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#' head(c)
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#' }
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#'
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@ -165,11 +165,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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eucast_rules <- function(x,
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col_mo = NULL,
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info = interactive(),
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expected_phenotypes")),
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verbose = FALSE,
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version_breakpoints = 14.0,
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version_expected_phenotypes = 1.2,
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version_expertrules = 3.3,
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# TODO version_resistant_phenotypes = 1.2,
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ampc_cephalosporin_resistance = NA,
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only_sir_columns = FALSE,
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custom_rules = NULL,
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@ -178,11 +178,11 @@ eucast_rules <- function(x,
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meet_criteria(x, allow_class = "data.frame")
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meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5), is_in = c("breakpoints", "expert", "other", "all", "custom"))
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meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5, 6), is_in = c("breakpoints", "expected_phenotypes", "expert", "other", "all", "custom"))
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meet_criteria(verbose, allow_class = "logical", has_length = 1)
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meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
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meet_criteria(version_expected_phenotypes, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPECTED_PHENOTYPES)))
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meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES)))
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# meet_criteria(version_resistant_phenotypes, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)))
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meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
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@ -209,13 +209,8 @@ eucast_rules <- function(x,
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}
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breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]]
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expected_phenotypes_info <- EUCAST_VERSION_EXPECTED_PHENOTYPES[[which(as.double(names(EUCAST_VERSION_EXPECTED_PHENOTYPES)) == version_expected_phenotypes)]]
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expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
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# resistantphenotypes_info <- EUCAST_VERSION_RESISTANTPHENOTYPES[[which(as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)) == version_resistant_phenotypes)]]
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# support old setting (until AMR v1.3.0)
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if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) {
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rules <- getOption("AMR.eucast_rules")
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}
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if (interactive() && isTRUE(verbose) && isTRUE(info)) {
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txt <- paste0(
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@ -390,6 +385,24 @@ eucast_rules <- function(x,
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}
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suppressWarnings(as.sir(x))
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}
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expand_groups <- function(entry) {
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parts <- trimws(strsplit(entry, ",")[[1]])
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group_names <- tolower(AMR::microorganisms.groups$mo_group_name)
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mo_names <- AMR::microorganisms.groups$mo_name
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group_names_lc <- tolower(group_names)
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result <- unlist(lapply(parts, function(part) {
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match_idx <- which(group_names_lc == tolower(part))
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if (length(match_idx) > 0) {
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mo_names[match_idx]
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} else {
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part
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}
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}))
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# only the ones with genus or genus/species, not subspecies (as genus_species will be matched)
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spaces <- vapply(FUN.VALUE = integer(1), strsplit(result, " "), length)
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result <- result[spaces < 3]
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return(paste0(unique(result), collapse = ", "))
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}
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# Preparing the data ------------------------------------------------------
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@ -442,15 +455,6 @@ eucast_rules <- function(x,
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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}
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if (any(x$genus == "Staphylococcus", na.rm = TRUE)) {
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all_staph <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
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all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL, info = FALSE))
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}
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if (any(x$genus == "Streptococcus", na.rm = TRUE)) {
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all_strep <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Streptococcus"), , drop = FALSE]
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all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL, info = FALSE))
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}
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n_added <- 0
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n_changed <- 0
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@ -577,7 +581,17 @@ eucast_rules <- function(x,
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} else {
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if (isTRUE(info)) {
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cat("\n")
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message_("Skipping inheritance rules defined by this AMR package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
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message_(paste0(
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font_red("Skipping inhibitor-inheritance rules defined by this AMR package: setting "),
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font_green_bg(" S "),
|
||||
font_red(" to drug+inhibitor where drug is "),
|
||||
font_green_bg(" S "),
|
||||
font_red(", and setting "),
|
||||
font_rose_bg(" R "),
|
||||
font_red(" to drug where drug+inhibitor is "),
|
||||
font_rose_bg(" R "),
|
||||
font_red(". Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
|
||||
))
|
||||
}
|
||||
}
|
||||
|
||||
@ -592,26 +606,43 @@ eucast_rules <- function(x,
|
||||
eucast_notification_shown <- FALSE
|
||||
if (!is.null(list(...)$eucast_rules_df)) {
|
||||
# this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
|
||||
eucast_rules_df <- list(...)$eucast_rules_df
|
||||
eucast_rules_df_total <- list(...)$eucast_rules_df
|
||||
} else {
|
||||
# otherwise internal data file, created in data-raw/_pre_commit_checks.R
|
||||
eucast_rules_df <- EUCAST_RULES_DF
|
||||
eucast_rules_df_total <- EUCAST_RULES_DF
|
||||
}
|
||||
|
||||
## filter on user-set guideline versions ----
|
||||
eucast_rules_df <- data.frame()
|
||||
if (any(c("all", "breakpoints") %in% rules)) {
|
||||
eucast_rules_df <- subset(
|
||||
eucast_rules_df,
|
||||
reference.rule_group %unlike% "breakpoint" |
|
||||
(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
|
||||
)
|
||||
eucast_rules_df <- eucast_rules_df %pm>%
|
||||
rbind_AMR(eucast_rules_df_total %pm>%
|
||||
subset(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
|
||||
# eucast_rules_df <- subset(
|
||||
# eucast_rules_df,
|
||||
# reference.rule_group %unlike% "breakpoint" |
|
||||
# (reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
|
||||
# )
|
||||
}
|
||||
if (any(c("all", "expected_phenotypes") %in% rules)) {
|
||||
eucast_rules_df <- eucast_rules_df %pm>%
|
||||
rbind_AMR(eucast_rules_df_total %pm>%
|
||||
subset(reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes))
|
||||
# eucast_rules_df <- subset(
|
||||
# eucast_rules_df,
|
||||
# reference.rule_group %unlike% "expected" |
|
||||
# (reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes)
|
||||
# )
|
||||
}
|
||||
if (any(c("all", "expert") %in% rules)) {
|
||||
eucast_rules_df <- subset(
|
||||
eucast_rules_df,
|
||||
reference.rule_group %unlike% "expert" |
|
||||
(reference.rule_group %like% "expert" & reference.version == version_expertrules)
|
||||
)
|
||||
eucast_rules_df <- eucast_rules_df %pm>%
|
||||
rbind_AMR(eucast_rules_df_total %pm>%
|
||||
subset(reference.rule_group %like% "expert" & reference.version == version_expertrules))
|
||||
# eucast_rules_df <- subset(
|
||||
# eucast_rules_df,
|
||||
# reference.rule_group %unlike% "expert" |
|
||||
# (reference.rule_group %like% "expert" & reference.version == version_expertrules)
|
||||
# )
|
||||
}
|
||||
## filter out AmpC de-repressed cephalosporin-resistant mutants ----
|
||||
# no need to filter on version number here - the rules contain these version number, so are inherently filtered
|
||||
@ -657,6 +688,9 @@ eucast_rules <- function(x,
|
||||
if (rule_group_current %like% "breakpoint" && !any(c("all", "breakpoints") %in% rules)) {
|
||||
next
|
||||
}
|
||||
if (rule_group_current %like% "expected" && !any(c("all", "expected_phenotypes") %in% rules)) {
|
||||
next
|
||||
}
|
||||
if (rule_group_current %like% "expert" && !any(c("all", "expert") %in% rules)) {
|
||||
next
|
||||
}
|
||||
@ -677,6 +711,7 @@ eucast_rules <- function(x,
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
if (i == 1) {
|
||||
rule_previous <- ""
|
||||
rule_group_previous <- ""
|
||||
@ -712,15 +747,25 @@ eucast_rules <- function(x,
|
||||
)
|
||||
),
|
||||
ifelse(
|
||||
rule_group_current %like% "expert",
|
||||
rule_group_current %like% "expected",
|
||||
paste0(
|
||||
"\n",
|
||||
word_wrap(
|
||||
expertrules_info$title, " (",
|
||||
font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"
|
||||
expected_phenotypes_info$title, " (",
|
||||
font_red(paste0(expected_phenotypes_info$version_txt, ", ", expected_phenotypes_info$year)), ")\n"
|
||||
)
|
||||
),
|
||||
""
|
||||
ifelse(
|
||||
rule_group_current %like% "expert",
|
||||
paste0(
|
||||
"\n",
|
||||
word_wrap(
|
||||
expertrules_info$title, " (",
|
||||
font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"
|
||||
)
|
||||
),
|
||||
"" # Default empty string if none of the conditions are met
|
||||
)
|
||||
)
|
||||
)
|
||||
), "\n")
|
||||
@ -743,47 +788,15 @@ eucast_rules <- function(x,
|
||||
if_mo_property <- trimws(eucast_rules_df[i, "if_mo_property", drop = TRUE])
|
||||
like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE])
|
||||
mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE])
|
||||
source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]
|
||||
source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
|
||||
target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
|
||||
target_value <- eucast_rules_df[i, "to_value", drop = TRUE]
|
||||
|
||||
# be sure to comprise all coagulase-negative/-positive staphylococci when they are mentioned
|
||||
if (mo_value %like% "coagulase" && any(x$genus == "Staphylococcus", na.rm = TRUE)) {
|
||||
if (mo_value %like% "negative") {
|
||||
eucast_rules_df[i, "this_value"] <- paste0(
|
||||
"^(", paste0(
|
||||
all_staph[which(all_staph$CNS_CPS %like% "negative"),
|
||||
"fullname",
|
||||
drop = TRUE
|
||||
],
|
||||
collapse = "|"
|
||||
),
|
||||
")$"
|
||||
)
|
||||
} else {
|
||||
eucast_rules_df[i, "this_value"] <- paste0(
|
||||
"^(", paste0(
|
||||
all_staph[which(all_staph$CNS_CPS %like% "positive"),
|
||||
"fullname",
|
||||
drop = TRUE
|
||||
],
|
||||
collapse = "|"
|
||||
),
|
||||
")$"
|
||||
)
|
||||
}
|
||||
like_is_one_of <- "like"
|
||||
}
|
||||
# be sure to comprise all beta-haemolytic Streptococci (Lancefield groups A, B, C and G) when they are mentioned
|
||||
if (mo_value %like% "group [ABCG]" && any(x$genus == "Streptococcus", na.rm = TRUE)) {
|
||||
eucast_rules_df[i, "this_value"] <- paste0(
|
||||
"^(", paste0(
|
||||
all_strep[which(all_strep$Lancefield %like% "group [ABCG]"),
|
||||
"fullname",
|
||||
drop = TRUE
|
||||
],
|
||||
collapse = "|"
|
||||
),
|
||||
")$"
|
||||
)
|
||||
like_is_one_of <- "like"
|
||||
# if amo_value contains a group name, expand that name with all species in it
|
||||
if (any(trimws(strsplit(mo_value, ",")[[1]]) %in% AMR::microorganisms.groups$mo_group_name, na.rm = TRUE)) {
|
||||
like_is_one_of <- "one_of"
|
||||
mo_value <- expand_groups(mo_value)
|
||||
}
|
||||
|
||||
if (like_is_one_of == "is") {
|
||||
@ -802,13 +815,8 @@ eucast_rules <- function(x,
|
||||
stop("invalid value for column 'like.is.one_of'", call. = FALSE)
|
||||
}
|
||||
|
||||
source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]
|
||||
source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
|
||||
target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
|
||||
target_value <- eucast_rules_df[i, "to_value", drop = TRUE]
|
||||
|
||||
if (is.na(source_antibiotics)) {
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value),
|
||||
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value | x$fullname %like% mo_value),
|
||||
error = function(e) integer(0)
|
||||
)
|
||||
} else {
|
||||
@ -820,25 +828,17 @@ eucast_rules <- function(x,
|
||||
rows <- integer(0)
|
||||
} else if (length(source_antibiotics) == 1) {
|
||||
rows <- tryCatch(
|
||||
which(x[, if_mo_property, drop = TRUE] %like% mo_value &
|
||||
which((x[, if_mo_property, drop = TRUE] %like% mo_value | x$fullname %like% mo_value) &
|
||||
as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
|
||||
error = function(e) integer(0)
|
||||
)
|
||||
} else if (length(source_antibiotics) == 2) {
|
||||
rows <- tryCatch(
|
||||
which(x[, if_mo_property, drop = TRUE] %like% mo_value &
|
||||
which((x[, if_mo_property, drop = TRUE] %like% mo_value | x$fullname %like% mo_value) &
|
||||
as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L] &
|
||||
as.sir_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
|
||||
error = function(e) integer(0)
|
||||
)
|
||||
# nolint start
|
||||
# } else if (length(source_antibiotics) == 3) {
|
||||
# rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
# & as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
||||
# & as.sir_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
|
||||
# & as.sir_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
|
||||
# error = function(e) integer(0))
|
||||
# nolint end
|
||||
} else {
|
||||
stop_("only 2 antimicrobials supported for source_antibiotics")
|
||||
}
|
||||
@ -855,7 +855,10 @@ eucast_rules <- function(x,
|
||||
rule_text, rule_group_current, rule_current,
|
||||
ifelse(rule_group_current %like% "breakpoint",
|
||||
paste0(breakpoints_info$title, " ", breakpoints_info$version_txt, ", ", breakpoints_info$year),
|
||||
paste0(expertrules_info$title, " ", expertrules_info$version_txt, ", ", expertrules_info$year)
|
||||
ifelse(rule_group_current %like% "expected",
|
||||
paste0(expected_phenotypes_info$title, " ", expected_phenotypes_info$version_txt, ", ", expected_phenotypes_info$year),
|
||||
paste0(expertrules_info$title, " ", expertrules_info$version_txt, ", ", expertrules_info$year)
|
||||
)
|
||||
)
|
||||
),
|
||||
rows = rows,
|
||||
@ -1130,7 +1133,12 @@ edit_sir <- function(x,
|
||||
if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir), na.rm = TRUE)) {
|
||||
track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
|
||||
}
|
||||
non_SIR <- is.na(new_edits[rows, cols]) | !(new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
|
||||
isNA <- is.na(new_edits[rows, cols])
|
||||
isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
|
||||
non_SIR <- !isSIR
|
||||
if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
|
||||
warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
|
||||
}
|
||||
tryCatch(
|
||||
# insert into original table
|
||||
if (isTRUE(overwrite)) {
|
||||
|
||||
2
R/mic.R
2
R/mic.R
@ -333,7 +333,7 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
|
||||
x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators))
|
||||
|
||||
if (isTRUE(as.mic)) {
|
||||
if (keep_operators == "edges" && length(x) > 1) {
|
||||
if (keep_operators == "edges" && length(unique(x)) > 1) {
|
||||
x[x == min(x, na.rm = TRUE)] <- paste0("<=", x[x == min(x, na.rm = TRUE)])
|
||||
x[x == max(x, na.rm = TRUE)] <- paste0(">=", x[x == max(x, na.rm = TRUE)])
|
||||
}
|
||||
|
||||
58
R/plotting.R
58
R/plotting.R
@ -243,31 +243,47 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
|
||||
as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
|
||||
}
|
||||
scale$transform_df <- function(self, df) {
|
||||
self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
|
||||
# create new breaks and labels here
|
||||
lims <- range(self$mic_values_rescaled, na.rm = TRUE)
|
||||
# support inner and outer 'mic_range' settings (e.g., the data ranges 0.5-8 and 'mic_range' is set to 0.025-32)
|
||||
if (!is.null(mic_range) && !is.na(mic_range[1]) && !is.na(lims[1]) && mic_range[1] < lims[1]) {
|
||||
lims[1] <- mic_range[1]
|
||||
}
|
||||
if (!is.null(mic_range) && !is.na(mic_range[2]) && !is.na(lims[2]) && mic_range[2] > lims[2]) {
|
||||
lims[2] <- mic_range[2]
|
||||
}
|
||||
ind_min <- which(COMMON_MIC_VALUES <= lims[1])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES <= lims[1]] - lims[1]))] # Closest index where COMMON_MIC_VALUES <= lims[1]
|
||||
ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2]
|
||||
if (!aest %in% colnames(df)) {
|
||||
# support for geom_hline() and geom_vline()
|
||||
if ("yintercept" %in% colnames(df)) {
|
||||
aest_val <- "yintercept"
|
||||
} else if ("xintercept" %in% colnames(df)) {
|
||||
aest_val <- "xintercept"
|
||||
} else {
|
||||
stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
|
||||
}
|
||||
out <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
|
||||
if (!is.null(self$mic_values_rescaled) && any(out < min(self$mic_values_rescaled, na.rm = TRUE) | out > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
|
||||
warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
|
||||
}
|
||||
df[[aest_val]] <- log2(as.double(out))
|
||||
} else {
|
||||
self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
|
||||
# create new breaks and labels here
|
||||
lims <- range(self$mic_values_rescaled, na.rm = TRUE)
|
||||
# support inner and outer 'mic_range' settings (e.g., the data ranges 0.5-8 and 'mic_range' is set to 0.025-32)
|
||||
if (!is.null(mic_range) && !is.na(mic_range[1]) && !is.na(lims[1]) && mic_range[1] < lims[1]) {
|
||||
lims[1] <- mic_range[1]
|
||||
}
|
||||
if (!is.null(mic_range) && !is.na(mic_range[2]) && !is.na(lims[2]) && mic_range[2] > lims[2]) {
|
||||
lims[2] <- mic_range[2]
|
||||
}
|
||||
ind_min <- which(COMMON_MIC_VALUES <= lims[1])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES <= lims[1]] - lims[1]))] # Closest index where COMMON_MIC_VALUES <= lims[1]
|
||||
ind_max <- which(COMMON_MIC_VALUES >= lims[2])[which.min(abs(COMMON_MIC_VALUES[COMMON_MIC_VALUES >= lims[2]] - lims[2]))] # Closest index where COMMON_MIC_VALUES >= lims[2]
|
||||
|
||||
self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
|
||||
self$mic_values_levels <- as.mic(COMMON_MIC_VALUES[ind_min:ind_max])
|
||||
|
||||
if (keep_operators %in% c("edges", "all") && length(self$mic_values_levels) > 1) {
|
||||
self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
|
||||
self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
|
||||
}
|
||||
if (keep_operators %in% c("edges", "all") && length(unique(self$mic_values_levels)) > 1) {
|
||||
self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
|
||||
self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
|
||||
}
|
||||
|
||||
self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
|
||||
if (aest == "y" && "group" %in% colnames(df)) {
|
||||
df$group <- as.integer(factor(df$x))
|
||||
self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
|
||||
if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) {
|
||||
df$group <- as.integer(factor(df$x))
|
||||
}
|
||||
df[[aest]] <- self$mic_values_log
|
||||
}
|
||||
df[[aest]] <- self$mic_values_log
|
||||
df
|
||||
}
|
||||
|
||||
|
||||
@ -146,10 +146,10 @@ random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
|
||||
}
|
||||
out <- as.mic(sample(mic_range_new, size = size, replace = TRUE))
|
||||
# 50% chance that lowest will get <= and highest will get >=
|
||||
if (stats::runif(1) > 0.5) {
|
||||
if (stats::runif(1) > 0.5 && length(unique(out)) > 1) {
|
||||
out[out == min(out)] <- paste0("<=", out[out == min(out)])
|
||||
}
|
||||
if (stats::runif(1) > 0.5) {
|
||||
if (stats::runif(1) > 0.5 && length(unique(out)) > 1) {
|
||||
out[out == max(out)] <- paste0(">=", out[out == max(out)])
|
||||
}
|
||||
return(out)
|
||||
|
||||
151
R/sir.R
151
R/sir.R
@ -464,6 +464,7 @@ is_sir_eligible <- function(x, threshold = 0.05) {
|
||||
#' @rdname as.sir
|
||||
#' @export
|
||||
#' @param S,I,R,NI,SDD a case-independent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters and whitespaces are removed from the input.
|
||||
#' @param info a [logical] to print information about the process
|
||||
# extra param: warn (logical, to never throw a warning)
|
||||
as.sir.default <- function(x,
|
||||
S = "^(S|U)+$",
|
||||
@ -471,7 +472,14 @@ as.sir.default <- function(x,
|
||||
R = "^(R)+$",
|
||||
NI = "^(N|NI|V)+$",
|
||||
SDD = "^(SDD|D|H)+$",
|
||||
info = TRUE,
|
||||
...) {
|
||||
meet_criteria(S, allow_class = "character", has_length = 1)
|
||||
meet_criteria(I, allow_class = "character", has_length = 1)
|
||||
meet_criteria(R, allow_class = "character", has_length = 1)
|
||||
meet_criteria(NI, allow_class = "character", has_length = 1)
|
||||
meet_criteria(SDD, allow_class = "character", has_length = 1)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
if (inherits(x, "sir")) {
|
||||
return(as_sir_structure(x))
|
||||
}
|
||||
@ -591,6 +599,7 @@ as.sir.mic <- function(x,
|
||||
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
|
||||
host = NULL,
|
||||
verbose = FALSE,
|
||||
info = TRUE,
|
||||
conserve_capped_values = NULL,
|
||||
...) {
|
||||
as_sir_method(
|
||||
@ -610,6 +619,8 @@ as.sir.mic <- function(x,
|
||||
breakpoint_type = breakpoint_type,
|
||||
host = host,
|
||||
verbose = verbose,
|
||||
info = info,
|
||||
conserve_capped_values = conserve_capped_values,
|
||||
...
|
||||
)
|
||||
}
|
||||
@ -629,6 +640,7 @@ as.sir.disk <- function(x,
|
||||
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
|
||||
host = NULL,
|
||||
verbose = FALSE,
|
||||
info = TRUE,
|
||||
...) {
|
||||
as_sir_method(
|
||||
method_short = "disk",
|
||||
@ -667,6 +679,7 @@ as.sir.data.frame <- function(x,
|
||||
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
|
||||
host = NULL,
|
||||
verbose = FALSE,
|
||||
info = TRUE,
|
||||
conserve_capped_values = NULL) {
|
||||
meet_criteria(x, allow_class = "data.frame") # will also check for dimensions > 0
|
||||
meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), allow_NULL = TRUE)
|
||||
@ -681,6 +694,7 @@ as.sir.data.frame <- function(x,
|
||||
meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1)
|
||||
meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
meet_criteria(verbose, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1)
|
||||
x.bak <- x
|
||||
for (i in seq_len(ncol(x))) {
|
||||
# don't keep factors, overwriting them is hard
|
||||
@ -697,10 +711,10 @@ as.sir.data.frame <- function(x,
|
||||
|
||||
# -- host
|
||||
if (missing(breakpoint_type) && any(host %in% clinical_breakpoints$host[!clinical_breakpoints$host %in% c("human", "ECOFF")], na.rm = TRUE)) {
|
||||
message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
|
||||
if (isTRUE(info)) message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
|
||||
breakpoint_type <- "animal"
|
||||
} else if (any(!suppressMessages(convert_host(host)) %in% c("human", "ECOFF"), na.rm = TRUE)) {
|
||||
message_("Assuming `breakpoint_type = \"animal\"`.")
|
||||
if (isTRUE(info)) message_("Assuming `breakpoint_type = \"animal\"`.")
|
||||
breakpoint_type <- "animal"
|
||||
}
|
||||
if (breakpoint_type == "animal") {
|
||||
@ -745,13 +759,15 @@ as.sir.data.frame <- function(x,
|
||||
} else {
|
||||
plural <- c("", "s", "a ")
|
||||
}
|
||||
message_(
|
||||
"Assuming value", plural[1], " ",
|
||||
vector_and(values, quotes = TRUE),
|
||||
" in column '", font_bold(col_specimen),
|
||||
"' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
|
||||
".\n Use `as.sir(uti = FALSE)` to prevent this."
|
||||
)
|
||||
if (isTRUE(info)) {
|
||||
message_(
|
||||
"Assuming value", plural[1], " ",
|
||||
vector_and(values, quotes = TRUE),
|
||||
" in column '", font_bold(col_specimen),
|
||||
"' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
|
||||
".\n Use `as.sir(uti = FALSE)` to prevent this."
|
||||
)
|
||||
}
|
||||
} else {
|
||||
# no data about UTI's found
|
||||
uti <- NULL
|
||||
@ -833,6 +849,8 @@ as.sir.data.frame <- function(x,
|
||||
breakpoint_type = breakpoint_type,
|
||||
host = host,
|
||||
verbose = verbose,
|
||||
info = info,
|
||||
conserve_capped_values = conserve_capped_values,
|
||||
is_data.frame = TRUE
|
||||
)
|
||||
} else if (types[i] == "disk") {
|
||||
@ -854,6 +872,7 @@ as.sir.data.frame <- function(x,
|
||||
breakpoint_type = breakpoint_type,
|
||||
host = host,
|
||||
verbose = verbose,
|
||||
info = info,
|
||||
is_data.frame = TRUE
|
||||
)
|
||||
} else if (types[i] == "sir") {
|
||||
@ -863,24 +882,28 @@ as.sir.data.frame <- function(x,
|
||||
if (!all(x[, ab_cols[i], drop = TRUE] %in% c("S", "SDD", "I", "R", "NI", NA), na.rm = TRUE)) {
|
||||
show_message <- TRUE
|
||||
# only print message if values are not already clean
|
||||
message_("Cleaning values in column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE
|
||||
)
|
||||
if (isTRUE(info)) {
|
||||
message_("Cleaning values in column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
} else if (!is.sir(x.bak[, ab_cols[i], drop = TRUE])) {
|
||||
show_message <- TRUE
|
||||
# only print message if class not already set
|
||||
message_("Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE, language = NULL), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE
|
||||
)
|
||||
if (isTRUE(info)) {
|
||||
message_("Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE, language = NULL), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
}
|
||||
x[, ab_cols[i]] <- as.sir.default(x = as.character(x[, ab_cols[i], drop = TRUE]))
|
||||
if (show_message == TRUE) {
|
||||
if (show_message == TRUE && isTRUE(info)) {
|
||||
message(font_green_bg(" OK "))
|
||||
}
|
||||
}
|
||||
@ -963,6 +986,7 @@ as_sir_method <- function(method_short,
|
||||
breakpoint_type,
|
||||
host,
|
||||
verbose,
|
||||
info,
|
||||
conserve_capped_values = NULL,
|
||||
...) {
|
||||
if (isTRUE(conserve_capped_values)) {
|
||||
@ -984,6 +1008,7 @@ as_sir_method <- function(method_short,
|
||||
meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1, .call_depth = -2)
|
||||
meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE, .call_depth = -2)
|
||||
meet_criteria(verbose, allow_class = "logical", has_length = 1, .call_depth = -2)
|
||||
meet_criteria(info, allow_class = "logical", has_length = 1, .call_depth = -2)
|
||||
|
||||
# backward compatibilty
|
||||
dots <- list(...)
|
||||
@ -996,7 +1021,7 @@ as_sir_method <- function(method_short,
|
||||
|
||||
guideline_coerced <- get_guideline(guideline, reference_data)
|
||||
|
||||
if (message_not_thrown_before("as.sir", "sir_interpretation_history")) {
|
||||
if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
|
||||
message()
|
||||
message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all the details of the breakpoint interpretations.\n\n", add_fn = font_green)
|
||||
}
|
||||
@ -1007,13 +1032,13 @@ as_sir_method <- function(method_short,
|
||||
if (breakpoint_type == "animal") {
|
||||
if (is.null(host)) {
|
||||
host <- "dogs"
|
||||
if (message_not_thrown_before("as.sir", "host_missing")) {
|
||||
if (isTRUE(info) && message_not_thrown_before("as.sir", "host_missing")) {
|
||||
message_("Animal hosts not set in `host`, assuming `host = \"dogs\"`, since these have the highest breakpoint availability.\n\n")
|
||||
}
|
||||
}
|
||||
} else {
|
||||
if (!is.null(host) && !all(toupper(as.character(host)) %in% c("HUMAN", "ECOFF"))) {
|
||||
if (message_not_thrown_before("as.sir", "assumed_breakpoint_animal")) {
|
||||
if (isTRUE(info) && message_not_thrown_before("as.sir", "assumed_breakpoint_animal")) {
|
||||
message_("Assuming `breakpoint_type = \"animal\"`, since `host` is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set `guideline = \"CLSI\"`?", ""), "\n\n")
|
||||
}
|
||||
breakpoint_type <- "animal"
|
||||
@ -1038,12 +1063,12 @@ as_sir_method <- function(method_short,
|
||||
}
|
||||
host.bak <- host
|
||||
host <- convert_host(host)
|
||||
if (any(is.na(host) & !is.na(host.bak)) && message_not_thrown_before("as.sir", "missing_hosts")) {
|
||||
if (any(is.na(host) & !is.na(host.bak)) && isTRUE(info) && message_not_thrown_before("as.sir", "missing_hosts")) {
|
||||
warning_("The following animal host(s) could not be coerced: ", vector_and(host.bak[is.na(host) & !is.na(host.bak)]), immediate = TRUE)
|
||||
message() # new line
|
||||
}
|
||||
# TODO add a switch to turn this off? In interactive sessions perhaps ask the user. Default should be On.
|
||||
# if (breakpoint_type == "animal" && message_not_thrown_before("as.sir", "host_missing_breakpoints")) {
|
||||
# if (breakpoint_type == "animal" && isTRUE(info) && message_not_thrown_before("as.sir", "host_missing_breakpoints")) {
|
||||
# if (guideline_coerced %like% "CLSI") {
|
||||
# message_("Please note that in the absence of specific veterinary breakpoints for certain animal hosts, the CLSI guideline VET09 will be applied where possible.\n\n")
|
||||
# }
|
||||
@ -1144,11 +1169,13 @@ as_sir_method <- function(method_short,
|
||||
# be sure to take current taxonomy, as the 'clinical_breakpoints' data set only contains current taxonomy
|
||||
mo <- suppressWarnings(suppressMessages(as.mo(mo, keep_synonyms = FALSE, info = FALSE)))
|
||||
if (all(is.na(ab))) {
|
||||
message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE),
|
||||
". Rename this column to a valid name or code, and check the output with `as.ab()`.",
|
||||
add_fn = font_red,
|
||||
as_note = FALSE
|
||||
)
|
||||
if (isTRUE(info)) {
|
||||
message_("Returning NAs for unknown antibiotic: ", vector_and(ab.bak, sort = FALSE, quotes = TRUE),
|
||||
". Rename this column to a valid name or code, and check the output with `as.ab()`.",
|
||||
add_fn = font_red,
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
return(as.sir(rep(NA, length(x))))
|
||||
}
|
||||
if (length(mo) == 1) {
|
||||
@ -1168,8 +1195,10 @@ as_sir_method <- function(method_short,
|
||||
uti <- rep(uti, length(x))
|
||||
}
|
||||
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
|
||||
if (message_not_thrown_before("as.sir", "intrinsic")) {
|
||||
warning_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
|
||||
if (isTRUE(info) && message_not_thrown_before("as.sir", "intrinsic")) {
|
||||
message_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.",
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
@ -1269,7 +1298,7 @@ as_sir_method <- function(method_short,
|
||||
add_intrinsic_resistance_to_AMR_env()
|
||||
}
|
||||
|
||||
if (nrow(df_unique) < 10 || nrow(breakpoints) == 0) {
|
||||
if (isTRUE(info) && nrow(df_unique) < 10 || nrow(breakpoints) == 0) {
|
||||
# only print intro under 10 items, otherwise progressbar will print this and then it will be printed double
|
||||
message_(intro_txt, appendLF = FALSE, as_note = FALSE)
|
||||
}
|
||||
@ -1279,14 +1308,16 @@ as_sir_method <- function(method_short,
|
||||
|
||||
if (nrow(breakpoints) == 0) {
|
||||
# apparently no breakpoints found
|
||||
message(
|
||||
paste0(font_rose_bg(" WARNING "), "\n"),
|
||||
font_black(paste0(
|
||||
" ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
|
||||
suppressMessages(suppressWarnings(ab_name(unique(ab_coerced), language = NULL, tolower = TRUE))),
|
||||
" (", unique(ab_coerced), ")."
|
||||
), collapse = "\n")
|
||||
)
|
||||
if (isTRUE(info)) {
|
||||
message(
|
||||
paste0(font_rose_bg(" WARNING "), "\n"),
|
||||
font_black(paste0(
|
||||
" ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
|
||||
suppressMessages(suppressWarnings(ab_name(unique(ab_coerced), language = NULL, tolower = TRUE))),
|
||||
" (", unique(ab_coerced), ")."
|
||||
), collapse = "\n")
|
||||
)
|
||||
}
|
||||
|
||||
load_mo_uncertainties(metadata_mo)
|
||||
return(rep(NA_sir_, nrow(df)))
|
||||
@ -1609,26 +1640,28 @@ as_sir_method <- function(method_short,
|
||||
|
||||
close(p)
|
||||
# printing messages
|
||||
if (has_progress_bar == TRUE) {
|
||||
# the progress bar has overwritten the intro text, so:
|
||||
message_(intro_txt, appendLF = FALSE, as_note = FALSE)
|
||||
}
|
||||
if (length(notes) > 0) {
|
||||
if (isTRUE(rise_warning)) {
|
||||
message(font_rose_bg(" WARNING "))
|
||||
} else {
|
||||
message(font_yellow_bg(" NOTE "))
|
||||
if (isTRUE(info)) {
|
||||
if (has_progress_bar == TRUE) {
|
||||
# the progress bar has overwritten the intro text, so:
|
||||
message_(intro_txt, appendLF = FALSE, as_note = FALSE)
|
||||
}
|
||||
notes <- unique(notes)
|
||||
if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
|
||||
for (i in seq_along(notes)) {
|
||||
message(word_wrap(" ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
|
||||
if (length(notes) > 0) {
|
||||
if (isTRUE(rise_warning)) {
|
||||
message(font_rose_bg(" WARNING "))
|
||||
} else {
|
||||
message(font_yellow_bg(" NOTE "))
|
||||
}
|
||||
notes <- unique(notes)
|
||||
if (isTRUE(verbose) || length(notes) == 1 || NROW(AMR_env$sir_interpretation_history) == 0) {
|
||||
for (i in seq_along(notes)) {
|
||||
message(word_wrap(" ", AMR_env$bullet_icon, " ", notes[i], add_fn = font_black))
|
||||
}
|
||||
} else {
|
||||
message(word_wrap(" ", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
|
||||
}
|
||||
} else {
|
||||
message(word_wrap(" ", AMR_env$bullet_icon, " There were multiple notes. Print or View `sir_interpretation_history()` to examine them, or use `as.sir(..., verbose = TRUE)` next time to directly print them here.", add_fn = font_black))
|
||||
message(font_green_bg(" OK "))
|
||||
}
|
||||
} else {
|
||||
message(font_green_bg(" OK "))
|
||||
}
|
||||
|
||||
load_mo_uncertainties(metadata_mo)
|
||||
|
||||
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
BIN
data-raw/Expected_Resistant_Phenotypes_v1.2_20230113.pdf
Normal file
BIN
data-raw/Expected_Resistant_Phenotypes_v1.2_20230113.pdf
Normal file
Binary file not shown.
@ -448,6 +448,9 @@ pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pr
|
||||
pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
|
||||
filter(group %like% "trimethoprim") %>%
|
||||
pull(ab)
|
||||
pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
|
||||
filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>%
|
||||
pull(ab)
|
||||
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
|
||||
pre_commit_lst$AB_BETALACTAMS <- sort(c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS, pre_commit_lst$AB_MONOBACTAMS))
|
||||
pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
|
||||
# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, betalactams_with_inhibitor, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
|
||||
# and all separate EARS-Net letter codes such as AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
|
||||
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'.
|
||||
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'. If 'this_value' exists in AMR::microorganisms.groups$mo_group_name it will be expanded in eucast_rules() to all relevant species occuring in microorganisms.groups$mo_name before further processing of the line in this file.
|
||||
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
|
||||
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 and later
|
||||
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 9 LINES SKIPPED <<<<<
|
||||
@ -302,11 +302,11 @@ genus_species is Streptococcus pneumoniae ERY S "AZM, CLR, RXT" S Streptococcus
|
||||
genus_species is Streptococcus pneumoniae ERY R "AZM, CLR, RXT" R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae TCY-S S "DOX, MNO" S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae TCY-S R "DOX, MNO" R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" PEN-S S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" PEN-S R "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" AMP S "AMX, AMC, SAM, PIP, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" AMP I "AMX, AMC, SAM, PIP, TZP" I Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis" AMP R "AMX, AMC, SAM, PIP, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Viridans Group Streptococcus (VGS)" PEN-S S "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Viridans Group Streptococcus (VGS)" PEN-S R "AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Viridans Group Streptococcus (VGS)" AMP S "AMX, AMC, SAM, PIP, TZP" S Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Viridans Group Streptococcus (VGS)" AMP I "AMX, AMC, SAM, PIP, TZP" I Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species one_of "Viridans Group Streptococcus (VGS)" AMP R "AMX, AMC, SAM, PIP, TZP" R Viridans group streptococci Breakpoints 12 "paste(""Streptococcus"", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == ""B_STRPT_VIRI"")]), collapse = "", "")"
|
||||
genus_species is Haemophilus influenzae PEN-S S "AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP" S Haemophilus influenzae Breakpoints 12 "x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == ""EUCAST 2022"" & clinical_breakpoints$mo == as.mo(""H. influenzae""))]), ""IMR"", ""MEV""); sort(x[x %in% betalactams()])"
|
||||
genus_species is Haemophilus influenzae "PEN-S, BLA-S" "R, R" "AMP, AMX, PIP" R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 12
|
||||
@ -487,11 +487,11 @@ genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pn
|
||||
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 13.1
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 13.1 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 13.1 will be expanded in eucast_rules()
|
||||
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 13.1 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
|
||||
genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 13.1
|
||||
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 13.1
|
||||
@ -673,11 +673,11 @@ genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pn
|
||||
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 14
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 14 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules()
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 14 will be expanded in eucast_rules()
|
||||
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 14 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
|
||||
genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 14
|
||||
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 14
|
||||
@ -783,6 +783,92 @@ genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoin
|
||||
genus_species is Brucella melitensis TCY-S R DOX R Brucella melitensis Breakpoints 14
|
||||
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 14
|
||||
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 14
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
genus_species one_of Citrobacter koseri, Citrobacter amalonaticus AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Citrobacter freundii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species one_of Enterobacter cloacae complex AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Escherichia hermannii AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Hafnia alvei AMP, AMX, PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Klebsiella aerogenes AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species one_of Klebsiella pneumoniae complex AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Klebsiella oxytoca AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Leclercia adecarboxylata FOS R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Morganella morganii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Plesiomonas shigelloides AMX, AMP, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Proteus mirabilis tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Proteus penneri AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Proteus vulgaris AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Providencia rettgeri AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Providencia stuartii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus is Raoultella AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Serratia marcescens AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Yersinia enterocolitica AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas hydrophila AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas veronii AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas dhakensis AMP, AMX, SAM, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas caviae AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas jandaei AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species one_of Citrobacter koseri, Citrobacter amalonaticus AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Citrobacter freundii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species one_of Enterobacter cloacae complex AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Escherichia hermannii AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Hafnia alvei AMP, AMX, PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Klebsiella aerogenes AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species one_of Klebsiella pneumoniae complex AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Klebsiella oxytoca AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Leclercia adecarboxylata FOS R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Morganella morganii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Plesiomonas shigelloides AMX, AMP, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Proteus mirabilis tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Proteus penneri AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Proteus vulgaris AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Providencia rettgeri AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Providencia stuartii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus is Raoultella AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Serratia marcescens AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Yersinia enterocolitica AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas hydrophila AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas veronii AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas dhakensis AMP, AMX, SAM, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas caviae AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus_species is Aeromonas jandaei AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
|
||||
genus one_of Acinetobacter, Achromobacter, Burkholderia, Elizabethkingia, Elizabethkingia, Ochrobactrum, Pseudomonas, Stenotrophomonas, Chryseobacterium PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species one_of Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter nosocomialis AMP, AMX, AMC, CTX, CRO, ATM, ETP, TMP, FOS, TCY, DOX R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Achromobacter xylosoxidans AMP, AMX, CTX, CRO, ATM, ETP R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species one_of Burkholderia cepacia complex AMP, AMX, AMC, SAM, TIC, TCC, PIP, TZP, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, PLB, COL R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Elizabethkingia meningoseptica AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, PLB, COL R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Elizabethkingia anophelis AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Ochrobactrum anthropi AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Pseudomonas aeruginosa AMP, AMX, AMC, SAM, CTX, CRO, ETP, CHL, TMP, KAN, NEO, tetracyclines, TGC R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Stenotrophomonas maltophilia AMP, AMX, AMC, SAM, TIC, PIP, TZP, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus is Chryseobacterium AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, PLB, COL R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Haemophilus influenzae FUS, streptogramins R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Moraxella catarrhalis R TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus is Neisseria TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species one_of Campylobacter jejuni, Campylobacter coli FUS, streptogramins, TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
|
||||
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species one_of Coagulase-negative Staphylococcus (CoNS), Staphylococcus aureus CAZ R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, sulfonamides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species one_of Enterococcus gallinarum, Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, sulfonamides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, sulfonamides R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus is Corynebacterium FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus one_of Leuconostoc, Pediococcus VAN, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species is Lactobacillus casei VAN, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
fullname is Lactobacillus casei rhamnosus VAN, FOS R Table 4: Expected resistant phenotype in gram-positive bacteria Expected phenotypes 1.2
|
||||
genus_species one_of Clostridium ramosum, Clostridium innocuum VAN R Table 5: Expected resistant phenotype in anaerobes Expected phenotypes 1.2
|
||||
order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
@ -958,7 +1044,7 @@ genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules
|
||||
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
|
||||
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
@ -1076,7 +1162,7 @@ genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules
|
||||
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.3
|
||||
genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
|
||||
|
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|
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|
||||
930e15623071edb2196fcf8b2a259380
|
||||
cb89a8b02473f40365a46e62fce5ec93
|
||||
|
||||
Binary file not shown.
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@ -12182,21 +12182,21 @@
|
||||
"Aestuariimicrobium" "Nalidixic acid"
|
||||
"Aestuariimicrobium" "Polymyxin B"
|
||||
"Aestuariimicrobium" "Temocillin"
|
||||
"Aestuariimicrobium ganziense" "Aztreonam"
|
||||
"Aestuariimicrobium ganziense" "Colistin"
|
||||
"Aestuariimicrobium ganziense" "Nalidixic acid"
|
||||
"Aestuariimicrobium ganziense" "Polymyxin B"
|
||||
"Aestuariimicrobium ganziense" "Temocillin"
|
||||
"Aestuariimicrobium kwangyangense" "Aztreonam"
|
||||
"Aestuariimicrobium kwangyangense" "Colistin"
|
||||
"Aestuariimicrobium kwangyangense" "Nalidixic acid"
|
||||
"Aestuariimicrobium kwangyangense" "Polymyxin B"
|
||||
"Aestuariimicrobium kwangyangense" "Temocillin"
|
||||
"Aestuariimicrobium soli" "Aztreonam"
|
||||
"Aestuariimicrobium soli" "Colistin"
|
||||
"Aestuariimicrobium soli" "Nalidixic acid"
|
||||
"Aestuariimicrobium soli" "Polymyxin B"
|
||||
"Aestuariimicrobium soli" "Temocillin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Temocillin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Temocillin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Temocillin"
|
||||
"Affinibrenneria" "Acetylmidecamycin"
|
||||
"Affinibrenneria" "Acetylspiramycin"
|
||||
"Affinibrenneria" "Avoparcin"
|
||||
@ -89868,20 +89868,20 @@
|
||||
"Liquorilactobacillus capillatus" "Nalidixic acid"
|
||||
"Liquorilactobacillus capillatus" "Polymyxin B"
|
||||
"Liquorilactobacillus capillatus" "Temocillin"
|
||||
"Lactobacillus casei pseudoplantarum" "Aztreonam"
|
||||
"Lactobacillus casei pseudoplantarum" "Colistin"
|
||||
"Lactobacillus casei pseudoplantarum" "Nalidixic acid"
|
||||
"Lactobacillus casei pseudoplantarum" "Polymyxin B"
|
||||
"Lactobacillus casei pseudoplantarum" "Teicoplanin"
|
||||
"Lactobacillus casei pseudoplantarum" "Temocillin"
|
||||
"Lactobacillus casei pseudoplantarum" "Vancomycin"
|
||||
"Lactobacillus casei casei" "Aztreonam"
|
||||
"Lactobacillus casei casei" "Colistin"
|
||||
"Lactobacillus casei casei" "Nalidixic acid"
|
||||
"Lactobacillus casei casei" "Polymyxin B"
|
||||
"Lactobacillus casei casei" "Teicoplanin"
|
||||
"Lactobacillus casei casei" "Temocillin"
|
||||
"Lactobacillus casei casei" "Vancomycin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Teicoplanin"
|
||||
"Temocillin"
|
||||
"Vancomycin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Teicoplanin"
|
||||
"Temocillin"
|
||||
"Vancomycin"
|
||||
"Limosilactobacillus caviae" "Aztreonam"
|
||||
"Limosilactobacillus caviae" "Colistin"
|
||||
"Limosilactobacillus caviae" "Nalidixic acid"
|
||||
@ -293754,16 +293754,16 @@
|
||||
"Streptosporangium yunnanense" "Nalidixic acid"
|
||||
"Streptosporangium yunnanense" "Polymyxin B"
|
||||
"Streptosporangium yunnanense" "Temocillin"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Aztreonam"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Colistin"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Nalidixic acid"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Polymyxin B"
|
||||
"Streptoverticillium cinnamoneum lanosum" "Temocillin"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Aztreonam"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Colistin"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Nalidixic acid"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Polymyxin B"
|
||||
"Streptoverticillium cinnamoneum sparsum" "Temocillin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Temocillin"
|
||||
"Aztreonam"
|
||||
"Colistin"
|
||||
"Nalidixic acid"
|
||||
"Polymyxin B"
|
||||
"Temocillin"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Aztreonam"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Colistin"
|
||||
"Streptoverticillium olivoreticuli olivoreticuli" "Nalidixic acid"
|
||||
|
||||
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@ -1 +1 @@
|
||||
a16b8db2140952b8a5848989afdccb53
|
||||
dfdbbebfe1a542270d63b94c12889860
|
||||
|
||||
Binary file not shown.
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@ -311,6 +311,19 @@
|
||||
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella orale"
|
||||
"B_HACEK" "B_KGLLA_ORLS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella oralis"
|
||||
"B_HACEK" "B_KGLLA_POTS" "Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK)" "Kingella potus"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_AFRC" "Klebsiella pneumoniae complex" "Klebsiella africana"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_PNMN" "Klebsiella pneumoniae complex" "Klebsiella pneumoniae"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_PNMN_OZAN" "Klebsiella pneumoniae complex" "Klebsiella pneumoniae ozaenae"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_PNMN_PNMN" "Klebsiella pneumoniae complex" "Klebsiella pneumoniae pneumoniae"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_PNMN_RHNS" "Klebsiella pneumoniae complex" "Klebsiella pneumoniae rhinoscleromatis"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_QSPN" "Klebsiella pneumoniae complex" "Klebsiella quasipneumoniae"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_QSPN_QSPN" "Klebsiella pneumoniae complex" "Klebsiella quasipneumoniae quasipneumoniae"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_QSPN_SMLP" "Klebsiella pneumoniae complex" "Klebsiella quasipneumoniae similipneumoniae"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_QSVR" "Klebsiella pneumoniae complex" "Klebsiella quasivariicola"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_VRCL" "Klebsiella pneumoniae complex" "Klebsiella variicola"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_VRCL_TRPC" "Klebsiella pneumoniae complex" "Klebsiella variicola tropica"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_VRCL_LNSS" "Klebsiella pneumoniae complex" "Klebsiella variicola tropicalensis"
|
||||
"B_KLBSL_PNMN-C" "B_KLBSL_VRCL_VRCL" "Klebsiella pneumoniae complex" "Klebsiella variicola variicola"
|
||||
"F_MYRZY_GLLR-C" "F_CANDD_FRMN" "Meyerozyma guilliermondii complex" "Candida fermentati"
|
||||
"F_MYRZY_GLLR-C" "F_MYRZY_CRBB" "Meyerozyma guilliermondii complex" "Meyerozyma caribbica"
|
||||
"F_MYRZY_GLLR-C" "F_MYRZY_CRPP" "Meyerozyma guilliermondii complex" "Meyerozyma carpophila"
|
||||
|
||||
Binary file not shown.
@ -1 +1 @@
|
||||
9c53db03dcf9c98ef571fcc6c16d0a68
|
||||
5908f9e6e7687dfb8301d27fb26d1790
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -1831,11 +1831,11 @@
|
||||
"B_AESTR_LTRL" "Aestuariibacter litoralis" "synonym" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Alteromonadales" "Alteromonadaceae" "Aestuariibacter" "litoralis" "" "species" "Tanaka et al., 2010" "aerobe" "LPSN" "788348" "515053" "791011" "3222678" 2 ""
|
||||
"B_AESTR_SLXG" "Aestuariibacter salexigens" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Alteromonadales" "Alteromonadaceae" "Aestuariibacter" "salexigens" "" "species" "Yi et al., 2004" "aerobe" "LPSN" "772927" "515053" "3222678" 2 "426337003"
|
||||
"B_RBCLM1" "Aestuariibaculum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "" "" "genus" "Hameed et al., 2014" "aerobe" "LPSN" "518286" "524" "8124539" "4898201" 2 ""
|
||||
"B_RBCLM1_B_RBCLM1_LTLN" "Aestuariibaculum lutulentum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "lutulentum" "" "species" "Gao et al., 2024" "aerobe" "LPSN" "43727" "518286" "8124539" 2 ""
|
||||
"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_MRNM" "Aestuariibaculum marinum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "marinum" "" "species" "Choi et al., 2019" "aerobe" "LPSN" "798029" "518286" "11167655" "8124539" 2 ""
|
||||
"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_SCPM" "Aestuariibaculum scopimerae" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "scopimerae" "" "species" "Lee et al., 2021" "aerobe" "LPSN" "18922" "518286" "8124539" 2 ""
|
||||
"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_SDMN" "Aestuariibaculum sediminum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "sediminum" "" "species" "Wu et al., 2022" "aerobe" "LPSN" "28837" "518286" "11894177" "8124539" 2 ""
|
||||
"B_RBCLM1_B_RBCLM1_B_RBCLM1_B_RBCLM1_SNCH" "Aestuariibaculum suncheonense" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "suncheonense" "" "species" "Jeong et al., 2013" "aerobe" "LPSN" "790362" "518286" "7885799" "8124539" 2 ""
|
||||
"B_RBCLM1_LTLN" "Aestuariibaculum lutulentum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "lutulentum" "" "species" "Gao et al., 2024" "aerobe" "LPSN" "43727" "518286" "8124539" 2 ""
|
||||
"B_RBCLM1_MRNM" "Aestuariibaculum marinum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "marinum" "" "species" "Choi et al., 2019" "aerobe" "LPSN" "798029" "518286" "11167655" "8124539" 2 ""
|
||||
"B_RBCLM1_SCPM" "Aestuariibaculum scopimerae" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "scopimerae" "" "species" "Lee et al., 2021" "aerobe" "LPSN" "18922" "518286" "8124539" 2 ""
|
||||
"B_RBCLM1_SDMN" "Aestuariibaculum sediminum" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "sediminum" "" "species" "Wu et al., 2022" "aerobe" "LPSN" "28837" "518286" "11894177" "8124539" 2 ""
|
||||
"B_RBCLM1_SNCH" "Aestuariibaculum suncheonense" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariibaculum" "suncheonense" "" "species" "Jeong et al., 2013" "aerobe" "LPSN" "790362" "518286" "7885799" "8124539" 2 ""
|
||||
"B_STRBS" "Aestuariibius" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Roseobacteraceae" "Aestuariibius" "" "" "genus" "Park et al., 2018" "LPSN" "520366" "11172" 2 ""
|
||||
"B_STRBS_INSL" "Aestuariibius insulae" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Roseobacteraceae" "Aestuariibius" "insulae" "" "species" "Park et al., 2018" "LPSN" "797657" "520366" 2 ""
|
||||
"B_AESTRC" "Aestuariicella" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Alteromonadales" "" "Aestuariicella" "" "" "genus" "Xue et al., 2022" "LPSN" "518743" "5070" "7614213" 2 ""
|
||||
@ -1848,9 +1848,9 @@
|
||||
"B_HBTNS" "Aestuariihabitans" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Roseobacteraceae" "Aestuariihabitans" "" "" "genus" "Yoon et al., 2014" "aerobe" "LPSN" "518472" "11172" "7574420" 2 ""
|
||||
"B_HBTNS_BLGY" "Aestuariihabitans beolgyonensis" "accepted" "Bacteria" "Pseudomonadota" "Alphaproteobacteria" "Rhodobacterales" "Roseobacteraceae" "Aestuariihabitans" "beolgyonensis" "" "species" "Yoon et al., 2014" "aerobe" "LPSN" "791419" "518472" "7574420" 2 ""
|
||||
"B_MCRBM1" "Aestuariimicrobium" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "" "" "genus" "Chen et al., 2018" "facultative anaerobe" "LPSN" "517663" "1114" "4884973" "8088" 2 ""
|
||||
"B_MCRBM1_B_MCRBM1_B_MCRBM1_GNZN" "Aestuariimicrobium ganziense" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "ganziense" "" "species" "likely facultative anaerobe" "GBIF" "517663" "11500818" "4884973" 2 ""
|
||||
"B_MCRBM1_B_MCRBM1_B_MCRBM1_B_MCRBM1_KWNG" "Aestuariimicrobium kwangyangense" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "kwangyangense" "" "species" "Jung et al., 2007" "aerobe" "LPSN" "786691" "517663" "5905030" "4884973" 2 ""
|
||||
"B_MCRBM1_B_MCRBM1_B_MCRBM1_B_MCRBM1_SOLI" "Aestuariimicrobium soli" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "soli" "" "species" "Chen et al., 2018" "facultative anaerobe" "LPSN" "797883" "517663" "4884973" 2 ""
|
||||
"B_MCRBM1_GNZN" "Aestuariimicrobium ganziense" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "ganziense" "" "species" "likely facultative anaerobe" "GBIF" "517663" "11500818" "4884973" 2 ""
|
||||
"B_MCRBM1_KWNG" "Aestuariimicrobium kwangyangense" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "kwangyangense" "" "species" "Jung et al., 2007" "aerobe" "LPSN" "786691" "517663" "5905030" "4884973" 2 ""
|
||||
"B_MCRBM1_SOLI" "Aestuariimicrobium soli" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Propionibacteriales" "Propionibacteriaceae" "Aestuariimicrobium" "soli" "" "species" "Chen et al., 2018" "facultative anaerobe" "LPSN" "797883" "517663" "4884973" 2 ""
|
||||
"B_TRMNS" "Aestuariimonas" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariimonas" "" "" "genus" "Park et al., 2018" "aerobe" "LPSN" "519333" "524" "4898201" 2 ""
|
||||
"B_TRMNS_INSL" "Aestuariimonas insulae" "accepted" "Bacteria" "Bacteroidota" "Flavobacteriia" "Flavobacteriales" "Flavobacteriaceae" "Aestuariimonas" "insulae" "" "species" "Park et al., 2018" "aerobe" "LPSN" "796399" "519333" 2 ""
|
||||
"B_[FAM]_ASTRRHBD" "Aestuariirhabdaceae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Oceanospirillales" "Aestuariirhabdaceae" "" "" "" "family" "Khan et al., 2020" "LPSN" "4854" "5074" "11127023" 2 ""
|
||||
@ -33646,6 +33646,7 @@
|
||||
"B_KLBSL_PSTR" "Klebsiella pasteurii" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "pasteurii" "" "species" "Merla et al., 2020" "likely facultative anaerobe" "LPSN" "5622" "515890" "12165548" "3221927" "11145273" 1 ""
|
||||
"B_KLBSL_PLNT" "Klebsiella planticola" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "planticola" "" "species" "Bagley et al., 1982" "facultative anaerobe" "LPSN" "777150" "515890" "5427566" "3221927" 1 ""
|
||||
"B_KLBSL_PNMN" "Klebsiella pneumoniae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "pneumoniae" "" "species" "Trevisan, 1887" "facultative anaerobe" "LPSN" "777151" "515890" "3221874" "3221927" 1 "1098101000112102,446870005,1098201000112108,409801009,56415008,714315002,713926009"
|
||||
"B_KLBSL_PNMN-C" "Klebsiella pneumoniae complex" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "pneumoniae complex" "" "species group" "facultative anaerobe" "Manually added" "515890" "3221927" 1 ""
|
||||
"B_KLBSL_PNMN_OZAN" "Klebsiella pneumoniae ozaenae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "pneumoniae" "ozaenae" "subspecies" "Orskov, 1984" "LPSN" "777152" "777151" "5427614" "3221874" 1 "65186004"
|
||||
"B_KLBSL_PNMN_PNMN" "Klebsiella pneumoniae pneumoniae" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "pneumoniae" "pneumoniae" "subspecies" "Orskov, 1984" "LPSN" "777153" "777151" "7234532" "3221874" 1 "18400002"
|
||||
"B_KLBSL_PNMN_RHNS" "Klebsiella pneumoniae rhinoscleromatis" "accepted" "Bacteria" "Pseudomonadota" "Gammaproteobacteria" "Enterobacterales" "Enterobacteriaceae" "Klebsiella" "pneumoniae" "rhinoscleromatis" "subspecies" "Orskov, 1984" "LPSN" "777154" "777151" "5427616" "3221874" 1 "17688001"
|
||||
@ -34472,12 +34473,12 @@
|
||||
"B_LCTBC_CMLL" "Lactobacillus camelliae" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "camelliae" "" "species" "Tanasupawat et al., 2007" "likely facultative anaerobe" "LPSN" "786434" "517058" "10738" "8081695" "3223445" 1.5 ""
|
||||
"B_LCTBC_CPLL" "Lactobacillus capillatus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "capillatus" "" "species" "Chao et al., 2008" "likely facultative anaerobe" "LPSN" "787617" "517058" "10739" "7603537" "3223445" 1.5 ""
|
||||
"B_LCTBC_CRNS" "Lactobacillus carnis" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "carnis" "" "species" "Shaw et al., 1986" "likely facultative anaerobe" "LPSN" "777267" "517058" "774486" "3223445" 1.5 ""
|
||||
"B_LCTBC_CASE_PSDP" "Lactobacillus casei" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "" "species" "Hansen et al., 1971" "likely facultative anaerobe" "LPSN" "777268" "517058" "10711" "3227248" "3223445" 1.15 "1017006,113779003"
|
||||
"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_ALCT" "Lactobacillus casei alactosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "alactosus" "subspecies" "Mills et al., 1973" "LPSN" "777269" "777268" "777272" "3227250" "3227248" "3227330" 1.15 ""
|
||||
"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_CASE" "Lactobacillus casei casei" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "casei" "subspecies" "Abo-Elnaga et al., 1965" "LPSN" "777270" "777268" "7234596" "3227248" "3227248" 1.15 "28315003"
|
||||
"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_PSDP" "Lactobacillus casei pseudoplantarum" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "pseudoplantarum" "subspecies" "Abo-Elnaga et al., 1965" "LPSN" "777272" "777268" "3227251" "3227248" "3227330" 1.15 "58249006"
|
||||
"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_RHMN" "Lactobacillus casei rhamnosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "rhamnosus" "subspecies" "Hansen, 1968" "LPSN" "777273" "777268" "10740" "3227212" "3227248" "3227211" 1.15 ""
|
||||
"B_LCTBC_CASE_PSDP_PSDP_PSDP_PSDP_TLRN" "Lactobacillus casei tolerans" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "tolerans" "subspecies" "Abo-Elnaga et al., 1965" "LPSN" "777274" "777268" "10878" "3227332" "3227248" "3227331" 1.15 "5234000"
|
||||
"B_LCTBC_CASE" "Lactobacillus casei" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "" "species" "Hansen et al., 1971" "likely facultative anaerobe" "LPSN" "777268" "517058" "10711" "3227248" "3223445" 1.15 "1017006,113779003"
|
||||
"B_LCTBC_CASE_ALCT" "Lactobacillus casei alactosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "alactosus" "subspecies" "Mills et al., 1973" "LPSN" "777269" "777268" "777272" "3227250" "3227248" "3227330" 1.15 ""
|
||||
"B_LCTBC_CASE_CASE" "Lactobacillus casei casei" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "casei" "subspecies" "Abo-Elnaga et al., 1965" "LPSN" "777270" "777268" "7234596" "3227248" "3227248" 1.15 "28315003"
|
||||
"B_LCTBC_CASE_PSDP" "Lactobacillus casei pseudoplantarum" "accepted" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "pseudoplantarum" "subspecies" "Abo-Elnaga et al., 1965" "LPSN" "777272" "777268" "3227251" "3227248" "3227330" 1.15 "58249006"
|
||||
"B_LCTBC_CASE_RHMN" "Lactobacillus casei rhamnosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "rhamnosus" "subspecies" "Hansen, 1968" "LPSN" "777273" "777268" "10740" "3227212" "3227248" "3227211" 1.15 ""
|
||||
"B_LCTBC_CASE_TLRN" "Lactobacillus casei tolerans" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "casei" "tolerans" "subspecies" "Abo-Elnaga et al., 1965" "LPSN" "777274" "777268" "10878" "3227332" "3227248" "3227331" 1.15 "5234000"
|
||||
"B_LCTBC_CTNF" "Lactobacillus catenaforme" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "catenaforme" "" "species" "Moore et al., 1970" "likely facultative anaerobe" "LPSN" "798354" "517058" "777275" "3223445" 1.5 ""
|
||||
"B_LCTBC_CTNFR" "Lactobacillus catenaformis" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "catenaformis" "" "species" "Moore et al., 1970" "likely facultative anaerobe" "LPSN" "777275" "517058" "789495" "3223445" 1.15 ""
|
||||
"B_LCTBC_CAVI" "Lactobacillus caviae" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "caviae" "" "species" "Killer et al., 2017" "likely facultative anaerobe" "LPSN" "795698" "517058" "10866" "9674251" "3223445" 1.5 ""
|
||||
@ -34701,9 +34702,9 @@
|
||||
"B_LCTBC_SAKE" "Lactobacillus sake" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sake" "" "species" "Torriani et al., 1996" "likely facultative anaerobe" "LPSN" "784069" "517058" "777388" "3223445" 1.5 ""
|
||||
"B_LCTBC_SAKE_CRNS" "Lactobacillus sake carnosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sake" "carnosus" "subspecies" "Torriani et al., 1996" "LPSN" "784070" "784069" "777389" 1.5 ""
|
||||
"B_LCTBC_SAKE_SAKE" "Lactobacillus sake sake" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sake" "sake" "subspecies" "Torriani et al., 1996" "LPSN" "784071" "784069" "777390" 1.5 ""
|
||||
"B_LCTBC_SKEI_SAKE" "Lactobacillus sakei" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "" "species" "Klein et al., 1996" "likely facultative anaerobe" "LPSN" "777388" "517058" "10710" "3227207" "3223445" 1.5 "39861009,113799009,113800008"
|
||||
"B_LCTBC_SKEI_SAKE_SAKE_SAKE_SAKE_CRNS" "Lactobacillus sakei carnosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "carnosus" "subspecies" "Torriani et al., 1996" "LPSN" "777389" "777388" "10881" "3227207" 1.5 ""
|
||||
"B_LCTBC_SKEI_SAKE_SAKE_SAKE_SAKE_SAKE" "Lactobacillus sakei sakei" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "sakei" "subspecies" "Torriani et al., 1996" "LPSN" "777390" "777388" "10877" "3227207" 1.5 ""
|
||||
"B_LCTBC_SKEI" "Lactobacillus sakei" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "" "species" "Klein et al., 1996" "likely facultative anaerobe" "LPSN" "777388" "517058" "10710" "3227207" "3223445" 1.5 "39861009,113799009,113800008"
|
||||
"B_LCTBC_SKEI_CRNS" "Lactobacillus sakei carnosus" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "carnosus" "subspecies" "Torriani et al., 1996" "LPSN" "777389" "777388" "10881" "3227207" 1.5 ""
|
||||
"B_LCTBC_SKEI_SAKE" "Lactobacillus sakei sakei" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "sakei" "sakei" "subspecies" "Torriani et al., 1996" "LPSN" "777390" "777388" "10877" "3227207" 1.5 ""
|
||||
"B_LCTBC_SLTL" "Lactobacillus salitolerans" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "salitolerans" "" "species" "Tohno et al., 2019" "likely facultative anaerobe" "LPSN" "800710" "517058" "10660" "3223445" 1.5 ""
|
||||
"B_LCTBC_SLVR" "Lactobacillus salivarius" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "salivarius" "" "species" "Li et al., 2006" "likely facultative anaerobe" "LPSN" "784072" "517058" "10714" "3227229" "3223445" 1.5 "37809002"
|
||||
"B_LCTBC_SLVR_SLCN" "Lactobacillus salivarius salicinius" "synonym" "Bacteria" "Bacillota" "Bacilli" "Lactobacillales" "Lactobacillaceae" "Lactobacillus" "salivarius" "salicinius" "subspecies" "Rogosa et al., 1953" "LPSN" "777391" "784072" "10714" "3227230" "3227229" "3227229" 1.5 "86840000"
|
||||
@ -61351,9 +61352,9 @@
|
||||
"B_RSVRG_MRTM" "Roseivirga maritima" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "maritima" "" "species" "Jung et al., 2016" "aerobe" "LPSN" "794295" "517334" 2 ""
|
||||
"B_RSVRG_MSKN" "Roseivirga misakiensis" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "misakiensis" "" "species" "Garcia-Lopez et al., 2020" "aerobe" "LPSN" "7880" "517334" 2 ""
|
||||
"B_RSVRG_PCFC" "Roseivirga pacifica" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "pacifica" "" "species" "Garcia-Lopez et al., 2020" "aerobe" "LPSN" "7873" "517334" 2 ""
|
||||
"B_RSVRG_SHNS_AQPN" "Roseivirga seohaensis" "synonym" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "seohaensis" "" "species" "Garcia-Lopez et al., 2019" "aerobe" "LPSN" "784819" "517334" "784818" "7234517" "9629563" 2 ""
|
||||
"B_RSVRG_SHNS_AQPN_AQPN_AQPN_AQPN_AQPN" "Roseivirga seohaensis aquiponti" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "seohaensis" "aquiponti" "subspecies" "Selvaratnam et al., 2016" "LPSN" "794907" "784819" "9507856" "7234517" 2 ""
|
||||
"B_RSVRG_SHNS_AQPN_AQPN_AQPN_AQPN_SHNS" "Roseivirga seohaensis seohaensis" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "seohaensis" "seohaensis" "subspecies" "Selvaratnam et al., 2016" "LPSN" "794906" "784819" "9629563" "7234517" 2 ""
|
||||
"B_RSVRG_SHNS" "Roseivirga seohaensis" "synonym" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "seohaensis" "" "species" "Garcia-Lopez et al., 2019" "aerobe" "LPSN" "784819" "517334" "784818" "7234517" "9629563" 2 ""
|
||||
"B_RSVRG_SHNS_AQPN" "Roseivirga seohaensis aquiponti" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "seohaensis" "aquiponti" "subspecies" "Selvaratnam et al., 2016" "LPSN" "794907" "784819" "9507856" "7234517" 2 ""
|
||||
"B_RSVRG_SHNS_SHNS" "Roseivirga seohaensis seohaensis" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "seohaensis" "seohaensis" "subspecies" "Selvaratnam et al., 2016" "LPSN" "794906" "784819" "9629563" "7234517" 2 ""
|
||||
"B_RSVRG_SPNG" "Roseivirga spongicola" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "spongicola" "" "species" "Hahnke et al., 2016" "aerobe" "LPSN" "784820" "517334" 2 ""
|
||||
"B_RSVRG_THRM" "Roseivirga thermotolerans" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "Roseivirga" "thermotolerans" "" "species" "Garcia-Lopez et al., 2020" "aerobe" "LPSN" "7881" "517334" 2 ""
|
||||
"B_[FAM]_ROSEVRGC" "Roseivirgaceae" "accepted" "Bacteria" "Bacteroidota" "Cytophagia" "Cytophagales" "Roseivirgaceae" "" "" "" "family" "Garcia-Lopez et al., 2020" "LPSN" "7785" "5018" "7571564" 2 ""
|
||||
@ -68974,8 +68975,8 @@
|
||||
"B_SMYCS_CVRN" "Streptomyces cavernae" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cavernae" "" "species" "Fang et al., 2020" "aerobe" "LPSN" "5701" "517119" "11121506" "3223560" 1.5 ""
|
||||
"B_SMYCS_CVSC" "Streptomyces caviscabies" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "caviscabies" "" "species" "Goyer et al., 1996" "likely facultative anaerobe" "LPSN" "781532" "517119" "781730" "3224180" "3223560" "3224177" 1.25 ""
|
||||
"B_SMYCS_CVRN1" "Streptomyces cavourensis" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cavourensis" "" "species" "Skarbek et al., 1978" "likely facultative anaerobe" "LPSN" "785000" "517119" "3223903" "3223560" "3224107" 1.5 "439655009"
|
||||
"B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_CVRN" "Streptomyces cavourensis cavourensis" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cavourensis" "cavourensis" "subspecies" "Skarbek et al., 1978" "LPSN" "781533" "785000" "785000" "7073676" "3223903" "3224107" 1.5 ""
|
||||
"B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_B_SMYCS_CVRN1_WSHN" "Streptomyces cavourensis washingtonensis" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cavourensis" "washingtonensis" "subspecies" "Skarbek et al., 1978" "LPSN" "781534" "785000" "781600" "3223905" "3223903" "3223678" 1.5 ""
|
||||
"B_SMYCS_CVRN1_CVRN" "Streptomyces cavourensis cavourensis" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cavourensis" "cavourensis" "subspecies" "Skarbek et al., 1978" "LPSN" "781533" "785000" "785000" "7073676" "3223903" "3224107" 1.5 ""
|
||||
"B_SMYCS_CVRN1_WSHN" "Streptomyces cavourensis washingtonensis" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cavourensis" "washingtonensis" "subspecies" "Skarbek et al., 1978" "LPSN" "781534" "785000" "781600" "3223905" "3223903" "3223678" 1.5 ""
|
||||
"B_SMYCS_CLLS" "Streptomyces cellostaticus" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cellostaticus" "" "species" "Nouioui et al., 2018" "likely facultative anaerobe" "LPSN" "781536" "517119" "3223772" "3223560" 1.5 "441384008"
|
||||
"B_SMYCS_CLLL" "Streptomyces celluloflavus" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "celluloflavus" "" "species" "Madhaiyan et al., 2020" "likely facultative anaerobe" "LPSN" "781537" "517119" "3223631" "3223560" 1.5 "439645005"
|
||||
"B_SMYCS_YTCS" "Streptomyces cellulolyticus" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptomyces" "cellulolyticus" "" "species" "1997" "likely facultative anaerobe" "LPSN" "785001" "517119" "3224135" "3223560" 1.5 "439191003"
|
||||
@ -69924,11 +69925,11 @@
|
||||
"B_SCLLM_BLDC" "Streptoverticillium baldaccii" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "baldaccii" "" "species" "Farina et al., 1966" "LPSN" "782192" "516693" "781490" 2 ""
|
||||
"B_SCLLM_BVRT" "Streptoverticillium biverticillatum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "biverticillatum" "" "species" "Farina et al., 1966" "LPSN" "782193" "516693" "781748" 2 ""
|
||||
"B_SCLLM_BLST" "Streptoverticillium blastmyceticum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "blastmyceticum" "" "species" "Locci et al., 1969" "LPSN" "782194" "516693" "781498" 2 ""
|
||||
"B_SCLLM_CNNM_LNSM" "Streptoverticillium cinnamoneum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "" "species" "Baldacci et al., 1966" "LPSN" "782196" "516693" "781561" 2 ""
|
||||
"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_ALBS" "Streptoverticillium cinnamoneum albosporum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "albosporum" "subspecies" "Thirumalachar, 1968" "LPSN" "782197" "782196" "781562" 2 ""
|
||||
"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_CNNM" "Streptoverticillium cinnamoneum cinnamoneum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "cinnamoneum" "subspecies" "Thirumalachar, 1968" "LPSN" "782199" "782196" "781563" 2 ""
|
||||
"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_LNSM" "Streptoverticillium cinnamoneum lanosum" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "lanosum" "subspecies" "Thirumalachar, 1968" "LPSN" "782200" "782196" 2 ""
|
||||
"B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM_SPRS" "Streptoverticillium cinnamoneum sparsum" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "sparsum" "subspecies" "Thirumalachar, 1968" "LPSN" "782201" "782196" 2 ""
|
||||
"B_SCLLM_CNNM" "Streptoverticillium cinnamoneum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "" "species" "Baldacci et al., 1966" "LPSN" "782196" "516693" "781561" 2 ""
|
||||
"B_SCLLM_CNNM_ALBS" "Streptoverticillium cinnamoneum albosporum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "albosporum" "subspecies" "Thirumalachar, 1968" "LPSN" "782197" "782196" "781562" 2 ""
|
||||
"B_SCLLM_CNNM_CNNM" "Streptoverticillium cinnamoneum cinnamoneum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "cinnamoneum" "subspecies" "Thirumalachar, 1968" "LPSN" "782199" "782196" "781563" 2 ""
|
||||
"B_SCLLM_CNNM_LNSM" "Streptoverticillium cinnamoneum lanosum" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "lanosum" "subspecies" "Thirumalachar, 1968" "LPSN" "782200" "782196" 2 ""
|
||||
"B_SCLLM_CNNM_SPRS" "Streptoverticillium cinnamoneum sparsum" "accepted" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "cinnamoneum" "sparsum" "subspecies" "Thirumalachar, 1968" "LPSN" "782201" "782196" 2 ""
|
||||
"B_SCLLM_DSTL" "Streptoverticillium distallicum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "distallicum" "" "species" "Locci et al., 1969" "LPSN" "782202" "516693" "781875" 2 ""
|
||||
"B_SCLLM_EHMN" "Streptoverticillium ehimense" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "ehimense" "" "species" "Locci et al., 1969" "LPSN" "782203" "516693" "781400" 2 ""
|
||||
"B_SCLLM_ERCD" "Streptoverticillium eurocidicum" "synonym" "Bacteria" "Actinomycetota" "Actinomycetes" "Kitasatosporales" "Streptomycetaceae" "Streptoverticillium" "eurocidicum" "" "species" "Locci et al., 1969" "LPSN" "782204" "516693" "781631" 2 ""
|
||||
@ -72428,8 +72429,8 @@
|
||||
"B_[FAM]_THRMSLFD" "Thermosulfidibacteraceae" "accepted" "Bacteria" "Aquificota" "Aquificia" "Thermosulfidibacterales" "Thermosulfidibacteraceae" "" "" "" "family" "Chuvochina et al., 2024" "LPSN" "43615" "43708" "10786899" 2 ""
|
||||
"B_[ORD]_THRMSLFD" "Thermosulfidibacterales" "accepted" "Bacteria" "Aquificota" "Aquificia" "Thermosulfidibacterales" "" "" "" "" "order" "Chuvochina et al., 2024" "LPSN" "43708" "37120" 2 ""
|
||||
"B_TRMNS1" "Thermosulfurimonas" "accepted" "Bacteria" "Thermodesulfobacteriota" "Thermodesulfobacteria" "Thermodesulfobacteriales" "Thermodesulfobacteriaceae" "Thermosulfurimonas" "" "" "genus" "Slobodkin et al., 2012" "anaerobe" "LPSN" "518269" "1440" "11114975" "9543" 2 ""
|
||||
"B_TRMNS1_B_TRMNS1_B_TRMNS1_B_TRMNS1_DSMT" "Thermosulfurimonas dismutans" "accepted" "Bacteria" "Thermodesulfobacteriota" "Thermodesulfobacteria" "Thermodesulfobacteriales" "Thermodesulfobacteriaceae" "Thermosulfurimonas" "dismutans" "" "species" "Slobodkin et al., 2012" "anaerobe" "LPSN" "790271" "518269" "7901824" "11114975" 2 ""
|
||||
"B_TRMNS1_B_TRMNS1_B_TRMNS1_B_TRMNS1_B_TRMNS1_MARN" "Thermosulfurimonas marina" "accepted" "Bacteria" "Thermodesulfobacteriota" "Thermodesulfobacteria" "Thermodesulfobacteriales" "Thermodesulfobacteriaceae" "Thermosulfurimonas" "marina" "" "species" "Frolova et al., 2019" "anaerobe" "LPSN" "5307" "518269" "11114975" 2 ""
|
||||
"B_TRMNS1_DSMT" "Thermosulfurimonas dismutans" "accepted" "Bacteria" "Thermodesulfobacteriota" "Thermodesulfobacteria" "Thermodesulfobacteriales" "Thermodesulfobacteriaceae" "Thermosulfurimonas" "dismutans" "" "species" "Slobodkin et al., 2012" "anaerobe" "LPSN" "790271" "518269" "7901824" "11114975" 2 ""
|
||||
"B_TRMNS1_MARN" "Thermosulfurimonas marina" "accepted" "Bacteria" "Thermodesulfobacteriota" "Thermodesulfobacteria" "Thermodesulfobacteriales" "Thermodesulfobacteriaceae" "Thermosulfurimonas" "marina" "" "species" "Frolova et al., 2019" "anaerobe" "LPSN" "5307" "518269" "11114975" 2 ""
|
||||
"B_TPHLS" "Thermosulfuriphilus" "accepted" "Bacteria" "Thermodesulfobacteriota" "" "" "" "Thermosulfuriphilus" "" "" "genus" "Slobodkina et al., 2017" "LPSN" "519252" "25893" 2 ""
|
||||
"B_TPHLS_AMMN" "Thermosulfuriphilus ammonigenes" "accepted" "Bacteria" "Thermodesulfobacteriota" "" "" "" "Thermosulfuriphilus" "ammonigenes" "" "species" "Slobodkina et al., 2017" "LPSN" "795868" "519252" 2 ""
|
||||
"B_[FAM]_THRMSYNC" "Thermosynechococcaceae" "accepted" "Bacteria" "Cyanobacteria" "Cyanobacteriia" "Thermosynechococcales" "Thermosynechococcaceae" "" "" "" "family" "Komarek et al., 2020" "LPSN" "39015" "10683622" "10831881" 2 ""
|
||||
|
||||
Binary file not shown.
@ -2107,6 +2107,11 @@ taxonomy$rank[which(taxonomy$fullname %like% "unknown")] <- "(unknown rank)"
|
||||
|
||||
# Some final checks -------------------------------------------------------------------------------
|
||||
|
||||
# this happened in early 2025, check that MO codes do not have repeated elements
|
||||
# fixed it then like this: microorganisms$mo <- gsub("B_SCLLM_CNNM_LNSM_LNSM_LNSM_LNSM", "B_SCLLM_CNNM", microorganisms$mo)
|
||||
taxonomy |> filter(mo %like% "_.*_.*_.*_") |> View()
|
||||
|
||||
|
||||
fix_old_mos <- function(dataset) {
|
||||
df <- dataset %>% mutate(mo = as.character(mo))
|
||||
df$mo[which(!df$mo %in% taxonomy$mo)] <- df %>% filter(!mo %in% taxonomy$mo) %>% mutate(name = mo_name(mo, keep_synonyms = TRUE), new_mo = taxonomy$mo[match(name, taxonomy$fullname)]) %>% pull(new_mo)
|
||||
|
||||
@ -27,8 +27,9 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# this data set is being used in the clinical_breakpoints data set, and thus by as.sir().
|
||||
# it prevents the breakpoints table from being extremely long for species that are part of a species group.
|
||||
# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().
|
||||
# It prevents the breakpoints table from being extremely long for species that are part of a species group.
|
||||
# Also used by eucast_rules() to expand group names.
|
||||
|
||||
library(dplyr)
|
||||
library(readr)
|
||||
@ -143,6 +144,10 @@ microorganisms.groups <- whonet_organisms %>%
|
||||
filter(mo_group != "B_CTRBC_FRND-C") %>%
|
||||
bind_rows(tibble(mo_group = as.mo("B_CTRBC_FRND-C"),
|
||||
mo = paste("Citrobacter", c("freundii", "braakii", "gillenii", "murliniae", "portucalensis", "sedlakii", "werkmanii", "youngae")) %>% as.mo(keep_synonyms = TRUE))) %>%
|
||||
# Klebsiella pneumoniae complex
|
||||
filter(mo_group != "B_KLBSL_PNMN-C") %>%
|
||||
bind_rows(tibble(mo_group = as.mo("B_KLBSL_PNMN-C"),
|
||||
mo = paste("Klebsiella", c("africana", "pneumoniae", "quasipneumoniae", "quasivariicola", "variicola")) %>% as.mo(keep_synonyms = TRUE))) %>%
|
||||
# Yersinia pseudotuberculosis complex in the NCBI Taxonomy Browser:
|
||||
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1649845
|
||||
filter(mo_group != "B_YERSN_PSDT-C") %>%
|
||||
@ -164,22 +169,19 @@ for (group in unique(microorganisms.groups$mo_group)) {
|
||||
filter(mo %like% spp & rank == "subspecies") %>%
|
||||
pull(mo)
|
||||
# add them
|
||||
microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = group, mo = mos))
|
||||
microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = as.mo(group), mo = mos))
|
||||
}
|
||||
|
||||
# add full names, arrange and clean
|
||||
microorganisms.groups <- microorganisms.groups %>%
|
||||
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE, language = NULL),
|
||||
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
|
||||
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
|
||||
arrange(mo_group_name, mo_name) %>%
|
||||
filter(mo_group != mo) %>%
|
||||
distinct() %>%
|
||||
filter(mo_group != mo) %>%
|
||||
distinct() %>%
|
||||
dataset_UTF8_to_ASCII()
|
||||
mo_uncertainties()
|
||||
|
||||
# add subspecies to all species
|
||||
|
||||
|
||||
class(microorganisms.groups$mo_group) <- c("mo", "character")
|
||||
class(microorganisms.groups$mo) <- c("mo", "character")
|
||||
usethis::use_data(microorganisms.groups, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -72,12 +72,15 @@ Other contributors:
|
||||
\item Dmytro Mykhailenko [contributor]
|
||||
\item Eric H. L. C. M. Hazenberg [contributor]
|
||||
\item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
|
||||
\item Jane Hawkey (\href{https://orcid.org/0000-0001-9661-5293}{ORCID}) [contributor]
|
||||
\item Jason Stull (\href{https://orcid.org/0000-0002-9028-8153}{ORCID}) [contributor]
|
||||
\item Javier Sanchez (\href{https://orcid.org/0000-0003-2605-8094}{ORCID}) [contributor]
|
||||
\item Jonas Salm [contributor]
|
||||
\item Judith M. Fonville [contributor]
|
||||
\item Kathryn Holt (\href{https://orcid.org/0000-0003-3949-2471}{ORCID}) [contributor]
|
||||
\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
|
||||
\item Matthew Saab [contributor]
|
||||
\item Natacha Couto (\href{https://orcid.org/0000-0002-9152-5464}{ORCID}) [contributor]
|
||||
\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
|
||||
\item Rogier P. Schade [contributor]
|
||||
\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
|
||||
|
||||
@ -30,6 +30,7 @@
|
||||
\alias{quinolones}
|
||||
\alias{rifamycins}
|
||||
\alias{streptogramins}
|
||||
\alias{sulfonamides}
|
||||
\alias{tetracyclines}
|
||||
\alias{trimethoprims}
|
||||
\alias{ureidopenicillins}
|
||||
@ -107,6 +108,8 @@ rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
|
||||
|
||||
streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
|
||||
|
||||
sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)
|
||||
|
||||
tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
|
||||
return_all = TRUE, ...)
|
||||
|
||||
@ -203,6 +206,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
|
||||
\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), 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[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
|
||||
\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13)
|
||||
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC)
|
||||
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
|
||||
\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)
|
||||
|
||||
@ -33,7 +33,7 @@ is.sir(x)
|
||||
is_sir_eligible(x, threshold = 0.05)
|
||||
|
||||
\method{as.sir}{default}(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
|
||||
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", ...)
|
||||
NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = TRUE, ...)
|
||||
|
||||
\method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
|
||||
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
|
||||
@ -44,7 +44,7 @@ is_sir_eligible(x, threshold = 0.05)
|
||||
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
|
||||
include_PKPD = getOption("AMR_include_PKPD", TRUE),
|
||||
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
|
||||
verbose = FALSE, conserve_capped_values = NULL, ...)
|
||||
verbose = FALSE, info = TRUE, conserve_capped_values = NULL, ...)
|
||||
|
||||
\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
|
||||
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
|
||||
@ -54,7 +54,7 @@ is_sir_eligible(x, threshold = 0.05)
|
||||
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
|
||||
include_PKPD = getOption("AMR_include_PKPD", TRUE),
|
||||
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
|
||||
verbose = FALSE, ...)
|
||||
verbose = FALSE, info = TRUE, ...)
|
||||
|
||||
\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
|
||||
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
|
||||
@ -65,7 +65,7 @@ is_sir_eligible(x, threshold = 0.05)
|
||||
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
|
||||
include_PKPD = getOption("AMR_include_PKPD", TRUE),
|
||||
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
|
||||
verbose = FALSE, conserve_capped_values = NULL)
|
||||
verbose = FALSE, info = TRUE, conserve_capped_values = NULL)
|
||||
|
||||
sir_interpretation_history(clean = FALSE)
|
||||
}
|
||||
@ -78,6 +78,8 @@ sir_interpretation_history(clean = FALSE)
|
||||
|
||||
\item{S, I, R, NI, SDD}{a case-independent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters and whitespaces are removed from the input.}
|
||||
|
||||
\item{info}{a \link{logical} to print information about the process}
|
||||
|
||||
\item{mo}{a vector (or column name) with \link{character}s that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
|
||||
|
||||
\item{ab}{a vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
@ -51,7 +51,7 @@ df
|
||||
#> 1 Escherichia coli R S S
|
||||
#> 2 Klebsiella pneumoniae R S S
|
||||
|
||||
eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
|
||||
eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
|
||||
#> mo TZP ampi cipro
|
||||
#> 1 Escherichia coli R R S
|
||||
#> 2 Klebsiella pneumoniae R R S
|
||||
@ -65,7 +65,7 @@ There is one exception in columns used for the rules: all column names of the \l
|
||||
\if{html}{\out{<div class="sourceCode r">}}\preformatted{y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
|
||||
TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
|
||||
|
||||
eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
|
||||
eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
|
||||
#> mo TZP ampi cipro
|
||||
#> 1 Escherichia coli R S S
|
||||
#> 2 Klebsiella pneumoniae R R S
|
||||
@ -86,7 +86,7 @@ x
|
||||
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
|
||||
}\if{html}{\out{</div>}}
|
||||
|
||||
These 34 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
|
||||
These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
|
||||
\itemize{
|
||||
\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
|
||||
\item aminopenicillins\cr(amoxicillin and ampicillin)
|
||||
@ -118,6 +118,7 @@ These 34 antimicrobial groups are allowed in the rules (case-insensitive) and ca
|
||||
\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, 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 streptogramins\cr(pristinamycin and quinupristin/dalfopristin)
|
||||
\item sulfonamides\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadimethoxine, sulfadimidine, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfamoxole, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, and sulfathiourea)
|
||||
\item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tetracycline screening test, and tigecycline)
|
||||
\item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tetracycline screening test)
|
||||
\item trimethoprims\cr(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)
|
||||
@ -138,6 +139,7 @@ eucast_rules(example_isolates,
|
||||
rules = "custom",
|
||||
custom_rules = x,
|
||||
info = FALSE,
|
||||
overwrite = TRUE,
|
||||
verbose = TRUE
|
||||
)
|
||||
|
||||
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@ -3,9 +3,9 @@
|
||||
\docType{data}
|
||||
\name{microorganisms}
|
||||
\alias{microorganisms}
|
||||
\title{Data Set with 78 678 Taxonomic Records of Microorganisms}
|
||||
\title{Data Set with 78 679 Taxonomic Records of Microorganisms}
|
||||
\format{
|
||||
A \link[tibble:tibble]{tibble} with 78 678 observations and 26 variables:
|
||||
A \link[tibble:tibble]{tibble} with 78 679 observations and 26 variables:
|
||||
\itemize{
|
||||
\item \code{mo}\cr ID of microorganism as used by this package. \emph{\strong{This is a unique identifier.}}
|
||||
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. \emph{\strong{This is a unique identifier.}}
|
||||
@ -14,7 +14,7 @@ A \link[tibble:tibble]{tibble} with 78 678 observations and 26 variables:
|
||||
\item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}
|
||||
\item \code{ref}\cr Author(s) and year of related scientific publication. This contains only the \emph{first surname} and year of the \emph{latest} authors, e.g. "Wallis \emph{et al.} 2006 \emph{emend.} Smith and Jones 2018" becomes "Smith \emph{et al.}, 2018". This field is directly retrieved from the source specified in the column \code{source}. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.
|
||||
\item \code{oxygen_tolerance} \cr Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see \emph{Source}). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 68.3\% of all ~39 000 bacteria in the data set contain an oxygen tolerance.
|
||||
\item \code{source}\cr Either "GBIF", "LPSN", "MycoBank", or "manually added" (see \emph{Source})
|
||||
\item \code{source}\cr Either "GBIF", "LPSN", "Manually added", "MycoBank", or "manually added" (see \emph{Source})
|
||||
\item \code{lpsn}\cr Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, \emph{Acetobacter ascendens} has LPSN Record number 7864 and 11011. Only the first is available in the \code{microorganisms} data set. \emph{\strong{This is a unique identifier}}, though available for only ~33 000 records.
|
||||
\item \code{lpsn_parent}\cr LPSN identifier of the parent taxon
|
||||
\item \code{lpsn_renamed_to}\cr LPSN identifier of the currently valid taxon
|
||||
@ -80,7 +80,7 @@ Included taxonomic data from \href{https://lpsn.dsmz.de}{LPSN}, \href{https://ww
|
||||
For convenience, some entries were added manually:
|
||||
\itemize{
|
||||
\item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H
|
||||
\item 36 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
|
||||
\item 37 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set
|
||||
\item 1 entry of \emph{Blastocystis} (\emph{B. hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
|
||||
\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
|
||||
\item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
|
||||
|
||||
@ -3,9 +3,9 @@
|
||||
\docType{data}
|
||||
\name{microorganisms.groups}
|
||||
\alias{microorganisms.groups}
|
||||
\title{Data Set with 521 Microorganisms In Species Groups}
|
||||
\title{Data Set with 534 Microorganisms In Species Groups}
|
||||
\format{
|
||||
A \link[tibble:tibble]{tibble} with 521 observations and 4 variables:
|
||||
A \link[tibble:tibble]{tibble} with 534 observations and 4 variables:
|
||||
\itemize{
|
||||
\item \code{mo_group}\cr ID of the species group / microbiological complex
|
||||
\item \code{mo}\cr ID of the microorganism belonging in the species group / microbiological complex
|
||||
|
||||
@ -88,13 +88,16 @@ $(document).ready(function() {
|
||||
x = x.replace("Eric", prefix + "nl" + suffix + "Eric");
|
||||
x = x.replace("Erwin", prefix + "nl" + suffix + "Erwin");
|
||||
x = x.replace("Gwen", prefix + "en" + suffix + "Gwen");
|
||||
x = x.replace("Jane", prefix + "au" + suffix + "Jane");
|
||||
x = x.replace("Jason", prefix + "ca" + suffix + "Jason");
|
||||
x = x.replace("Javier", prefix + "ca" + suffix + "Javier");
|
||||
x = x.replace("Jonas", prefix + "de" + suffix + "Jonas");
|
||||
x = x.replace("Judith", prefix + "nl" + suffix + "Judith");
|
||||
x = x.replace("Kathryn", prefix + "en" + suffix + "Kathryn");
|
||||
x = x.replace("Larisse", prefix + "sa" + suffix + "Larisse");
|
||||
x = x.replace("Matthew", prefix + "ca" + suffix + "Matthew");
|
||||
x = x.replace("Matthijs", prefix + "nl" + suffix + "Matthijs");
|
||||
x = x.replace("Natacha", prefix + "en" + suffix + "Natacha");
|
||||
x = x.replace("Peter", prefix + "en" + suffix + "Peter");
|
||||
x = x.replace("Rogier", prefix + "nl" + suffix + "Rogier");
|
||||
x = x.replace("Sofia", prefix + "sv" + suffix + "Sofia");
|
||||
@ -122,12 +125,15 @@ $(document).ready(function() {
|
||||
x = x.replace("Corinna", "Dr. Corinna");
|
||||
x = x.replace("Dennis", "Dr. Dennis");
|
||||
x = x.replace("Gwen", "Prof. Gwen");
|
||||
x = x.replace("Jane", "Dr. Jane");
|
||||
x = x.replace("Jason", "Dr. Jason");
|
||||
x = x.replace("Javier", "Prof. Javier");
|
||||
x = x.replace("Jonas", "Dr. Jonas");
|
||||
x = x.replace("Judith", "Dr. Judith");
|
||||
x = x.replace("Katryn", "Prof. Katryn");
|
||||
x = x.replace("Larisse", "Dr. Larisse");
|
||||
x = x.replace("Matthijs", "Dr. Matthijs");
|
||||
x = x.replace("Natacha", "Dr. Natacha");
|
||||
x = x.replace("Peter", "Dr. Peter");
|
||||
x = x.replace("Rogier", "Dr. Rogier");
|
||||
x = x.replace("Sofia", "Dr. Sofia");
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user