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(v3.0.1.9084) Fix breakpoint infer rules

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dr. M.S. (Matthijs) Berends
2026-07-09 17:14:59 +02:00
parent ea996c8361
commit 9237bfbc19
24 changed files with 545 additions and 318 deletions
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4
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR
Version: 3.0.1.9083
Date: 2026-07-03
Version: 3.0.1.9084
Date: 2026-07-09
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9083
# AMR 3.0.1.9084
Planned as v3.1.0, end of June 2026.

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R/interpretive_rules.R
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@@ -110,13 +110,8 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @references
#' - EUCAST Expert Rules. Version 2.0, 2012.\cr
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
#' - EUCAST Expected Phenotypes. [(link)](https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. [(link)](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/)
#' @inheritSection AMR Download Our Reference Data
#' @examples
#' \donttest{

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R/tidymodels.R
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@@ -126,8 +126,7 @@ step_mic_log2 <- function(
trained = FALSE,
columns = NULL,
skip = FALSE,
id = recipes::rand_id("mic_log2")
) {
id = recipes::rand_id("mic_log2")) {
recipes::add_step(
recipe,
step_mic_log2_new(
@@ -202,8 +201,7 @@ step_sir_numeric <- function(
trained = FALSE,
columns = NULL,
skip = FALSE,
id = recipes::rand_id("sir_numeric")
) {
id = recipes::rand_id("sir_numeric")) {
recipes::add_step(
recipe,
step_sir_numeric_new(

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data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R
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@@ -503,6 +503,72 @@ dim(breakpoints_new)
dim(clinical_breakpoints)
# Correct anaerobic bacteria in EUCAST ----
eucast_anaerobe_corrections <- tibble::tribble(
~guideline, ~type, ~host, ~method, ~site, ~mo, ~rank_index, ~ab, ~ref_tbl, ~disk_dose, ~breakpoint_S, ~breakpoint_R, ~uti, ~is_SDD,
# Prevotella spp.
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("AMP"), "Prevotella", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("AMP"), "Prevotella", "2 mcg", 25, 25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("SAM"), "Prevotella", "10/10 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("AMX"), "Prevotella", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("AMC"), "Prevotella", "2/1 mcg", 24, 24, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("ETP"), "Prevotella", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("ETP"), "Prevotella", "10 mcg", 29, 29, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Prevotella"), 3, as.ab("IPM"), "Prevotella", NA, 0.125, 0.125, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Prevotella"), 3, as.ab("IPM"), "Prevotella", "10 mcg", 35, 35, FALSE, FALSE,
# Fusobacterium necrophorum
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMP"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMP"), "F. necrophorum", "2 mcg", 27, 27, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("SAM"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("SAM"), "F. necrophorum", "10/10 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMX"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMC"), "F. necrophorum", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("AMC"), "F. necrophorum", "2/1 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("ETP"), "F. necrophorum", NA, 0.06, 0.06, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("ETP"), "F. necrophorum", "10 mcg", 35, 35, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("IPM"), "F. necrophorum", NA, 0.125, 0.125, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Fusobacterium necrophorum"), 2, as.ab("IPM"), "F. necrophorum", "10 mcg", 36, 36, FALSE, FALSE,
# Clostridium perfringens
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMP"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMP"), "C. perfringens", "2 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("SAM"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("SAM"), "C. perfringens", "10/10 mcg", 27, 27, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMX"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMC"), "C. perfringens", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("AMC"), "C. perfringens", "2/1 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("ETP"), "C. perfringens", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("ETP"), "C. perfringens", "10 mcg", 24, 24, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Clostridium perfringens"), 2, as.ab("IPM"), "C. perfringens", NA, 0.5, 0.5, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Clostridium perfringens"), 2, as.ab("IPM"), "C. perfringens", "10 mcg", 25, 25, FALSE, FALSE,
# Cutibacterium acnes
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMP"), "C. acnes", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMP"), "C. acnes", "2 mcg", 23, 23, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("SAM"), "C. acnes", "10/10 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMX"), "C. acnes", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("AMC"), "C. acnes", "2/1 mcg", 24, 24, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("CTX"), "C. acnes", "5 mcg", 26, 26, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("CRO"), "C. acnes", NA, 0.06, 0.06, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("CRO"), "C. acnes", "30 mcg", 33, 33, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("ETP"), "C. acnes", NA, 0.25, 0.25, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("ETP"), "C. acnes", "10 mcg", 28, 28, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("IPM"), "C. acnes", NA, 0.03, 0.03, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("IPM"), "C. acnes", "10 mcg", 39, 39, FALSE, FALSE,
"EUCAST 2025", "human", "human", "MIC", NA, as.mo("Cutibacterium acnes"), 2, as.ab("LNZ"), "C. acnes", NA, 2, 2, FALSE, FALSE,
"EUCAST 2025", "human", "human", "DISK", NA, as.mo("Cutibacterium acnes"), 2, as.ab("LNZ"), "C. acnes", "10 mcg", 34, 34, FALSE, FALSE
)
breakpoints_new <- clinical_breakpoints |>
bind_rows(eucast_anaerobe_corrections) |>
bind_rows(eucast_anaerobe_corrections |> mutate(guideline = "EUCAST 2026")) |>
bind_rows(eucast_anaerobe_corrections |> mutate(guideline = "EUCAST 2023")) |>
bind_rows(eucast_anaerobe_corrections |> mutate(guideline = "EUCAST 2024"))
# SAVE TO PACKAGE ----
# determine rank again now that some changes were made on taxonomic level (genus -> species)

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7bcb6eaf7e2da23ac552acbfd12b3e62
634c5e23bed1e92783eeb4739c0d1486

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data-raw/interpretive_rules.tsv
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@@ -90,7 +90,7 @@ EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX
EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I
EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S
EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I
EUCAST Breakpoints 10 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R
@@ -199,7 +199,7 @@ EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX
EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I
EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 11 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S
EUCAST Breakpoints 11 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I
@@ -260,7 +260,7 @@ EUCAST Breakpoints 12 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AM
EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))])); sort(x[x %in% penicillins()]) |> toString()
EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
@@ -331,6 +331,9 @@ EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-
EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus TCY-S R DOX, MNO R
EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S
EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I
EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R
@@ -351,8 +354,8 @@ EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Strep
EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R
EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S
EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06
@@ -381,7 +384,6 @@ EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans
EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
EUCAST Breakpoints 13 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S
EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I
EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R
@@ -391,19 +393,19 @@ EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus
EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP S AMX S
EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP I AMX I
EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP R AMX R
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusibacterium necrophorum") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Clostridium perfringens") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
@@ -451,7 +453,7 @@ EUCAST Breakpoints 14 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AM
EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) |> sort() |> toString()
EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Haemophilus influenzae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% penicillins()] |> sort() |> toString()
EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
@@ -521,8 +523,11 @@ EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus coagulase-n
EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S
EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S MRSA isolates are in this file safely denoted as FOX resistant
EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S
EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I
EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R
@@ -543,8 +548,8 @@ EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Strep
EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R
EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S
EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(c("SAM", "PIP", "TZP", "PHN", "IMR", "MEV", clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$mo == as.mo("S. pneumoniae"))])); x[x %in% betalactams()] |> sort() |> toString() AND REMOVE CEC
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(c("SAM", "PIP", "TZP", "PHN", "IMR", "MEV", clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$mo == as.mo("S. pneumoniae"))])); x[x %in% betalactams()] |> sort() |> toString() AND REMOVE CEC
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06
@@ -582,19 +587,19 @@ EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus
EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & mo_genus(clinical_breakpoints$mo) == "Prevotella" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP S AMX S
EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP I AMX I
EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP R AMX R
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Fusibacterium necrophorum") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Clostridium perfringens"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Clostridium perfringens") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
@@ -643,7 +648,7 @@ EUCAST Breakpoints 15 Enterococcus genus is Enterococcus AMP R AMX, AMC R
EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CAZ, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TEM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("Haemophilus influenzae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% penicillins()] |> sort() |> toString()
EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
@@ -708,9 +713,12 @@ EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudin
EUCAST Breakpoints 15 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S S MFX S
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
EUCAST Breakpoints 15 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
EUCAST Breakpoints 15 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S
EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I
EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R
@@ -731,8 +739,8 @@ EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Strep
EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R
EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S
EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, BPR, CFM, CPD, CPT, CRO, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PHN, PIP, PIP, SAM, TZP, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, BPR, CFM, CPD, CPT, CRO, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PHN, PIP, PIP, SAM, TZP, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, FPE, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV", "FPE")) |> toString()
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, FPE, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV", "FPE")) |> toString()
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06
@@ -770,19 +778,19 @@ EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus
EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & mo_genus(clinical_breakpoints$mo) == "Prevotella" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP S AMX S
EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP I AMX I
EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP R AMX R
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Fusibacterium necrophorum") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Clostridium perfringens"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Clostridium perfringens") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
@@ -831,7 +839,7 @@ EUCAST Breakpoints 16 Enterococcus genus is Enterococcus AMP R AMX, AMC R
EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CAZ, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TEM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Haemophilus influenzae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% penicillins()] |> sort() |> toString()
EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
@@ -897,9 +905,12 @@ EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudin
EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S I carbapenems I Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
EUCAST Breakpoints 16 Staphylococcus genus_species one_of Staphylococcus pseudintermedius, Staphylococcus schleiferi, Staphylococcus coagulans OXA-S R carbapenems R Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S S MFX S
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX I
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
EUCAST Breakpoints 16 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S
EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I
EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R
@@ -920,8 +931,8 @@ EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Strep
EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R
EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S
EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, BPR, CFM, CPD, CPT, CRO, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PHN, PIP, PIP, SAM, TZP, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, BPR, CFM, CPD, CPT, CRO, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PHN, PIP, PIP, SAM, TZP, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, FPE, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV", "FPE")) |> toString()
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, FPE, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV", "FPE")) |> toString()
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
EUCAST Breakpoints 16 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06
@@ -959,19 +970,19 @@ EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococc
EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
EUCAST Breakpoints 13.1 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP S AMX S
EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP I AMX I
EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella AMP R AMX R
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusibacterium necrophorum") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Clostridium perfringensm"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Clostridium perfringens") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()]) |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% betalactams()] |> sort() |> toString()
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
@@ -1015,7 +1026,7 @@ EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX,
EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
EUCAST Breakpoints 13.1 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Haemophilus influenzae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); x[x %in% penicillins()] |> sort() |> toString()
EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
EUCAST Breakpoints 13.1 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
@@ -1084,7 +1095,10 @@ EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus NOR-S S CIP, LVX
EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S
EUCAST Breakpoints 13.1 Staphylococcus genus_species is Staphylococcus aureus FOX-S, VAN R, S TLV S MRSA isolates are in this file safely denoted as FOX resistant
EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
EUCAST Breakpoints 13.1 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN S penicillins S
EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN I penicillins I
EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group C, Streptococcus Group G PEN R penicillins R
@@ -1105,8 +1119,8 @@ EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Str
EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R
EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S S DOX, MNO S
EUCAST Breakpoints 13.1 Streptococcus groups A, B, C, G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY-S R DOX, MNO R
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV"))
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
EUCAST Breakpoints 13.1 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06
@@ -1135,25 +1149,6 @@ EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridan
EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S will be expanded in eucast_rules()
EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I will be expanded in eucast_rules()
EUCAST Breakpoints 13.1 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R will be expanded in eucast_rules()
EUCAST Breakpoints 13.0 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 13.0 Anaerobic bacteria genus is Prevotella AMP S AMX S
EUCAST Breakpoints 13.0 Anaerobic bacteria genus is Prevotella AMP I AMX I
EUCAST Breakpoints 13.0 Anaerobic bacteria genus is Prevotella AMP R AMX R
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I
EUCAST Breakpoints 13.0 Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R
EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN I AMX S
EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN R AMX R
EUCAST Breakpoints Corynebacterium diphtheriae/ulcerans genus_species one_of Corynebacterium diphtheriae, Corynebacterium ulcerans PEN S CTX S
@@ -1455,13 +1450,7 @@ EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus M
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus TCY S DOX, MNO, TGC S
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus LNZ S TZD S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S Weird that this rules in in the Strep A/B/C/G document, while it's not in the Strep viridans document - document title itself it for "S. species"
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Viridans Group Streptococcus (VGS) PEN R aminopenicillins, CTX, CRO R Weird that this rules in in the Strep A/B/C/G document, while it's not in the Strep viridans document - document title itself it for "S. species"
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S AMC, AMP, AMX, CEC, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IPM, MEM, PEN S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)) & clinical_breakpoints$mo == as.mo("S. pneumoniae"))]); x[x %in% betalactams()] |> toString()
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S AMC, AMP, AMX, CEC, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IPM, MEM, PEN S x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("S. pneumoniae") & clinical_breakpoints$host == "human" & (clinical_breakpoints$site != "Screen" | is.na(clinical_breakpoints$site)))]); sort(c(x[x %in% betalactams()])) |> toString()
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX I
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S MFX S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae ERY, CLI S, S macrolides, lincosamides S
@@ -1470,6 +1459,12 @@ EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species i
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY R DOX, MNO R
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S Weird that this rules in in the Strep A/B/C/G document, while it's not in the Strep viridans document - document title itself it for "S. species"
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Viridans Group Streptococcus (VGS) PEN R aminopenicillins, CTX, CRO R Weird that this rules in in the Strep A/B/C/G document, while it's not in the Strep viridans document - document title itself it for "S. species"
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus species genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R
EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R
EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R
EUCAST Expert Rules 3.3 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R
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index.md
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@@ -27,9 +27,12 @@
<div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;">
<small><a href="https://amr-for-r.org/">amr-for-r.org</a></small>
</p>
<p style="text-align:right; width: 50%;">
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">doi.org/10.18637/jss.v104.i03</a></small>
</p>
@@ -57,7 +60,7 @@ times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation
in scientific research.
After installing this package, R knows [**~97 000 distinct microbial
species**](./reference/microorganisms.html) (updated mei 2026) and all
species**](./reference/microorganisms.html) (updated May 2026) and all
[**~620 antimicrobial and antiviral
drugs**](./reference/antimicrobials.html) by name and code (including
ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all
@@ -168,13 +171,11 @@ example_isolates %>%
#> ℹ Using column mo as input for `mo_fullname()`
#> ℹ Using column mo as input for `mo_is_gram_negative()`
#> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
#> Resistant Phenotypes' v1.2 (2023). This note will be shown
#> once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
#> This note will be shown once per session.
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
#> # A tibble: 35 × 7
#> bacteria GEN TOB AMK KAN IPM MEM
#> <chr> <sir> <sir> <sir> <sir> <sir> <sir>
@@ -224,8 +225,8 @@ wisca(example_isolates,
```
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:------------------------|:-------------------------------------|:-------------------------------------|
| 70.1% (65.1-75.4%) | 93.6% (92.1-95%) | 89.8% (87.3-92.4%) |
|:---|:---|:---|
| 70% (64.8-75.2%) | 93.6% (92-95.1%) | 89.9% (87.1-92.5%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
@@ -239,10 +240,10 @@ wisca(example_isolates,
```
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:----------------|:------------------------|:-------------------------------------|:-------------------------------------|
| Clinical | 74.4% (68.2-79.9%) | 93.6% (91.9-95.1%) | 90.4% (86.9-93.3%) |
| ICU | 57% (48.6-65.9%) | 86.8% (83.4-89.8%) | 82.9% (77.5-87.1%) |
| Outpatient | 57.5% (45.9-69.3%) | 76.6% (70.6-82.3%) | 67.9% (57.6-77.2%) |
|:---|:---|:---|:---|
| Clinical | 74.6% (69.3-80.3%) | 93.6% (92.1-95%) | 90.4% (87-93.2%) |
| ICU | 56.9% (48.2-66.3%) | 86.7% (83.4-89.7%) | 82.9% (78.1-87.3%) |
| Outpatient | 57.3% (45.8-69.1%) | 76.6% (70.6-81.9%) | 67.9% (58-76.9%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
@@ -251,12 +252,11 @@ for tracking resistance per species over time:
antibiogram(example_isolates,
mo_transform = "gramstain",
antimicrobials = c("AMC", carbapenems(), "TZP"))
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
#> (meropenem)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
```
| Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
|:--------------|:----------------------------|:--------------------|:---------------------|:------------------------|
|:---|:---|:---|:---|:---|
| Gram-negative | 76% (73-79%,N=726) | 99% (98-100%,N=631) | 100% (99-100%,N=626) | 88% (85-91%,N=641) |
| Gram-positive | 76% (74-79%,N=1138) | 81% (75-85%,N=257) | 77% (70-82%,N=203) | 86% (82-89%,N=345) |
@@ -270,7 +270,7 @@ antibiogram(example_isolates,
```
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:--------------|:------------------------|:-------------------------------------|:-------------------------------------|
|:---|:---|:---|:---|
| Gram-negative | 88% (85-91%,N=641) | 99% (97-99%,N=691) | 98% (97-99%,N=693) |
| Gram-positive | 86% (82-89%,N=345) | 98% (96-98%,N=1044) | 95% (93-97%,N=550) |
@@ -367,16 +367,15 @@ out <- example_isolates %>%
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
summarise(across(c(aminoglycosides(), polymyxins()),
resistance))
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
#> (tobramycin), AMK (amikacin), and KAN (kanamycin)
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
#> (kanamycin)
#> ℹ For `polymyxins()` using column COL (colistin)
#> Warning: There was 1 warning in `summarise()`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()),
#> resistance)`.
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
#> ℹ In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group:
#> ward = "Outpatient" (whilst `minimum = 30`).
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
#> 30`).
out
#> # A tibble: 3 × 6
#> ward GEN TOB AMK KAN COL

2
man/AMR.Rd
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@@ -12,7 +12,7 @@ The \code{AMR} package is a peer-reviewed, \href{https://amr-for-r.org/#copyrigh
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~97 000 distinct microbial species}} (updated mei 2026) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antimicrobial and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen} and the \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~97 000 distinct microbial species}} (updated May 2026) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antimicrobial and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen} and the \href{https://www.umcg.nl}{University Medical Center Groningen}.
The \code{AMR} package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}

2
man/clinical_breakpoints.Rd
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@@ -5,7 +5,7 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 45 555 observations and 14 variables:
A \link[tibble:tibble]{tibble} with 45 735 observations and 14 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"}

2
man/g.test.Rd
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@@ -46,7 +46,7 @@ A list with class \code{"htest"} containing the following
\code{(observed - expected) / sqrt(expected)}.}
\item{stdres}{standardized residuals,
\code{(observed - expected) / sqrt(V)}, where \code{V} is the
residual cell variance {(\if{html}{\out{<a href="#reference+chisq.test.Rd+R+3AAgresti+3A2007" class="citation">}}Agresti 2007\if{html}{\out{</a>}}, section 2.4.5)}
residual cell variance (Agresti, 2007, section 2.4.5
for the case where \code{x} is a matrix, \code{n * p * (1 - p)} otherwise).}
}
\description{

5
man/ggplot_pca.Rd
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@@ -59,9 +59,8 @@ ggplot_pca(
}
\item{pc.biplot}{
If true, use what {\if{html}{\cite{}\out{<a href="#reference+biplot.princomp.Rd+R+3AGabriel+3A1971" class="citation">}}Gabriel (1971)\if{html}{\out{</a>}}} refers to as a
\dQuote{principal component biplot},
with \code{lambda = 1} and observations scaled up by sqrt(n) and
If true, use what Gabriel (1971) refers to as a "principal component
biplot", with \code{lambda = 1} and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.

9
man/interpretive_rules.Rd
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@@ -173,12 +173,7 @@ eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
\itemize{
\item EUCAST Expert Rules. Version 2.0, 2012.\cr
Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
\item EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{(link)}
\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{(link)}
\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx}{(link)}
\item EUCAST Expected Phenotypes. \href{https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}{(link)}
}
}