(v3.0.1.9085) website

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9081
-Date: 2026-06-27
+Version: 3.0.1.9085
+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

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9081
+# AMR 3.0.1.9085
 
 Planned as v3.1.0, end of June 2026.
 

R/interpretive_rules.R

@@ -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{

README.Rmd

@@ -22,7 +22,7 @@ Please visit our comprehensive package website <https://amr-for-r.org> to read m
 Overview:
 
 * Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
-* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
+* **Peer-reviewed**, used in over 175 countries, cited over 100 times, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
 * Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
 * Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
 * Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
@@ -32,7 +32,9 @@ Overview:
 
 ----
 
-The `AMR` package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
+The `AMR` package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods.
+
+**Our aim has always been to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
 
 The `AMR` package 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). **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 [University of Groningen](https://www.rug.nl) and the [University Medical Center Groningen](https://www.umcg.nl).
 

README.md

@@ -10,8 +10,8 @@ Overview:
 
 - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
   data analysis in a One Health approach
-- **Peer-reviewed**, used in over 175 countries, available in 28
-  languages
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
+  available in 28 languages
 - Generates **antibiograms** - WISCA for empiric coverage estimates, or
   traditional/syndromic for AMR surveillance
 - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -32,10 +32,11 @@ The `AMR` package is a peer-reviewed, free and open-source R package
 with zero dependencies to simplify the analysis and prediction of
 Antimicrobial Resistance (AMR) and to work with microbial and
 antimicrobial data and properties, by using evidence-based methods.
-**Our aim is to provide a standard** for clean and reproducible AMR data
-analysis, that can therefore empower epidemiological analyses to
-continuously enable surveillance and treatment evaluation in any
-setting.
+
+**Our aim has always been to provide a standard** for clean and
+reproducible AMR data analysis, that can therefore empower
+epidemiological analyses to continuously enable surveillance and
+treatment evaluation in any setting.
 
 The `AMR` package supports and can read any data format, including
 WHONET data. This package works on Windows, macOS and Linux with all

data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R

@@ -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)

data-raw/clin_break.md5

@@ -1 +1 @@
-7bcb6eaf7e2da23ac552acbfd12b3e62
+634c5e23bed1e92783eeb4739c0d1486

data-raw/interpretive_rules.tsv

@@ -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	

index.Rmd

@@ -20,7 +20,7 @@ AMR:::reset_all_thrown_messages()
 # The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a>
 
 * Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
-* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
+* **Peer-reviewed**, used in over 175 countries, cited over 100 times, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
 * Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
 * Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
 * Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
@@ -41,9 +41,9 @@ AMR:::reset_all_thrown_messages()
 
 ## Introduction
 
-The `AMR` package is a peer-reviewed, [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of [many different researchers](./authors.html) from around the globe to make this a successful and durable project!
+The `AMR` package is a peer-reviewed, [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods.
 
-This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
+**Our aim has always been to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of [many different researchers](./authors.html) from around the globe to make this a successful and durable project! The `AMR` package was already cited [over 100 times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC) in scientific research.
 
 After installing this package, R knows [**`r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species**](./reference/microorganisms.html) (updated `r format(AMR:::TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial and antiviral drugs**](./reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))` and EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))` 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). **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 [University of Groningen](https://www.rug.nl) and the [University Medical Center Groningen](https://www.umcg.nl).
 

index.md

@@ -5,8 +5,8 @@
 
 - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
   data analysis in a One Health approach
-- **Peer-reviewed**, used in over 175 countries, available in 28
-  languages
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
+  available in 28 languages
 - Generates **antibiograms** - WISCA for empiric coverage estimates, or
   traditional/syndromic for AMR surveillance
 - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -46,19 +46,17 @@ R package with [zero
 dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify
 the analysis and prediction of Antimicrobial Resistance (AMR) and to
 work with microbial and antimicrobial data and properties, by using
-evidence-based methods. **Our aim is to provide a standard** for clean
-and reproducible AMR data analysis, that can therefore empower
+evidence-based methods.
+
+**Our aim has always been to provide a standard** for clean and
+reproducible AMR data analysis, that can therefore empower
 epidemiological analyses to continuously enable surveillance and
 treatment evaluation in any setting. We are a team of [many different
 researchers](./authors.html) from around the globe to make this a
-successful and durable project!
-
-This work was published in the Journal of Statistical Software (Volume
-104(3); [DOI
-10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and
-formed the basis of two PhD theses ([DOI
-10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and
-[DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
+successful and durable project! The `AMR` package was already cited
+[over 100
+times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
+in scientific research.
 
 After installing this package, R knows [**~97 000 distinct microbial
 species**](./reference/microorganisms.html) (updated mei 2026) and all
@@ -229,7 +227,7 @@ wisca(example_isolates,
 
 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:------------------------|:-------------------------------------|:-------------------------------------|
-| 70% (64.7-75.2%)        | 93.6% (92.2-95.1%)                   | 89.8% (87-92.5%)                     |
+| 70% (64.8-75.1%)        | 93.6% (92.1-95%)                     | 89.9% (86.9-92.3%)                   |
 
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -244,9 +242,9 @@ wisca(example_isolates,
 
 | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:----------------|:------------------------|:-------------------------------------|:-------------------------------------|
-| Clinical        | 74.6% (68.6-80.6%)      | 93.7% (92.1-95.1%)                   | 90.4% (87-93.1%)                     |
-| ICU             | 57% (48.6-65.7%)        | 86.8% (83.6-89.8%)                   | 82.9% (78.1-87.3%)                   |
-| Outpatient      | 56.9% (45.9-68.2%)      | 76.7% (70.6-82.3%)                   | 68% (57.6-77.2%)                     |
+| Clinical        | 74.7% (69-80.3%)        | 93.6% (92-95.2%)                     | 90.4% (86.8-93.1%)                   |
+| ICU             | 56.9% (48.7-66%)        | 86.8% (83.6-90%)                     | 82.8% (78.3-87.3%)                   |
+| Outpatient      | 57.2% (46-68.2%)        | 76.5% (70.3-82.2%)                   | 67.7% (57.3-77.2%)                   |
 
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -349,11 +347,6 @@ example_isolates %>%
   summarise(across(c(GEN, TOB),
                    list(total_R = resistance,
                         conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-#> ℹ `resistance()` assumes the EUCAST guideline and thus
-#>   considers the 'I' category susceptible. Set the `guideline`
-#>   argument or the `AMR_guideline` option to either "CLSI" or
-#>   "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> # A tibble: 3 × 5
 #>   ward       GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
 #>   <chr>            <dbl> <chr>              <dbl> <chr>       

man/clinical_breakpoints.Rd

@@ -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"}

man/interpretive_rules.Rd

@@ -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)}
 }
 }