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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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66
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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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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