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(v3.0.1.9059) Update taxonomy of microorganisms
This commit is contained in:
Matthijs Berends
GitHub
@@ -451,7 +451,7 @@ EUCAST Breakpoints 14 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AM
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EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
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EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
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EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
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EUCAST Breakpoints 14 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$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2024" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) |> sort() |> toString()
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EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
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EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
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EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
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@@ -543,8 +543,8 @@ EUCAST Breakpoints 14 Streptococcus groups A, B, C, G genus_species one_of Strep
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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
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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
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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
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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, 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"))
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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, 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"))
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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
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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
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EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
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EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
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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
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@@ -582,19 +582,19 @@ EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus
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EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
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EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
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EUCAST Breakpoints 15 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
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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 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP S AMX S
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP I AMX I
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP R AMX R
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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 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
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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 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
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EUCAST Breakpoints 15 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$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
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@@ -643,7 +643,7 @@ EUCAST Breakpoints 15 Enterococcus genus is Enterococcus AMP R AMX, AMC R
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EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
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EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
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EUCAST Breakpoints 15 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
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EUCAST Breakpoints 15 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$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CAZ, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TEM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) |> toString()
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EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
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EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
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EUCAST Breakpoints 15 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
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@@ -731,8 +731,8 @@ EUCAST Breakpoints 15 Streptococcus groups A, B, C, G genus_species one_of Strep
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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
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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
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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
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EUCAST Breakpoints 15 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"))
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EUCAST Breakpoints 15 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"))
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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()
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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()
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EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
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EUCAST Breakpoints 15 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
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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
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@@ -770,7 +770,7 @@ EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus
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EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
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EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
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EUCAST Breakpoints 16 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
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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 2024" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP S AMX S
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EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP I AMX I
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EUCAST Breakpoints 16 Anaerobic bacteria genus is Prevotella AMP R AMX R
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@@ -778,11 +778,11 @@ EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necropho
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
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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 2024" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
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EUCAST Breakpoints 16 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$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
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EUCAST Breakpoints 16 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
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@@ -831,7 +831,7 @@ EUCAST Breakpoints 16 Enterococcus genus is Enterococcus AMP R AMX, AMC R
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EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
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EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
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EUCAST Breakpoints 16 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
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EUCAST Breakpoints 16 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$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CAZ, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TEM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2026" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()]) |> toString()
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EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
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EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
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EUCAST Breakpoints 16 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
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@@ -920,8 +920,8 @@ EUCAST Breakpoints 16 Streptococcus groups A, B, C, G genus_species one_of Strep
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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
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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
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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
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EUCAST Breakpoints 16 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"))
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EUCAST Breakpoints 16 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"))
|
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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 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 +959,19 @@ 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 2023" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
EUCAST Breakpoints 13.1 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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 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 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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 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 2023" & clinical_breakpoints$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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 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 2023" & clinical_breakpoints$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
|
||||
EUCAST Breakpoints 13.1 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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 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
|
||||
@@ -1135,25 +1135,25 @@ 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 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$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
EUCAST Breakpoints Anaerobic bacteria genus is Prevotella AMP S AMX S
|
||||
EUCAST Breakpoints Anaerobic bacteria genus is Prevotella AMP I AMX I
|
||||
EUCAST Breakpoints Anaerobic bacteria genus is Prevotella AMP R AMX R
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
|
||||
EUCAST Breakpoints 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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX S CRO S
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX I CRO I
|
||||
EUCAST Breakpoints Anaerobic bacteria genus_species is Cutibacterium acnes CTX R CRO R
|
||||
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
|
||||
@@ -1414,19 +1414,20 @@ EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria
|
||||
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Lactobacillus VAN, TEC R
|
||||
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Clostridium (ramosum|innocuum) VAN R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus_species is Campylobacter ERY R CLR, AZM R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY R CLR, AZM R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Regex means that K. aerogenes is not matched.
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CXM S CXM, cephalosporins_2nd R Also includes the C. freundii complex - these Citrobacter species were not literally mentioned in the document, but the complex was.
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R This is Enterobacterales except Salmonella spp.
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Morganella morganii) TGC R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ S CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Proteus|Morganella morganii) TGC R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei) CTX S CTX, CRO, CAZ, TZP This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei) CRO S CTX, CRO, CAZ, TZP This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei) CAZ S CTX, CRO, CAZ, TZP This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei) TZP S CTX, CRO, CAZ, TZP This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Serratia|Morganella morganii|Providencia) CTX S CTX, CRO, CAZ This is rule 4 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Serratia|Morganella morganii|Providencia) CRO S CTX, CRO, CAZ This is rule 4 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) fullname like ^(Serratia|Morganella morganii|Providencia) CAZ S CTX, CRO, CAZ This is rule 4 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Enterococcus genus is Enterococcus NOR S CIP, LVX S
|
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@@ -1441,30 +1442,34 @@ EUCAST Expert Rules 3.3 Expert Rules on Moraxella catarrhalis genus_species is M
|
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EUCAST Expert Rules 3.3 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL R fluoroquinolones R
|
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EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella cephalosporins_2nd R
|
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EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella aminoglycosides R
|
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EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella PEF S CIP S
|
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EUCAST Expert Rules 3.3 Expert Rules on Salmonella genus is Salmonella PEF R CIP R
|
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EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R betalactams R
|
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EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S
|
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EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R all penicillins without beta-lactamse inhibitor
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R AMC, AMP, AMX, APL, APX, ATM, AXS, AZA, AZD, AZL, BAM, BIA, BNB, BNP, CAC, CAR, CAT, CAZ, CCL, CCP, CCV, CCX, CDC, CDR, CEB, CEC, CED, CEM, CEP, CEQ, CFA, CFM, CFM1, CFP, CFR, CFS, CFZ, CHE, CIC, CID, CLM, CLO, CMX, CMZ, CND, CPA, CPC, CPD, CPI, CPL, CPM, CPO, CPR, CPX, CRB, CRD, CRN, CRO, CSE, CSL, CSU, CTA, CTB, CTC, CTF, CTL, CTS, CTT, CTX, CTZ, CXA, CXM, CZA, CZD, CZL, CZO, CZP, CZT, CZX, DIC, DIT, DIX, DIZ, DOR, EPC, ETP, FDC, FEP, FLC, FOV, FOX, FPE, FPT, FPZ, FTA, HAP, HET, IMR, IPM, LEN, LEX, LOR, LTM, MAN, MEC, MEM, MET, MEV, MEZ, MSU, MTM, NAF, OXA, PAN, PEN, PHE, PHN, PIP, PIS, PME, PNM, PNO, PRB, PRC, PRP, PSU, PVM, RIA, RID, RIT, RZM, SAM, SBC, SLT6, SRX, TAL, TAN, TBP, TCC, TEM, TIC, TIO, TMN, TZP, ZOP R Betalactams without ceftaroline and ceftobiprole = betalactams()[!betalactams() %in% c("CPT", "BPR")]
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor, carbapenems S Must be S to all betactams with recognised anti-staphylococcal activity
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R all penicillins without beta-lactamse inhibitor and excluding isoxazolylpenicillines
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus ERY, CLI S macrolides, lincosamides S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX I
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus NOR S MFX S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus LVX R fluoroquinolones R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Staphylococcus genus is Staphylococcus MFX R fluoroquinolones R
|
||||
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 VAN S lipoglycopeptides S
|
||||
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 A, B, C and G 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 A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus A, B, C and G 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 PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX, 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 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 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
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR R LVX, MFX R
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R
|
||||
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 pneumoniae genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S
|
||||
EUCAST Expert Rules 3.3 Expert Rules on Viridans Group Streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S
|
||||
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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Reference in New Issue
Block a user