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(v3.0.1.9084) Fix breakpoint infer rules
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@@ -90,7 +90,7 @@ EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX
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EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
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EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I
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EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
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EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
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EUCAST Breakpoints 10 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
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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
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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
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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
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@@ -199,7 +199,7 @@ EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX
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EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
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EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY I AZM, CLR, RXT I
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EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
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EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
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EUCAST Breakpoints 11 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
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EUCAST Breakpoints 11 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
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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
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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
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@@ -260,7 +260,7 @@ EUCAST Breakpoints 12 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AM
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EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
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EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
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EUCAST Breakpoints 12 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
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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$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))])); sort(x[x %in% penicillins()]) |> toString()
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EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S, BLA-S R, R AMP, AMX, PIP R
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EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC S SAM S
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EUCAST Breakpoints 12 Haemophilus influenzae genus_species is Haemophilus influenzae AMC I SAM I
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@@ -331,6 +331,9 @@ EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-
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EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
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EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
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EUCAST Breakpoints 12 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
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EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus TCY-S R DOX, MNO R
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EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
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EUCAST Breakpoints 12 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
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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
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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
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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
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@@ -351,8 +354,8 @@ EUCAST Breakpoints 12 Streptococcus groups A, B, C, G genus_species one_of Strep
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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
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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
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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
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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"))
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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"))
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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()
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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$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
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EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S S CEC I
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EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S CEC I
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EUCAST Breakpoints 12 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA-S R PEN, PHN R from flowchart: when OXA < 20 or PEN > 0.06
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@@ -381,7 +384,6 @@ EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans
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EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP S AMX, AMC, SAM, PIP, TZP S paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
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EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP I AMX, AMC, SAM, PIP, TZP I paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
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EUCAST Breakpoints 12 Viridans group streptococci genus_species one_of Viridans Group Streptococcus (VGS) AMP R AMX, AMC, SAM, PIP, TZP R paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
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EUCAST Breakpoints 13 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
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EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP S AMX S
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EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP I AMX I
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EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae AMP R AMX R
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@@ -391,19 +393,19 @@ EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus
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EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S S fluoroquinolones S
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EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S I fluoroquinolones I
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EUCAST Breakpoints 14 Aerococcus sanguinicola/urinae genus_species is Aerococcus sanguinicola, Aerococcus urinae NOR-S R fluoroquinolones R
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EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()])
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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()
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EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP S AMX S
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EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP I AMX I
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EUCAST Breakpoints 14 Anaerobic bacteria genus is Prevotella AMP R AMX R
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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$mo == as.mo("Fusobacterium necrophorum"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$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$site)))]); x[x %in% betalactams()] |> sort() |> toString()
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP S AMX S
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP I AMX I
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Fusobacterium necrophorum AMP R AMX R
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$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()])
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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()
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP S AMX S
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP I AMX I
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Clostridium perfringens AMP R AMX R
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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$mo == as.mo("Cutibacterium acnes"))]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM", "TZP", "CTX", "CRO"); sort(x[x %in% betalactams()])
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes PEN S AMC, AMP, AMX, CRO, CTX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$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$site)))]); x[x %in% betalactams()] |> sort() |> toString()
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP S AMX S
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP I AMX I
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EUCAST Breakpoints 14 Anaerobic bacteria genus_species is Cutibacterium acnes AMP R AMX R
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@@ -451,7 +453,7 @@ EUCAST Breakpoints 14 Enterococcus genus is Enterococcus AMP R AMP, SAM, AMX, AM
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EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S S CIP, LVX S
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EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S I CIP, LVX I
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EUCAST Breakpoints 14 Enterococcus genus is Enterococcus NOR-S R CIP, LVX R
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EUCAST Breakpoints 14 Haemophilus influenzae genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CEC, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S x <- c(unique(clinical_breakpoints$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 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()
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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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@@ -521,8 +523,11 @@ EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus coagulase-n
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EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus VAN S DAL, ORI S
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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
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EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus ERY S AZM, CLR, RXT S
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EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY-S S DOX, MNO S
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EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY S DOX, MNO S
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EUCAST Breakpoints 14 Staphylococcus genus_species is Staphylococcus aureus FOX-S S CTX, CRO I
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EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
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EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus ERY R AZM, CLR, RXT R
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EUCAST Breakpoints 14 Staphylococcus genus is Staphylococcus NOR-S R CIP, MFX, LVX R
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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
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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
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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
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@@ -543,8 +548,8 @@ 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, 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 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$ab != as.ab("cefaclor"))]); sort(c(x[x %in% betalactams()], "SAM", "PIP", "TZP", "PHN", "IMR", "MEV")) |> toString()
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EUCAST Breakpoints 14 Streptococcus pneumoniae genus_species is Streptococcus pneumoniae PEN S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, PHN, PIP, SAM, TZP S x <- unique(clinical_breakpoints$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()
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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 +587,19 @@ 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 2025" & mo_genus(clinical_breakpoints$mo) == "Prevotella")]), "AMP", "SAM", "AMX", "AMC", "PIP", "ETP", "IPM"); sort(x[x %in% betalactams()]) |> toString()
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, SAM, TZP S x <- unique(clinical_breakpoints$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$site)))]); x[x %in% betalactams()] |> sort() |> toString()
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP S AMX S
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP I AMX I
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EUCAST Breakpoints 15 Anaerobic bacteria genus is Prevotella AMP R AMX R
|
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EUCAST Breakpoints 15 Anaerobic bacteria genus_species is Fusobacterium necrophorum PEN S AMC, AMP, AMX, ETP, IPM, MEM, PEN, PIP, SAM, TZP S x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2025" & clinical_breakpoints$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
|
||||
|
||||
|
Can't render this file because it has a wrong number of fields in line 10.
|
Reference in New Issue
Block a user