added in 11
added in 11
added in 11
x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(H. influenzae))])); sort(x[x %in% penicillins()]) |> toString()
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
MRSA isolates are in this file safely denoted as FOX resistant
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
x <- unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == EUCAST 2022 & clinical_breakpoints$mo == as.mo(S. pneumoniae) & clinical_breakpoints$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV)) |> toString()
x <- unique(clinical_breakpoints$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()
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
paste(Streptococcus, mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == B_STRPT_VIRI)]), collapse = , )
paste(Streptococcus, mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == B_STRPT_VIRI)]), collapse = , )
paste(Streptococcus, mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == B_STRPT_VIRI)]), collapse = , )
paste(Streptococcus, mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == B_STRPT_VIRI)]), collapse = , )
paste(Streptococcus, mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == B_STRPT_VIRI)]), collapse = , )
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()
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()
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()
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()
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()
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
MRSA isolates are in this file safely denoted as FOX resistant
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
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$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV)) |> toString()
x <- unique(clinical_breakpoints$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()
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
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()
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()
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()
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()
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()
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
MRSA isolates are in this file safely denoted as FOX resistant
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
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$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV)) |> toString()
x <- unique(clinical_breakpoints$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()
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
will be expanded in eucast_rules()
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()
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()
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()
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()
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()
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, ceftolozan/tazobactam))]))
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
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$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV, FPE)) |> toString()
x <- unique(clinical_breakpoints$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()
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
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()
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()
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()
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()
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()
penicillins()[!penicillins() %in% betalactams_with_inhibitor()]
See last sentence: Isolates that test resistant to cefoxitin are resistant to all penicillins
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(CZO, FEP, CTX, CRO, CXM, cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, cefiderocol, ceftolozan/tazobactam))])) |> toString()
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, cefiderocol, ceftolozan/tazobactam))])) |> toString()
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, cefiderocol, ceftolozan/tazobactam))])) |> toString()
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(CZO, FEP, CTX, CRO, CXM, cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, cefiderocol, ceftolozan/tazobactam))])) |> toString()
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, cefiderocol, ceftolozan/tazobactam))])) |> toString()
sort(c(cephalosporins()[!cephalosporins() %in% as.ab(c(cefalexin, ceftazidim, ceftazidim/avibactam, ceftibuten, cefiderocol, ceftolozan/tazobactam))])) |> toString()
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
Not explicitly mentioned in guidelines in this section, but previous section about these 3 species do mention OXA as preferred method
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
penicillins()[!penicillins() %in% c(PHN, isoxazolylpenicillins())]
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
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$ab != as.ab(cefaclor))]); sort(c(x[x %in% betalactams()], SAM, PIP, TZP, PHN, IMR, MEV, FPE)) |> toString()
x <- unique(clinical_breakpoints$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()
from flowchart: when OXA < 20 or PEN > 0.06
from flowchart: when OXA < 20 or PEN > 0.06
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
does not explicitly state that it is for other fluoroquinolones
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
MO group name will be expanded in eucast_rules()
originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
This is Enterobacterales except Salmonella spp.
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
all penicillins without beta-lactamse inhibitor
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
Additional rules from header added in separate rule (genus is one of…)
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
These last ones are all true sulfonamides
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Since R to sulfonamides - TMP result is equal with combinations
Regex means that K. aerogenes is not matched.
Also includes the C. freundii complex - these Citrobacter species were not literally mentioned in the document, but the complex was.
This is Enterobacterales except Salmonella spp.
This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 3 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 4 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 4 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
This is rule 4 of EUCAST Expert Rules v3.3 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
Betalactams without ceftaroline and ceftobiprole = betalactams()[!betalactams() %in% c(CPT, BPR)]
Must be S to all betactams with recognised anti-staphylococcal activity
all penicillins without beta-lactamse inhibitor and excluding isoxazolylpenicillines
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()
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
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