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expert rules 12.0
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data-raw/Dosages_v_12.0_Breakpoint_Tables.pdf
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data-raw/Dosages_v_12.0_Breakpoint_Tables.pdf
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data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx
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data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx
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@ -42,7 +42,7 @@ old_globalenv <- ls(envir = globalenv())
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# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
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EUCAST_RULES_DF <- utils::read.delim(
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file = "data-raw/eucast_rules.tsv",
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skip = 10,
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skip = 9,
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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@ -1,4 +1,171 @@
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"ab" "name" "type" "dose" "dose_times" "administration" "notes" "original_txt" "eucast_version"
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"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 12
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"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 12
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"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv" 12
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"AMX" "Amoxicillin" "high_dosage" "0.75-1 g" 3 "oral" "" "0.75-1 g x 3 oral" 12
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"AMX" "Amoxicillin" "standard_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 12
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"AMX" "Amoxicillin" "uncomplicated_uti" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 12
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"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "2 g + 0.2 g" 3 "iv" "" "(2 g amoxicillin + 0.2 g clavulanic acid) x 3 iv" 12
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"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "1 g + 0.2 g" 3 "iv" "" "(1 g amoxicillin + 0.2 g clavulanic acid) x 3-4 iv" 12
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"AMC" "Amoxicillin/clavulanic acid" "high_dosage" "0.875 g + 0.125 g" 3 "oral" "" "(0.875 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 12
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"AMC" "Amoxicillin/clavulanic acid" "standard_dosage" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 12
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"AMC" "Amoxicillin/clavulanic acid" "uncomplicated_uti" "0.5 g + 0.125 g" 3 "oral" "" "(0.5 g amoxicillin + 0.125 g clavulanic acid) x 3 oral" 12
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"AMP" "Ampicillin" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 12
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"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 12
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"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 12
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"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 12
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"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 12
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"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 12
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"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 12
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"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 12
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"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 12
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"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 12
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"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 12
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"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 12
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"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 12
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"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 12
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"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 12
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"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 12
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"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 12
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"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 12
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"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 12
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"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 12
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"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 12
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"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 12
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"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 12
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"CTX" "Cefotaxime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 12
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"CTX" "Cefotaxime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 12
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"CPD" "Cefpodoxime" "standard_dosage" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 12
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"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 12
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"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 12
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"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 12
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"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 12
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"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 12
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"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 12
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"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 12
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"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 12
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"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 12
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"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam) x 3 iv over 1 hour" 12
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"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 12
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"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 12
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"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 12
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"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 12
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"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 12
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"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 12
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"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 12
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"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 12
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"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 12
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"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 12
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"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 12
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"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 12
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"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 12
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"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 12
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"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 12
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"CLR" "Clarithromycin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 12
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"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 12
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"CLI" "Clindamycin" "high_dosage" "0.9 g" 3 "iv" "" "0.9 g x 3 iv" 12
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"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 12
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"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "" "0.3 g x 4 oral" 12
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"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 12
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"CLO" "Cloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 12
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"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 12
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"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 12
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"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 12
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"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv with a loading dose of 9 MU" 12
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"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1 If needed, 0.5 g x 1 iv over 30 minutes on day 8" 12
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"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 12
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"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 12
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"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 12
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"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 12
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"DIC" "Dicloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 12
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"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 12
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"DIC" "Dicloxacillin" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 12
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"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 12
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"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 12
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"DOR" "Doripenem" "standard_dosage" "0.5 g" 3 "iv" "over 1 hour" "0.5 g x 3 iv over 1 hour" 12
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"DOX" "Doxycycline" "high_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 12
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"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 12
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"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 12
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"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 12
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"ERY" "Erythromycin" "high_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 12
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"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 12
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"ERY" "Erythromycin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 12
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"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 12
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"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 12
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"FLC" "Flucloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 12
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"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv (or 1 g x 6 iv)" 12
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"FLC" "Flucloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 12
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"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 12
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"FOS" "Fosfomycin" "high_dosage" "8 g" 3 "iv" "" "8 g x 3 iv" 12
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"FOS" "Fosfomycin" "standard_dosage" "4 g" 3 "iv" "" "4 g x 3 iv" 12
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"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 12
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"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 12
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"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 12
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"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 12
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"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 12
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"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 12
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"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 12
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"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 12
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"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 12
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"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 12
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"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 12
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"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 12
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"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 12
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"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 12
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"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 12
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"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 12
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"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 12
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"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 12
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"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 12
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"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 12
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"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 12
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"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 12
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"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 12
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"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 12
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"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 12
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"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 12
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"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 12
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"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 12
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"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 12
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"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 12
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"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 12
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"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv over 3 hours" 12
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"OXA" "Oxacillin" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 12
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"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 12
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"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 12
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"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv by extended 3-hour infusion" 12
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"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 12
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"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv by extended 3-hour infusion" 12
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"TZP" "Piperacillin/tazobactam" "standard_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv 30-minute infusion or x 3 iv by extended 4-hour infusion" 12
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"QDA" "Quinupristin/dalfopristin" "high_dosage" "7.5 mg/kg" 3 "iv" "" "7.5 mg/kg x 3 iv" 12
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||||
"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 12
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"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 12
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"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 12
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"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 12
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"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 12
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||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 12
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||||
"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 12
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||||
"TEC" "Teicoplanin" "high_dosage" "0.8 g" 1 "iv" "" "0.8 g x 1 iv" 12
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||||
"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 12
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||||
"TLV" "Telavancin" "standard_dosage" "10 mg/kg" 1 "iv" "over 1 hour" "10 mg/kg x 1 iv over 1 hour" 12
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||||
"TLT" "Telithromycin" "standard_dosage" "0.8 g" 1 "oral" "" "0.8 g x 1 oral" 12
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||||
"TEM" "Temocillin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 12
|
||||
"TEM" "Temocillin" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 12
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||||
"TCY" "Tetracycline" "high_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 12
|
||||
"TCY" "Tetracycline" "standard_dosage" "0.25 g" 4 "oral" "" "0.25 g x 4 oral" 12
|
||||
"TIC" "Ticarcillin" "high_dosage" "3 g" 6 "iv" "" "3 g x 6 iv" 12
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||||
"TIC" "Ticarcillin" "standard_dosage" "3 g" 4 "iv" "" "3 g x 4 iv" 12
|
||||
"TCC" "Ticarcillin/clavulanic acid" "high_dosage" "3 g + 0.1 g" 6 "iv" "" "(3 g ticarcillin + 0.1 g clavulanic acid) x 6 iv" 12
|
||||
"TCC" "Ticarcillin/clavulanic acid" "standard_dosage" "3 g + 0.1-0.2 g" 4 "iv" "" "(3 g ticarcillin + 0.1-0.2 g clavulanic acid) x 4 iv" 12
|
||||
"TGC" "Tigecycline" "standard_dosage" "0.1 g" "loading dose followed by 50 mg x 2 iv" "0.1 g loading dose followed by 50 mg x 2 iv" 12
|
||||
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 12
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 12
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 12
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 11
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 11
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv" 11
|
||||
|
||||
Binary file not shown.
@ -1,12 +1,11 @@
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
|
||||
# 'betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
|
||||
# 'fluoroquinolones', 'glycopeptides', 'glycopeptides_except_lipo', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'tetracyclines_except_TGC', 'ureidopenicillins',
|
||||
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
|
||||
# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
|
||||
# and all separate EARS-Net letter codes such as AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
|
||||
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
||||
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
|
||||
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
|
||||
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
|
||||
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 and later
|
||||
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 9 LINES SKIPPED <<<<<
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group reference.version note
|
||||
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
|
||||
@ -176,12 +175,12 @@ genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhal
|
||||
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 11
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints 11
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints 11
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints 11
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints 11
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints 11
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints 11
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TIC S Anaerobic Gram-positives Breakpoints 11
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TIC I Anaerobic Gram-positives Breakpoints 11
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TIC R Anaerobic Gram-positives Breakpoints 11
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TIC S Anaerobic Gram-negatives Breakpoints 11
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TIC I Anaerobic Gram-negatives Breakpoints 11
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TIC R Anaerobic Gram-negatives Breakpoints 11
|
||||
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 11
|
||||
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 11
|
||||
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 11
|
||||
@ -224,6 +223,133 @@ genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei
|
||||
genus is Bacillus NOR S fluoroquinolones S Bacillus Breakpoints 11 added in 11
|
||||
genus is Bacillus NOR I fluoroquinolones I Bacillus Breakpoints 11 added in 11
|
||||
genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11
|
||||
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 12
|
||||
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 12
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 12
|
||||
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 12
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus NOR S MFX S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus NOR S CIP, LVX I Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus NOR R MFX, CIP, LVX R Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints 12
|
||||
genus is Staphylococcus TCY R DOX, MNO R Staphylococcus Breakpoints 12
|
||||
genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints 12
|
||||
genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints 12
|
||||
genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 12
|
||||
genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 12
|
||||
genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 12
|
||||
genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 12
|
||||
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 Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae NOR R MFX, LVX R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 12
|
||||
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints 12
|
||||
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints 12
|
||||
genus_species like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Haemophilus influenzae Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NOR S CIP, LVX, MFX, OFX S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NOR R CIP, LVX, MFX, OFX R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Moraxella catarrhalis TCY R DOX, MNO R Moraxella catarrhalis Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints 12
|
||||
genus_species is Pasteurella multocida NOR S CIP, LVX S Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Pasteurella multocida NOR R CIP, LVX R Streptococcus pneumoniae Breakpoints 12
|
||||
genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints 12
|
||||
genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints 12
|
||||
genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints 12
|
||||
genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints 12
|
||||
genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints 12
|
||||
genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints 12
|
||||
genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints 12
|
||||
genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints 12
|
||||
genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints 12
|
||||
genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints 12
|
||||
genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints 12
|
||||
genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola AMP S AMX S Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola AMP I AMX I Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola AMP R AMX R Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints 12
|
||||
genus_species is Aerococcus urinae AMP S AMX S Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus urinae AMP I AMX I Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus urinae AMP R AMX R Aerococcus sanguinicola Breakpoints 12
|
||||
genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints 12
|
||||
genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints 12
|
||||
genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints 12
|
||||
genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints 12
|
||||
genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints 12
|
||||
genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 12
|
||||
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 12
|
||||
genus is Vibrio PEF S CIP, LVX S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF I CIP, LVX I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio PEF R CIP, LVX R Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio ERY S AZM S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio ERY I AZM I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio ERY R AZM R Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio TCY S DOX S Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio TCY I DOX I Vibrio spp. Breakpoints 12
|
||||
genus is Vibrio TCY R DOX R Vibrio spp. Breakpoints 12
|
||||
genus is Bacillus NOR S CIP, LVX S Bacillus Breakpoints 12
|
||||
genus is Bacillus NOR R CIP, LVX R Bacillus Breakpoints 12
|
||||
genus_species is Burkholderia pseudomallei TCY S DOX I Burkholderia pseudomallei Breakpoints 12
|
||||
genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 12
|
||||
order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
|
||||
@ -373,7 +499,9 @@ genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rul
|
||||
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species is Staphylococcus aureus FOX S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.2 all penicillins without beta-lactamse inhibitor
|
||||
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
|
||||
@ -491,7 +619,9 @@ genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rul
|
||||
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.3
|
||||
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus_species is Staphylococcus aureus FOX S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.3 all penicillins without beta-lactamse inhibitor
|
||||
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
@ -33,12 +33,12 @@ library(cleaner)
|
||||
|
||||
# URL:
|
||||
# https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Dosages_v_11.0_Breakpoint_Tables.pdf
|
||||
# download the PDF file, open in Acrobat Pro and export as Excel workbook
|
||||
breakpoints_version <- 11
|
||||
# download the PDF file, open in Adobe Acrobat and export as Excel workbook
|
||||
breakpoints_version <- 12
|
||||
|
||||
dosage_source <- read_excel("data-raw/Dosages_v_11.0_Breakpoint_Tables.xlsx", skip = 5, na = "None") %>%
|
||||
dosage_source <- read_excel("data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx", skip = 4, na = "None") %>%
|
||||
format_names(snake_case = TRUE, penicillins = "drug") %>%
|
||||
filter(!tolower(standard_dosage) %in% c("standard dosage_source", "under review")) %>%
|
||||
filter(!tolower(standard_dosage) %in% c("standard dosage", "standard dosage_source", "under review")) %>%
|
||||
filter(!is.na(standard_dosage)) %>%
|
||||
# keep only one drug in the table
|
||||
arrange(desc(drug)) %>%
|
||||
@ -125,7 +125,7 @@ get_dosage_lst <- function(col_data) {
|
||||
standard <- get_dosage_lst(dosage_source$standard_dosage)
|
||||
high <- get_dosage_lst(dosage_source$high_dosage)
|
||||
uti <- get_dosage_lst(dosage_source$uncomplicated_uti)
|
||||
dosage <- bind_rows(
|
||||
dosage_new <- bind_rows(
|
||||
# standard dose
|
||||
data.frame(
|
||||
ab = dosage_source$ab,
|
||||
@ -171,6 +171,9 @@ dosage <- bind_rows(
|
||||
arrange(name, administration, type) %>%
|
||||
filter(!is.na(dose), dose != ".") %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
rownames(dosage) <- NULL
|
||||
rownames(dosage_new) <- NULL
|
||||
|
||||
dosage <- bind_rows(dosage_new, AMR::dosage) %>%
|
||||
dataset_UTF8_to_ASCII()
|
||||
|
||||
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2)
|
||||
|
||||
Reference in New Issue
Block a user