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Update clinical breakpoints and fix some as.mo() bugs (#117)
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115 * docs * implement ecoffs * unit tests
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data-raw/Dosages_v_13.0_Breakpoint_Tables.pdf
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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" 13
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"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
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"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv" 13
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"AMX" "Amoxicillin" "high_dosage" "0.75-1 g" 3 "oral" "" "0.75-1 g x 3 oral" 13
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"AMX" "Amoxicillin" "standard_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
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"AMX" "Amoxicillin" "uncomplicated_uti" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
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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" 13
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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" 13
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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" 13
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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" 13
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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" 13
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"AMP" "Ampicillin" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13
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"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
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"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 13
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"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 13
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"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 13
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"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 13
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"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13
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"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
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"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 13
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"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 13
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"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 13
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"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 13
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"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 13
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"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 13
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"LEX" "Cefalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 13
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"LEX" "Cefalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 13
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"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
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"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
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"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
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"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 13
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"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 13
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"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 13
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"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 13
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"CTX" "Cefotaxime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
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"CTX" "Cefotaxime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
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"CPD" "Cefpodoxime" "standard_dosage" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 13
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"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 13
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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" 13
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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" 13
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"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 13
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"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 13
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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" 13
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"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 13
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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" 13
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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" 13
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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" 13
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"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 13
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"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 13
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"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 13
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"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 13
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"CXM" "Cefuroxime" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
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"CXM" "Cefuroxime" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13
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"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13
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"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 13
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"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
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"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 13
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"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
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"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 13
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"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 13
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"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 13
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"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
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"CLR" "Clarithromycin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
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"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 13
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"CLI" "Clindamycin" "high_dosage" "0.9 g" 3 "iv" "" "0.9 g x 3 iv" 13
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"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 13
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"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "" "0.3 g x 4 oral" 13
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"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 13
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"CLO" "Cloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
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"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
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"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
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"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 13
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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" 13
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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" 13
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"DAP" "Daptomycin" "standard_dosage" "4 mg/kg" 1 "iv" "" "4 mg/kg x 1 iv" 13
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"DAP" "Daptomycin" "standard_dosage" "6 mg/kg" 1 "iv" "" "6 mg/kg x 1 iv" 13
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"DFX" "Delafloxacin" "standard_dosage" "0.3 g" 2 "iv" "" "0.3 g x 2 iv" 13
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"DFX" "Delafloxacin" "standard_dosage" "0.45 g" 2 "oral" "" "0.45 g x 2 oral" 13
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"DIC" "Dicloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
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"DIC" "Dicloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
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"DIC" "Dicloxacillin" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 13
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"DIC" "Dicloxacillin" "standard_dosage" "0.5-1 g" 4 "oral" "" "0.5-1 g x 4 oral" 13
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"DOR" "Doripenem" "high_dosage" "1 g" 3 "iv" "over 1 hour" "1 g x 3 iv over 1 hour" 13
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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" 13
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"DOX" "Doxycycline" "high_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 13
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"DOX" "Doxycycline" "standard_dosage" "0.1 g" 1 "oral" "" "0.1 g x 1 oral" 13
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"ERV" "Eravacycline" "standard_dosage" "1 mg/kg" 2 "iv" "" "1 mg/kg x 2 iv" 13
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"ETP" "Ertapenem" "standard_dosage" "1 g" 1 "iv" "over 30 minutes" "1 g x 1 iv over 30 minutes" 13
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"ERY" "Erythromycin" "high_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
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"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2-4 iv" 13
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"ERY" "Erythromycin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
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"ERY" "Erythromycin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2-4 oral" 13
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"FDX" "Fidaxomicin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 13
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"FLC" "Flucloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 13
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"FLC" "Flucloxacillin" "standard_dosage" "2 g" 4 "iv" "" "2 g x 4 iv (or 1 g x 6 iv)" 13
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"FLC" "Flucloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 13
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"FLC" "Flucloxacillin" "standard_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 13
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"FOS" "Fosfomycin" "high_dosage" "8 g" 3 "iv" "" "8 g x 3 iv" 13
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"FOS" "Fosfomycin" "standard_dosage" "4 g" 3 "iv" "" "4 g x 3 iv" 13
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"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 13
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"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 13
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"FUS" "Fusidic acid" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
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"FUS" "Fusidic acid" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
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"GEN" "Gentamicin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13
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"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 13
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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" 13
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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" 13
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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" 13
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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" 13
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"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 13
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"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 13
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"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 13
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"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 13
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"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 13
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"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 13
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"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 13
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"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 13
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"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 13
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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" 13
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"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 13
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"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 13
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"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 13
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"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 13
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"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 13
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"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 13
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"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 13
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"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 13
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"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 13
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"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 13
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"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 13
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"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv over 3 hours" 13
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"OXA" "Oxacillin" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 13
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"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 13
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"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 13
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"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv by extended 3-hour infusion" 13
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"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 13
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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" 13
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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" 13
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"QDA" "Quinupristin/dalfopristin" "high_dosage" "7.5 mg/kg" 3 "iv" "" "7.5 mg/kg x 3 iv" 13
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"QDA" "Quinupristin/dalfopristin" "standard_dosage" "7.5 mg/kg" 2 "iv" "" "7.5 mg/kg x 2 iv" 13
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"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "iv" "" "0.6 g x 1 iv" 13
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"RIF" "Rifampicin" "standard_dosage" "0.6 g" 1 "oral" "" "0.6 g x 1 oral" 13
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"RXT" "Roxithromycin" "standard_dosage" "0.15 g" 2 "oral" "" "0.15 g x 2 oral" 13
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"SPT" "Spectinomycin" "standard_dosage" "2 g" 1 "im" "" "2 g x 1 im" 13
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"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "iv" "" "0.2 g x 1 iv" 13
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"TZD" "Tedizolid" "standard_dosage" "0.2 g" 1 "oral" "" "0.2 g x 1 oral" 13
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"TEC" "Teicoplanin" "high_dosage" "0.8 g" 1 "iv" "" "0.8 g x 1 iv" 13
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"TEC" "Teicoplanin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 13
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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" 13
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"TLT" "Telithromycin" "standard_dosage" "0.8 g" 1 "oral" "" "0.8 g x 1 oral" 13
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"TEM" "Temocillin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 13
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"TEM" "Temocillin" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 13
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"TCY" "Tetracycline" "high_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 13
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"TCY" "Tetracycline" "standard_dosage" "0.25 g" 4 "oral" "" "0.25 g x 4 oral" 13
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"TIC" "Ticarcillin" "high_dosage" "3 g" 6 "iv" "" "3 g x 6 iv" 13
|
||||
"TIC" "Ticarcillin" "standard_dosage" "3 g" 4 "iv" "" "3 g x 4 iv" 13
|
||||
"TCC" "Ticarcillin/clavulanic acid" "high_dosage" "3 g + 0.1 g" 6 "iv" "" "(3 g ticarcillin + 0.1 g clavulanic acid) x 6 iv" 13
|
||||
"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" 13
|
||||
"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" 13
|
||||
"TOB" "Tobramycin" "standard_dosage" "6-7 mg/kg" 1 "iv" "" "6-7 mg/kg x 1 iv" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 13
|
||||
"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" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13
|
||||
"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" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13
|
||||
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 13
|
||||
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 13
|
||||
"AMK" "Amikacin" "standard_dosage" "25-30 mg/kg" 1 "iv" "" "25-30 mg/kg x 1 iv" 12
|
||||
"AMX" "Amoxicillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 12
|
||||
"AMX" "Amoxicillin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3-4 iv" 12
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -73,6 +73,7 @@ whonet_organisms.bak <- whonet_organisms
|
||||
# generate the mo codes and add their names
|
||||
whonet_organisms <- whonet_organisms.bak %>%
|
||||
mutate(mo = as.mo(gsub("(sero[a-z]*| complex| nontypable| non[-][a-zA-Z]+|var[.]| not .*|sp[.],.*|, .*variant.*|, .*toxin.*|, microaer.*| beta-haem[.])", "", ORGANISM),
|
||||
minimum_matching_score = 0.6,
|
||||
keep_synonyms = TRUE,
|
||||
language = "en"),
|
||||
mo = case_when(ORGANISM %like% "Anaerobic" & ORGANISM %like% "negative" ~ as.mo("B_ANAER-NEG"),
|
||||
@ -86,17 +87,21 @@ whonet_organisms <- whonet_organisms.bak %>%
|
||||
new_mo_codes <- whonet_organisms %>%
|
||||
mutate(
|
||||
first_part = sapply(ORGANISM, function(x) strsplit(gsub("[^a-zA-Z _-]+", "", x), " ")[[1]][1], USE.NAMES = FALSE),
|
||||
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic")
|
||||
keep = mo_name %like_case% first_part | ORGANISM %like% "Gram " | ORGANISM == "Other" | ORGANISM %like% "anaerobic") %>%
|
||||
filter(keep == TRUE) %>%
|
||||
transmute(code = toupper(ORGANISM_CODE),
|
||||
mo = mo)
|
||||
# update microorganisms.codes with the latest WHONET codes
|
||||
microorganisms.codes <- microorganisms.codes %>%
|
||||
microorganisms.codes2 <- microorganisms.codes %>%
|
||||
# remove all old WHONET codes, whether we (in the end) keep them or not
|
||||
filter(!toupper(code) %in% toupper(whonet_organisms$ORGANISM_CODE)) %>%
|
||||
filter(!toupper(code) %in% toupper(new_mo_codes$code)) %>%
|
||||
# and add the new ones
|
||||
bind_rows(new_mo_codes %>%
|
||||
filter(keep == TRUE) %>%
|
||||
transmute(code = toupper(ORGANISM_CODE),
|
||||
mo = mo)) %>%
|
||||
bind_rows(new_mo_codes) %>%
|
||||
arrange(code)
|
||||
# new codes:
|
||||
microorganisms.codes2$code[which(!microorganisms.codes2$code %in% microorganisms.codes$code)]
|
||||
mo_name(microorganisms.codes2$mo[which(!microorganisms.codes2$code %in% microorganisms.codes$code)], keep_synonyms = TRUE)
|
||||
microorganisms.codes <- microorganisms.codes2
|
||||
|
||||
# Run this part to update ASIARS-Net:
|
||||
# start
|
||||
@ -140,11 +145,11 @@ whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na =
|
||||
|
||||
breakpoints <- whonet_breakpoints %>%
|
||||
mutate(code = toupper(ORGANISM_CODE)) %>%
|
||||
left_join(bind_rows(microorganisms.codes,
|
||||
left_join(bind_rows(microorganisms.codes %>% filter(!code %in% c("ALL", "GEN")),
|
||||
# GEN (Generic) and ALL (All) are PK/PD codes
|
||||
data.frame(code = c("ALL", "GEN"),
|
||||
mo = rep(as.mo("UNKNOWN"), 2))))
|
||||
# these ones lack a MO name, they cannot be used:
|
||||
# these ones lack an MO name, they cannot be used:
|
||||
unknown <- breakpoints %>%
|
||||
filter(is.na(mo)) %>%
|
||||
pull(code) %>%
|
||||
@ -159,9 +164,13 @@ breakpoints %>%
|
||||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
|
||||
count(YEAR, GUIDELINES, WHONET_ABX_CODE) %>%
|
||||
arrange(desc(YEAR))
|
||||
breakpoints %>%
|
||||
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
|
||||
pull(WHONET_ABX_CODE) %>%
|
||||
unique()
|
||||
# we cannot use them
|
||||
breakpoints <- breakpoints %>%
|
||||
filter(WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE)
|
||||
# breakpoints <- breakpoints %>%
|
||||
# filter(WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE)
|
||||
# now check with our own antibiotics
|
||||
breakpoints %>%
|
||||
filter(!toupper(WHONET_ABX_CODE) %in% antibiotics$ab) %>%
|
||||
@ -171,19 +180,19 @@ breakpoints %>%
|
||||
|
||||
breakpoints_new <- breakpoints %>%
|
||||
# only last available 10 years
|
||||
filter(YEAR > max(YEAR) - 10) %>%
|
||||
# filter(YEAR > max(YEAR) - 10) %>%
|
||||
transmute(
|
||||
guideline = paste(GUIDELINES, YEAR),
|
||||
method = TEST_METHOD,
|
||||
site = gsub(".*(UTI|urinary|urine).*", "UTI", SITE_OF_INFECTION, ignore.case = TRUE),
|
||||
site = SITE_OF_INFECTION,
|
||||
mo,
|
||||
rank_index = case_when(
|
||||
is.na(mo_rank(mo)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
|
||||
mo_rank(mo) %like% "(infra|sub)" ~ 1,
|
||||
mo_rank(mo) == "species" ~ 2,
|
||||
mo_rank(mo) == "genus" ~ 3,
|
||||
mo_rank(mo) == "family" ~ 4,
|
||||
mo_rank(mo) == "order" ~ 5,
|
||||
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
|
||||
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
|
||||
TRUE ~ 6
|
||||
),
|
||||
ab = as.ab(WHONET_ABX_CODE),
|
||||
@ -191,7 +200,7 @@ breakpoints_new <- breakpoints %>%
|
||||
disk_dose = POTENCY,
|
||||
breakpoint_S = S,
|
||||
breakpoint_R = R,
|
||||
uti = ifelse(is.na(site), FALSE, site == "UTI")
|
||||
uti = ifelse(is.na(site), FALSE, gsub(".*(UTI|urinary|urine).*", "UTI", site) == "UTI")
|
||||
) %>%
|
||||
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
|
||||
mutate(disk_dose = disk_dose %>%
|
||||
@ -206,8 +215,18 @@ breakpoints_new <- breakpoints %>%
|
||||
breakpoints_new %>%
|
||||
mutate(id = paste(guideline, ab, mo, method, site)) %>%
|
||||
filter(id %in% .$id[which(duplicated(id))])
|
||||
# remove duplicates
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE)
|
||||
|
||||
# clean disk zones and MICs
|
||||
# fix reference table names
|
||||
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl))
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
mutate(ref_tbl = case_when(is.na(ref_tbl) & guideline %like% "EUCAST 202" ~ lead(ref_tbl),
|
||||
is.na(ref_tbl) ~ "Unknown",
|
||||
TRUE ~ ref_tbl))
|
||||
|
||||
# clean disk zones
|
||||
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S", drop = TRUE]))
|
||||
breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE]))
|
||||
|
||||
@ -227,7 +246,7 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <-
|
||||
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
|
||||
# EUCAST 2022 guideline: S <= 8 and R > 8
|
||||
# WHONET file: S <= 8 and R >= 16
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
# this will make an MIC of 12 I, which should be R, so:
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "MIC" & log2(breakpoint_R) - log2(breakpoint_S) != 0,
|
||||
@ -235,6 +254,7 @@ breakpoints_new <- breakpoints_new %>%
|
||||
breakpoint_R
|
||||
))
|
||||
# fix disks as well
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "DISK")
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "DISK" & breakpoint_S - breakpoint_R != 0,
|
||||
breakpoint_R + 1,
|
||||
@ -244,7 +264,7 @@ breakpoints_new <- breakpoints_new %>%
|
||||
breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
|
||||
|
||||
# check again
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
# compare with current version
|
||||
clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
|
||||
|
||||
@ -252,6 +272,72 @@ clinical_breakpoints %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "
|
||||
dim(breakpoints_new)
|
||||
dim(clinical_breakpoints)
|
||||
|
||||
# ECOFFs ----
|
||||
|
||||
# ECOFF = Epidemiological Cut-Off
|
||||
whonet_ecoff <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
|
||||
filter(BREAKPOINT_TYPE == "ECOFF", GUIDELINES %in% c("CLSI", "EUCAST"))
|
||||
|
||||
ecoff <- whonet_ecoff %>%
|
||||
filter(!ORGANISM_CODE %in% c("clu", "BFX", "PFX", "kma", "cdh")) %>%
|
||||
transmute(guideline = paste(GUIDELINES, YEAR),
|
||||
mo = as.mo(ORGANISM_CODE, keep_synonyms = TRUE),
|
||||
ab = as.ab(WHONET_ABX_CODE),
|
||||
method = TEST_METHOD,
|
||||
ecoff = as.double(ECV_ECOFF)) %>%
|
||||
filter(!is.na(ecoff)) %>%
|
||||
distinct()
|
||||
|
||||
# join to breakpoints
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
bind_rows(breakpoints_new %>%
|
||||
right_join(ecoff, by = c("guideline", "mo", "ab", "method"))) %>%
|
||||
mutate(ref_tbl = ifelse(is.na(ref_tbl), "ECOFF", ref_tbl)) %>%
|
||||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
|
||||
arrange(desc(guideline), ab, mo, method) %>%
|
||||
mutate(rank_index = case_when(
|
||||
is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
|
||||
mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "species" ~ 2,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "genus" ~ 3,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "family" ~ 4,
|
||||
mo_rank(mo, keep_synonyms = TRUE) == "order" ~ 5,
|
||||
TRUE ~ 6
|
||||
)) %>%
|
||||
mutate(uti = ifelse(is.na(uti), FALSE, uti)) %>%
|
||||
relocate(ecoff, .after = breakpoint_R)
|
||||
|
||||
breakpoints_new.bak <- mutate(uti = ifelse(is.na(uti), FALSE, uti), .after = ecoff)
|
||||
|
||||
# EXTEND CoNS/CoPS/GAS/GBS ----
|
||||
|
||||
# extend all coagulase-postive/-negative staphylococci
|
||||
CoNS <- breakpoints_new %>% filter(mo == as.mo("CoNS"))
|
||||
for (m in MO_CONS[mo_subspecies(MO_CONS, keep_synonyms = TRUE) == ""]) {
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
bind_rows(CoNS %>%
|
||||
mutate(mo = m))
|
||||
}
|
||||
CoPS <- breakpoints_new %>% filter(mo == as.mo("CoPS"))
|
||||
for (m in MO_COPS[mo_subspecies(MO_COPS, keep_synonyms = TRUE) == ""]) {
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
bind_rows(CoPS %>%
|
||||
mutate(mo = m))
|
||||
}
|
||||
# do the same for group A and B streptococci
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
bind_rows(breakpoints_new %>%
|
||||
filter(mo == as.mo("Streptococcus Group A")) %>%
|
||||
mutate(mo = as.mo("Streptococcus pyogenes"))) %>%
|
||||
bind_rows(breakpoints_new %>%
|
||||
filter(mo == as.mo("Streptococcus Group B")) %>%
|
||||
mutate(mo = as.mo("Streptococcus agalactiae")))
|
||||
# remove duplicates again for CoNS/CoPS/GBS and arrange
|
||||
breakpoints_new <- breakpoints_new %>%
|
||||
mutate(mo = as.mo(mo, keep_synonyms = TRUE)) %>%
|
||||
distinct(guideline, ab, mo, method, site, .keep_all = TRUE) %>%
|
||||
arrange(desc(guideline), ab, mo, method)
|
||||
|
||||
|
||||
# Save to package ----
|
||||
|
||||
|
||||
@ -32,9 +32,9 @@ library(readxl)
|
||||
library(cleaner)
|
||||
|
||||
# URL:
|
||||
# https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Dosages_v_11.0_Breakpoint_Tables.pdf
|
||||
# https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/Dosages_v_13.0_Breakpoint_Tables.pdf
|
||||
# download the PDF file, open in Adobe Acrobat and export as Excel workbook
|
||||
breakpoints_version <- 12
|
||||
breakpoints_version <- 13
|
||||
|
||||
dosage_source <- read_excel("data-raw/Dosages_v_12.0_Breakpoint_Tables.xlsx", skip = 4, na = "None") %>%
|
||||
format_names(snake_case = TRUE, penicillins = "drug") %>%
|
||||
@ -170,10 +170,9 @@ dosage_new <- bind_rows(
|
||||
) %>%
|
||||
arrange(name, administration, type) %>%
|
||||
filter(!is.na(dose), dose != ".") %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
rownames(dosage_new) <- NULL
|
||||
|
||||
dosage <- bind_rows(dosage_new, AMR::dosage) %>%
|
||||
# this makes it a tibble as well:
|
||||
dataset_UTF8_to_ASCII()
|
||||
|
||||
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2)
|
||||
dosage <- bind_rows(dosage_new, AMR::dosage)
|
||||
|
||||
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
|
||||
|
||||
BIN
data-raw/v_13.0_Breakpoint_Tables.xlsx
Normal file
BIN
data-raw/v_13.0_Breakpoint_Tables.xlsx
Normal file
Binary file not shown.
Reference in New Issue
Block a user