mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 20:02:04 +02:00
(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
This commit is contained in:
Binary file not shown.
BIN
data-raw/Dosages_v_11.0_Breakpoint_Tables.xlsx
Normal file
BIN
data-raw/Dosages_v_11.0_Breakpoint_Tables.xlsx
Normal file
Binary file not shown.
@ -1 +1 @@
|
||||
a30faa0e4475d440d1bb8e44e6857062
|
||||
fa68ab044001078f290218a7de6cc5c4
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -37,6 +37,8 @@
|
||||
"BEK" 439318 "Bekanamycin" "Aminoglycosides" "" "c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")" "character(0)"
|
||||
"BNB" "J01CE08" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "" 3.6 "g" ""
|
||||
"BNP" "J01CE10" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"bicillin v\", \"biphecillin\")" 2 "g" "character(0)"
|
||||
"PEN" "J01CE01" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
|
||||
)" 3.6 "g" "3913-1"
|
||||
"BES" 10178705 "Besifloxacin" "Quinolones" "" "besifloxacin" "character(0)"
|
||||
"BIA" 71339 "Biapenem" "Carbapenems" "" "c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")" "character(0)"
|
||||
"BCZ" 65807 "Bicyclomycin (Bicozamycin)" "Other antibacterials" "" "c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")" "character(0)"
|
||||
@ -328,8 +330,6 @@
|
||||
"PAZ" "J01MA18" 65957 "Pazufloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "" "c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")" 1 "g" "character(0)"
|
||||
"PEF" "J01MA03" 51081 "Pefloxacin" "Quinolones" "Quinolone antibacterials" "Fluoroquinolones" "c(\"\", \"pefl\")" "c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")" 0.8 "g" 0.8 "g" "3906-5"
|
||||
"PNM" "J01CE06" 10250769 "Penamecillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")" 1.05 "g" "character(0)"
|
||||
"PEN" "J01CE01" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "Combinations of antibacterials" "Combinations of antibacterials" "c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")" "c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
|
||||
)" 3.6 "g" "3913-1"
|
||||
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "" "" ""
|
||||
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "" "" ""
|
||||
"PNM1" "J01AA10" 54686187 "Penimepicycline" "Tetracyclines" "Tetracyclines" "Tetracyclines" "" "c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")" "character(0)"
|
||||
@ -354,6 +354,7 @@
|
||||
"POS" "J02AC04" 468595 "Posaconazole" "Antifungals/antimycotics" "Antimycotics for systemic use" "Triazole derivatives" "posa" "c(\"noxafil\", \"posaconazole\", \"posaconazole sp\", \"posconazole\")" 0.3 "g" 0.3 "g" "c(\"53731-6\", \"80545-7\")"
|
||||
"PRA" 9802884 "Pradofloxacin" "Quinolones" "" "pradofloxacin" "character(0)"
|
||||
"PRX" 71455 "Premafloxacin" "Quinolones" "" "premafloxacin" "character(0)"
|
||||
"PMD" "J04AK08" 456199 "Pretomanid" "Antimycobacterials" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "" "" ""
|
||||
"PRM" 6446787 "Primycin" "Macrolides/lincosamides" "" "" ""
|
||||
"PRI" "J01FG01" 11979535 "Pristinamycin" "Macrolides/lincosamides" "Macrolides, lincosamides and streptogramins" "Streptogramins" "c(\"\", \"pris\")" "c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")" 2 "g" "character(0)"
|
||||
"PRB" "J01CE09" 5903 "Procaine benzylpenicillin" "Beta-lactams/penicillins" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "c(\"depocillin\", \"duphapen\", \"hostacillin\", \"hydracillin\", \"jenacillin o\", \"nopcaine\", \"penicillin procaine\", \"retardillin\", \"vetspen\", \"vitablend\")" 0.6 "g" "character(0)"
|
||||
|
||||
Binary file not shown.
@ -115,6 +115,115 @@ genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 10
|
||||
genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints 10
|
||||
genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints 10
|
||||
genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 10
|
||||
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 11
|
||||
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 11
|
||||
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 11
|
||||
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 11
|
||||
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus FOX R carbapenems, cephalosporins_except_CAZ R Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints 11
|
||||
genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints 11
|
||||
genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints 11
|
||||
genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints 11
|
||||
genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 11
|
||||
genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 11
|
||||
genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 11
|
||||
genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 11
|
||||
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
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 11
|
||||
genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints 11
|
||||
genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints 11
|
||||
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_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
|
||||
genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints 11
|
||||
genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints 11
|
||||
genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints 11
|
||||
genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints 11
|
||||
genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints 11
|
||||
genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints 11
|
||||
genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints 11
|
||||
genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints 11
|
||||
genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints 11
|
||||
genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints 11
|
||||
genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints 11
|
||||
genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints 11
|
||||
genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints 11
|
||||
genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints 11
|
||||
genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints 11
|
||||
genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints 11
|
||||
genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints 11
|
||||
genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints 11
|
||||
genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints 11
|
||||
genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints 11
|
||||
genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints 11
|
||||
genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints 11
|
||||
genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints 11
|
||||
genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints 11
|
||||
genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints 11
|
||||
genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints 11
|
||||
genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints 11
|
||||
genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints 11
|
||||
genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints 11
|
||||
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 PEN, glycopeptides, 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
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
@ -25,6 +25,7 @@
|
||||
|
||||
library(openxlsx)
|
||||
library(dplyr)
|
||||
library(tidyr)
|
||||
library(cleaner)
|
||||
library(AMR)
|
||||
|
||||
@ -32,9 +33,18 @@ library(AMR)
|
||||
|
||||
read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
|
||||
message("Getting sheet ", sheet)
|
||||
message("\nGetting sheet: ", sheet)
|
||||
sheet.bak <- sheet
|
||||
|
||||
uncertainties <- NULL
|
||||
add_uncertainties <- function(old, new) {
|
||||
if (is.null(old)) {
|
||||
new
|
||||
} else {
|
||||
bind_rows(old, new)
|
||||
}
|
||||
}
|
||||
|
||||
raw_data <- read.xlsx(xlsxFile = file,
|
||||
sheet = sheet,
|
||||
colNames = FALSE,
|
||||
@ -42,6 +52,12 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
skipEmptyCols = FALSE,
|
||||
fillMergedCells = TRUE,
|
||||
na.strings = c("", "-", "NA", "IE", "IP"))
|
||||
probable_rows <- suppressWarnings(raw_data %>% mutate_all(as.double) %>% summarise_all(~sum(!is.na(.))) %>% unlist() %>% max())
|
||||
if (probable_rows == 0) {
|
||||
message("NO ROWS FOUND")
|
||||
message("------------------------")
|
||||
return(NULL)
|
||||
}
|
||||
|
||||
# in the info header in the Excel file, EUCAST mentions which genera are targeted
|
||||
if (sheet %like% "anaerob.*Gram.*posi") {
|
||||
@ -69,7 +85,8 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
} else if (sheet %like% "PK.*PD") {
|
||||
sheet <- "UNKNOWN"
|
||||
}
|
||||
mo_sheet <- paste0(as.mo(unlist(strsplit(sheet, "_"))), collapse = "|")
|
||||
mo_sheet <- paste0(suppressMessages(as.mo(unlist(strsplit(sheet, "_")))), collapse = "|")
|
||||
if (!is.null(mo_uncertainties())) uncertainties <- add_uncertainties(uncertainties, mo_uncertainties())
|
||||
|
||||
set_columns_names <- function(x, cols) {
|
||||
colnames(x) <- cols[1:length(colnames(x))]
|
||||
@ -80,7 +97,8 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
for (i in seq_len(length(x))) {
|
||||
y <- trimws(unlist(strsplit(x[i], "(,|and)")))
|
||||
y <- trimws(gsub("[(].*[)]", "", y))
|
||||
y <- suppressWarnings(as.mo(y, allow_uncertain = FALSE))
|
||||
y <- suppressWarnings(suppressMessages(as.mo(y, allow_uncertain = FALSE)))
|
||||
if (!is.null(mo_uncertainties())) uncertainties <<- add_uncertainties(uncertainties, mo_uncertainties())
|
||||
y <- y[!is.na(y) & y != "UNKNOWN"]
|
||||
x[i] <- paste(y, collapse = "|")
|
||||
}
|
||||
@ -153,7 +171,8 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
mutate(drug = gsub(" ?[(, ].*$", "", drug),
|
||||
drug = gsub("[1-9]+$", "", drug),
|
||||
ab = as.ab(drug)) %>%
|
||||
select(ab, mo, everything(), -drug)
|
||||
select(ab, mo, everything(), -drug) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
|
||||
# new row for every different MO mentioned
|
||||
for (i in 1:nrow(cleaned)) {
|
||||
@ -162,7 +181,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
mo_vect <- unlist(strsplit(mo, "|", fixed = TRUE))
|
||||
cleaned[i, "mo"] <- mo_vect[1]
|
||||
for (j in seq_len(length(mo_vect))) {
|
||||
cleaned <- bind_rows(cleaned, cleaned[i ,])
|
||||
cleaned <- bind_rows(cleaned, cleaned[i , , drop = FALSE])
|
||||
cleaned[nrow(cleaned), "mo"] <- mo_vect[j]
|
||||
}
|
||||
}
|
||||
@ -190,41 +209,26 @@ read_EUCAST <- function(sheet, file, guideline_name) {
|
||||
ref_tbl = sheet.bak,
|
||||
disk_dose = ifelse(!is.na(disk_dose), paste0(disk_dose, "ug"), NA_character_),
|
||||
breakpoint_S,
|
||||
breakpoint_R)
|
||||
breakpoint_R) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
|
||||
if (!is.null(uncertainties)) {
|
||||
print(uncertainties %>% distinct(input, mo, .keep_all = TRUE))
|
||||
}
|
||||
|
||||
message("Estimated: ", probable_rows, ", gained: ", cleaned %>% count(ab) %>% nrow())
|
||||
message("------------------------")
|
||||
cleaned
|
||||
}
|
||||
|
||||
sheets_to_analyse <- c("Enterobacterales",
|
||||
"Pseudomonas",
|
||||
"S.maltophilia",
|
||||
"Acinetobacter",
|
||||
"Staphylococcus",
|
||||
"Enterococcus",
|
||||
"Streptococcus A,B,C,G",
|
||||
"S.pneumoniae",
|
||||
"Viridans group streptococci",
|
||||
"H.influenzae",
|
||||
"M.catarrhalis",
|
||||
"N.gonorrhoeae",
|
||||
"N.meningitidis",
|
||||
"Anaerobes, Grampositive",
|
||||
"C.difficile",
|
||||
"Anaerobes, Gramnegative",
|
||||
"H.pylori",
|
||||
"L.monocytogenes",
|
||||
"P.multocida",
|
||||
"C.jejuni_C.coli",
|
||||
"Corynebacterium",
|
||||
"A.sanguinicola_A.urinae",
|
||||
"K.kingae",
|
||||
"Aeromonas",
|
||||
"B.pseudomallei",
|
||||
"M.tuberculosis",
|
||||
"PK PD breakpoints")
|
||||
|
||||
file <- "data-raw/v_10.0_Breakpoint_Tables.xlsx"
|
||||
guideline_name <- "EUCAST 2020"
|
||||
# Actual import -----------------------------------------------------------
|
||||
|
||||
file <- "data-raw/v_11.0_Breakpoint_Tables.xlsx"
|
||||
sheets <- readxl::excel_sheets(file)
|
||||
guideline_name <- "EUCAST 2021"
|
||||
|
||||
sheets_to_analyse <- sheets[!sheets %in% c("Content", "Changes", "Notes", "Guidance", "Dosages", "Technical uncertainty", "Topical agents")]
|
||||
|
||||
# takes the longest time:
|
||||
new_EUCAST <- read_EUCAST(sheet = sheets_to_analyse[1],
|
||||
|
||||
@ -606,6 +606,20 @@ antibiotics <- antibiotics %>%
|
||||
TRUE ~ group))
|
||||
antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones"
|
||||
|
||||
# add pretomanid
|
||||
antibiotics <- antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
bind_rows(antibiotics %>%
|
||||
mutate(ab = as.character(ab)) %>%
|
||||
filter(ab == "SMF") %>%
|
||||
mutate(ab = "PMD",
|
||||
atc = "J04AK08",
|
||||
cid = 456199,
|
||||
name = "Pretomanid",
|
||||
abbreviations = list(""),
|
||||
oral_ddd = NA_real_))
|
||||
|
||||
|
||||
# update DDDs from WHOCC website
|
||||
ddd_oral <- double(length = nrow(antibiotics))
|
||||
ddd_iv <- double(length = nrow(antibiotics))
|
||||
|
||||
130
data-raw/reproduction_of_eucast_dosage.R
Normal file
130
data-raw/reproduction_of_eucast_dosage.R
Normal file
@ -0,0 +1,130 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis for R #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
||||
# Developed at the University of Groningen, the Netherlands, in #
|
||||
# collaboration with non-profit organisations Certe Medical #
|
||||
# Diagnostics & Advice, and University Medical Center Groningen. #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
library(dplyr)
|
||||
library(readxl)
|
||||
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
|
||||
|
||||
dosage_source <- read_excel("data-raw/Dosages_v_11.0_Breakpoint_Tables.xlsx", skip = 5, na = "None") %>%
|
||||
format_names(snake_case = TRUE, penicillins = "drug") %>%
|
||||
filter(!tolower(standard_dosage) %in% c("standard dosage_source", "under review")) %>%
|
||||
filter(!is.na(standard_dosage)) %>%
|
||||
# keep only one drug in the table
|
||||
arrange(desc(drug)) %>%
|
||||
mutate(drug = gsub("(.*) ([(]|iv|oral).*", "\\1", drug)) %>%
|
||||
#distinct(drug, .keep_all = TRUE) %>%
|
||||
arrange(drug) %>%
|
||||
mutate(ab = as.ab(drug),
|
||||
ab_name = ab_name(ab, language = NULL))
|
||||
|
||||
get_dosage_lst <- function(col_data) {
|
||||
standard <- col_data %>%
|
||||
# remove new lines
|
||||
gsub(" ?(\n|\t)+ ?", " ", .) %>%
|
||||
# keep only the first suggestion, replace all after 'or' and more informative texts
|
||||
gsub("(.*?) (or|with|loading|depending|over|by) .*", "\\1", .) %>%
|
||||
# remove (1 MU)
|
||||
gsub(" [(][0-9] [A-Z]+[)]", "", .) %>%
|
||||
# remove parentheses
|
||||
gsub("[)(]", "", .) %>%
|
||||
# remove drug names
|
||||
gsub(" [a-z]{5,99}( |$)", " ", .) %>%
|
||||
gsub(" [a-z]{5,99}( |$)", " ", .) %>%
|
||||
gsub(" (acid|dose)", "", .)# %>%
|
||||
# keep lowest value only (25-30 mg -> 25 mg)
|
||||
# gsub("[-].*? ", " ", .)
|
||||
|
||||
dosage_lst <- lapply(strsplit(standard, " x "),
|
||||
function(x) {
|
||||
dose <- x[1]
|
||||
if (dose %like% "under") {
|
||||
dose <- NA_character_
|
||||
}
|
||||
admin <- x[2]
|
||||
|
||||
list(
|
||||
dose = trimws(dose),
|
||||
dose_times = gsub("^([0-9.]+).*", "\\1", admin),
|
||||
administration = clean_character(admin),
|
||||
notes = "",
|
||||
original_txt = ""
|
||||
)
|
||||
})
|
||||
for (i in seq_len(length(col_data))) {
|
||||
dosage_lst[[i]]$original_txt <- gsub("\n", " ", col_data[i])
|
||||
if (col_data[i] %like% " (or|with|loading|depending|over) ") {
|
||||
dosage_lst[[i]]$notes <- gsub("\n", " ", gsub(".* ((or|with|loading|depending|over) .*)", "\\1", col_data[i]))
|
||||
}
|
||||
}
|
||||
dosage_lst
|
||||
}
|
||||
|
||||
standard <- get_dosage_lst(dosage_source$standard_dosage)
|
||||
high <- get_dosage_lst(dosage_source$high_dosage)
|
||||
uti <- get_dosage_lst(dosage_source$uncomplicated_uti)
|
||||
dosage <- bind_rows(
|
||||
data.frame(
|
||||
ab = dosage_source$ab,
|
||||
name = dosage_source$ab_name,
|
||||
type = "standard_dosage",
|
||||
dose = sapply(standard, function(x) x$dose),
|
||||
dose_times = sapply(standard, function(x) x$dose_times),
|
||||
administration = sapply(standard, function(x) x$administration),
|
||||
notes = sapply(standard, function(x) x$notes),
|
||||
original_txt = sapply(standard, function(x) x$original_txt),
|
||||
stringsAsFactors = FALSE
|
||||
),
|
||||
data.frame(
|
||||
ab = dosage_source$ab,
|
||||
name = dosage_source$ab_name,
|
||||
type = "high_dosage",
|
||||
dose = sapply(high, function(x) x$dose),
|
||||
dose_times = sapply(high, function(x) x$dose_times),
|
||||
administration = sapply(high, function(x) x$administration),
|
||||
notes = sapply(high, function(x) x$notes),
|
||||
original_txt = sapply(high, function(x) x$original_txt),
|
||||
stringsAsFactors = FALSE
|
||||
),
|
||||
data.frame(
|
||||
ab = dosage_source$ab,
|
||||
name = dosage_source$ab_name,
|
||||
type = "uncomplicated_uti",
|
||||
dose = sapply(uti, function(x) x$dose),
|
||||
dose_times = sapply(uti, function(x) x$dose_times),
|
||||
administration = sapply(uti, function(x) x$administration),
|
||||
notes = sapply(uti, function(x) x$notes),
|
||||
original_txt = sapply(uti, function(x) x$original_txt),
|
||||
stringsAsFactors = FALSE
|
||||
)) %>%
|
||||
mutate(eucast_version = breakpoints_version) %>%
|
||||
arrange(name, administration, type) %>%
|
||||
filter(!is.na(dose), dose != ".")
|
||||
|
||||
usethis::use_data(dosage, internal = FALSE, overwrite = TRUE, version = 2)
|
||||
@ -77,6 +77,7 @@ clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
|
||||
|
||||
# add new EUCAST with read_EUCAST.R
|
||||
# 2020-04-14 did that now for 2019 and 2020
|
||||
|
||||
rsi_trans <- rsi_trans %>%
|
||||
filter(guideline != "EUCAST 2019") %>%
|
||||
bind_rows(new_EUCAST) %>%
|
||||
@ -88,6 +89,17 @@ rsi_trans <- rsi_trans %>%
|
||||
ab = as.ab(ab)) %>%
|
||||
arrange(desc(guideline), ab, mo, method)
|
||||
|
||||
# 2021-01-12 did that now for 2021
|
||||
rsi_trans <- rsi_trans %>%
|
||||
mutate(mo = as.character(mo)) %>%
|
||||
bind_rows(new_EUCAST) %>%
|
||||
mutate(uti = site %like% "(UTI|urinary)") %>%
|
||||
as.data.frame(stringsAsFactors = FALSE) %>%
|
||||
# force classes again
|
||||
mutate(mo = as.mo(mo),
|
||||
ab = as.ab(ab)) %>%
|
||||
arrange(desc(guideline), ab, mo, method)
|
||||
|
||||
# save to package
|
||||
rsi_translation <- rsi_trans
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE)
|
||||
|
||||
@ -1 +1 @@
|
||||
c589396a6728f7c72def07b4dfb35e28
|
||||
f816b536ddd71d00e1adcdaba97d0329
|
||||
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
@ -19,7 +19,8 @@ de CoPS KPS TRUE FALSE
|
||||
de Gram-negative Gramnegativ FALSE FALSE
|
||||
de Gram-positive Grampositiv FALSE FALSE
|
||||
de Bacteria Bakterien FALSE FALSE
|
||||
de Fungi Hefen/Pilze FALSE FALSE
|
||||
de Fungi Pilze FALSE FALSE
|
||||
de Yeasts Hefen FALSE FALSE
|
||||
de Protozoa Protozoen FALSE FALSE
|
||||
de biogroup Biogruppe FALSE FALSE
|
||||
de biotype Biotyp FALSE FALSE
|
||||
@ -49,8 +50,9 @@ nl CoPS CPS TRUE FALSE
|
||||
nl Gram-negative Gram-negatief FALSE FALSE
|
||||
nl Gram-positive Gram-positief FALSE FALSE
|
||||
nl Bacteria Bacteriën FALSE FALSE
|
||||
nl Fungi Schimmels/gisten FALSE FALSE
|
||||
nl Protozoa protozoën FALSE FALSE
|
||||
nl Fungi Schimmels FALSE FALSE
|
||||
nl Yeasts Gisten FALSE FALSE
|
||||
nl Protozoa Protozoën FALSE FALSE
|
||||
nl biogroup biogroep FALSE FALSE
|
||||
nl vegetative vegetatief FALSE FALSE
|
||||
nl ([([ ]*?)group \\1groep FALSE FALSE
|
||||
@ -83,6 +85,7 @@ es Gram-negative Gram negativo FALSE FALSE
|
||||
es Gram-positive Gram positivo FALSE FALSE
|
||||
es Bacteria Bacterias FALSE FALSE
|
||||
es Fungi Hongos FALSE FALSE
|
||||
es Yeasts Levaduras FALSE FALSE
|
||||
es Protozoa Protozoarios FALSE FALSE
|
||||
es biogroup biogrupo FALSE FALSE
|
||||
es biotype biotipo FALSE FALSE
|
||||
@ -110,7 +113,8 @@ it unknown rank grado sconosciuto FALSE FALSE
|
||||
it Gram-negative Gram negativo FALSE FALSE
|
||||
it Gram-positive Gram positivo FALSE FALSE
|
||||
it Bacteria Batteri FALSE FALSE
|
||||
it Fungi Fungo FALSE FALSE
|
||||
it Fungi Funghi FALSE FALSE
|
||||
it Yeasts Lieviti FALSE FALSE
|
||||
it Protozoa Protozoi FALSE FALSE
|
||||
it biogroup biogruppo FALSE FALSE
|
||||
it biotype biotipo FALSE FALSE
|
||||
@ -139,6 +143,7 @@ fr Gram-negative Gram négatif FALSE FALSE
|
||||
fr Gram-positive Gram positif FALSE FALSE
|
||||
fr Bacteria Bactéries FALSE FALSE
|
||||
fr Fungi Champignons FALSE FALSE
|
||||
fr Yeasts Levures FALSE FALSE
|
||||
fr Protozoa Protozoaires FALSE FALSE
|
||||
fr biogroup biogroupe FALSE FALSE
|
||||
fr vegetative végétatif FALSE FALSE
|
||||
@ -166,6 +171,7 @@ pt Gram-negative Gram negativo FALSE FALSE
|
||||
pt Gram-positive Gram positivo FALSE FALSE
|
||||
pt Bacteria Bactérias FALSE FALSE
|
||||
pt Fungi Fungos FALSE FALSE
|
||||
pt Yeasts Leveduras FALSE FALSE
|
||||
pt Protozoa Protozoários FALSE FALSE
|
||||
pt biogroup biogrupo FALSE FALSE
|
||||
pt biotype biótipo FALSE FALSE
|
||||
|
||||
|
BIN
data-raw/v_11.0_Breakpoint_Tables.xlsx
Normal file
BIN
data-raw/v_11.0_Breakpoint_Tables.xlsx
Normal file
Binary file not shown.
Reference in New Issue
Block a user