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(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)

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dr. M.S. (Matthijs) Berends
2021-01-12 22:08:04 +01:00
parent 3b84b8be75
commit d014955ce0
93 changed files with 3631 additions and 374 deletions
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109
data-raw/eucast_rules.tsv
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@ -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

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