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(v0.6.1.9050) support staged install
This commit is contained in:
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data-raw/eucast_rules.tsv
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data-raw/eucast_rules.tsv
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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
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order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints
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order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints
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order is Enterobacteriales AMP R AMX R Enterobacteriales (Order) Breakpoints
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genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints
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genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints
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genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints
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genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints
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genus is Staphylococcus FOX S carbapenems, cephalosporins_without_CAZ S Staphylococcus Breakpoints
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genus is Staphylococcus FOX I carbapenems, cephalosporins_without_CAZ I Staphylococcus Breakpoints
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genus is Staphylococcus FOX R carbapenems, cephalosporins_without_CAZ R Staphylococcus Breakpoints
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genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Staphylococcus Breakpoints
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genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints
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genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints
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genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints
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genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints
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genus_species is Enterococcus faecium AMP R all_betalactams R Enterococcus Breakpoints
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genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints
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genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints
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genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints
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genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints
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genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints
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genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_without_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_without_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_without_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX, MFX S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints
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genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints
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genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints
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genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Streptococcus pneumoniae Breakpoints
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genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ PEN S AMP, AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints
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genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP S AMX, AMC, PIP, TZP S Viridans group streptococci Breakpoints
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genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP I AMX, AMC, PIP, TZP I Viridans group streptococci Breakpoints
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genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ AMP R AMX, AMC, PIP, TZP R Viridans group streptococci Breakpoints
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genus_species is Haemophilus influenzae AMP S AMX, PIP S Haemophilus influenzae Breakpoints
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genus_species is ^Haemophilus influenzae AMP I AMX, PIP I Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae AMP R AMX, PIP R Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae PEN S AMP, AMX, AMC, PIP, TZP S Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae AMC S TZP S Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae AMC I TZP I Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae AMC R TZP R Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae NAL S CIP, LVX, MFX, OFX S Haemophilus influenzae Breakpoints
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genus_species is Haemophilus influenzae TCY S DOX, MNO S Haemophilus influenzae Breakpoints
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genus_species is Moraxella catarrhalis AMC S TZP S Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis AMC I TZP I Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis AMC R TZP R Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis NAL S CIP, LVX, MFX, OFX S Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram positives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram positives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram positives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram negatives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram negatives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram negatives Breakpoints
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genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints
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genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints
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genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints
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genus_species is Campylobacter coli ERY S AZM, CLR S Campylobacter coli Breakpoints
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genus_species is Campylobacter coli ERY I AZM, CLR I Campylobacter coli Breakpoints
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genus_species is Campylobacter coli ERY R AZM, CLR R Campylobacter coli Breakpoints
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genus_species is Campylobacter coli TCY S DOX S Campylobacter coli Breakpoints
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genus_species is Campylobacter coli TCY I DOX I Campylobacter coli Breakpoints
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genus_species is Campylobacter coli TCY R DOX R Campylobacter coli Breakpoints
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genus_species is Campylobacter jejuni ERY S AZM, CLR S Campylobacter jejuni Breakpoints
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genus_species is Campylobacter jejuni ERY I AZM, CLR I Campylobacter jejuni Breakpoints
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genus_species is Campylobacter jejuni ERY R AZM, CLR R Campylobacter jejuni Breakpoints
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genus_species is Campylobacter jejuni TCY S DOX S Campylobacter jejuni Breakpoints
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genus_species is Campylobacter jejuni TCY I DOX I Campylobacter jejuni Breakpoints
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genus_species is Campylobacter jejuni TCY R DOX R Campylobacter jejuni Breakpoints
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genus_species is Aerococcus sanguinicola NOR S fluoroquinolones S Aerococcus sanguinicola Breakpoints
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genus_species is Aerococcus sanguinicola NOR I fluoroquinolones I Aerococcus sanguinicola Breakpoints
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genus_species is Aerococcus sanguinicola NOR R fluoroquinolones R Aerococcus sanguinicola Breakpoints
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genus_species is Aerococcus sanguinicola CIP S LVX S Aerococcus sanguinicola Breakpoints
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genus_species is Aerococcus sanguinicola CIP I LVX I Aerococcus sanguinicola Breakpoints
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genus_species is Aerococcus sanguinicola CIP R LVX R Aerococcus urinae Breakpoints
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genus_species is Aerococcus urinae NOR S fluoroquinolones S Aerococcus urinae Breakpoints
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genus_species is Aerococcus urinae NOR I fluoroquinolones I Aerococcus urinae Breakpoints
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genus_species is Aerococcus urinae NOR R fluoroquinolones R Aerococcus urinae Breakpoints
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genus_species is Aerococcus urinae CIP S LVX S Aerococcus urinae Breakpoints
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genus_species is Aerococcus urinae CIP I LVX I Aerococcus urinae Breakpoints
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genus_species is Aerococcus urinae CIP R LVX R Aerococcus urinae Breakpoints
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genus_species is Kingella kingae PEN S AMP, AMX S Kingella kingae Breakpoints
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genus_species is Kingella kingae PEN I AMP, AMX I Kingella kingae Breakpoints
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genus_species is Kingella kingae PEN R AMP, AMX R Kingella kingae Breakpoints
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genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints
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genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints
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genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints
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genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints
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family is Enterobacteriaceae PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Enterobacter aerogenes aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Escherichia hermanni aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus_species is Yersinia pseudotuberculosis poly, COL R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
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genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordatella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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fullname like ^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules
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genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
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||||
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
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||||
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
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||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
gramstain is Gram positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus capitis CAZ, FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus aureus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Staphylococcus epidermidis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Staphylococcus coagulase-negative CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Staphylococcus hominis CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Staphylococcus haemolyticus CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus intermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Staphylococcus pseudintermedius CAZ R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus is Streptococcus FUS, CAZ, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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||||
genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_without_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus is Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) PEN S aminopenicillins, cephalosporins_without_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
|
||||
genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
|
||||
genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules
|
||||
family is Enterobacteriaceae TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods Expert Rules
|
||||
genus is .* ERY S AZM, CLR S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
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||||
genus is .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
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||||
genus is .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
|
||||
genus is Staphylococcus TOB R KAN, amik R Table 12: Interpretive rules for aminoglycosides Expert Rules
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||||
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules
|
||||
family is Enterobacteriaceae GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
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||||
family is Enterobacteriaceae GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules
|
||||
genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
|
||||
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
|
||||
family is Enterobacteriaceae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
|
||||
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
|
||||
genus is .* AMC R AMP, AMX R Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R Other rules
|
||||
genus is .* TZP R PIP R Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R Other rules
|
||||
genus is .* SXT R TMP R Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R Other rules
|
||||
genus is .* AMP S AMC S Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S Other rules
|
||||
genus is .* AMX S AMC S Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S Other rules
|
||||
genus is .* PIP S TZP S Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S Other rules
|
||||
genus is .* TMP S SXT S Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S Other rules
|
||||
|
40
data-raw/internals.R
Normal file
40
data-raw/internals.R
Normal file
@ -0,0 +1,40 @@
|
||||
# EUCAST rules ----
|
||||
# For editing the reference file, these values can all be used for target antibiotics:
|
||||
# "aminoglycosides", "tetracyclines", "polymyxins", "macrolides", "glycopeptides",
|
||||
# "streptogramins", "cephalosporins", "cephalosporins_without_CAZ", "carbapenems",
|
||||
# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
|
||||
# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
|
||||
# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
||||
# This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
|
||||
# LiPuma JJ, 2015 (PMID 16217180).
|
||||
eucast_rules_file <- dplyr::arrange(
|
||||
.data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
strip.white = TRUE,
|
||||
na = c(NA, "", NULL)),
|
||||
reference.rule_group,
|
||||
reference.rule)
|
||||
|
||||
# Translations -----
|
||||
translations_file <- utils::read.table(file = "data-raw/translations.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
header = TRUE,
|
||||
blank.lines.skip = TRUE,
|
||||
fill = TRUE,
|
||||
strip.white = TRUE,
|
||||
encoding = "UTF-8",
|
||||
fileEncoding = "UTF-8",
|
||||
na.strings = c(NA, "", NULL))
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::use_data(eucast_rules_file, translations_file,
|
||||
internal = TRUE,
|
||||
overwrite = TRUE,
|
||||
version = 2)
|
||||
|
||||
# Remove from global environment ----
|
||||
rm(eucast_rules_file)
|
||||
rm(translations_file)
|
||||
305
data-raw/reproduction_of_antibiotics.R
Normal file
305
data-raw/reproduction_of_antibiotics.R
Normal file
@ -0,0 +1,305 @@
|
||||
|
||||
library(dplyr)
|
||||
|
||||
# got EARS-Net codes (= ECDC/WHO codes) from here:
|
||||
|
||||
# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
|
||||
# opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
|
||||
# and exported table 'DRGLST' to MS Excel
|
||||
library(readxl)
|
||||
DRGLST <- read_excel("DRGLST.xlsx")
|
||||
abx <- DRGLST %>%
|
||||
select(ab = WHON5_CODE,
|
||||
name = ANTIBIOTIC) %>%
|
||||
# remove the ones without WHONET code
|
||||
filter(!is.na(ab)) %>%
|
||||
distinct(name, .keep_all = TRUE) %>%
|
||||
# add the ones without WHONET code
|
||||
bind_rows(
|
||||
DRGLST %>%
|
||||
select(ab = WHON5_CODE,
|
||||
name = ANTIBIOTIC) %>%
|
||||
filter(is.na(ab)) %>%
|
||||
distinct(name, .keep_all = TRUE)
|
||||
# add new ab code later
|
||||
) %>%
|
||||
arrange(name)
|
||||
|
||||
# add old ATC codes
|
||||
ab_old <- AMR::antibiotics %>%
|
||||
mutate(official = gsub("( and |, )", "/", official),
|
||||
abbr = tolower(paste(ifelse(is.na(abbr), "", abbr),
|
||||
ifelse(is.na(certe), "", certe),
|
||||
ifelse(is.na(umcg), "", umcg),
|
||||
sep = "|")))
|
||||
for (i in 1:nrow(ab_old)) {
|
||||
abbr <- ab_old[i, "abbr"]
|
||||
abbr <- strsplit(abbr, "|", fixed = TRUE) %>% unlist() %>% unique()
|
||||
abbr <- abbr[abbr != ""]
|
||||
#print(abbr)
|
||||
if (length(abbr) == 0) {
|
||||
ab_old[i, "abbr"] <- NA_character_
|
||||
} else {
|
||||
ab_old[i, "abbr"] <- paste(abbr, collapse = "|")
|
||||
}
|
||||
}
|
||||
|
||||
# create reference data set: to be able to map ab to atc
|
||||
abx_atc1 <- abx %>%
|
||||
mutate(name_lower = tolower(name)) %>%
|
||||
left_join(ab_old %>%
|
||||
select(ears_net, atc), by = c(ab = "ears_net")) %>%
|
||||
rename(atc1 = atc) %>%
|
||||
left_join(ab_old %>%
|
||||
mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
|
||||
transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
|
||||
rename(atc2 = atc) %>%
|
||||
left_join(ab_old %>%
|
||||
mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
|
||||
mutate(official = gsub("f", "ph", official)) %>%
|
||||
transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
|
||||
rename(atc3 = atc) %>%
|
||||
left_join(ab_old %>%
|
||||
mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
|
||||
mutate(official = gsub("t", "th", official)) %>%
|
||||
transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
|
||||
rename(atc4 = atc) %>%
|
||||
left_join(ab_old %>%
|
||||
mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
|
||||
mutate(official = gsub("f", "ph", official)) %>%
|
||||
mutate(official = gsub("t", "th", official)) %>%
|
||||
transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
|
||||
rename(atc5 = atc) %>%
|
||||
left_join(ab_old %>%
|
||||
mutate(official = gsub(", combinations", "", official, fixed = TRUE)) %>%
|
||||
mutate(official = gsub("f", "ph", official)) %>%
|
||||
mutate(official = gsub("t", "th", official)) %>%
|
||||
mutate(official = gsub("ine$", "in", official)) %>%
|
||||
transmute(official = tolower(official), atc), by = c(name_lower = "official")) %>%
|
||||
rename(atc6 = atc) %>%
|
||||
mutate(atc = case_when(!is.na(atc1) ~ atc1,
|
||||
!is.na(atc2) ~ atc2,
|
||||
!is.na(atc3) ~ atc3,
|
||||
!is.na(atc4) ~ atc4,
|
||||
!is.na(atc4) ~ atc5,
|
||||
TRUE ~ atc6)) %>%
|
||||
distinct(ab, name, .keep_all = TRUE) %>%
|
||||
select(ab, atc, name)
|
||||
|
||||
abx_atc2 <- ab_old %>%
|
||||
filter(!atc %in% abx_atc1$atc,
|
||||
is.na(ears_net),
|
||||
!is.na(atc_group1),
|
||||
!atc_group1 %like% ("virus|vaccin|viral|immun"),
|
||||
!official %like% "(combinations| with )") %>%
|
||||
mutate(ab = NA_character_) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE) %>%
|
||||
select(ab, atc, name = official)
|
||||
|
||||
abx2 <- bind_rows(abx_atc1, abx_atc2)
|
||||
|
||||
rm(abx_atc1)
|
||||
rm(abx_atc2)
|
||||
|
||||
abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(gsub("[/0-9-]",
|
||||
" ",
|
||||
abx2$name[is.na(abx2$ab)]),
|
||||
minlength = 3,
|
||||
method = "left.kept",
|
||||
strict = TRUE))
|
||||
|
||||
n_distinct(abx2$ab)
|
||||
|
||||
abx2 <- abx2 %>% arrange(ab)
|
||||
seqnr <- 0
|
||||
# add follow up nrs
|
||||
for (i in 2:nrow(abx2)) {
|
||||
if (abx2[i, "ab"] == abx2[i - 1, "ab"]) {
|
||||
seqnr <- seqnr + 1
|
||||
abx2[i, "seqnr"] <- seqnr
|
||||
} else {
|
||||
seqnr <- 0
|
||||
}
|
||||
}
|
||||
for (i in 2:nrow(abx2)) {
|
||||
if (!is.na(abx2[i, "seqnr"])) {
|
||||
abx2[i, "ab"] <- paste0(abx2[i, "ab"], abx2[i, "seqnr"])
|
||||
}
|
||||
}
|
||||
abx2 <- abx2 %>% select(-seqnr) %>% arrange(name)
|
||||
|
||||
# everything unique??
|
||||
nrow(abx2) == n_distinct(abx2$ab)
|
||||
|
||||
# get ATC properties
|
||||
abx2 <- abx2 %>%
|
||||
left_join(ab_old %>%
|
||||
select(atc, abbr, atc_group1, atc_group2,
|
||||
oral_ddd, oral_units, iv_ddd, iv_units))
|
||||
|
||||
abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE)))
|
||||
|
||||
# vector with official names, returns vector with CIDs
|
||||
get_CID <- function(ab) {
|
||||
CID <- rep(NA_integer_, length(ab))
|
||||
p <- progress_estimated(n = length(ab), min_time = 0)
|
||||
for (i in 1:length(ab)) {
|
||||
p$tick()$print()
|
||||
|
||||
CID[i] <- tryCatch(
|
||||
data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(ab[i], reserved = TRUE),
|
||||
"/cids/TXT?name_type=complete"),
|
||||
showProgress = FALSE)[[1]][1],
|
||||
error = function(e) NA_integer_)
|
||||
if (is.na(CID[i])) {
|
||||
# try with removing the text in brackets
|
||||
CID[i] <- tryCatch(
|
||||
data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
|
||||
"/cids/TXT?name_type=complete"),
|
||||
showProgress = FALSE)[[1]][1],
|
||||
error = function(e) NA_integer_)
|
||||
}
|
||||
if (is.na(CID[i])) {
|
||||
# try match on word and take the lowest CID value (sorted)
|
||||
ab[i] <- gsub("[^a-z0-9]+", " ", ab[i], ignore.case = TRUE)
|
||||
CID[i] <- tryCatch(
|
||||
data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
||||
URLencode(ab[i], reserved = TRUE),
|
||||
"/cids/TXT?name_type=word"),
|
||||
showProgress = FALSE)[[1]][1],
|
||||
error = function(e) NA_integer_)
|
||||
}
|
||||
Sys.sleep(0.1)
|
||||
}
|
||||
CID
|
||||
}
|
||||
|
||||
# get CIDs (2-3 min)
|
||||
CIDs <- get_CID(abx2$name)
|
||||
# These could not be found:
|
||||
abx2[is.na(CIDs),] %>% View()
|
||||
|
||||
# returns list with synonyms (brand names), with CIDs as names
|
||||
get_synonyms <- function(CID, clean = TRUE) {
|
||||
synonyms <- rep(NA_character_, length(CID))
|
||||
p <- progress_estimated(n = length(CID), min_time = 0)
|
||||
|
||||
for (i in 1:length(CID)) {
|
||||
p$tick()$print()
|
||||
|
||||
synonyms_txt <- ""
|
||||
|
||||
if (is.na(CID[i])) {
|
||||
next
|
||||
}
|
||||
|
||||
synonyms_txt <- tryCatch(
|
||||
data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
|
||||
CID[i],
|
||||
"/synonyms/TXT"),
|
||||
sep = "\n",
|
||||
showProgress = FALSE)[[1]],
|
||||
error = function(e) NA_character_)
|
||||
|
||||
Sys.sleep(0.1)
|
||||
|
||||
if (clean == TRUE) {
|
||||
# remove text between brackets
|
||||
synonyms_txt <- trimws(gsub("[(].*[)]", "",
|
||||
gsub("[[].*[]]", "",
|
||||
gsub("[(].*[]]", "",
|
||||
gsub("[[].*[)]", "", synonyms_txt)))))
|
||||
synonyms_txt <- gsub("Co-", "Co", synonyms_txt, fixed = TRUE)
|
||||
# only length 6 to 20 and no txt with reading marks or numbers and must start with capital letter (= brand)
|
||||
synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(6:20)
|
||||
& !grepl("[-&{},_0-9/]", synonyms_txt)
|
||||
& grepl("^[A-Z]", synonyms_txt, ignore.case = FALSE)]
|
||||
synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
|
||||
}
|
||||
synonyms_txt <- unique(trimws(synonyms_txt[tolower(synonyms_txt) %in% unique(tolower(synonyms_txt))]))
|
||||
synonyms[i] <- list(sort(synonyms_txt))
|
||||
}
|
||||
names(synonyms) <- CID
|
||||
synonyms
|
||||
}
|
||||
|
||||
# get brand names from PubChem (2-3 min)
|
||||
synonyms <- get_synonyms(CIDs)
|
||||
synonyms <- lapply(synonyms,
|
||||
function(x) {
|
||||
if (length(x) == 0 | all(is.na(x))) {
|
||||
""
|
||||
} else {
|
||||
x
|
||||
}})
|
||||
|
||||
# add them to data set
|
||||
antibiotics <- abx2 %>%
|
||||
left_join(DRGLST %>%
|
||||
select(ab = WHON5_CODE, CLASS, SUBCLASS) %>%
|
||||
distinct(ab, .keep_all = TRUE), by = "ab") %>%
|
||||
transmute(ab,
|
||||
atc,
|
||||
cid = CIDs,
|
||||
# no capital after a slash: Ampicillin/Sulbactam -> Ampicillin/sulbactam
|
||||
name = name %>%
|
||||
gsub("([/-])([A-Z])", "\\1\\L\\2", ., perl = TRUE) %>%
|
||||
gsub("edta", "EDTA", ., ignore.case = TRUE),
|
||||
group = case_when(
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "am(ph|f)enicol" ~ "Amphenicols",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "aminoglycoside" ~ "Aminoglycosides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "carbapenem" | name %like% "(imipenem|meropenem)" ~ "Carbapenems",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "First-generation cephalosporin" ~ "Cephalosporins (1st gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Second-generation cephalosporin" ~ "Cephalosporins (2nd gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Third-generation cephalosporin" ~ "Cephalosporins (3rd gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "Fourth-generation cephalosporin" ~ "Cephalosporins (4th gen.)",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(tuberculosis|mycobacter)" ~ "Antimycobacterials",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "cephalosporin" ~ "Cephalosporins",
|
||||
name %like% "^Ce" & is.na(atc_group1) & paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "beta-?lactam" ~ "Cephalosporins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(beta-?lactam|penicillin)" ~ "Beta-lactams/penicillins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "quinolone" ~ "Quinolones",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "glycopeptide" ~ "Glycopeptides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "macrolide" ~ "Macrolides/lincosamides",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "tetracycline" ~ "Tetracyclines",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "trimethoprim" ~ "Trimethoprims",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "polymyxin" ~ "Polymyxins",
|
||||
paste(atc_group1, atc_group2, CLASS, SUBCLASS) %like% "(fungal|mycot)" ~ "Antifungals/antimycotics",
|
||||
TRUE ~ "Other antibacterials"
|
||||
),
|
||||
atc_group1, atc_group2,
|
||||
abbreviations = unname(abbr),
|
||||
synonyms = unname(synonyms),
|
||||
oral_ddd, oral_units,
|
||||
iv_ddd, iv_units) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE)
|
||||
|
||||
# some exceptions
|
||||
antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]] <- list(c("dox", "doxy"))
|
||||
antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c("clox"))
|
||||
antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "CFC")) # cefaclor old WHONET4 code
|
||||
# 'Polymixin B' (POL) and 'Polymyxin B' (PLB) both exist, so:
|
||||
antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B"))
|
||||
antibiotics <- filter(antibiotics, ab != "POL")
|
||||
# 'Latamoxef' (LTM) and 'Moxalactam (Latamoxef)' (MOX) both exist, so:
|
||||
antibiotics[which(antibiotics$ab == "LTM"), "abbreviations"][[1]] <- list(c("MOX", "moxa"))
|
||||
antibiotics <- filter(antibiotics, ab != "MOX")
|
||||
# RFP and RFP1 (the J0 one) both mean 'rifapentine', although 'rifp' is not recognised, so:
|
||||
antibiotics <- filter(antibiotics, ab != "RFP")
|
||||
antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP"
|
||||
antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp"))
|
||||
# ESBL E-test codes:
|
||||
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
|
||||
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
|
||||
antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c("xpml"))
|
||||
antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "xpm"))
|
||||
antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
|
||||
antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
|
||||
|
||||
class(antibiotics$ab) <- "ab"
|
||||
class(antibiotics$atc) <- "atc"
|
||||
|
||||
dim(antibiotics) # for R/data.R
|
||||
usethis::use_data(antibiotics, overwrite = TRUE)
|
||||
rm(antibiotics)
|
||||
501
data-raw/reproduction_of_microorganisms.R
Normal file
501
data-raw/reproduction_of_microorganisms.R
Normal file
@ -0,0 +1,501 @@
|
||||
# Reproduction of the `microorganisms` data set
|
||||
|
||||
# Data retrieved from the Catalogue of Life (CoL) through the Encyclopaedia of Life:
|
||||
# https://opendata.eol.org/dataset/catalogue-of-life/
|
||||
# (download the resource file with a name like "Catalogue of Life yyyy-mm-dd")
|
||||
# and from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
|
||||
# https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads.html
|
||||
# (download the latest "Complete List" as xlsx file)
|
||||
|
||||
library(dplyr)
|
||||
library(AMR)
|
||||
|
||||
# unzip and extract taxon.tab (around 1.5 GB) from the CoL archive, then:
|
||||
data_col <- data.table::fread("Downloads/taxon.tab")
|
||||
|
||||
# read the xlsx file from DSMZ (only around 2.5 MB):
|
||||
data_dsmz <- readxl::read_xlsx("Downloads/DSMZ_bactnames.xlsx")
|
||||
|
||||
# the CoL data is over 3.7M rows:
|
||||
data_col %>% freq(kingdom)
|
||||
# Item Count Percent Cum. Count Cum. Percent
|
||||
# --- ---------- ---------- -------- ----------- -------------
|
||||
# 1 Animalia 2,225,627 59.1% 2,225,627 59.1%
|
||||
# 2 Plantae 1,177,412 31.3% 3,403,039 90.4%
|
||||
# 3 Fungi 290,145 7.7% 3,693,184 98.1%
|
||||
# 4 Chromista 47,126 1.3% 3,740,310 99.3%
|
||||
# 5 Bacteria 14,478 0.4% 3,754,788 99.7%
|
||||
# 6 Protozoa 6,060 0.2% 3,760,848 99.9%
|
||||
# 7 Viruses 3,827 0.1% 3,764,675 100.0%
|
||||
# 8 Archaea 610 0.0% 3,765,285 100.0%
|
||||
|
||||
# clean data_col
|
||||
data_col <- data_col %>%
|
||||
as_tibble() %>%
|
||||
select(col_id = taxonID,
|
||||
col_id_new = acceptedNameUsageID,
|
||||
fullname = scientificName,
|
||||
kingdom,
|
||||
phylum,
|
||||
class,
|
||||
order,
|
||||
family,
|
||||
genus,
|
||||
species = specificEpithet,
|
||||
subspecies = infraspecificEpithet,
|
||||
rank = taxonRank,
|
||||
ref = scientificNameAuthorship,
|
||||
species_id = furtherInformationURL)
|
||||
data_col$source <- "CoL"
|
||||
|
||||
# clean data_dsmz
|
||||
data_dsmz <- data_dsmz %>%
|
||||
as_tibble() %>%
|
||||
transmute(col_id = NA_integer_,
|
||||
col_id_new = NA_integer_,
|
||||
fullname = "",
|
||||
# kingdom = "",
|
||||
# phylum = "",
|
||||
# class = "",
|
||||
# order = "",
|
||||
# family = "",
|
||||
genus = ifelse(is.na(GENUS), "", GENUS),
|
||||
species = ifelse(is.na(SPECIES), "", SPECIES),
|
||||
subspecies = ifelse(is.na(SUBSPECIES), "", SUBSPECIES),
|
||||
rank = ifelse(species == "", "genus", "species"),
|
||||
ref = AUTHORS,
|
||||
species_id = as.character(RECORD_NO),
|
||||
source = "DSMZ")
|
||||
|
||||
# DSMZ only contains genus/(sub)species, try to find taxonomic properties based on genus and data_col
|
||||
ref_taxonomy <- data_col %>%
|
||||
filter(genus %in% data_dsmz$genus,
|
||||
family != "") %>%
|
||||
distinct(genus, .keep_all = TRUE) %>%
|
||||
select(kingdom, phylum, class, order, family, genus)
|
||||
|
||||
data_dsmz <- data_dsmz %>%
|
||||
left_join(ref_taxonomy, by = "genus") %>%
|
||||
mutate(kingdom = "Bacteria",
|
||||
phylum = ifelse(is.na(phylum), "(unknown phylum)", phylum),
|
||||
class = ifelse(is.na(class), "(unknown class)", class),
|
||||
order = ifelse(is.na(order), "(unknown order)", order),
|
||||
family = ifelse(is.na(family), "(unknown family)", family),
|
||||
)
|
||||
|
||||
# combine everything
|
||||
data_total <- data_col %>%
|
||||
bind_rows(data_dsmz)
|
||||
|
||||
rm(data_col)
|
||||
rm(data_dsmz)
|
||||
rm(ref_taxonomy)
|
||||
|
||||
MOs <- data_total %>%
|
||||
filter(
|
||||
(
|
||||
# we only want all MICROorganisms and no viruses
|
||||
!kingdom %in% c("Animalia", "Plantae", "Viruses")
|
||||
# and not all fungi: Aspergillus, Candida, Trichphyton and Pneumocystis are the most important,
|
||||
# so only keep these orders from the fungi:
|
||||
& !(kingdom == "Fungi"
|
||||
& !order %in% c("Eurotiales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
|
||||
)
|
||||
# or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
|
||||
| genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Anisakis", "Apophysomyces",
|
||||
"Arachnia", "Ascaris", "Aureobacterium", "Aureobasidium", "Balantidum", "Bilophilia", "Branhamella", "Brochontrix",
|
||||
"Brugia", "Calymmatobacterium", "Catabacter", "Cdc", "Chilomastix", "Chryseomonas", "Cladophialophora", "Cladosporium",
|
||||
"Clonorchis", "Cordylobia", "Curvularia", "Demodex", "Dermatobia", "Diphyllobothrium", "Dracunculus", "Echinococcus",
|
||||
"Enterobius", "Euascomycetes", "Exophiala", "Fasciola", "Fusarium", "Hendersonula", "Hymenolepis", "Kloeckera",
|
||||
"Koserella", "Larva", "Leishmania", "Lelliottia", "Loa", "Lumbricus", "Malassezia", "Metagonimus", "Molonomonas",
|
||||
"Mucor", "Nattrassia", "Necator", "Novospingobium", "Onchocerca", "Opistorchis", "Paragonimus", "Paramyxovirus",
|
||||
"Pediculus", "Phoma", "Phthirus", "Pityrosporum", "Pseudallescheria", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula",
|
||||
"Salinococcus", "Sanguibacteroides", "Schistosoma", "Scopulariopsis", "Scytalidium", "Sporobolomyces", "Stomatococcus",
|
||||
"Strongyloides", "Syncephalastraceae", "Taenia", "Torulopsis", "Trichinella", "Trichobilharzia", "Trichomonas",
|
||||
"Trichosporon", "Trichuris", "Trypanosoma", "Wuchereria")
|
||||
# or the taxonomic entry is old - the species was renamed
|
||||
| !is.na(col_id_new)
|
||||
)
|
||||
|
||||
# filter old taxonomic names so only the ones with an existing reference will be kept
|
||||
MOs <- MOs %>%
|
||||
filter(is.na(col_id_new) | (!is.na(col_id_new) & col_id_new %in% MOs$col_id))
|
||||
|
||||
MOs <- MOs %>%
|
||||
# remove text if it contains 'Not assigned' like phylum in viruses
|
||||
mutate_all(~gsub("Not assigned", "", .))
|
||||
|
||||
MOs <- MOs %>%
|
||||
# Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011':
|
||||
mutate(authors2 = iconv(ref, from = "UTF-8", to = "ASCII//TRANSLIT"),
|
||||
# remove leading and trailing brackets
|
||||
authors2 = gsub("^[(](.*)[)]$", "\\1", authors2),
|
||||
# only take part after brackets if there's a name
|
||||
authors2 = ifelse(grepl(".*[)] [a-zA-Z]+.*", authors2),
|
||||
gsub(".*[)] (.*)", "\\1", authors2),
|
||||
authors2),
|
||||
# get year from last 4 digits
|
||||
lastyear = as.integer(gsub(".*([0-9]{4})$", "\\1", authors2)),
|
||||
# can never be later than now
|
||||
lastyear = ifelse(lastyear > as.integer(format(Sys.Date(), "%Y")),
|
||||
NA,
|
||||
lastyear),
|
||||
# get authors without last year
|
||||
authors = gsub("(.*)[0-9]{4}$", "\\1", authors2),
|
||||
# remove nonsense characters from names
|
||||
authors = gsub("[^a-zA-Z,'& -]", "", authors),
|
||||
# remove trailing and leading spaces
|
||||
authors = trimws(authors),
|
||||
# only keep first author and replace all others by 'et al'
|
||||
authors = gsub("(,| and| et| &| ex| emend\\.?) .*", " et al.", authors),
|
||||
# et al. always with ending dot
|
||||
authors = gsub(" et al\\.?", " et al.", authors),
|
||||
authors = gsub(" ?,$", "", authors),
|
||||
# don't start with 'sensu' or 'ehrenb'
|
||||
authors = gsub("^(sensu|Ehrenb.?) ", "", authors, ignore.case = TRUE),
|
||||
# no initials, only surname
|
||||
authors = gsub("^([A-Z]+ )+", "", authors, ignore.case = FALSE),
|
||||
# combine author and year if year is available
|
||||
ref = ifelse(!is.na(lastyear),
|
||||
paste0(authors, ", ", lastyear),
|
||||
authors),
|
||||
# fix beginning and ending
|
||||
ref = gsub(", $", "", ref),
|
||||
ref = gsub("^, ", "", ref)
|
||||
)
|
||||
|
||||
# Remove non-ASCII characters (these are not allowed by CRAN)
|
||||
MOs <- MOs %>%
|
||||
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
|
||||
as_tibble(stringsAsFactors = FALSE)
|
||||
|
||||
# Split old taxonomic names - they refer in the original data to a new `taxonID` with `acceptedNameUsageID`
|
||||
MOs.old <- MOs %>%
|
||||
filter(!is.na(col_id_new),
|
||||
ref != "",
|
||||
source != "DSMZ") %>%
|
||||
transmute(col_id,
|
||||
col_id_new,
|
||||
fullname =
|
||||
trimws(
|
||||
gsub("(.*)[(].*", "\\1",
|
||||
stringr::str_replace(
|
||||
string = fullname,
|
||||
pattern = stringr::fixed(authors2),
|
||||
replacement = "")) %>%
|
||||
gsub(" (var|f|subsp)[.]", "", .)),
|
||||
ref) %>%
|
||||
filter(!is.na(fullname)) %>%
|
||||
distinct(fullname, .keep_all = TRUE) %>%
|
||||
arrange(col_id)
|
||||
|
||||
MOs <- MOs %>%
|
||||
filter(is.na(col_id_new) | source == "DSMZ") %>%
|
||||
transmute(col_id,
|
||||
fullname = trimws(case_when(rank == "family" ~ family,
|
||||
rank == "order" ~ order,
|
||||
rank == "class" ~ class,
|
||||
rank == "phylum" ~ phylum,
|
||||
rank == "kingdom" ~ kingdom,
|
||||
TRUE ~ paste(genus, species, subspecies))),
|
||||
kingdom,
|
||||
phylum,
|
||||
class,
|
||||
order,
|
||||
family,
|
||||
genus = gsub(":", "", genus),
|
||||
species,
|
||||
subspecies,
|
||||
rank,
|
||||
ref,
|
||||
species_id = gsub(".*/([a-f0-9]+)", "\\1", species_id),
|
||||
source) %>%
|
||||
#distinct(fullname, .keep_all = TRUE) %>%
|
||||
filter(!grepl("unassigned", fullname, ignore.case = TRUE))
|
||||
|
||||
# Filter out the DSMZ records that were renamed and are now in MOs.old
|
||||
MOs <- MOs %>%
|
||||
filter(!(source == "DSMZ" & fullname %in% MOs.old$fullname),
|
||||
!(source == "DSMZ" & fullname %in% (MOs %>% filter(source == "CoL") %>% pull(fullname)))) %>%
|
||||
distinct(fullname, .keep_all = TRUE)
|
||||
|
||||
# Add abbreviations so we can easily know which ones are which ones.
|
||||
# These will become valid and unique microbial IDs for the AMR package.
|
||||
MOs <- MOs %>%
|
||||
group_by(kingdom) %>%
|
||||
mutate(abbr_other = case_when(
|
||||
rank == "family" ~ paste0("[FAM]_",
|
||||
abbreviate(family,
|
||||
minlength = 8,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE)),
|
||||
rank == "order" ~ paste0("[ORD]_",
|
||||
abbreviate(order,
|
||||
minlength = 8,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE)),
|
||||
rank == "class" ~ paste0("[CLS]_",
|
||||
abbreviate(class,
|
||||
minlength = 8,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE)),
|
||||
rank == "phylum" ~ paste0("[PHL]_",
|
||||
abbreviate(phylum,
|
||||
minlength = 8,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE)),
|
||||
rank == "kingdom" ~ paste0("[KNG]_", kingdom),
|
||||
TRUE ~ NA_character_
|
||||
)) %>%
|
||||
# abbreviations may be same for genera between kingdoms,
|
||||
# because each abbreviation starts with the the first character(s) of the kingdom
|
||||
mutate(abbr_genus = abbreviate(genus,
|
||||
minlength = 5,
|
||||
use.classes = TRUE,
|
||||
method = "both.sides",
|
||||
strict = FALSE)) %>%
|
||||
ungroup() %>%
|
||||
group_by(genus) %>%
|
||||
# species abbreviations may be the same between genera
|
||||
# because the genus abbreviation is part of the abbreviation
|
||||
mutate(abbr_species = abbreviate(species,
|
||||
minlength = 3,
|
||||
use.classes = FALSE,
|
||||
method = "both.sides")) %>%
|
||||
ungroup() %>%
|
||||
group_by(genus, species) %>%
|
||||
mutate(abbr_subspecies = abbreviate(subspecies,
|
||||
minlength = 3,
|
||||
use.classes = FALSE,
|
||||
method = "both.sides")) %>%
|
||||
ungroup() %>%
|
||||
# remove trailing underscores
|
||||
mutate(mo = gsub("_+$", "",
|
||||
toupper(paste(ifelse(kingdom %in% c("Animalia", "Plantae"),
|
||||
substr(kingdom, 1, 2),
|
||||
substr(kingdom, 1, 1)),
|
||||
ifelse(is.na(abbr_other),
|
||||
paste(abbr_genus,
|
||||
abbr_species,
|
||||
abbr_subspecies,
|
||||
sep = "_"),
|
||||
abbr_other),
|
||||
sep = "_")))) %>%
|
||||
mutate(mo = ifelse(duplicated(.$mo),
|
||||
# these one or two must be unique too
|
||||
paste0(mo, "1"),
|
||||
mo),
|
||||
fullname = ifelse(fullname == "",
|
||||
trimws(paste(genus, species, subspecies)),
|
||||
fullname)) %>%
|
||||
# put `mo` in front, followed by the rest
|
||||
select(mo, everything(), -abbr_other, -abbr_genus, -abbr_species, -abbr_subspecies)
|
||||
|
||||
|
||||
# add non-taxonomic entries
|
||||
MOs <- MOs %>%
|
||||
bind_rows(
|
||||
# Unknowns
|
||||
data.frame(mo = "UNKNOWN",
|
||||
col_id = NA_integer_,
|
||||
fullname = "(unknown name)",
|
||||
kingdom = "(unknown kingdom)",
|
||||
phylum = "(unknown phylum)",
|
||||
class = "(unknown class)",
|
||||
order = "(unknown order)",
|
||||
family = "(unknown family)",
|
||||
genus = "(unknown genus)",
|
||||
species = "(unknown species)",
|
||||
subspecies = "(unknown subspecies)",
|
||||
rank = "(unknown rank)",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added",
|
||||
stringsAsFactors = FALSE),
|
||||
data.frame(mo = "B_GRAMN",
|
||||
col_id = NA_integer_,
|
||||
fullname = "(unknown Gram negatives)",
|
||||
kingdom = "Bacteria",
|
||||
phylum = "(unknown phylum)",
|
||||
class = "(unknown class)",
|
||||
order = "(unknown order)",
|
||||
family = "(unknown family)",
|
||||
genus = "(unknown Gram negatives)",
|
||||
species = "(unknown species)",
|
||||
subspecies = "(unknown subspecies)",
|
||||
rank = "species",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added",
|
||||
stringsAsFactors = FALSE),
|
||||
data.frame(mo = "B_GRAMP",
|
||||
col_id = NA_integer_,
|
||||
fullname = "(unknown Gram positives)",
|
||||
kingdom = "Bacteria",
|
||||
phylum = "(unknown phylum)",
|
||||
class = "(unknown class)",
|
||||
order = "(unknown order)",
|
||||
family = "(unknown family)",
|
||||
genus = "(unknown Gram positives)",
|
||||
species = "(unknown species)",
|
||||
subspecies = "(unknown subspecies)",
|
||||
rank = "species",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added",
|
||||
stringsAsFactors = FALSE),
|
||||
# CoNS
|
||||
MOs %>%
|
||||
filter(genus == "Staphylococcus", species == "epidermidis") %>% .[1,] %>%
|
||||
mutate(mo = gsub("EPI", "CNS", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "coagulase-negative",
|
||||
fullname = "Coagulase-negative Staphylococcus (CoNS)",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
# CoPS
|
||||
MOs %>%
|
||||
filter(genus == "Staphylococcus", species == "epidermidis") %>% .[1,] %>%
|
||||
mutate(mo = gsub("EPI", "CPS", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "coagulase-positive",
|
||||
fullname = "Coagulase-positive Staphylococcus (CoPS)",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
# Streptococci groups A, B, C, F, H, K
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "pyogenes") %>% .[1,] %>%
|
||||
# we can keep all other details, since S. pyogenes is the only member of group A
|
||||
mutate(mo = gsub("PYO", "GRA", mo),
|
||||
species = "group A" ,
|
||||
fullname = "Streptococcus group A"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
# we can keep all other details, since S. agalactiae is the only member of group B
|
||||
mutate(mo = gsub("AGA", "GRB", mo),
|
||||
species = "group B" ,
|
||||
fullname = "Streptococcus group B"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "dysgalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("DYS", "GRC", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "group C" ,
|
||||
fullname = "Streptococcus group C",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("AGA", "GRD", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "group D" ,
|
||||
fullname = "Streptococcus group D",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("AGA", "GRF", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "group F" ,
|
||||
fullname = "Streptococcus group F",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("AGA", "GRG", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "group G" ,
|
||||
fullname = "Streptococcus group G",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("AGA", "GRH", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "group H" ,
|
||||
fullname = "Streptococcus group H",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("AGA", "GRK", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "group K" ,
|
||||
fullname = "Streptococcus group K",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added"),
|
||||
# Beta haemolytic Streptococci
|
||||
MOs %>%
|
||||
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
||||
mutate(mo = gsub("AGA", "HAE", mo),
|
||||
col_id = NA_integer_,
|
||||
species = "beta-haemolytic" ,
|
||||
fullname = "Beta-haemolytic Streptococcus",
|
||||
ref = NA_character_,
|
||||
species_id = "",
|
||||
source = "manually added")
|
||||
)
|
||||
|
||||
|
||||
# everything distinct?
|
||||
sum(duplicated(MOs$mo))
|
||||
colnames(MOs)
|
||||
|
||||
# set prevalence per species
|
||||
MOs <- MOs %>%
|
||||
mutate(prevalence = case_when(
|
||||
class == "Gammaproteobacteria"
|
||||
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
|
||||
| mo == "UNKNOWN"
|
||||
~ 1,
|
||||
phylum %in% c("Proteobacteria",
|
||||
"Firmicutes",
|
||||
"Actinobacteria",
|
||||
"Sarcomastigophora")
|
||||
| genus %in% c("Aspergillus",
|
||||
"Bacteroides",
|
||||
"Candida",
|
||||
"Capnocytophaga",
|
||||
"Chryseobacterium",
|
||||
"Cryptococcus",
|
||||
"Elisabethkingia",
|
||||
"Flavobacterium",
|
||||
"Fusobacterium",
|
||||
"Giardia",
|
||||
"Leptotrichia",
|
||||
"Mycoplasma",
|
||||
"Prevotella",
|
||||
"Rhodotorula",
|
||||
"Treponema",
|
||||
"Trichophyton",
|
||||
"Ureaplasma")
|
||||
| rank %in% c("kingdom", "phylum", "class", "order", "family")
|
||||
~ 2,
|
||||
TRUE ~ 3
|
||||
))
|
||||
|
||||
# save it
|
||||
MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
|
||||
MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
|
||||
class(MOs$mo) <- "mo"
|
||||
|
||||
saveRDS(MOs, "microorganisms.rds")
|
||||
saveRDS(MOs.old, "microorganisms.old.rds")
|
||||
|
||||
# on the server:
|
||||
usethis::use_data(microorganisms, overwrite = TRUE)
|
||||
usethis::use_data(microorganisms.old, overwrite = TRUE)
|
||||
rm(microorganisms)
|
||||
rm(microorganisms.old)
|
||||
# and update the year in R/data.R
|
||||
52
data-raw/reproduction_of_rsi_translation.R
Normal file
52
data-raw/reproduction_of_rsi_translation.R
Normal file
@ -0,0 +1,52 @@
|
||||
library(dplyr)
|
||||
library(readxl)
|
||||
|
||||
# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
|
||||
# opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
|
||||
# and exported table 'DRGLST1' to MS Excel
|
||||
DRGLST1 <- read_excel("DRGLST1.xlsx")
|
||||
rsi_translation <- DRGLST1 %>%
|
||||
# only keep CLSI and EUCAST guidelines:
|
||||
filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
|
||||
# set a nice layout:
|
||||
transmute(guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
|
||||
method = TESTMETHOD,
|
||||
mo = as.mo(ORG_CODE),
|
||||
ab = as.ab(WHON5_CODE),
|
||||
ref_tbl = REF_TABLE,
|
||||
dose_disk = POTENCY,
|
||||
S_disk = as.disk(DISK_S),
|
||||
R_disk = as.disk(DISK_R),
|
||||
S_mic = as.mic(MIC_S),
|
||||
R_mic = as.mic(MIC_R)) %>%
|
||||
filter(!is.na(mo) & !is.na(ab)) %>%
|
||||
arrange(desc(guideline), mo, ab)
|
||||
|
||||
# create 2 tables: MIC and disk
|
||||
tbl_mic <- rsi_translation %>%
|
||||
filter(method == "MIC") %>%
|
||||
select(-ends_with("_disk")) %>%
|
||||
mutate(joinstring = paste(guideline, mo, ab))
|
||||
tbl_disk <- rsi_translation %>%
|
||||
filter(method == "DISK") %>%
|
||||
select(-S_mic, -R_mic) %>%
|
||||
mutate(joinstring = paste(guideline, mo, ab)) %>%
|
||||
select(joinstring, ends_with("_disk"))
|
||||
|
||||
# merge them so every record is a unique combination of method, mo and ab
|
||||
rsi_translation <- tbl_mic %>%
|
||||
left_join(tbl_disk,
|
||||
by = "joinstring") %>%
|
||||
select(-joinstring, -method) %>%
|
||||
as.data.frame(stringsAsFactors = FALSE) %>%
|
||||
# force classes again
|
||||
mutate(mo = as.mo(mo),
|
||||
ab = as.ab(ab),
|
||||
S_mic = as.mic(S_mic),
|
||||
R_mic = as.mic(R_mic),
|
||||
S_disk = as.disk(S_disk),
|
||||
R_disk = as.disk(R_disk))
|
||||
|
||||
# save to package
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE)
|
||||
rm(rsi_translation)
|
||||
371
data-raw/translations.tsv
Normal file
371
data-raw/translations.tsv
Normal file
@ -0,0 +1,371 @@
|
||||
lang pattern replacement fixed ignore.case
|
||||
de Coagulase-negative Staphylococcus Koagulase-negative Staphylococcus FALSE FALSE
|
||||
de Coagulase-positive Staphylococcus Koagulase-positive Staphylococcus FALSE FALSE
|
||||
de Beta-haemolytic Streptococcus Beta-hämolytischer Streptococcus FALSE FALSE
|
||||
de unknown Gram negatives unbekannte Gramnegativen FALSE FALSE
|
||||
de unknown Gram positives unbekannte Grampositiven FALSE FALSE
|
||||
de unknown name unbekannte Name FALSE FALSE
|
||||
de unknown kingdom unbekanntes Reich FALSE FALSE
|
||||
de unknown phylum unbekannter Stamm FALSE FALSE
|
||||
de unknown class unbekannte Klasse FALSE FALSE
|
||||
de unknown order unbekannte Ordnung FALSE FALSE
|
||||
de unknown family unbekannte Familie FALSE FALSE
|
||||
de unknown genus unbekannte Gattung FALSE FALSE
|
||||
de unknown species unbekannte Art FALSE FALSE
|
||||
de unknown subspecies unbekannte Unterart FALSE FALSE
|
||||
de unknown rank unbekannter Rang FALSE FALSE
|
||||
de (CoNS) (KNS) TRUE FALSE
|
||||
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 Protozoa Protozoen FALSE FALSE
|
||||
de biogroup Biogruppe FALSE FALSE
|
||||
de biotype Biotyp FALSE FALSE
|
||||
de vegetative vegetativ FALSE FALSE
|
||||
de ([([ ]*?)group \\1Gruppe FALSE FALSE
|
||||
de ([([ ]*?)Group \\1Gruppe FALSE FALSE
|
||||
nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE
|
||||
nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE
|
||||
nl Beta-haemolytic Streptococcus Beta-hemolytische Streptococcus FALSE FALSE
|
||||
nl unknown Gram negatives onbekende Gram-negatieven FALSE FALSE
|
||||
nl unknown Gram positives onbekende Gram-positieven FALSE FALSE
|
||||
nl unknown name onbekende naam FALSE FALSE
|
||||
nl unknown kingdom onbekend koninkrijk FALSE FALSE
|
||||
nl unknown phylum onbekend fylum FALSE FALSE
|
||||
nl unknown class onbekende klasse FALSE FALSE
|
||||
nl unknown order onbekende orde FALSE FALSE
|
||||
nl unknown family onbekende familie FALSE FALSE
|
||||
nl unknown genus onbekend geslacht FALSE FALSE
|
||||
nl unknown species onbekende soort FALSE FALSE
|
||||
nl unknown subspecies onbekende ondersoort FALSE FALSE
|
||||
nl unknown rank onbekende rang FALSE FALSE
|
||||
nl (CoNS) (CNS) TRUE FALSE
|
||||
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 biogroup biogroep FALSE FALSE
|
||||
nl vegetative vegetatief FALSE FALSE
|
||||
nl ([([ ]*?)group \\1groep FALSE FALSE
|
||||
nl ([([ ]*?)Group \\1Groep FALSE FALSE
|
||||
es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
|
||||
es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
|
||||
es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
|
||||
es unknown Gram negatives Gram negativos desconocidos FALSE FALSE
|
||||
es unknown Gram positives Gram positivos desconocidos FALSE FALSE
|
||||
es unknown name nombre desconocido FALSE FALSE
|
||||
es unknown kingdom reino desconocido FALSE FALSE
|
||||
es unknown phylum filo desconocido FALSE FALSE
|
||||
es unknown class clase desconocida FALSE FALSE
|
||||
es unknown order orden desconocido FALSE FALSE
|
||||
es unknown family familia desconocida FALSE FALSE
|
||||
es unknown genus género desconocido FALSE FALSE
|
||||
es unknown species especie desconocida FALSE FALSE
|
||||
es unknown subspecies subespecie desconocida FALSE FALSE
|
||||
es unknown rank rango desconocido FALSE FALSE
|
||||
es (CoNS) (SCN) TRUE FALSE
|
||||
es (CoPS) (SCP) TRUE FALSE
|
||||
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 Protozoa Protozoarios FALSE FALSE
|
||||
es biogroup biogrupo FALSE FALSE
|
||||
es biotype biotipo FALSE FALSE
|
||||
es vegetative vegetativo FALSE FALSE
|
||||
es ([([ ]*?)group \\1grupo FALSE FALSE
|
||||
es ([([ ]*?)Group \\1Grupo FALSE FALSE
|
||||
it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE
|
||||
it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE
|
||||
it Beta-haemolytic Streptococcus Streptococcus Beta-emolitico FALSE FALSE
|
||||
it unknown Gram negatives Gram negativi sconosciuti FALSE FALSE
|
||||
it unknown Gram positives Gram positivi sconosciuti FALSE FALSE
|
||||
it unknown name nome sconosciuto FALSE FALSE
|
||||
it unknown kingdom regno sconosciuto FALSE FALSE
|
||||
it unknown phylum phylum sconosciuto FALSE FALSE
|
||||
it unknown class classe sconosciuta FALSE FALSE
|
||||
it unknown order ordine sconosciuto FALSE FALSE
|
||||
it unknown family famiglia sconosciuta FALSE FALSE
|
||||
it unknown genus genere sconosciuto FALSE FALSE
|
||||
it unknown species specie sconosciute FALSE FALSE
|
||||
it unknown subspecies sottospecie sconosciute FALSE FALSE
|
||||
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 Protozoa Protozoi FALSE FALSE
|
||||
it biogroup biogruppo FALSE FALSE
|
||||
it biotype biotipo FALSE FALSE
|
||||
it vegetative vegetativo FALSE FALSE
|
||||
it ([([ ]*?)group \\1gruppo FALSE FALSE
|
||||
it ([([ ]*?)Group \\1Gruppo FALSE FALSE
|
||||
fr Coagulase-negative Staphylococcus Staphylococcus à coagulase négative FALSE FALSE
|
||||
fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE
|
||||
fr Beta-haemolytic Streptococcus Streptococcus Bêta-hémolytique FALSE FALSE
|
||||
fr unknown Gram negatives Gram négatifs inconnus FALSE FALSE
|
||||
fr unknown Gram positives Gram positifs inconnus FALSE FALSE
|
||||
fr unknown name nom inconnu FALSE FALSE
|
||||
fr unknown kingdom règme inconnu FALSE FALSE
|
||||
fr unknown phylum embranchement inconnu FALSE FALSE
|
||||
fr unknown class classe inconnue FALSE FALSE
|
||||
fr unknown order ordre inconnu FALSE FALSE
|
||||
fr unknown family famille inconnue FALSE FALSE
|
||||
fr unknown genus genre inconnu FALSE FALSE
|
||||
fr unknown species espèce inconnue FALSE FALSE
|
||||
fr unknown subspecies sous-espèce inconnue FALSE FALSE
|
||||
fr unknown rank rang inconnu FALSE FALSE
|
||||
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 Protozoa Protozoaires FALSE FALSE
|
||||
fr biogroup biogroupe FALSE FALSE
|
||||
fr vegetative végétatif FALSE FALSE
|
||||
fr ([([ ]*?)group \\1groupe FALSE FALSE
|
||||
fr ([([ ]*?)Group \\1Groupe FALSE FALSE
|
||||
pt Coagulase-negative Staphylococcus Staphylococcus coagulase negativo FALSE FALSE
|
||||
pt Coagulase-positive Staphylococcus Staphylococcus coagulase positivo FALSE FALSE
|
||||
pt Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
|
||||
pt unknown Gram negatives Gram negativos desconhecidos FALSE FALSE
|
||||
pt unknown Gram positives Gram positivos desconhecidos FALSE FALSE
|
||||
pt unknown name nome desconhecido FALSE FALSE
|
||||
pt unknown kingdom reino desconhecido FALSE FALSE
|
||||
pt unknown phylum filo desconhecido FALSE FALSE
|
||||
pt unknown class classe desconhecida FALSE FALSE
|
||||
pt unknown order ordem desconhecido FALSE FALSE
|
||||
pt unknown family família desconhecida FALSE FALSE
|
||||
pt unknown genus gênero desconhecido FALSE FALSE
|
||||
pt unknown species espécies desconhecida FALSE FALSE
|
||||
pt unknown subspecies subespécies desconhecida FALSE FALSE
|
||||
pt unknown rank classificação desconhecido FALSE FALSE
|
||||
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 Protozoa Protozoários FALSE FALSE
|
||||
pt biogroup biogrupo FALSE FALSE
|
||||
pt biotype biótipo FALSE FALSE
|
||||
pt vegetative vegetativo FALSE FALSE
|
||||
pt ([([ ]*?)group \\1grupo FALSE FALSE
|
||||
pt ([([ ]*?)Group \\1Grupo FALSE FALSE
|
||||
|
||||
nl 4-aminosalicylic acid 4-aminosalicylzuur
|
||||
nl Adefovir dipivoxil Adefovir
|
||||
nl Aldesulfone sodium Aldesulfon
|
||||
nl Amikacin Amikacine
|
||||
nl Amoxicillin Amoxicilline
|
||||
nl Amoxicillin/beta-lactamase inhibitor Amoxicilline/enzymremmer
|
||||
nl Amphotericin B Amfotericine B
|
||||
nl Ampicillin Ampicilline
|
||||
nl Ampicillin/beta-lactamase inhibitor Ampicilline/enzymremmer
|
||||
nl Anidulafungin Anidulafungine
|
||||
nl Azidocillin Azidocilline
|
||||
nl Azithromycin Azitromycine
|
||||
nl Azlocillin Azlocilline
|
||||
nl Bacampicillin Bacampicilline
|
||||
nl Bacitracin Bacitracine
|
||||
nl Benzathine benzylpenicillin Benzylpenicillinebenzathine
|
||||
nl Benzathine phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine
|
||||
nl Benzylpenicillin Benzylpenicilline
|
||||
nl Calcium aminosalicylate Aminosalicylzuur
|
||||
nl Capreomycin Capreomycine
|
||||
nl Carbenicillin Carbenicilline
|
||||
nl Carindacillin Carindacilline
|
||||
nl Caspofungin Caspofungine
|
||||
nl Cefacetrile Cefacetril
|
||||
nl Cefalexin Cefalexine
|
||||
nl Cefalotin Cefalotine
|
||||
nl Cefamandole Cefamandol
|
||||
nl Cefapirin Cefapirine
|
||||
nl Cefazedone Cefazedon
|
||||
nl Cefazolin Cefazoline
|
||||
nl Cefepime Cefepim
|
||||
nl Cefixime Cefixim
|
||||
nl Cefmenoxime Cefmenoxim
|
||||
nl Cefmetazole Cefmetazol
|
||||
nl Cefodizime Cefodizim
|
||||
nl Cefonicid Cefonicide
|
||||
nl Cefoperazone Cefoperazon
|
||||
nl Cefoperazone/beta-lactamase inhibitor Cefoperazon/enzymremmer
|
||||
nl Cefotaxime Cefotaxim
|
||||
nl Cefoxitin Cefoxitine
|
||||
nl Cefpirome Cefpirom
|
||||
nl Cefpodoxime Cefpodoxim
|
||||
nl Cefsulodin Cefsulodine
|
||||
nl Ceftazidime Ceftazidim
|
||||
nl Ceftezole Ceftezol
|
||||
nl Ceftizoxime Ceftizoxim
|
||||
nl Ceftriaxone Ceftriaxon
|
||||
nl Cefuroxime Cefuroxim
|
||||
nl Cefuroxime/metronidazole Cefuroxim/andere antibacteriele middelen
|
||||
nl Chloramphenicol Chlooramfenicol
|
||||
nl Chlortetracycline Chloortetracycline
|
||||
nl Cinoxacin Cinoxacine
|
||||
nl Ciprofloxacin Ciprofloxacine
|
||||
nl Clarithromycin Claritromycine
|
||||
nl Clavulanic acid Clavulaanzuur
|
||||
nl clavulanic acid clavulaanzuur
|
||||
nl Clindamycin Clindamycine
|
||||
nl Clometocillin Clometocilline
|
||||
nl Clotrimazole Clotrimazol
|
||||
nl Cloxacillin Cloxacilline
|
||||
nl Colistin Colistine
|
||||
nl Dapsone Dapson
|
||||
nl Daptomycin Daptomycine
|
||||
nl Dibekacin Dibekacine
|
||||
nl Dicloxacillin Dicloxacilline
|
||||
nl Dirithromycin Diritromycine
|
||||
nl Econazole Econazol
|
||||
nl Enoxacin Enoxacine
|
||||
nl Epicillin Epicilline
|
||||
nl Erythromycin Erytromycine
|
||||
nl Ethambutol/isoniazid Ethambutol/isoniazide
|
||||
nl Fleroxacin Fleroxacine
|
||||
nl Flucloxacillin Flucloxacilline
|
||||
nl Fluconazole Fluconazol
|
||||
nl Flucytosine Fluorocytosine
|
||||
nl Flurithromycin Fluritromycine
|
||||
nl Fosfomycin Fosfomycine
|
||||
nl Fusidic acid Fusidinezuur
|
||||
nl Gatifloxacin Gatifloxacine
|
||||
nl Gemifloxacin Gemifloxacine
|
||||
nl Gentamicin Gentamicine
|
||||
nl Grepafloxacin Grepafloxacine
|
||||
nl Hachimycin Hachimycine
|
||||
nl Hetacillin Hetacilline
|
||||
nl Imipenem/cilastatin Imipenem/enzymremmer
|
||||
nl Inosine pranobex Inosiplex
|
||||
nl Isepamicin Isepamicine
|
||||
nl Isoconazole Isoconazol
|
||||
nl Isoniazid Isoniazide
|
||||
nl Itraconazole Itraconazol
|
||||
nl Josamycin Josamycine
|
||||
nl Kanamycin Kanamycine
|
||||
nl Ketoconazole Ketoconazol
|
||||
nl Levofloxacin Levofloxacine
|
||||
nl Lincomycin Lincomycine
|
||||
nl Lomefloxacin Lomefloxacine
|
||||
nl Lysozyme Lysozym
|
||||
nl Mandelic acid Amandelzuur
|
||||
nl Metampicillin Metampicilline
|
||||
nl Meticillin Meticilline
|
||||
nl Metisazone Metisazon
|
||||
nl Metronidazole Metronidazol
|
||||
nl Mezlocillin Mezlocilline
|
||||
nl Micafungin Micafungine
|
||||
nl Miconazole Miconazol
|
||||
nl Midecamycin Midecamycine
|
||||
nl Miocamycin Miocamycine
|
||||
nl Moxifloxacin Moxifloxacine
|
||||
nl Mupirocin Mupirocine
|
||||
nl Nalidixic acid Nalidixinezuur
|
||||
nl Neomycin Neomycine
|
||||
nl Netilmicin Netilmicine
|
||||
nl Nitrofurantoin Nitrofurantoine
|
||||
nl Norfloxacin Norfloxacine
|
||||
nl Novobiocin Novobiocine
|
||||
nl Nystatin Nystatine
|
||||
nl Ofloxacin Ofloxacine
|
||||
nl Oleandomycin Oleandomycine
|
||||
nl Ornidazole Ornidazol
|
||||
nl Oxacillin Oxacilline
|
||||
nl Oxolinic acid Oxolinezuur
|
||||
nl Oxytetracycline Oxytetracycline
|
||||
nl Pazufloxacin Pazufloxacine
|
||||
nl Pefloxacin Pefloxacine
|
||||
nl Penamecillin Penamecilline
|
||||
nl Penicillin Penicilline
|
||||
nl Pheneticillin Feneticilline
|
||||
nl Phenoxymethylpenicillin Fenoxymethylpenicilline
|
||||
nl Pipemidic acid Pipemidinezuur
|
||||
nl Piperacillin Piperacilline
|
||||
nl Piperacillin/beta-lactamase inhibitor Piperacilline/enzymremmer
|
||||
nl Piromidic acid Piromidinezuur
|
||||
nl Pivampicillin Pivampicilline
|
||||
nl Polymyxin B Polymyxine B
|
||||
nl Posaconazole Posaconazol
|
||||
nl Pristinamycin Pristinamycine
|
||||
nl Procaine benzylpenicillin Benzylpenicillineprocaine
|
||||
nl Propicillin Propicilline
|
||||
nl Prulifloxacin Prulifloxacine
|
||||
nl Quinupristin/dalfopristin Quinupristine/dalfopristine
|
||||
nl Ribostamycin Ribostamycine
|
||||
nl Rifabutin Rifabutine
|
||||
nl Rifampicin Rifampicine
|
||||
nl Rifampicin/pyrazinamide/ethambutol/isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide
|
||||
nl Rifampicin/pyrazinamide/isoniazid Rifampicine/pyrazinamide/isoniazide
|
||||
nl Rifampicin/isoniazid Rifampicine/isoniazide
|
||||
nl Rifamycin Rifamycine
|
||||
nl Rifaximin Rifaximine
|
||||
nl Rokitamycin Rokitamycine
|
||||
nl Rosoxacin Rosoxacine
|
||||
nl Roxithromycin Roxitromycine
|
||||
nl Rufloxacin Rufloxacine
|
||||
nl Sisomicin Sisomicine
|
||||
nl Sodium aminosalicylate Aminosalicylzuur
|
||||
nl Sparfloxacin Sparfloxacine
|
||||
nl Spectinomycin Spectinomycine
|
||||
nl Spiramycin Spiramycine
|
||||
nl Spiramycin/metronidazole Spiramycine/metronidazol
|
||||
nl Staphylococcus immunoglobulin Stafylokokkenimmunoglobuline
|
||||
nl Streptoduocin Streptoduocine
|
||||
nl Streptomycin Streptomycine
|
||||
nl Streptomycin/isoniazid Streptomycine/isoniazide
|
||||
nl Sulbenicillin Sulbenicilline
|
||||
nl Sulfadiazine/tetroxoprim Sulfadiazine/tetroxoprim
|
||||
nl Sulfadiazine/trimethoprim Sulfadiazine/trimethoprim
|
||||
nl Sulfadimidine/trimethoprim Sulfadimidine/trimethoprim
|
||||
nl Sulfafurazole Sulfafurazol
|
||||
nl Sulfaisodimidine Sulfisomidine
|
||||
nl Sulfalene Sulfaleen
|
||||
nl Sulfamazone Sulfamazon
|
||||
nl Sulfamerazine/trimethoprim Sulfamerazine/trimethoprim
|
||||
nl Sulfamethizole Sulfamethizol
|
||||
nl Sulfamethoxazole Sulfamethoxazol
|
||||
nl Sulfamethoxazole/trimethoprim Sulfamethoxazol/trimethoprim
|
||||
nl Sulfametoxydiazine Sulfamethoxydiazine
|
||||
nl Sulfametrole/trimethoprim Sulfametrol/trimethoprim
|
||||
nl Sulfamoxole Sulfamoxol
|
||||
nl Sulfamoxole/trimethoprim Sulfamoxol/trimethoprim
|
||||
nl Sulfaperin Sulfaperine
|
||||
nl Sulfaphenazole Sulfafenazol
|
||||
nl Sulfathiazole Sulfathiazol
|
||||
nl Sulfathiourea Sulfathioureum
|
||||
nl Sultamicillin Sultamicilline
|
||||
nl Talampicillin Talampicilline
|
||||
nl Teicoplanin Teicoplanine
|
||||
nl Telithromycin Telitromycine
|
||||
nl Temafloxacin Temafloxacine
|
||||
nl Temocillin Temocilline
|
||||
nl Tenofovir disoproxil Tenofovir
|
||||
nl Terizidone Terizidon
|
||||
nl Thiamphenicol Thiamfenicol
|
||||
nl Thioacetazone/isoniazid Thioacetazon/isoniazide
|
||||
nl Ticarcillin Ticarcilline
|
||||
nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer
|
||||
nl Tinidazole Tinidazol
|
||||
nl Tobramycin Tobramycine
|
||||
nl Troleandomycin Troleandomycine
|
||||
nl Trovafloxacin Trovafloxacine
|
||||
nl Vancomycin Vancomycine
|
||||
nl Voriconazole Voriconazol
|
||||
nl Aminoglycosides Aminoglycosiden TRUE FALSE
|
||||
nl Amphenicols Amfenicolen TRUE FALSE
|
||||
nl Antifungals/antimycotics Antifungica/antimycotica TRUE FALSE
|
||||
nl Antimycobacterials Antimycobacteriele middelen TRUE FALSE
|
||||
nl Beta-lactams/penicillins Beta-lactams/penicillines TRUE FALSE
|
||||
nl Cephalosporins (1st gen.) Cefalosporines (1e gen.) TRUE FALSE
|
||||
nl Cephalosporins (2nd gen.) Cefalosporines (2e gen.) TRUE FALSE
|
||||
nl Cephalosporins (3rd gen.) Cefalosporines (3e gen.) TRUE FALSE
|
||||
nl Cephalosporins (4th gen.) Cefalosporines (4e gen.) TRUE FALSE
|
||||
nl Cephalosporins Cefalosporines TRUE FALSE
|
||||
nl Glycopeptides Glycopeptiden TRUE FALSE
|
||||
nl Macrolides/lincosamides Macroliden/lincosamiden TRUE FALSE
|
||||
nl Other antibacterials Overige antibiotica TRUE FALSE
|
||||
nl Polymyxins Polymyxines TRUE FALSE
|
||||
nl Quinolones Quinolonen TRUE FALSE
|
||||
|
Can't render this file because it has a wrong number of fields in line 157.
|
Reference in New Issue
Block a user