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(v1.7.1.9055) added EUCAST 3.3 and all LPSN records numbers
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@ -7,7 +7,7 @@
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# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
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# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
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# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
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# -------------------------------------------------------------------------------------------------------------------------------
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# -------------------------------------------------------------------------------------------------------------------------------
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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 reference.version note
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order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
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order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
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@ -303,7 +303,7 @@ fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) am
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fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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@ -415,3 +415,121 @@ fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacte
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fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
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fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
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fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.2 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
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order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Escherichia hermannii aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Hafnia alvei aminopenicillins, AMC, polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Yersinia pseudotuberculosis polymyxins R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Aeromonas hydrophila aminopenicillins, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Aeromonas veronii aminopenicillins, SAM, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Aeromonas dhakensis aminopenicillins, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus_species is Aeromonas caviae aminopenicillins, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.3
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genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3
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fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP, ATM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Elizabethkingia anophelis aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus is Chryseobacterium aminopenicillins, AMC, SAM, TIC, TCC, CRO, CTX, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
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genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
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genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
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genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
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fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.3
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gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Staphylococcus xylosus CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Staphylococcus capitis CAZ, FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Staphylococcus aureus CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Staphylococcus coagulase-negative CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus is Streptococcus FUS, CAZ, aminoglycosides R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides
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genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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fullname like ^Enterococcus (gallinarum|casseliflavus) FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides
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fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 These last ones are all true sulfonamides
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genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3 Since R to sulfonamides - TMP result is equal with combinations
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genus is Corynebacterium FOS R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus one_of Leuconostoc, Pediococcus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus is Lactobacillus VAN, TEC R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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fullname like ^Clostridium (ramosum|innocuum) VAN R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.3
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genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R Expert Rules on Enterobacterales Expert Rules 3.3
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genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S Expert Rules on Enterobacterales Expert Rules 3.3
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fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R Expert Rules on Enterobacterales Expert Rules 3.3
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fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R Expert Rules on Enterobacterales Expert Rules 3.3
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genus one_of Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella CIP R fluoroquinolones R Expert Rules on Enterobacterales Expert Rules 3.3 This is Enterobacterales except Salmonella spp.
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fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules on Enterobacterales Expert Rules 3.3
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genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.3
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genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.3
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genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
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genus_species one_of Staphylococcus aureus, Staphylococcus lugdunensis PEN R AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC R Expert Rules on Staphylococcus Expert Rules 3.3 all penicillins without beta-lactamse inhibitor
|
||||
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.3
|
||||
genus is Staphylococcus LVX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus MFX R fluoroquinolones R Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus TCY S DOX, MNO, TGC S Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus TCY R DOX, MNO R Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus VAN S lipoglycopeptides S Expert Rules on Staphylococcus Expert Rules 3.3
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genus is Staphylococcus LNZ S TZD S Expert Rules on Staphylococcus Expert Rules 3.3
|
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fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.3
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fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.3
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genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.3
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genus_species is Enterococcus faecium CLI R Expert Rules on Enterococcus Expert Rules 3.3
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
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genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
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genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
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||||
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
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||||
genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
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genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
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genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
fullname 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 aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.3
|
||||
genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.3
|
||||
genus_species is Campylobacter ERY R CLR, AZM R Expert Rules on Campylobacter Expert Rules 3.3
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX S CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO S CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ S CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CTX I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CRO I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia) CAZ I CTX, CRO, CAZ Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) Expert Rules 3.3 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
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141537
data-raw/microorganisms.txt
141537
data-raw/microorganisms.txt
File diff suppressed because it is too large
Load Diff
@ -1 +1 @@
|
||||
e8251824eec0b72d037b3dbfcdbe444a
|
||||
dbe572abad4a2dc85db8cb146b74beb9
|
||||
|
||||
@ -25,6 +25,8 @@
|
||||
|
||||
# Go to https://lpsn.dsmz.de/downloads (register first) and download the latest CSV file.
|
||||
|
||||
file_location <- "data-raw/taxonomy.csv"
|
||||
|
||||
library(tidyverse)
|
||||
library(AMR)
|
||||
|
||||
@ -111,7 +113,7 @@ abbreviate_mo <- function(x, minlength = 5, prefix = "", ...) {
|
||||
|
||||
# Read data ---------------------------------------------------------------
|
||||
|
||||
taxonomy <- read_csv("~/Downloads/taxonomy.csv")
|
||||
taxonomy <- read_csv(file_location)
|
||||
|
||||
# Create synonyms ---------------------------------------------------------
|
||||
|
||||
@ -129,8 +131,7 @@ new_synonyms <- taxonomy %>%
|
||||
filter(fullname != fullname_new) %>%
|
||||
# this part joins this table to itself to correct for entries that had >1 renames,
|
||||
# such as:
|
||||
# Bacteroides tectum -> Bacteroides tectus
|
||||
# Bacteroides tectus -> Bacteroides pyogenes
|
||||
# Bacteroides tectum -> Bacteroides tectus -> Bacteroides pyogenes
|
||||
left_join(., .,
|
||||
by = c("fullname_new" = "fullname"),
|
||||
suffix = c("", ".2")) %>%
|
||||
@ -359,6 +360,20 @@ MOs <- MOs %>%
|
||||
MOs <- MOs %>%
|
||||
df_remove_nonASCII()
|
||||
|
||||
# Add LPSN record IDs -----------------------------------------------------
|
||||
|
||||
records_ids <- taxonomy %>%
|
||||
mutate(across(1:3, function(x) { x[is.na(x)] <- ""; x}),
|
||||
fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet))) %>%
|
||||
transmute(fullname, species_id = as.numeric(record_no))
|
||||
message("Adding ", sum(records_ids$fullname %in% microorganisms$fullname), " LPSN record IDs")
|
||||
MOs <- MOs %>%
|
||||
select(-species_id) %>%
|
||||
left_join(records_ids, by = "fullname") %>%
|
||||
relocate(species_id, .after = ref) %>%
|
||||
mutate(source = case_when(!is.na(species_id) ~ "LPSN",
|
||||
source %unlike% "manual" ~ "CoL",
|
||||
TRUE ~ source))
|
||||
|
||||
# Merge synonyms ----------------------------------------------------------
|
||||
|
||||
|
||||
Reference in New Issue
Block a user