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(v3.0.1.9089) Remove old expert rules that conflict with expected resistant phenotypes

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dr. M.S. (Matthijs) Berends
2026-09-03 15:53:29 +02:00
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DESCRIPTION
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Package: AMR Package: AMR
Version: 3.0.1.9088 Version: 3.0.1.9089
Date: 2026-09-03 Date: 2026-09-03
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 3.0.1.9088 # AMR 3.0.1.9089
Planned as v3.1.0, end of September 2026. Planned as v3.1.0, end of September 2026.

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R/aa_globals.R
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@@ -79,18 +79,6 @@ EUCAST_VERSION_EXPERT_RULES <- list(
year = 2021, year = 2021,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'", title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/" url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
),
"3.2" = list(
version_txt = "v3.2",
year = 2020,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
),
"3.1" = list(
version_txt = "v3.1",
year = 2016,
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
) )
) )
EUCAST_VERSION_EXPECTED_PHENOTYPES <- list( EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(

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R/sysdata.rda
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data-raw/interpretive_rules.tsv
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@@ -1217,197 +1217,6 @@ EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-pos
EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Lactobacillus casei VAN, FOS R EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria genus_species is Lactobacillus casei VAN, FOS R
EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria fullname is Lactobacillus casei rhamnosus VAN, FOS R EUCAST Expected phenotypes 1.2 Table 4: Expected resistant phenotype in gram-positive bacteria fullname is Lactobacillus casei rhamnosus VAN, FOS R
EUCAST Expected phenotypes 1.2 Table 5: Expected resistant phenotype in anaerobes genus_species one_of Clostridium ramosum, Clostridium innocuum VAN R EUCAST Expected phenotypes 1.2 Table 5: Expected resistant phenotype in anaerobes genus_species one_of Clostridium ramosum, Clostridium innocuum VAN R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R originally Enterobacter aerogenes, but was renamed to Klebsiella aerogenes
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Escherichia hermannii aminopenicillins, TIC R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus is Klebsiella aminopenicillins, TIC R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Morganella morganii aminopenicillins, AMC, CZO, DOX, MNO, TCY, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Proteus penneri aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus is Raoultella aminopenicillins, TIC R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R
EUCAST Expert Rules 3.1 Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) genus_species is Yersinia pseudotuberculosis PLB, COL R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, FOX, CXM, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter baumannii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria 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, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Brucella anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, DOX, MNO, TCY, TGC R
EUCAST Expert Rules 3.1 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides_except_lipo, LIN, DAP, LNZ R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Moraxella catarrhalis TMP R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus is Neisseria TMP R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter jejuni FUS, streptogramins, TMP R
EUCAST Expert Rules 3.1 Table 03: Intrinsic resistance in other Gram-negative bacteria genus_species is Campylobacter coli FUS, streptogramins, TMP R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria gramstain is Gram-positive ATM, polymyxins, NAL R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus aureus CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus epidermidis CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus hominis CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus haemolyticus CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus intermedius CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Staphylococcus pseudintermedius CAZ R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus faecalis FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, TMP, SXT R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus gallinarum FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, TMP, SXT R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Corynebacterium FOS R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Listeria monocytogenes cephalosporins R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus is Lactobacillus glycopeptides_except_lipo R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Clostridium ramosum VAN R
EUCAST Expert Rules 3.1 Table 04: Intrinsic resistance in Gram-positive bacteria genus_species is Clostridium innocuum VAN R
EUCAST Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S
EUCAST Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus is Enterococcus AMP R ureidopenicillins, carbapenems R
EUCAST Expert Rules 3.1 Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci genus is Enterococcus AMX R ureidopenicillins, carbapenems R
EUCAST Expert Rules 3.1 Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) order is Enterobacterales TIC, PIP R, S PIP R
EUCAST Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY S AZM, CLR S
EUCAST Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY I AZM, CLR I
EUCAST Expert Rules 3.1 Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins genus like .* ERY R AZM, CLR R
EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides genus is Staphylococcus TOB R KAN, AMK R
EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides genus is Staphylococcus GEN R aminoglycosides R
EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides order is Enterobacterales GEN, TOB I, S GEN R
EUCAST Expert Rules 3.1 Table 12: Interpretive rules for aminoglycosides order is Enterobacterales GEN, TOB R, I TOB R
EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus is Staphylococcus MFX R fluoroquinolones R
EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R
EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones order is Enterobacterales CIP R fluoroquinolones R
EUCAST Expert Rules 3.1 Table 13: Interpretive rules for quinolones genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R
EUCAST Expert Rules 3.2 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S
EUCAST Expert Rules 3.2 Expert Rules on Campylobacter genus_species is Campylobacter ERY R CLR, AZM R
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP S PIP S
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Klebsiella(?! aerogenes)|Raoultella) PIP R
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia) CXM S CXM, cephalosporins_2nd R
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales 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 This is Enterobacterales except Salmonella spp.
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales fullname like ^(Serratia|Providencia|Morganella morganii) TGC R
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) 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 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) 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 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) 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 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) 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 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) 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 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
EUCAST Expert Rules 3.2 Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins) 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 This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
EUCAST Expert Rules 3.2 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMP R ureidopenicillins, IPM R
EUCAST Expert Rules 3.2 Expert Rules on Enterococcus fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R
EUCAST Expert Rules 3.2 Expert Rules on Enterococcus genus is Enterococcus NOR S CIP, LVX S
EUCAST Expert Rules 3.2 Expert Rules on Enterococcus genus is Enterococcus VAN S lipoglycopeptides S
EUCAST Expert Rules 3.2 Expert Rules on Enterococcus genus_species is Enterococcus faecium CLI R
EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae PEN S betalactams S
EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL S fluoroquinolones S
EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R
EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY S DOX, MNO S
EUCAST Expert Rules 3.2 Expert Rules on Haemophilus influenzae genus_species is Haemophilus influenzae TCY R DOX, MNO R
EUCAST Expert Rules 3.2 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL S fluoroquinolones S
EUCAST Expert Rules 3.2 Expert Rules on Moraxella catarrhalis genus_species is Moraxella catarrhalis NAL R fluoroquinolones R
EUCAST Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella cephalosporins_2nd R
EUCAST Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella aminoglycosides R
EUCAST Expert Rules 3.2 Expert Rules on Salmonella genus is Salmonella PEF R CIP R
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX R betalactams R
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus 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 all penicillins without beta-lactamse inhibitor
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus ERY, CLI S macrolides, lincosamides S
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus LVX R fluoroquinolones R
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus MFX R fluoroquinolones R
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus TCY S DOX, MNO, TGC S
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus TCY R DOX, MNO R
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus VAN S lipoglycopeptides S
EUCAST Expert Rules 3.2 Expert Rules on Staphylococcus genus is Staphylococcus LNZ S TZD S
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus A, B, C and G genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR S LVX, MFX S
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae NOR R LVX, MFX R
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae LVX R fluoroquinolones R
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY S DOX, MNO S
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae TCY R DOX, MNO R
EUCAST Expert Rules 3.2 Expert Rules on Streptococcus pneumoniae genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S
EUCAST Expert Rules 3.2 Expert Rules on Viridans Group Streptococci genus_species one_of Viridans Group Streptococcus (VGS) PEN S aminopenicillins, CTX, CRO S
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. order is Enterobacterales PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Enterobacter cloacae aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Escherichia hermannii aminopenicillins, TIC R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Hafnia alvei aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Klebsiella oxytoca aminopenicillins, TIC R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Leclercia adecarboxylata FOS R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus is Raoultella aminopenicillins, TIC R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Serratia marcescens aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia enterocolitica aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Yersinia pseudotuberculosis polymyxins R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas hydrophila aminopenicillins, AMC, SAM, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R
EUCAST Expert Rules 3.2 Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria 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
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus is Acinetobacter DOX, TCY R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria 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 Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Additional rules from header added in separate rule (genus is one of…)
EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R
EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R
EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R
EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R
EUCAST Expert Rules 3.2 Table 3: Intrinsic resistance in other gram-negative bacteria fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria gramstain is Gram-positive ATM, TEM, polymyxins, NAL R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus cohnii CAZ, NOV R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus xylosus CAZ, NOV R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus capitis CAZ, FOS R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus aureus CAZ R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Staphylococcus coagulase-negative CAZ R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Streptococcus FUS, CAZ, aminoglycosides R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecalis TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Enterococcus (gallinarum|casseliflavus) TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria 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 These last ones are all true sulfonamides
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP S SXT, SLT1, SLT2, SLT3, SLT4, SLT5 S Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP I SXT, SLT1, SLT2, SLT3, SLT4, SLT5 I Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Enterococcus faecium TMP R SXT, SLT1, SLT2, SLT3, SLT4, SLT5 R Since R to sulfonamides - TMP result is equal with combinations
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Corynebacterium FOS R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus_species is Listeria monocytogenes CAZ, cephalosporins_except_CAZ R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus one_of Leuconostoc, Pediococcus VAN, TEC R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria genus is Lactobacillus VAN, TEC R
EUCAST Expert Rules 3.2 Table 4: Intrinsic resistance in gram-positive bacteria fullname like ^Clostridium (ramosum|innocuum) VAN R
EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY S CLR, AZM S
EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY R CLR, AZM R EUCAST Expert Rules 3.3 Expert Rules on Campylobacter genus is Campylobacter ERY R CLR, AZM R
EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R EUCAST Expert Rules 3.3 Expert Rules on Enterobacterales genus_species one_of Escherichia coli, Proteus mirabilis AMP R PIP R
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@@ -64,9 +64,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be \code{"1.2"}.} \item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be \code{"1.2"}.}
\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be \code{"3.3"}, \code{"3.2"}, or \code{"3.1"}.} \item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be \code{"3.3"}.}
\item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.} \item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, and \emph{Klebsiella aerogenes}.}
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.} \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}