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(v1.6.0.9000) custom EUCAST rules

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dr. M.S. (Matthijs) Berends
2021-04-07 08:37:42 +02:00
parent 551f99dc8f
commit 7a3139f7cc
49 changed files with 1363 additions and 594 deletions
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54
data-raw/_internals.R
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@ -134,7 +134,7 @@ create_intr_resistance <- function() {
# Save internal data sets to R/sysdata.rda --------------------------------
# Save internal data to R/sysdata.rda -------------------------------------
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
@ -188,6 +188,35 @@ AB_lookup <- create_AB_lookup()
MO_lookup <- create_MO_lookup()
MO.old_lookup <- create_MO.old_lookup()
# antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab)
AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"]
FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone") %>% pull(ab)
LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
GLYCOPEPTIDES_EXCEPT_LIPO <- GLYCOPEPTIDES[!GLYCOPEPTIDES %in% LIPOGLYCOPEPTIDES]
LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide") %>% pull(ab) %>% c("PRL")
MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
TETRACYCLINES <- antibiotics %>% filter(atc_group2 %like% "tetracycline") %>% pull(ab)
TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
BETALACTAMS <- c(PENICILLINS, CEPHALOSPORINS, CARBAPENEMS)
DEFINED_AB_GROUPS <- ls(envir = globalenv())
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
# Export to package as internal data ----
usethis::use_data(eucast_rules_file,
translations_file,
@ -199,6 +228,29 @@ usethis::use_data(eucast_rules_file,
AB_lookup,
MO_lookup,
MO.old_lookup,
AMINOGLYCOSIDES,
AMINOPENICILLINS,
CARBAPENEMS,
CEPHALOSPORINS,
CEPHALOSPORINS_1ST,
CEPHALOSPORINS_2ND,
CEPHALOSPORINS_3RD,
CEPHALOSPORINS_EXCEPT_CAZ,
FLUOROQUINOLONES,
LIPOGLYCOPEPTIDES,
GLYCOPEPTIDES,
GLYCOPEPTIDES_EXCEPT_LIPO,
LINCOSAMIDES,
MACROLIDES,
OXAZOLIDINONES,
PENICILLINS,
POLYMYXINS,
STREPTOGRAMINS,
TETRACYCLINES,
TETRACYCLINES_EXCEPT_TGC,
UREIDOPENICILLINS,
BETALACTAMS,
DEFINED_AB_GROUPS,
internal = TRUE,
overwrite = TRUE,
version = 2,

66
data-raw/eucast_rules.tsv
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@ -1,7 +1,7 @@
# -------------------------------------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins',
# 'betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'glycopeptides_except_lipo', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'tetracyclines_except_TGC', 'ureidopenicillins',
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
@ -14,7 +14,7 @@ order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 10
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 10
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 10
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 10
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 10
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 10
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 10
@ -120,7 +120,7 @@ order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 11
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 11
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 11
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 11
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints 11
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 11
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 11
genus is Staphylococcus FOX S carbapenems, cephalosporins_except_CAZ S Staphylococcus Breakpoints 11
genus is Staphylococcus FOX I carbapenems, cephalosporins_except_CAZ I Staphylococcus Breakpoints 11
@ -224,7 +224,7 @@ genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei
genus is Bacillus NOR S fluoroquinolones S Bacillus Breakpoints 11 added in 11
genus is Bacillus NOR I fluoroquinolones I Bacillus Breakpoints 11 added in 11
genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
order is Enterobacterales PEN, glycopeptides_except_lipo, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
@ -232,17 +232,17 @@ genus_species is Klebsiella aerogenes aminopenicillins, AMC, CZO, FOX R Table
genus_species is Escherichia hermannii aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Hafnia alvei aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus is Klebsiella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Morganella morganii aminopenicillins, AMC, CZO, tetracyclines, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus penneri aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, tetracyclines, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Morganella morganii aminopenicillins, AMC, CZO, DOX, MNO, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus penneri aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Proteus vulgaris aminopenicillins, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia rettgeri aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Providencia stuartii aminopenicillins, AMC, CZO, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus is Raoultella aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Serratia marcescens aminopenicillins, AMC, CZO, FOX, CXM, DOX, TCY, polymyxins, NIT R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Yersinia enterocolitica aminopenicillins, AMC, TIC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 01: Intrinsic resistance in Enterobacterales (at the time: Enterobacteriaceae) Expert Rules 3.1
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, 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 3.1
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 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
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 3.1
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 3.1
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 3.1
@ -251,9 +251,9 @@ genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, E
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 Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
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 3.1
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 3.1
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 3.1
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, DOX, MNO, TCY, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus_species is Stenotrophomonas maltophilia aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules 3.1
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides_except_lipo, LIN, DAP, LNZ R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Haemophilus influenzae FUS, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus_species is Moraxella catarrhalis TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules 3.1
@ -279,8 +279,8 @@ genus_species is Enterococcus casseliflavus FUS, CAZ, cephalosporins_except_CA
genus_species is Enterococcus faecium FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, TMP, SXT R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Corynebacterium FOS R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus one_of Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus is Lactobacillus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
@ -298,7 +298,7 @@ genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules fo
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules 3.1
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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 3.2
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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
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
@ -308,13 +308,13 @@ genus_species is Klebsiella aerogenes aminopenicillins, AMC, SAM, CZO, CEP, LE
genus_species is Klebsiella oxytoca aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
fullname like ^Klebsiella( pneumoniae| quasipneumoniae| variicola)? aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Leclercia adecarboxylata FOS R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Morganella morganii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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 3.2
genus_species is Plesiomonas shigelloides aminopenicillins, AMC, SAM R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus mirabilis tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus penneri aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus vulgaris aminopenicillins, CZO, CEP, LEX, CFR, CXM, tetracyclines, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Providencia rettgeri aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Providencia stuartii aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Proteus mirabilis DOX, MNO, TCY, TGC, polymyxins, NIT R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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 3.2
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 3.2
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 3.2
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 3.2
genus is Raoultella aminopenicillins, TIC R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
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 3.2
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 3.2
@ -324,20 +324,20 @@ genus_species is Aeromonas veronii aminopenicillins, AMC, SAM, FOX R Table 1:
genus_species is Aeromonas dhakensis aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas caviae aminopenicillins, AMC, SAM, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp. Expert Rules 3.2
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
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 3.2
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 3.2 Additional rules from header added in separate rule (genus is one of…)
genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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 3.2 Additional rules from header added in separate rule (genus is one of…)
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
genus_species is Ochrobactrum 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 3.2 Additional rules from header added in separate rule (genus is one of…)
genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, tetracyclines, TGC R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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 3.2 Additional rules from header added in separate rule (genus is one of…)
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 3.2 Additional rules from header added in separate rule (genus is one of…)
genus_species is Haemophilus influenzae FUS, streptogramins, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Moraxella catarrhalis TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus is Neisseria TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
fullname like ^Campylobacter (jejuni|coli) FUS, streptogramins, TMP, glycopeptides, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
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 3.2
genus_species is Moraxella catarrhalis TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
genus is Neisseria TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones R Table 3: Intrinsic resistance in other gram-negative bacteria Expert Rules 3.2
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 3.2
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 3.2
gramstain is Gram-positive ATM, TEM, polymyxins, NAL R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
genus_species is Staphylococcus cohnii CAZ, NOV R Table 4: Intrinsic resistance in gram-positive bacteria Expert Rules 3.2
@ -372,8 +372,8 @@ fullname like ^(Serratia|Providencia|Morganella morganii) TGC R Expert Rules o
genus is Salmonella cephalosporins_2nd R Expert Rules on Salmonella Expert Rules 3.2
genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules 3.2
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 R all_betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 S all_betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
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 3.2 all penicillins without beta-lactamse inhibitor
genus is Staphylococcus ERY, CLI S macrolides, lincosamides S Expert Rules on Staphylococcus Expert Rules 3.2
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.2
@ -400,7 +400,7 @@ genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Strep
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
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 3.2
genus_species is Haemophilus influenzae PEN S all_betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2

Can't render this file because it contains an unexpected character in line 6 and column 96.

2
data-raw/reproduction_of_microorganisms_update.R
View File

@ -160,7 +160,7 @@ updated_microorganisms <- taxonomy %>%
TRUE ~ "subsp."),
ref = get_author_year(authors),
species_id = as.character(record_no),
source = "LSPN",
source = "LPSN",
prevalence = 0,
snomed = NA)

4
data-raw/translations.tsv
View File

@ -39,6 +39,10 @@ antibiotic TRUE TRUE FALSE Antibiotikum antibioticum antibiótico
Antibiotic TRUE TRUE FALSE Antibiotikum Antibioticum Antibiótico
Drug TRUE TRUE FALSE Medikament Middel Fármaco
drug TRUE TRUE FALSE Medikament middel fármaco
Frequency FALSE TRUE FALSE Zahl Aantal
Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L)
Disk diffusion diameter (mm) FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm)
Antimicrobial Interpretation FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie
4-aminosalicylic acid FALSE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico
Adefovir dipivoxil FALSE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil
Aldesulfone sodium FALSE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica

1 pattern regular_expr case_sensitive affect_mo_name de nl es it fr pt
39 Antibiotic TRUE TRUE FALSE Antibiotikum Antibioticum Antibiótico
40 Drug TRUE TRUE FALSE Medikament Middel Fármaco
41 drug TRUE TRUE FALSE Medikament middel fármaco
42 Frequency FALSE TRUE FALSE Zahl Aantal
43 Minimum Inhibitory Concentration (mg/L) FALSE FALSE FALSE Minimale Hemm-Konzentration (mg/L) Minimale inhiberende concentratie (mg/L)
44 Disk diffusion diameter (mm) FALSE FALSE FALSE Durchmesser der Scheibenzone (mm) Diameter diskzone (mm)
45 Antimicrobial Interpretation FALSE FALSE FALSE Antimikrobielle Auswertung Antimicrobiële interpretatie
46 4-aminosalicylic acid FALSE TRUE FALSE 4-Aminosalicylsäure 4-aminosalicylzuur Ácido 4-aminosalicílico
47 Adefovir dipivoxil FALSE TRUE FALSE Adefovir Dipivoxil Adefovir Adefovir dipivoxil
48 Aldesulfone sodium FALSE TRUE FALSE Aldesulfon-Natrium Aldesulfon Aldesulfona sódica