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(v0.8.0.9007) Enterobacterales order

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dr. M.S. (Matthijs) Berends
2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions
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16
data-raw/eucast_rules.tsv
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@ -5,13 +5,13 @@
# 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)
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J (2005, PMID 16217180).
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# -------------------------------------------------------------------------------------------------------------------------------
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
order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP R AMX R Enterobacteriales (Order) Breakpoints
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints
genus is Staphylococcus FOX R all_betalactams R Staphylococcus Breakpoints
@ -109,7 +109,7 @@ genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints
genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints
genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints
genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints
family is Enterobacteriaceae PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
genus_species is Enterobacter cloacae aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules
@ -177,11 +177,11 @@ genus is .* ERY I AZM, CLR I Table 11: Interpretive rules for macrolides, lincos
genus is .* ERY R AZM, CLR R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules
genus is Staphylococcus TOB R KAN, AMK R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus GEN R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules
family is Enterobacteriaceae GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
family is Enterobacteriaceae GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules
order is Enterobacterales GEN, TOB I, S GEN R Table 12: Interpretive rules for aminoglycosides Expert Rules
order is Enterobacterales GEN, TOB R, I TOB R Table 12: Interpretive rules for aminoglycosides Expert Rules
genus is Staphylococcus MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus_species is Streptococcus pneumoniae MFX R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
family is Enterobacteriaceae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
order is Enterobacterales CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus_species is Neisseria gonorrhoeae CIP R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules
genus is .* AMC R AMP, AMX R Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R Other rules
genus is .* TZP R PIP R Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R Other rules

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