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(v2.1.1.9111) add betalactams_with_inhibitor(), fixes #175

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dr. M.S. (Matthijs) Berends
2024-12-06 15:44:20 +01:00
parent 059618e710
commit 0488d00f20
18 changed files with 286 additions and 302 deletions
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16
data-raw/eucast_rules.tsv
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@ -1,6 +1,6 @@
# -------------------------------------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
# aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, betalactams_with_inhibitor, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
# and all separate EARS-Net letter codes such as 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)
@ -11,7 +11,7 @@ if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 10
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 S betalactams_with_inhibitor S Staphylococcus Breakpoints 10
genus is Staphylococcus PEN, FOX R, S OXA, FLC S 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
@ -117,7 +117,7 @@ genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 11
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 S betalactams_with_inhibitor S Staphylococcus Breakpoints 11
genus is Staphylococcus PEN, FOX R, S OXA, FLC S 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
@ -226,7 +226,7 @@ genus is Bacillus NOR R fluoroquinolones R Bacillus Breakpoints 11 added in 11
order is Enterobacterales AMP S AMX S Enterobacterales (Order) Breakpoints 12
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints 12
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints 12
genus is Staphylococcus PEN, FOX S AMP, AMX, PIP, TIC S Staphylococcus Breakpoints 12
genus is Staphylococcus PEN, FOX S betalactams_with_inhibitor S Staphylococcus Breakpoints 12
genus is Staphylococcus PEN, FOX R, S OXA, FLC S Staphylococcus Breakpoints 12
genus is Staphylococcus FOX R betalactams R Staphylococcus Breakpoints 12
genus_species is Staphylococcus saprophyticus AMP S AMX, AMC, PIP, TZP S Staphylococcus Breakpoints 12
@ -500,8 +500,8 @@ genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules
genus is Salmonella PEF R CIP R Expert Rules on Salmonella 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 FOX 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 is Staphylococcus aureus FOX S betalactams S Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX1 S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.2
genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor 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
@ -620,8 +620,8 @@ genus is Salmonella aminoglycosides R Expert Rules on Salmonella Expert Rules
genus is Salmonella PEF R CIP R Expert Rules on Salmonella Expert Rules 3.3
genus_species is Staphylococcus aureus FOX1 R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
genus_species is Staphylococcus aureus FOX R betalactams R Expert Rules on Staphylococcus Expert Rules 3.3
genus_species is Staphylococcus aureus FOX1 S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
genus_species is Staphylococcus aureus FOX S betalactams S Expert Rules on Staphylococcus Expert Rules 3.3
genus_species is Staphylococcus aureus FOX1 S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.3
genus_species is Staphylococcus aureus FOX S betalactams_with_inhibitor S Expert Rules on Staphylococcus Expert Rules 3.3
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
genus is Staphylococcus NOR S CIP, LVX, MFX, OFX S Expert Rules on Staphylococcus Expert Rules 3.3

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