P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-19 18:23:17 +02:00
Code Releases Activity

(v2.1.1.9226) update intrinsic_resistant, unit test fixes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-27 15:20:22 +01:00
parent e6f88241b2
commit 969a42cc8c
29 changed files with 139318 additions and 244254 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
data-raw/eucast_rules.tsv
View File

@ -783,36 +783,6 @@ genus_species is Brucella melitensis TCY-S S DOX S Brucella melitensis Breakpoin
genus_species is Brucella melitensis TCY-S R DOX R Brucella melitensis Breakpoints 14
genus_species is Burkholderia pseudomallei TCY-S S DOX I Burkholderia pseudomallei Breakpoints 14
genus_species is Burkholderia pseudomallei TCY-S R DOX R Burkholderia pseudomallei Breakpoints 14
genus_species one_of Citrobacter koseri, Citrobacter amalonaticus AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Citrobacter freundii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species one_of Enterobacter cloacae complex  AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Escherichia hermannii  AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Hafnia alvei  AMP, AMX, PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Klebsiella aerogenes AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species one_of Klebsiella pneumoniae complex AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Klebsiella oxytoca AMX, AMP, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Leclercia adecarboxylata FOS R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Morganella morganii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Plesiomonas shigelloides AMX, AMP, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Proteus mirabilis tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Proteus penneri AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Proteus vulgaris AMP, AMX, CZO, CEP, LEX, CFR, CXM, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Providencia rettgeri AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Providencia stuartii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, tetracyclines, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus is Raoultella AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Serratia marcescens AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, PLB, COL, NIT R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Yersinia enterocolitica AMP, AMX, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Yersinia pseudotuberculosis PLB, COL R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Aeromonas hydrophila AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Aeromonas veronii AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Aeromonas dhakensis AMP, AMX, SAM, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Aeromonas caviae AMP, AMX, SAM R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Aeromonas jandaei AMP, AMX, SAM, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
order is Enterobacterales PEN, glycopeptides, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species one_of Citrobacter koseri, Citrobacter amalonaticus AMP, AMX, TIC R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
genus_species is Citrobacter freundii AMP, AMX, AMC, SAM, CZO, CEP, LEX, CFR, FOX R Table 1: Expected resistant phenotype in Enterobacterales and Aeromonas spp. Expected phenotypes 1.2
@ -850,7 +820,7 @@ genus_species is Pseudomonas aeruginosa AMP, AMX, AMC, SAM, CTX, CRO, ETP, CHL
genus_species is Stenotrophomonas maltophilia AMP, AMX, AMC, SAM, TIC, PIP, TZP, CTX, CRO, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus is Chryseobacterium AMP, AMX, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, PLB, COL R Table 2: Expected resistant phenotype in non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus_species is Haemophilus influenzae FUS, streptogramins R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus_species is Moraxella catarrhalis R TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus_species is Moraxella catarrhalis TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus is Neisseria TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2
genus_species one_of Campylobacter jejuni, Campylobacter coli FUS, streptogramins, TMP R Table 3: Expected resistant phenotype in gram-negative bacteria other than Enterobacterales and non-fermentative gram-negative bacteria Expected phenotypes 1.2

Can't render this file because it has a wrong number of fields in line 9.