Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in eucast_rules().
Value
A list containing the custom rules
Details
Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the eucast_rules() function.
How it works
Basics
If you are familiar with the case_when() function of the dplyr package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the 'formula notation'. The rule itself is written before the tilde (~) and the consequence of the rule is written after the tilde:
x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
TZP == "R" ~ aminopenicillins == "R")These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:
x
#> A set of custom EUCAST rules:
#>
#> 1. If TZP is "S" then set to S :
#> amoxicillin (AMX), ampicillin (AMP)
#>
#> 2. If TZP is "R" then set to R :
#> amoxicillin (AMX), ampicillin (AMP)The rules (the part before the tilde, in above example TZP == "S" and TZP == "R") must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column TZP must exist. We will create a sample data set and test the rules set:
df <- data.frame(mo = c("Escherichia coli", "Klebsiella pneumoniae"),
TZP = as.rsi("R"),
ampi = as.rsi("S"),
cipro = as.rsi("S"))
df
#> mo TZP ampi cipro
#> 1 Escherichia coli R S S
#> 2 Klebsiella pneumoniae R S S
eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
#> mo TZP ampi cipro
#> 1 Escherichia coli R R S
#> 2 Klebsiella pneumoniae R R SUsing taxonomic properties in rules
There is one exception in variables used for the rules: all column names of the microorganisms data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "species_id", "source", "prevalence" and "snomed". Thus, this next example will work as well, despite the fact that the df data set does not contain a column genus:
y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
#> mo TZP ampi cipro
#> 1 Escherichia coli R S S
#> 2 Klebsiella pneumoniae R R SUsage of antibiotic group names
It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part after the tilde. In above examples, the antibiotic group aminopenicillins is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
"aminoglycosides"
(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)"aminopenicillins"
(amoxicillin and ampicillin)"antifungals"
(5-fluorocytosine, amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)"antimycobacterials"
(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, morinamide, p-aminosalicylic acid, pretomanid, prothionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone/isoniazid, tiocarlide and viomycin)"betalactams"
(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin and ticarcillin/clavulanic acid)"carbapenems"
(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)"cephalosporins"
(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)"cephalosporins_1st"
(cefacetrile, cefadroxil, cefaloridine, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephalexin, cephalothin, cephapirin and cephradine)"cephalosporins_2nd"
(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)"cephalosporins_3rd"
(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone and latamoxef)"cephalosporins_4th"
(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)"cephalosporins_5th"
(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor and ceftolozane/tazobactam)"cephalosporins_except_caz"
(cefacetrile, cefaclor, cefadroxil, cefaloridine, cefamandole, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/enzyme inhibitor, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cefuroxime axetil, cephalexin, cephalothin, cephapirin, cephradine, latamoxef and loracarbef)"fluoroquinolones"
(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)"glycopeptides"
(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)"glycopeptides_except_lipo"
(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)"lincosamides"
(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)"lipoglycopeptides"
(dalbavancin, oritavancin and telavancin)"macrolides"
(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin and tylvalosin)"oxazolidinones"
(cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)"penicillins"
(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, methicillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, phenethicillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)"polymyxins"
(colistin, polymyxin B and polymyxin B/polysorbate 80)"quinolones"
(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin and trovafloxacin)"streptogramins"
(pristinamycin and quinupristin/dalfopristin)"tetracyclines"
(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, tetracycline and tigecycline)"tetracyclines_except_tgc"
(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline and tetracycline)"trimethoprims"
(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim and trimethoprim/sulfamethoxazole)"ureidopenicillins"
(azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)
Examples
x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
x
#> A set of custom EUCAST rules:
#>
#> 1. If AMC is "R" and genus is "Klebsiella" then set to R :
#> amoxicillin (AMX), ampicillin (AMP)
#>
#> 2. If AMC is "I" and genus is "Klebsiella" then set to I :
#> amoxicillin (AMX), ampicillin (AMP)
# run the custom rule set (verbose = TRUE will return a logbook instead of the data set):
eucast_rules(example_isolates,
rules = "custom",
custom_rules = x,
info = FALSE,
verbose = TRUE)
#> row col mo_fullname old new
#> 1 33 AMP Klebsiella pneumoniae R I
#> 2 33 AMX Klebsiella pneumoniae R I
#> 3 34 AMP Klebsiella pneumoniae R I
#> 4 34 AMX Klebsiella pneumoniae R I
#> 5 531 AMP Klebsiella pneumoniae R I
#> 6 531 AMX Klebsiella pneumoniae R I
#> 7 1485 AMP Klebsiella oxytoca R I
#> 8 1485 AMX Klebsiella oxytoca R I
#> rule
#> 1 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 2 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 3 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 4 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 5 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 6 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 7 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> 8 report as 'I' when AMC is "I" and genus is "Klebsiella": amoxicillin, ampicillin
#> rule_group rule_name
#> 1 Custom EUCAST rules Custom EUCAST rule 2
#> 2 Custom EUCAST rules Custom EUCAST rule 2
#> 3 Custom EUCAST rules Custom EUCAST rule 2
#> 4 Custom EUCAST rules Custom EUCAST rule 2
#> 5 Custom EUCAST rules Custom EUCAST rule 2
#> 6 Custom EUCAST rules Custom EUCAST rule 2
#> 7 Custom EUCAST rules Custom EUCAST rule 2
#> 8 Custom EUCAST rules Custom EUCAST rule 2
#> rule_source
#> 1 Object 'x' consisting of 2 custom rules
#> 2 Object 'x' consisting of 2 custom rules
#> 3 Object 'x' consisting of 2 custom rules
#> 4 Object 'x' consisting of 2 custom rules
#> 5 Object 'x' consisting of 2 custom rules
#> 6 Object 'x' consisting of 2 custom rules
#> 7 Object 'x' consisting of 2 custom rules
#> 8 Object 'x' consisting of 2 custom rules
# combine rule sets
x2 <- c(x,
custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
x2
#> A set of custom EUCAST rules:
#>
#> 1. If AMC is "R" and genus is "Klebsiella" then set to R :
#> amoxicillin (AMX), ampicillin (AMP)
#>
#> 2. If AMC is "I" and genus is "Klebsiella" then set to I :
#> amoxicillin (AMX), ampicillin (AMP)
#>
#> 3. If TZP is "R" then set to R :
#> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM),
#> imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM),
#> meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN),
#> razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP)