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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Define Custom EUCAST Rules< / h1 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/R/custom_eucast_rules.R" class = "external-link" > < code > R/custom_eucast_rules.R< / code > < / a > < / small >
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< p > Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > .< / p >
< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "fu" > custom_eucast_rules< / span > < span class = "op" > (< / span > < span class = "va" > ...< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "arguments" > Arguments< a class = "anchor" aria-label = "anchor" href = "#arguments" > < / a > < / h2 >
< dl > < dt > ...< / dt >
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< dd > < p > rules in < a href = "https://rdrr.io/r/base/tilde.html" class = "external-link" > formula< / a > notation, see < em > Examples< / em > < / p > < / dd >
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< / dl > < / div >
< div class = "section level2" >
< h2 id = "value" > Value< a class = "anchor" aria-label = "anchor" href = "#value" > < / a > < / h2 >
< p > A < a href = "https://rdrr.io/r/base/list.html" class = "external-link" > list< / a > containing the custom rules< / p >
< / div >
< div class = "section level2" >
< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
< p > Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the < code > < a href = "eucast_rules.html" > eucast_rules()< / a > < / code > function.< / p >
< / div >
< div class = "section level2" >
< h2 id = "how-it-works" > How it works< a class = "anchor" aria-label = "anchor" href = "#how-it-works" > < / a > < / h2 >
< div class = "section" >
< h3 id = "basics" > Basics< a class = "anchor" aria-label = "anchor" href = "#basics" > < / a > < / h3 >
< p > If you are familiar with the < code > < a href = "https://dplyr.tidyverse.org/reference/case_when.html" class = "external-link" > case_when()< / a > < / code > function of the < code > dplyr< / code > package, you will recognise the input method to set your own rules. Rules must be set using what < span style = "R" > R< / span > considers to be the 'formula notation'. The rule itself is written < em > before< / em > the tilde (< code > ~< / code > ) and the consequence of the rule is written < em > after< / em > the tilde:< / p >
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< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/custom_eucast_rules.html" > custom_eucast_rules< / a > < / span > < span class = "op" > (< / span > < span class = "va" > TZP< / span > < span class = "op" > ==< / span > < span class = "st" > "S"< / span > < span class = "op" > ~< / span > < span class = "va" > aminopenicillins< / span > < span class = "op" > ==< / span > < span class = "st" > "S"< / span > ,< / span >
< span > < span class = "va" > TZP< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > ~< / span > < span class = "va" > aminopenicillins< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < p > < / p > < / div >
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< p > 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:< / p >
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< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "va" > x< / span > < / span >
< span > < span class = "co" > #> A set of custom EUCAST rules:< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> 1. If TZP is "S" then set to S :< / span > < / span >
< span > < span class = "co" > #> amoxicillin (AMX), ampicillin (AMP)< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> 2. If TZP is "R" then set to R :< / span > < / span >
< span > < span class = "co" > #> amoxicillin (AMX), ampicillin (AMP)< / span > < / span > < / code > < / pre > < p > < / p > < / div >
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< p > The rules (the part < em > before< / em > the tilde, in above example < code > TZP == "S"< / code > and < code > TZP == "R"< / code > ) 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 < code > TZP< / code > must exist. We will create a sample data set and test the rules set:< / p >
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< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "va" > df< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > mo < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Escherichia coli"< / span > , < span class = "st" > "Klebsiella pneumoniae"< / span > < span class = "op" > )< / span > ,< / span >
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< span > TZP < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > ,< / span >
< span > ampi < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S"< / span > < span class = "op" > )< / span > ,< / span >
< span > cipro < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/as.sir.html" > as.sir< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
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< span > < span class = "va" > df< / span > < / span >
< span > < span class = "co" > #> mo TZP ampi cipro< / span > < / span >
< span > < span class = "co" > #> 1 Escherichia coli R S S< / span > < / span >
< span > < span class = "co" > #> 2 Klebsiella pneumoniae R S S< / span > < / span >
< span > < / span >
< span > < span class = "fu" > < a href = "../reference/eucast_rules.html" > eucast_rules< / a > < / span > < span class = "op" > (< / span > < span class = "va" > df< / span > , rules < span class = "op" > =< / span > < span class = "st" > "custom"< / span > , custom_rules < span class = "op" > =< / span > < span class = "va" > x< / span > , info < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> mo TZP ampi cipro< / span > < / span >
< span > < span class = "co" > #> 1 Escherichia coli R R S< / span > < / span >
< span > < span class = "co" > #> 2 Klebsiella pneumoniae R R S< / span > < / span > < / code > < / pre > < p > < / p > < / div >
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< / div >
< div class = "section" >
< h3 id = "using-taxonomic-properties-in-rules" > Using taxonomic properties in rules< a class = "anchor" aria-label = "anchor" href = "#using-taxonomic-properties-in-rules" > < / a > < / h3 >
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< p > There is one exception in columns used for the rules: all column names of the < a href = "microorganisms.html" > microorganisms< / a > data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" and "snomed". Thus, this next example will work as well, despite the fact that the < code > df< / code > data set does not contain a column < code > genus< / code > :< / p >
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< p > < / p > < div class = "sourceCode r" > < pre > < code > < span > < span class = "va" > y< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/custom_eucast_rules.html" > custom_eucast_rules< / a > < / span > < span class = "op" > (< / span > < span class = "va" > TZP< / span > < span class = "op" > ==< / span > < span class = "st" > "S"< / span > < span class = "op" > & < / span > < span class = "va" > genus< / span > < span class = "op" > ==< / span > < span class = "st" > "Klebsiella"< / span > < span class = "op" > ~< / span > < span class = "va" > aminopenicillins< / span > < span class = "op" > ==< / span > < span class = "st" > "S"< / span > ,< / span >
< span > < span class = "va" > TZP< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > & < / span > < span class = "va" > genus< / span > < span class = "op" > ==< / span > < span class = "st" > "Klebsiella"< / span > < span class = "op" > ~< / span > < span class = "va" > aminopenicillins< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "fu" > < a href = "../reference/eucast_rules.html" > eucast_rules< / a > < / span > < span class = "op" > (< / span > < span class = "va" > df< / span > , rules < span class = "op" > =< / span > < span class = "st" > "custom"< / span > , custom_rules < span class = "op" > =< / span > < span class = "va" > y< / span > , info < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> mo TZP ampi cipro< / span > < / span >
< span > < span class = "co" > #> 1 Escherichia coli R S S< / span > < / span >
< span > < span class = "co" > #> 2 Klebsiella pneumoniae R R S< / span > < / span > < / code > < / pre > < p > < / p > < / div >
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< / div >
< div class = "section" >
< h3 id = "usage-of-antibiotic-group-names" > Usage of antibiotic group names< a class = "anchor" aria-label = "anchor" href = "#usage-of-antibiotic-group-names" > < / a > < / h3 >
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< p > It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part < em > after< / em > the tilde. In above examples, the antibiotic group < code > aminopenicillins< / code > is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.< / p > < ul > < li > < p > "aminoglycosides"< br > (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)< / p > < / li >
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< li > < p > "aminopenicillins"< br > (amoxicillin and ampicillin)< / p > < / li >
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< li > < p > "antifungals"< br > (amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole and voriconazole)< / p > < / li >
< li > < p > "antimycobacterials"< br > (4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide and viomycin)< / p > < / li >
< li > < p > "betalactams"< br > (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, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, 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/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, 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, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, 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)< / p > < / li >
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< li > < p > "carbapenems"< br > (biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil and tebipenem)< / p > < / li >
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< li > < p > "cephalosporins"< br > (cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, 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/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef and loracarbef)< / p > < / li >
< li > < p > "cephalosporins_1st"< br > (cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole and cephradine)< / p > < / li >
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< li > < p > "cephalosporins_2nd"< br > (cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil and loracarbef)< / p > < / li >
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< li > < p > "cephalosporins_3rd"< br > (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, ceftriaxone/beta-lactamase inhibitor and latamoxef)< / p > < / li >
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< li > < p > "cephalosporins_4th"< br > (cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome and cefquinome)< / p > < / li >
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< li > < p > "cephalosporins_5th"< br > (ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril and ceftolozane/tazobactam)< / p > < / li >
< li > < p > "cephalosporins_except_caz"< br > (cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, 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/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef and loracarbef)< / p > < / li >
< li > < p > "fluoroquinolones"< br > (besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, 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)< / p > < / li >
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< li > < p > "glycopeptides"< br > (avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin and vancomycin-macromethod)< / p > < / li >
< li > < p > "glycopeptides_except_lipo"< br > (avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin and vancomycin-macromethod)< / p > < / li >
< li > < p > "lincosamides"< br > (acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin and tylvalosin)< / p > < / li >
< li > < p > "lipoglycopeptides"< br > (dalbavancin, oritavancin and telavancin)< / p > < / li >
< li > < p > "macrolides"< br > (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)< / p > < / li >
< li > < p > "oxazolidinones"< br > (cadazolid, cycloserine, linezolid, tedizolid and thiacetazone)< / p > < / li >
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< li > < p > "penicillins"< br > (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, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin and ticarcillin/clavulanic acid)< / p > < / li >
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< li > < p > "polymyxins"< br > (colistin, polymyxin B and polymyxin B/polysorbate 80)< / p > < / li >
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< li > < p > "quinolones"< br > (besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, 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)< / p > < / li >
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< li > < p > "streptogramins"< br > (pristinamycin and quinupristin/dalfopristin)< / p > < / li >
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< li > < p > "tetracyclines"< br > (cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline and tigecycline)< / p > < / li >
< li > < p > "tetracyclines_except_tgc"< br > (cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline and tetracycline)< / p > < / li >
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< li > < p > "trimethoprims"< br > (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)< / p > < / li >
< li > < p > "ureidopenicillins"< br > (azlocillin, mezlocillin, piperacillin and piperacillin/tazobactam)< / p > < / li >
< / ul > < / div >
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< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "fu" > custom_eucast_rules< / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > AMC< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > & < / span > < span class = "va" > genus< / span > < span class = "op" > ==< / span > < span class = "st" > "Klebsiella"< / span > < span class = "op" > ~< / span > < span class = "va" > aminopenicillins< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "va" > AMC< / span > < span class = "op" > ==< / span > < span class = "st" > "I"< / span > < span class = "op" > & < / span > < span class = "va" > genus< / span > < span class = "op" > ==< / span > < span class = "st" > "Klebsiella"< / span > < span class = "op" > ~< / span > < span class = "va" > aminopenicillins< / span > < span class = "op" > ==< / span > < span class = "st" > "I"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "va" > x< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > A set of custom EUCAST rules:< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1. If AMC is "R" and genus is "Klebsiella" then set to R :< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > amoxicillin (AMX), ampicillin (AMP)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2. If AMC is "I" and genus is "Klebsiella" then set to I :< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > amoxicillin (AMX), ampicillin (AMP)< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # run the custom rule set (verbose = TRUE will return a logbook instead of the data set):< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "eucast_rules.html" > eucast_rules< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span > < / span >
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< span class = "r-in" > < span > rules < span class = "op" > =< / span > < span class = "st" > "custom"< / span > ,< / span > < / span >
< span class = "r-in" > < span > custom_rules < span class = "op" > =< / span > < span class = "va" > x< / span > ,< / span > < / span >
< span class = "r-in" > < span > info < span class = "op" > =< / span > < span class = "cn" > FALSE< / span > ,< / span > < / span >
< span class = "r-in" > < span > verbose < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 8 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > row col mo_fullname old new rule rule_…¹ rule_…² rule_…³< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < ord> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 33 AMP Klebsiella pneumoniae R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 33 AMX Klebsiella pneumoniae R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 34 AMP Klebsiella pneumoniae R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 34 AMX Klebsiella pneumoniae R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 531 AMP Klebsiella pneumoniae R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 531 AMX Klebsiella pneumoniae R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > < span style = "text-decoration: underline;" > 1< / span > 485 AMP Klebsiella oxytoca R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > < span style = "text-decoration: underline;" > 1< / span > 485 AMX Klebsiella oxytoca R I < span style = "color: #949494;" > "< / span > report… Custom… Custom… Object…< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # … with abbreviated variable names ¹ < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "co" > # combine rule sets< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "va" > x2< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > x< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > custom_eucast_rules< / span > < span class = "op" > (< / span > < span class = "va" > TZP< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > ~< / span > < span class = "va" > carbapenems< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-in" > < span > < span class = "va" > x2< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > A set of custom EUCAST rules:< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 1. If AMC is "R" and genus is "Klebsiella" then set to R :< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > amoxicillin (AMX), ampicillin (AMP)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 2. If AMC is "I" and genus is "Klebsiella" then set to I :< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > amoxicillin (AMX), ampicillin (AMP)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > 3. If TZP is "R" then set to R :< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM),< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM),< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN),< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP)< / span >
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< / main > < aside class = "col-md-3" > < nav id = "toc" > < h2 > On this page< / h2 >
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< p > < / p > < p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
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