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< meta property = "og:description" content = "Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables." / >
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< h1 > EUCAST rules< / h1 >
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< p > Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, < a href = 'http://eucast.org' > http://eucast.org< / a > ), see < em > Source< / em > . This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.< / p >
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< pre class = "usage" > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > col_mo< / span > < span class = 'kw' > =< / span > < span class = 'kw' > NULL< / span > , < span class = 'kw' > info< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > , < span class = 'kw' > rules< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "breakpoints"< / span > ,
< span class = 'st' > "expert"< / span > , < span class = 'st' > "other"< / span > , < span class = 'st' > "all"< / span > ), < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'kw' > amcl< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > amik< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > amox< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > ampi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > azit< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > azlo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > aztr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cefa< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfep< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cfot< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfox< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cfra< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfta< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > cftr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cfur< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > chlo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > cipr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > clar< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > clin< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > clox< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > coli< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > czol< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > dapt< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > doxy< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > erta< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > eryt< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > fosf< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > fusi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > gent< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > imip< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > kana< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > levo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > linc< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > line< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > mero< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > mezl< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > mino< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > moxi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > nali< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > neom< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > neti< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > nitr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > norf< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > novo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > oflo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > oxac< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > peni< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > pipe< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > pita< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > poly< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > pris< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > qida< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > rifa< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > roxi< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > siso< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > teic< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > tetr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > tica< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > tige< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > tobr< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > trim< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (),
< span class = 'kw' > trsu< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'kw' > vanc< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / span > (), < span class = 'no' > ...< / span > )
< span class = 'fu' > eucast_rules_file< / span > ()< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
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< th > x< / th >
< td > < p > data with antibiotic columns, like e.g. < code > amox< / code > and < code > amcl< / code > < / p > < / td >
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< / tr >
< tr >
< th > col_mo< / th >
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< td > < p > column name of the unique IDs of the microorganisms (see < code > < a href = 'as.mo.html' > mo< / a > < / code > ), defaults to the first column of class < code > mo< / code > . Values will be coerced using < code > < a href = 'as.mo.html' > as.mo< / a > < / code > .< / p > < / td >
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< / tr >
< tr >
< th > info< / th >
< td > < p > print progress< / p > < / td >
< / tr >
< tr >
< th > rules< / th >
< td > < p > a character vector that specifies which rules should be applied - one or more of < code > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c("breakpoints", "expert", "other", "all")< / a > < / code > < / p > < / td >
< / tr >
< tr >
< th > verbose< / th >
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< td > < p > a logical to indicate whether extensive info should be returned as a < code > data.frame< / code > with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative < code > data.frame< / code > with changes will be returned as output.< / p > < / td >
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< / tr >
< tr >
< th > amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc< / th >
< td > < p > column name of an antibiotic, see Antibiotics< / p > < / td >
< / tr >
< tr >
< th > ...< / th >
< td > < p > parameters that are passed on to < code > eucast_rules< / code > < / p > < / td >
< / tr >
< / table >
< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
< ul >
< li > < p > EUCAST Expert Rules. Version 2.0, 2012. < br / >
Leclercq et al. < strong > EUCAST expert rules in antimicrobial susceptibility testing.< / strong > < em > Clin Microbiol Infect.< / em > 2013;19(2):141-60. < br / >
< a href = 'https://doi.org/10.1111/j.1469-0691.2011.03703.x' > https://doi.org/10.1111/j.1469-0691.2011.03703.x< / a > < / p > < / li >
< li > < p > EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. < br / >
< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf< / a > < / p > < / li >
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< li > < p > EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. < br / >
< a href = 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx' > http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx< / a > < / p > < / li >
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< / ul >
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< p > For editing the reference file (which is available with < code > eucast_rules_file< / code > ), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: < code > "amcl, fluoroquinolones"< / code > . The mo_property can be any column name from the < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > data set, or < code > genus_species< / code > or < code > gramstain< / code > . This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).< / p >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
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< p > The input of < code > tbl_< / code > , possibly with edited values of antibiotics. Or, if < code > verbose = TRUE< / code > , a < code > data.frame< / code > with all original and new values of the affected bug-drug combinations.< / p >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > The file used for applying all EUCAST rules can be retrieved with < code > eucast_rules_file()< / code > . It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: < br / >
< code > AMR::EUCAST_RULES_FILE_LOCATION< / code > (without brackets).< / p >
< p > In the source code it is located under < a href = 'https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv' > < code > ./inst/eucast/eucast_rules.tsv< / code > < / a > .< / p >
< p > < strong > Note:< / strong > When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.< / p >
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< h2 class = "hasAnchor" id = "antibiotics" > < a class = "anchor" href = "#antibiotics" > < / a > Antibiotics< / h2 >
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< p > To define antibiotics column names, leave as it is to determine it automatically with < code > < a href = 'guess_ab_col.html' > guess_ab_col< / a > < / code > or input a text (case-insensitive) or use < code > NULL< / code > to skip a column (e.g. < code > tica = NULL< / code > ). Non-existing columns will anyway be skipped with a warning.< / p >
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< p > Abbrevations of the column containing antibiotics in the form: < strong > abbreviation< / strong > : generic name (< em > ATC code< / em > )< / p >
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< p > < strong > amcl< / strong > : amoxicillin+clavulanic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR02' > J01CR02< / a > ),
< strong > amik< / strong > : amikacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB06' > J01GB06< / a > ),
< strong > amox< / strong > : amoxicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA04' > J01CA04< / a > ),
< strong > ampi< / strong > : ampicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA01' > J01CA01< / a > ),
< strong > azit< / strong > : azithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA10' > J01FA10< / a > ),
< strong > azlo< / strong > : azlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA09' > J01CA09< / a > ),
< strong > aztr< / strong > : aztreonam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DF01' > J01DF01< / a > ),
< strong > cefa< / strong > : cefaloridine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB02' > J01DB02< / a > ),
< strong > cfep< / strong > : cefepime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DE01' > J01DE01< / a > ),
< strong > cfot< / strong > : cefotaxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD01' > J01DD01< / a > ),
< strong > cfox< / strong > : cefoxitin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC01' > J01DC01< / a > ),
< strong > cfra< / strong > : cefradine (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB09' > J01DB09< / a > ),
< strong > cfta< / strong > : ceftazidime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD02' > J01DD02< / a > ),
< strong > cftr< / strong > : ceftriaxone (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DD04' > J01DD04< / a > ),
< strong > cfur< / strong > : cefuroxime (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DC02' > J01DC02< / a > ),
< strong > chlo< / strong > : chloramphenicol (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01BA01' > J01BA01< / a > ),
< strong > cipr< / strong > : ciprofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA02' > J01MA02< / a > ),
< strong > clar< / strong > : clarithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA09' > J01FA09< / a > ),
< strong > clin< / strong > : clindamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF01' > J01FF01< / a > ),
< strong > clox< / strong > : flucloxacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CF05' > J01CF05< / a > ),
< strong > coli< / strong > : colistin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB01' > J01XB01< / a > ),
< strong > czol< / strong > : cefazolin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DB04' > J01DB04< / a > ),
< strong > dapt< / strong > : daptomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX09' > J01XX09< / a > ),
< strong > doxy< / strong > : doxycycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA02' > J01AA02< / a > ),
< strong > erta< / strong > : ertapenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH03' > J01DH03< / a > ),
< strong > eryt< / strong > : erythromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA01' > J01FA01< / a > ),
< strong > fosf< / strong > : fosfomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX01' > J01XX01< / a > ),
< strong > fusi< / strong > : fusidic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XC01' > J01XC01< / a > ),
< strong > gent< / strong > : gentamicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB03' > J01GB03< / a > ),
< strong > imip< / strong > : imipenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH51' > J01DH51< / a > ),
< strong > kana< / strong > : kanamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB04' > J01GB04< / a > ),
< strong > levo< / strong > : levofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA12' > J01MA12< / a > ),
< strong > linc< / strong > : lincomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FF02' > J01FF02< / a > ),
< strong > line< / strong > : linezolid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XX08' > J01XX08< / a > ),
< strong > mero< / strong > : meropenem (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01DH02' > J01DH02< / a > ),
< strong > mezl< / strong > : mezlocillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA10' > J01CA10< / a > ),
< strong > mino< / strong > : minocycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA08' > J01AA08< / a > ),
< strong > moxi< / strong > : moxifloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA14' > J01MA14< / a > ),
< strong > nali< / strong > : nalidixic acid (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MB02' > J01MB02< / a > ),
< strong > neom< / strong > : neomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB05' > J01GB05< / a > ),
< strong > neti< / strong > : netilmicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB07' > J01GB07< / a > ),
< strong > nitr< / strong > : nitrofurantoin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XE01' > J01XE01< / a > ),
< strong > norf< / strong > : norfloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA06' > J01MA06< / a > ),
< strong > novo< / strong > : novobiocin (an ATCvet code: < a href = 'https://www.whocc.no/atc_ddd_index/?code=QJ01XX95' > QJ01XX95< / a > ),
< strong > oflo< / strong > : ofloxacin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01MA01' > J01MA01< / a > ),
< strong > peni< / strong > : (benzyl)penicillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CE01' > J01CE01< / a > ),
< strong > pipe< / strong > : piperacillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA12' > J01CA12< / a > ),
< strong > pita< / strong > : piperacillin+tazobactam (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CR05' > J01CR05< / a > ),
< strong > poly< / strong > : polymyxin B (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XB02' > J01XB02< / a > ),
< strong > pris< / strong > : pristinamycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG01' > J01FG01< / a > ),
< strong > qida< / strong > : quinupristin/dalfopristin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FG02' > J01FG02< / a > ),
< strong > rifa< / strong > : rifampicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J04AB02' > J04AB02< / a > ),
< strong > roxi< / strong > : roxithromycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01FA06' > J01FA06< / a > ),
< strong > siso< / strong > : sisomicin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB08' > J01GB08< / a > ),
< strong > teic< / strong > : teicoplanin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA02' > J01XA02< / a > ),
< strong > tetr< / strong > : tetracycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA07' > J01AA07< / a > ),
< strong > tica< / strong > : ticarcillin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01CA13' > J01CA13< / a > ),
< strong > tige< / strong > : tigecycline (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01AA12' > J01AA12< / a > ),
< strong > tobr< / strong > : tobramycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01GB01' > J01GB01< / a > ),
< strong > trim< / strong > : trimethoprim (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EA01' > J01EA01< / a > ),
< strong > trsu< / strong > : sulfamethoxazole and trimethoprim (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01EE01' > J01EE01< / a > ),
< strong > vanc< / strong > : vancomycin (< a href = 'https://www.whocc.no/atc_ddd_index/?code=J01XA01' > J01XA01< / a > ).< / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
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< p > On our website < a href = 'https://msberends.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'co' > # NOT RUN {< / span >
< span class = 'no' > a< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > septic_patients< / span > )
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< span class = 'no' > a< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/data.frame' > data.frame< / a > < / span > (< span class = 'kw' > mo< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'https://www.rdocumentation.org/packages/base/topics/c' > c< / a > < / span > (< span class = 'st' > "Staphylococcus aureus"< / span > ,
< span class = 'st' > "Enterococcus faecalis"< / span > ,
< span class = 'st' > "Escherichia coli"< / span > ,
< span class = 'st' > "Klebsiella pneumoniae"< / span > ,
< span class = 'st' > "Pseudomonas aeruginosa"< / span > ),
< span class = 'kw' > vanc< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Vancomycin< / span >
< span class = 'kw' > amox< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Amoxicillin< / span >
< span class = 'kw' > coli< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Colistin< / span >
< span class = 'kw' > cfta< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Ceftazidime< / span >
< span class = 'kw' > cfur< / span > < span class = 'kw' > =< / span > < span class = 'st' > "-"< / span > , < span class = 'co' > # Cefuroxime< / span >
< span class = 'kw' > peni< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > , < span class = 'co' > # Benzylpenicillin< / span >
< span class = 'kw' > cfox< / span > < span class = 'kw' > =< / span > < span class = 'st' > "S"< / span > , < span class = 'co' > # Cefoxitin< / span >
< span class = 'kw' > stringsAsFactors< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > )
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< span class = 'no' > a< / span >
< span class = 'co' > # mo vanc amox coli cfta cfur peni cfox< / span >
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< span class = 'co' > # 1 Staphylococcus aureus - - - - - S S< / span >
< span class = 'co' > # 2 Enterococcus faecalis - - - - - S S< / span >
< span class = 'co' > # 3 Escherichia coli - - - - - S S< / span >
< span class = 'co' > # 4 Klebsiella pneumoniae - - - - - S S< / span >
< span class = 'co' > # 5 Pseudomonas aeruginosa - - - - - S S< / span >
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< span class = 'co' > # apply EUCAST rules: 18 results are forced as R or S< / span >
< span class = 'no' > b< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > a< / span > )
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< span class = 'no' > b< / span >
< span class = 'co' > # mo vanc amox coli cfta cfur peni cfox< / span >
< span class = 'co' > # 1 Staphylococcus aureus - S R R S S S< / span >
< span class = 'co' > # 2 Enterococcus faecalis - - R R R S R< / span >
< span class = 'co' > # 3 Escherichia coli R - - - - R S< / span >
< span class = 'co' > # 4 Klebsiella pneumoniae R R - - - R S< / span >
< span class = 'co' > # 5 Pseudomonas aeruginosa R R - - R R R< / span >
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< span class = 'co' > # do not apply EUCAST rules, but rather get a a data.frame< / span >
< span class = 'co' > # with 18 rows, containing all details about the transformations:< / span >
< span class = 'no' > c< / span > < span class = 'kw' > < -< / span > < span class = 'fu' > eucast_rules< / span > (< span class = 'no' > a< / span > , < span class = 'kw' > verbose< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > )
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< span class = 'co' > # }< / span > < / pre >
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