eucast_rules.RdApply 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.
eucast_rules(tbl, col_mo = NULL, info = TRUE, rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE, amcl = guess_ab_col(), amik = guess_ab_col(), amox = guess_ab_col(), ampi = guess_ab_col(), azit = guess_ab_col(), azlo = guess_ab_col(), aztr = guess_ab_col(), cefa = guess_ab_col(), cfep = guess_ab_col(), cfot = guess_ab_col(), cfox = guess_ab_col(), cfra = guess_ab_col(), cfta = guess_ab_col(), cftr = guess_ab_col(), cfur = guess_ab_col(), chlo = guess_ab_col(), cipr = guess_ab_col(), clar = guess_ab_col(), clin = guess_ab_col(), clox = guess_ab_col(), coli = guess_ab_col(), czol = guess_ab_col(), dapt = guess_ab_col(), doxy = guess_ab_col(), erta = guess_ab_col(), eryt = guess_ab_col(), fosf = guess_ab_col(), fusi = guess_ab_col(), gent = guess_ab_col(), imip = guess_ab_col(), kana = guess_ab_col(), levo = guess_ab_col(), linc = guess_ab_col(), line = guess_ab_col(), mero = guess_ab_col(), mezl = guess_ab_col(), mino = guess_ab_col(), moxi = guess_ab_col(), nali = guess_ab_col(), neom = guess_ab_col(), neti = guess_ab_col(), nitr = guess_ab_col(), norf = guess_ab_col(), novo = guess_ab_col(), oflo = guess_ab_col(), oxac = guess_ab_col(), peni = guess_ab_col(), pipe = guess_ab_col(), pita = guess_ab_col(), poly = guess_ab_col(), pris = guess_ab_col(), qida = guess_ab_col(), rifa = guess_ab_col(), roxi = guess_ab_col(), siso = guess_ab_col(), teic = guess_ab_col(), tetr = guess_ab_col(), tica = guess_ab_col(), tige = guess_ab_col(), tobr = guess_ab_col(), trim = guess_ab_col(), trsu = guess_ab_col(), vanc = guess_ab_col()) EUCAST_rules(...) interpretive_reading(...)
| tbl | table with antibiotic columns, like e.g. |
|---|---|
| col_mo | column name of the unique IDs of the microorganisms (see |
| info | print progress |
| rules | a character vector that specifies which rules should be applied - one or more of |
| verbose | a logical to indicate whether extensive info should be returned as a |
| 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 | column name of an antibiotic, see Antibiotics |
| ... | parameters that are passed on to |
EUCAST Expert Rules. Version 2.0, 2012.
Leclercq et al. EUCAST expert rules in antimicrobial susceptibility testing. Clin Microbiol Infect. 2013;19(2):141-60.
https://doi.org/10.1111/j.1469-0691.2011.03703.x
EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016.
http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf
EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019.
http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx
The input of tbl, possibly with edited values of antibiotics. Or, if verbose = TRUE, a data.frame with all original and new values of the affected bug-drug combinations.
To define antibiotics column names, leave as it is to determine it automatically with guess_ab_col or input a text (case-insensitive) or use NULL to skip a column (e.g. tica = NULL). Non-existing columns will anyway be skipped with a warning.
Abbrevations of the column containing antibiotics in the form: abbreviation: generic name (ATC code)
amcl: amoxicillin+clavulanic acid (J01CR02), amik: amikacin (J01GB06), amox: amoxicillin (J01CA04), ampi: ampicillin (J01CA01), azit: azithromycin (J01FA10), azlo: azlocillin (J01CA09), aztr: aztreonam (J01DF01), cefa: cefaloridine (J01DB02), cfep: cefepime (J01DE01), cfot: cefotaxime (J01DD01), cfox: cefoxitin (J01DC01), cfra: cefradine (J01DB09), cfta: ceftazidime (J01DD02), cftr: ceftriaxone (J01DD04), cfur: cefuroxime (J01DC02), chlo: chloramphenicol (J01BA01), cipr: ciprofloxacin (J01MA02), clar: clarithromycin (J01FA09), clin: clindamycin (J01FF01), clox: flucloxacillin (J01CF05), coli: colistin (J01XB01), czol: cefazolin (J01DB04), dapt: daptomycin (J01XX09), doxy: doxycycline (J01AA02), erta: ertapenem (J01DH03), eryt: erythromycin (J01FA01), fosf: fosfomycin (J01XX01), fusi: fusidic acid (J01XC01), gent: gentamicin (J01GB03), imip: imipenem (J01DH51), kana: kanamycin (J01GB04), levo: levofloxacin (J01MA12), linc: lincomycin (J01FF02), line: linezolid (J01XX08), mero: meropenem (J01DH02), mezl: mezlocillin (J01CA10), mino: minocycline (J01AA08), moxi: moxifloxacin (J01MA14), nali: nalidixic acid (J01MB02), neom: neomycin (J01GB05), neti: netilmicin (J01GB07), nitr: nitrofurantoin (J01XE01), norf: norfloxacin (J01MA06), novo: novobiocin (an ATCvet code: QJ01XX95), oflo: ofloxacin (J01MA01), peni: (benzyl)penicillin (J01CE01), pipe: piperacillin (J01CA12), pita: piperacillin+tazobactam (J01CR05), poly: polymyxin B (J01XB02), pris: pristinamycin (J01FG01), qida: quinupristin/dalfopristin (J01FG02), rifa: rifampicin (J04AB02), roxi: roxithromycin (J01FA06), siso: sisomicin (J01GB08), teic: teicoplanin (J01XA02), tetr: tetracycline (J01AA07), tica: ticarcillin (J01CA13), tige: tigecycline (J01AA12), tobr: tobramycin (J01GB01), trim: trimethoprim (J01EA01), trsu: sulfamethoxazole and trimethoprim (J01EE01), vanc: vancomycin (J01XA01).
On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.
# NOT RUN { a <- eucast_rules(septic_patients) a <- data.frame(mo = c("Staphylococcus aureus", "Enterococcus faecalis", "Escherichia coli", "Klebsiella pneumoniae", "Pseudomonas aeruginosa"), vanc = "-", # Vancomycin amox = "-", # Amoxicillin coli = "-", # Colistin cfta = "-", # Ceftazidime cfur = "-", # Cefuroxime peni = "S", # Benzylpenicillin cfox = "S", # Cefoxitin stringsAsFactors = FALSE) a # mo vanc amox coli cfta cfur peni cfox # 1 Staphylococcus aureus - - - - - S S # 2 Enterococcus faecalis - - - - - S S # 3 Escherichia coli - - - - - S S # 4 Klebsiella pneumoniae - - - - - S S # 5 Pseudomonas aeruginosa - - - - - S S # apply EUCAST rules: 18 results are forced as R or S b <- eucast_rules(a) b # mo vanc amox coli cfta cfur peni cfox # 1 Staphylococcus aureus - S R R S S S # 2 Enterococcus faecalis - - R R R S R # 3 Escherichia coli R - - - - R S # 4 Klebsiella pneumoniae R R - - - R S # 5 Pseudomonas aeruginosa R R - - R R R # do not apply EUCAST rules, but rather get a a data.frame # with 18 rows, containing all details about the transformations: c <- eucast_rules(a, verbose = TRUE) # }