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 = "amcl", amik = "amik", amox = "amox", ampi = "ampi", azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa", cfep = "cfep", cfot = "cfot", cfox = "cfox", cfra = "cfra", cfta = "cfta", cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr", clar = "clar", clin = "clin", clox = "clox", coli = "coli", czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta", eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent", imip = "imip", kana = "kana", levo = "levo", linc = "linc", line = "line", mero = "mero", mezl = "mezl", mino = "mino", moxi = "moxi", nali = "nali", neom = "neom", neti = "neti", nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo", oxac = "oxac", peni = "peni", pipe = "pipe", pita = "pita", poly = "poly", pris = "pris", qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic", tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc") 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 8.1, 2018.
http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx
The input of tbl, possibly with edited values of antibiotics. Or, if verbose = TRUE, a data.frame with verbose info.
To define antibiotics column names, 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: penicillin (J01RA01), 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).
a <- eucast_rules(septic_patients)#>#> Warning: These columns do not exist and will be ignored: azlo, aztr, cefa, cfra, clar, dapt, erta, fusi, levo, linc, mezl, mino, nali, neom, neti, novo, norf, oflo, pipe, poly, pris, qida, roxi, siso, tica. #> THIS MAY STRONGLY INFLUENCE THE OUTCOME.#> #> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) #> #> EUCAST Clinical Breakpoints (v8.1, 2018) #> Enterobacteriales (Order) (no changes) #> Staphylococcus (no changes) #> Enterococcus (no changes) #> Streptococcus groups A, B, C, G (no changes) #> Streptococcus pneumoniae (no changes) #> Viridans group streptococci (no changes) #> Haemophilus influenzae (no changes) #> Moraxella catarrhalis (no changes) #> Anaerobic Gram positives (no changes) #> Anaerobic Gram negatives (no changes) #> Pasteurella multocida (no changes) #> Campylobacter jejuni and C. coli (no changes) #> Aerococcus sanguinicola and A. urinae (no changes) #> Kingella kingae (no changes) #> #> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016) #> Table 1: Intrinsic resistance in Enterobacteriaceae (no changes) #> Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes) #> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes) #> Table 4: Intrinsic resistance in Gram-positive bacteria (no changes) #> Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes) #> Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes) #> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes) #> Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes) #> Table 12: Interpretive rules for aminoglycosides (no changes) #> Table 13: Interpretive rules for quinolones (no changes) #> #> Other rules #> Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes) #> Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes) #> Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes) #> Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes) #> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes) #> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes) #> #> => EUCAST rules affected 1,980 out of 2,000 rows -> changed 0 test results. #> #>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# 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 b <- eucast_rules(a, "mo") # 18 results are forced as R or S#> Warning: These columns do not exist and will be ignored: amcl, amik, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot, cftr, chlo, cipr, clar, clin, clox, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, oxac, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu. #> THIS MAY STRONGLY INFLUENCE THE OUTCOME.#> #> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)#> NOTE: Using column `amox` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.#> #> EUCAST Clinical Breakpoints (v8.1, 2018) #> Enterobacteriales (Order) (no changes) #> Staphylococcus (2 changes) #> Enterococcus (no changes) #> Streptococcus groups A, B, C, G (no changes) #> Streptococcus pneumoniae (no changes) #> Viridans group streptococci (no changes) #> Haemophilus influenzae (no changes) #> Moraxella catarrhalis (no changes) #> Anaerobic Gram positives (no changes) #> Anaerobic Gram negatives (no changes) #> Pasteurella multocida (no changes) #> Campylobacter jejuni and C. coli (no changes) #> Aerococcus sanguinicola and A. urinae (no changes) #> Kingella kingae (no changes) #> #> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016) #> Table 1: Intrinsic resistance in Enterobacteriaceae (5 changes) #> Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (5 changes) #> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes) #> Table 4: Intrinsic resistance in Gram-positive bacteria (6 changes) #> Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes) #> Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes) #> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes) #> Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes) #> Table 12: Interpretive rules for aminoglycosides (no changes) #> Table 13: Interpretive rules for quinolones (no changes) #> #> Other rules #> Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes) #> Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes) #> Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes) #> Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes) #> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes) #> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes) #> #> => EUCAST rules affected 5 out of 5 rows -> changed 18 test results. #> #>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# 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