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.

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(...)

Arguments

tbl

table with antibiotic columns, like e.g. amox and amcl

col_mo

column name of the unique IDs of the microorganisms (see mo), defaults to the first column of class mo. Values will be coerced using as.mo.

info

print progress

rules

a character vector that specifies which rules should be applied - one or more of c("breakpoints", "expert", "other", "all")

verbose

a logical to indicate whether extensive info should be returned as a data.frame with info about which rows and columns are effected

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_rules

Source

Value

The input of tbl, possibly with edited values of antibiotics. Or, if verbose = TRUE, a data.frame with verbose info.

Antibiotics

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).

Examples

a <- eucast_rules(septic_patients)
#> NOTE: Using column `mo` as input for `col_mo`.
#> 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) #> #> 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