Apply EUCAST rules

Source: R/eucast_rules.R

Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.

To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.

eucast_rules(
  x,
  col_mo = NULL,
  info = interactive(),
  rules = getOption("AMR.eucast_rules", default = c("breakpoints", "expert")),
  verbose = FALSE,
  ...
)

Arguments

x

data with antibiotic columns, like e.g. AMX and AMC
col_mo

column name of the IDs of the microorganisms (see as.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. Must be one or more of "breakpoints", "expert", "other", "all", and defaults to c("breakpoints", "expert"). The default value can be set to another value using e.g. options(AMR.eucast_rules = "all").
verbose

a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.
...

column name of an antibiotic, please see section Antibiotics below

Source

Value

The input of x, 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.

Details

Note: This function does not translate MIC values to RSI values. Use as.rsi() for that.
Note: When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, 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.

Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:

  • Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;

  • Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;

  • Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;

  • Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;

  • Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;

  • Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;

  • Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;

  • Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.

These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use eucast_rules(..., rules = "all"), or set the default behaviour of the [eucast_rules()] function with options(AMR.eucast_rules = "all") (or any other valid input value(s) to the rules parameter).

The file containing all EUCAST rules is located here: https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv.

Antibiotics

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. TIC = NULL to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.

The following antibiotics are used for the functions eucast_rules() and mdro(). These are shown below in the format 'antimicrobial ID: name (ATC code)', sorted by name:

AMK: amikacin (J01GB06), AMX: amoxicillin (J01CA04), AMC: amoxicillin/clavulanic acid (J01CR02), AMP: ampicillin (J01CA01), SAM: ampicillin/sulbactam (J01CR01), AZM: azithromycin (J01FA10), AZL: azlocillin (J01CA09), ATM: aztreonam (J01DF01), CAP: capreomycin (J04AB30), RID: cefaloridine (J01DB02), CZO: cefazolin (J01DB04), FEP: cefepime (J01DE01), CTX: cefotaxime (J01DD01), CTT: cefotetan (J01DC05), FOX: cefoxitin (J01DC01), CPT: ceftaroline (J01DI02), CAZ: ceftazidime (J01DD02), CRO: ceftriaxone (J01DD04), CXM: cefuroxime (J01DC02), CED: cephradine (J01DB09), CHL: chloramphenicol (J01BA01), CIP: ciprofloxacin (J01MA02), CLR: clarithromycin (J01FA09), CLI: clindamycin (J01FF01), COL: colistin (J01XB01), DAP: daptomycin (J01XX09), DOR: doripenem (J01DH04), DOX: doxycycline (J01AA02), ETP: ertapenem (J01DH03), ERY: erythromycin (J01FA01), ETH: ethambutol (J04AK02), FLC: flucloxacillin (J01CF05), FOS: fosfomycin (J01XX01), FUS: fusidic acid (J01XC01), GAT: gatifloxacin (J01MA16), GEN: gentamicin (J01GB03), GEH: gentamicin-high (no ATC code), IPM: imipenem (J01DH51), INH: isoniazid (J04AC01), KAN: kanamycin (J01GB04), LVX: levofloxacin (J01MA12), LIN: lincomycin (J01FF02), LNZ: linezolid (J01XX08), MEM: meropenem (J01DH02), MTR: metronidazole (J01XD01), MEZ: mezlocillin (J01CA10), MNO: minocycline (J01AA08), MFX: moxifloxacin (J01MA14), NAL: nalidixic acid (J01MB02), NEO: neomycin (J01GB05), NET: netilmicin (J01GB07), NIT: nitrofurantoin (J01XE01), NOR: norfloxacin (J01MA06), NOV: novobiocin (QJ01XX95), OFX: ofloxacin (J01MA01), OXA: oxacillin (J01CF04), PEN: penicillin G (J01CE01), PIP: piperacillin (J01CA12), TZP: piperacillin/tazobactam (J01CR05), PLB: polymyxin B (J01XB02), PRI: pristinamycin (J01FG01), PZA: pyrazinamide (J04AK01), QDA: quinupristin/dalfopristin (J01FG02), RIB: rifabutin (J04AB04), RIF: rifampicin (J04AB02), RFP: rifapentine (J04AB05), RXT: roxithromycin (J01FA06), SIS: sisomicin (J01GB08), STH: streptomycin-high (no ATC code), TEC: teicoplanin (J01XA02), TLV: telavancin (J01XA03), TCY: tetracycline (J01AA07), TIC: ticarcillin (J01CA13), TCC: ticarcillin/clavulanic acid (J01CR03), TGC: tigecycline (J01AA12), TOB: tobramycin (J01GB01), TMP: trimethoprim (J01EA01), SXT: trimethoprim/sulfamethoxazole (J01EE01), VAN: vancomycin (J01XA01).

Maturing lifecycle


The lifecycle of this function is maturing. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.

Read more on our website!

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.

Examples

# \donttest{
a <- data.frame(mo = c("Staphylococcus aureus",
                       "Enterococcus faecalis",
                       "Escherichia coli",
                       "Klebsiella pneumoniae",
                       "Pseudomonas aeruginosa"),
                VAN = "-",       # Vancomycin
                AMX = "-",       # Amoxicillin
                COL = "-",       # Colistin
                CAZ = "-",       # Ceftazidime
                CXM = "-",       # Cefuroxime
                PEN = "S",       # Penicillin G
                FOX = "S",       # Cefoxitin
                stringsAsFactors = FALSE)

a
#                       mo  VAN  AMX  COL  CAZ  CXM  PEN  FOX
# 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  VAN  AMX  COL  CAZ  CXM  PEN  FOX
# 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 data.frame
# with 18 rows, containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE)
# }