Get and Compare Antimicrobial Wild Type Distributions from EUCAST

These functions allow retrieval of antimicrobial wild type distributions, live from eucast.org.

Usage

get_eucast_amr_distribution(
  ab,
  mo = NULL,
  method = "MIC",
  as_freq_table = TRUE
)

get_eucast_mic_distribution(ab, mo = NULL, as_freq_table = TRUE)

get_eucast_disk_distribution(ab, mo = NULL, as_freq_table = TRUE)

compare_mic_with_eucast(mics, ab, mo = NULL)

compare_disk_with_eucast(disks, ab, mo = NULL)

Arguments

ab

antimicrobial, can be anything understood by ab_name()

mo

microorganism, can be anything understood by mo_name() (can be left blank)

method

either "MIC" or "disk"/"diff"

as_freq_table

either TRUE (default) or FALSE, to return result as frequency table

mics

MIC values, will be coerced with as.mic()

disks

Disk diffusion values, will be coerced with as.disk()

Details

The compare_*_with_eucast() functions allow to compare a user range with EUCAST distributions. Use ggplot2::autoplot() on the output to visualise the results.

Supported Antimicrobials

In December 2024, EUCAST had 176 distributions available, namely for these antimicrobials:

Amikacin, amoxicillin, amoxicillin/clavulanic acid, amphotericin B, ampicillin, ampicillin/sulbactam, anidulafungin, apramycin, aspoxicillin, avilamycin, azithromycin, aztreonam, aztreonam/avibactam, bacitracin, bedaquiline, benzylpenicillin, capreomycin, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefazolin, cefdinir, cefepime, cefepime/tazobactam, cefepime/zidebactam, cefiderocol, cefixime, cefoperazone, cefoperazone/sulbactam, cefoselis, cefotaxime, cefotetan, cefovecin, cefoxitin, cefpirome, cefpodoxime, cefpodoxime/clavulanic acid, cefquinome, ceftaroline, ceftazidime, ceftazidime/avibactam, ceftibuten, ceftiofur, ceftobiprole, ceftolozane/tazobactam, ceftriaxone, cefuroxime, cephradine, chloramphenicol, chlortetracycline, ciprofloxacin, clarithromycin, clavulanic acid, clinafloxacin, clindamycin, clofazimine, cloxacillin, colistin, cycloserine, dalbavancin, danofloxacin, daptomycin, delafloxacin, delamanid, dicloxacillin, difloxacin, doripenem, doxycycline, enrofloxacin, eravacycline, ertapenem, erythromycin, ethambutol, ethionamide, faropenem, fidaxomicin, florfenicol, flucloxacillin, fluconazole, flucytosine, flumequine, fosfomycin, fusidic acid, gamithromycin, gatifloxacin, gemifloxacin, gentamicin, imipenem, imipenem/relebactam, isavuconazole, isoniazid, itraconazole, kanamycin, ketoconazole, lefamulin, levofloxacin, lincomycin, linezolid, loracarbef, marbofloxacin, mecillinam, meropenem, meropenem/vaborbactam, metronidazole, micafungin, minocycline, moxifloxacin, mupirocin, nalidixic acid, narasin, neomycin, netilmicin, nitrofurantoin, nitroxoline, norfloxacin, norvancomycin, ofloxacin, omadacycline, orbifloxacin, oritavancin, oxacillin, oxolinic acid, oxytetracycline, pefloxacin, phenoxymethylpenicillin, piperacillin, piperacillin/tazobactam, pirlimycin, posaconazole, pradofloxacin, pristinamycin, pyrazinamide, quinupristin/dalfopristin, retapamulin, rezafungin, rifabutin, rifampicin, roxithromycin, secnidazole, sitafloxacin, spectinomycin, spiramycin, streptomycin, sulbactam, sulfadiazine, sulfamethoxazole, sulfisoxazole, tedizolid, teicoplanin, telavancin, telithromycin, temocillin, terbinafine, tetracycline, thiamphenicol, tiamulin, ticarcillin, ticarcillin/clavulanic acid, tigecycline, tildipirosin, tilmicosin, tobramycin, trimethoprim, trimethoprim/sulfamethoxazole, tulathromycin, tylosin, tylvalosin, vancomycin, viomycin, and voriconazole.

For the current list, run eucast_supported_ab_distributions().

Examples

if (FALSE) { # \dontrun{
get_eucast_mic_distribution("cipro")

# not returning as frequency table
get_eucast_mic_distribution("cipro", as_freq_table = FALSE)

# specify microorganism to only get results for that pathogen
get_eucast_mic_distribution("cipro", "K. pneumoniae")

get_eucast_disk_distribution("cipro", "K. pneumoniae")


# Plotting ----------------------------------------------------------------

mic_data <- get_eucast_mic_distribution("cipro", "K. pneumoniae")
mics <- rep(mic_data$mic, mic_data$count)
ggplot2::autoplot(mics, ab = "cipro", mo = "K. pneumoniae", title = "Look at my MICs!")


# Comparing With User Values ----------------------------------------------

my_mic_values <- AMR::random_mic(500)
comparison <- compare_mic_with_eucast(my_mic_values, ab = "cipro", mo = "K. pneumoniae")
comparison
ggplot2::autoplot(comparison)
} # }