Skip to contents

# Data Sets with 625 Antimicrobial Drugs

Source: `R/data.R`
`antimicrobials.Rd`

Two data sets containing all antimicrobials and antivirals. Use `as.ab()` or one of the `ab_*` functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.

The `antibiotics` data set has been renamed to `antimicrobials`. The old name will be removed in a future version.

## Usage

    antimicrobials

    antibiotics

    antivirals

## Format

### For the antimicrobials data set: a tibble with 505 observations and 14 variables:

- `ab`
  antimicrobial ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. This is a unique identifier.

- `cid`
  Compound ID as found in PubChem. This is a unique identifier.

- `name`
  Official name as used by WHONET/EARS-Net or the WHO. This is a unique identifier.

- `group`
  One or more short and concise group names, based on WHONET and WHOCC definitions

- `atc`
  ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02` (last updated 4th of May, 2025):

- `atc_group1`
  Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`

- `atc_group2`
  Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`

- `abbr`
  List of abbreviations as used in many countries, also for antimicrobial susceptibility testing (AST)

- `synonyms`
  Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID

ATC properties (last updated 4th of May, 2025):

- `oral_ddd`
  Defined Daily Dose (DDD), oral treatment, currently available for 180 drugs

- `oral_units`
  Units of `oral_ddd`

- `iv_ddd`
  Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 153 drugs

- `iv_units`
  Units of `iv_ddd`

LOINC:

- `loinc`
  All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use `ab_loinc()` to retrieve them quickly, see `ab_property()`.

### For the antivirals data set: a tibble with 120 observations and 11 variables:

- `av`
  Antiviral ID as used in this package (such as `ACI`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. This is a unique identifier. Combinations are codes that contain a `+` to indicate this, such as `ATA+COBI` for atazanavir/cobicistat.

- `name`
  Official name as used by WHONET/EARS-Net or the WHO. This is a unique identifier.

- `atc`
  ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, see Details

- `cid`
  Compound ID as found in PubChem. This is a unique identifier.

- `atc_group`
  Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC

- `synonyms`
  Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID

- `oral_ddd`
  Defined Daily Dose (DDD), oral treatment

- `oral_units`
  Units of `oral_ddd`

- `iv_ddd`
  Defined Daily Dose (DDD), parenteral treatment

- `iv_units`
  Units of `iv_ddd`

- `loinc`
  All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use `av_loinc()` to retrieve them quickly, see `av_property()`.

An object of class `deprecated_amr_dataset` (inherits from `tbl_df`, `tbl`, `data.frame`) with 505 rows and 14 columns.

An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with 120 rows and 11 columns.

## Details

Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`. Do note that ATC codes are not unique. For example, J01CR02 is officially the ATC code for "amoxicillin and beta-lactamase inhibitor". Consequently, these two items from the antimicrobials data set both return `"J01CR02"`:

    ab_atc("amoxicillin/clavulanic acid")
    ab_atc("amoxicillin/sulbactam")

Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and are consequently only available where a CID is available.

## Download Our Reference Data

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit our website for direct download links, or explore the actual files in our GitHub repository.

## WHOCC

This package contains all ~550 antibiotic, antimycotic and antiviral drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://atcddd.fhi.no) and the Pharmaceuticals Community Register of the European Commission (https://ec.europa.eu/health/documents/community-register/html/index_en.htm).

These have become the gold standard for international drug utilisation monitoring and research.

The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.

NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://atcddd.fhi.no/copyright_disclaimer/.

## References

- WHO Collaborating Centre for Drug Statistics Methodology, Guidelines for ATC classification and DDD assignment, Oslo Accessed from https://atcddd.fhi.no/atc_ddd_index/ on 4th of May, 2025.

- Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from https://loinc.org on 19th of October, 2023.

- European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/index_en.htm

## See also

microorganisms, intrinsic_resistant

## Examples

    antimicrobials
    #> # A tibble: 505 × 14
    #>    ab        cid name   group atc   atc_group1 atc_group2 abbreviations synonyms
    #>    <ab>    <dbl> <chr>  <lis> <lis> <chr>      <chr>      <list>        <list>
    #>  1 AMA      4649 4-ami… <chr> <chr> Drugs for… Aminosali… <chr [1]>     <chr>
    #>  2 ACM   6450012 Acety… <chr> <chr> NA         NA         <chr [1]>     <chr>
    #>  3 ASP  49787020 Acety… <chr> <chr> NA         NA         <chr [1]>     <chr>
    #>  4 ALS      8954 Aldes… <chr> <chr> Drugs for… Drugs for… <chr [1]>     <chr>
    #>  5 AMK     37768 Amika… <chr> <chr> Aminoglyc… Other ami… <chr [6]>     <chr>
    #>  6 AKF        NA Amika… <chr> <chr> NA         NA         <chr [1]>     <chr>
    #>  7 AMO     54260 Amoro… <chr> <chr> Antifunga… Other ant… <chr [1]>     <chr>
    #>  8 AMX     33613 Amoxi… <chr> <chr> Beta-lact… Penicilli… <chr [4]>     <chr>
    #>  9 AMC  23665637 Amoxi… <chr> <chr> Beta-lact… Combinati… <chr [6]>     <chr>
    #> 10 AXS    465441 Amoxi… <chr> <chr> NA         NA         <chr [1]>     <chr>
    #> # ℹ 495 more rows
    #> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,
    #> #   iv_units <chr>, loinc <list>
    antivirals
    #> # A tibble: 120 × 11
    #>    av       name      atc      cid atc_group synonyms oral_ddd oral_units iv_ddd
    #>    <av>     <chr>     <chr>  <dbl> <chr>     <list>      <dbl> <chr>       <dbl>
    #>  1 ABA      Abacavir  J05A… 4.41e5 Nucleosi… <chr>         0.6 g              NA
    #>  2 ACI      Aciclovir J05A… 1.35e8 Nucleosi… <chr>         4   g               4
    #>  3 ADD      Adefovir… J05A… 6.09e4 Nucleosi… <chr>        10   mg             NA
    #>  4 AME      Amenamev… J05A… 1.14e7 Other an… <chr>         0.4 g              NA
    #>  5 AMP      Amprenav… J05A… 6.50e4 Protease… <chr>         1.2 g              NA
    #>  6 ASU      Asunapre… J05A… 1.61e7 Antivira… <chr>         0.2 g              NA
    #>  7 ATA      Atazanav… J05A… 1.48e5 Protease… <chr>         0.3 g              NA
    #>  8 ATA+COBI Atazanav… J05A… 8.66e7 Antivira… <chr>        NA   NA             NA
    #>  9 ATA+RIT  Atazanav… J05A… 2.51e7 Antivira… <chr>         0.3 g              NA
    #> 10 BAM      Baloxavi… J05A… 1.24e8 Other an… <chr>        40   mg             NA
    #> # ℹ 110 more rows
    #> # ℹ 2 more variables: iv_units <chr>, loinc <list>