antimicrobials: Data Sets with 617 Antimicrobial Drugs

In AMR: Antimicrobial Resistance Data Analysis

Data Sets with 617 Antimicrobial Drugs

Description

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 497 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
  A short and concise group name, based on WHONET and WHOCC definitions

• atc
  ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02 (last updated May 4th, 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 May 4th, 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 497 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/reg_hum_atc.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/.

Source

• 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 May 4th, 2025.

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

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

See Also

microorganisms, intrinsic_resistant

Examples

antimicrobials
antivirals

AMR documentation built on June 8, 2025, 10:17 a.m.