Data set with ~450 antibiotics

A data set containing all antibiotics. Use as.ab or one of the ab_property functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic 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.

antibiotics

Format

A data.frame with 455 observations and 13 variables:

ab

Antibiotic ID as used in this package (like AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available

atc

ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02

cid

Compound ID as found in PubChem

name

Official name as used by WHONET/EARS-Net or the WHO

group

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

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 antibiotic susceptibility testing (AST)

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 ddd_units

iv_ddd

Defined Daily Dose (DDD), parenteral treatment

iv_units

Units of iv_ddd

Source

World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): https://www.whocc.no/atc_ddd_index/

WHONET 2019 software: http://www.whonet.org/software.html

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

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

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

WHOCC

This package contains all ~500 antimicrobial 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://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (http://ec.europa.eu/health/documents/community-register/html/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.

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.

See also

microorganisms