All reference data (about microorganisms, antibiotics, R/SI
interpretation, EUCAST rules, etc.) in this AMR package are
reliable, up-to-date and freely available. We continually export our
data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also
supply tab separated files that are machine-readable and suitable for
input in any software program, such as laboratory information
systems.
On this page, we explain how to download them and how the structure of the data sets look like.
If you are reading this page from within R, please visit our website, which is automatically updated with every code change.
A data set with 70,760 rows and 16 columns, containing the following
column names:
mo, fullname, kingdom, phylum,
class, order, family, genus,
species, subspecies, rank, ref,
species_id, source, prevalence and
snomed.
This data set is in R available as microorganisms, after
you load the AMR package.
It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set here.
Direct download links:
NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub. Advice? Use R instead.
Our full taxonomy of microorganisms is based on the authoritative and comprehensive:
Included (sub)species per taxonomic kingdom:
| Kingdom | Number of (sub)species |
|---|---|
| (unknown kingdom) | 1 |
| Animalia | 2,153 |
| Archaea | 694 |
| Bacteria | 22,852 |
| Chromista | 32,167 |
| Fungi | 9,582 |
Example rows when filtering on genus Escherichia:
| mo | fullname | kingdom | phylum | class | order | family | genus | species | subspecies | rank | ref | species_id | source | prevalence | snomed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B_ESCHR | Escherichia | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | genus | 515602 | LPSN | 1 | 64735005 | |||
| B_ESCHR_ALBR | Escherichia albertii | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | albertii | species | Huys et al., 2003 | 776053 | LPSN | 1 | 419388003 | |
| B_ESCHR_COLI | Escherichia coli | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | species | Castellani et al., 1919 | 776057 | LPSN | 1 | 1095001000112106, 715307006, 737528008, … | |
| B_ESCHR_FRGS | Escherichia fergusonii | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | fergusonii | species | Farmer et al., 1985 | 776059 | LPSN | 1 | 72461005 | |
| B_ESCHR_HRMN | Escherichia hermannii | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | hermannii | species | Brenner et al., 1983 | 776060 | LPSN | 1 | 85786000 | |
| B_ESCHR_MRMT | Escherichia marmotae | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | marmotae | species | Liu et al., 2015 | 792928 | LPSN | 1 | 14961000146107 |
A data set with 14,338 rows and 4 columns, containing the following
column names:
fullname, fullname_new, ref and
prevalence.
Note: remember that the ‘ref’ columns contains the
scientific reference to the old taxonomic entries, i.e. of column
‘fullname’. For the scientific reference of the new names,
i.e. of column ‘fullname_new’, see the
microorganisms data set.
This data set is in R available as microorganisms.old,
after you load the AMR package.
It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set here.
Direct download links:
This data set contains old, previously accepted taxonomic names. The
data sources are the same as the microorganisms data
set:
A data set with 464 rows and 14 columns, containing the following
column names:
ab, cid, name, group, atc,
atc_group1, atc_group2, abbreviations,
synonyms, oral_ddd, oral_units,
iv_ddd, iv_units and loinc.
This data set is in R available as antibiotics, after
you load the AMR package.
It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set here.
Direct download links:
This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.
| ab | cid | name | group | atc | atc_group1 | atc_group2 | abbreviations | synonyms | oral_ddd | oral_units | iv_ddd | iv_units | loinc |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AMK | 37768 | Amikacin | Aminoglycosides | D06AX12, J01GB06, S01AA21 | Aminoglycoside antibacterials | Other aminoglycosides | ak, ami, amik, … | amicacin, amikacillin, amikacin, … | 1.0 | g | 13546-7, 15098-7, 17798-0, … | ||
| AMX | 33613 | Amoxicillin | Beta-lactams/penicillins | J01CA04 | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | ac, amox, amx | actimoxi, amoclen, amolin, … | 1.5 | g | 3.0 | g | 16365-9, 25274-2, 3344-9, … |
| AMC | 23665637 | Amoxicillin/clavulanic acid | Beta-lactams/penicillins | J01CR02 | Beta-lactam antibacterials, penicillins | Combinations of penicillins, incl. beta-lactamase inhibitors | a/c, amcl, aml, … | amocla, amoclan, amoclav, … | 1.5 | g | 3.0 | g | |
| AMP | 6249 | Ampicillin | Beta-lactams/penicillins | J01CA01, S01AA19 | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | am, amp, ampi | acillin, adobacillin, amblosin, … | 2.0 | g | 6.0 | g | 21066-6, 3355-5, 33562-0, … |
| AZM | 447043 | Azithromycin | Macrolides/lincosamides | J01FA10, S01AA26 | Macrolides, lincosamides and streptogramins | Macrolides | az, azi, azit, … | aritromicina, azasite, azenil, … | 0.3 | g | 0.5 | g | 16420-2, 25233-8 |
| PEN | 5904 | Benzylpenicillin | Beta-lactams/penicillins | J01CE01, S01AA14 | Combinations of antibacterials | Combinations of antibacterials | bepe, pen, peni, … | abbocillin, ayercillin, bencilpenicilina, … | 3.6 | g | 3913-1 |
A data set with 102 rows and 9 columns, containing the following
column names:
atc, cid, name, atc_group,
synonyms, oral_ddd, oral_units,
iv_ddd and iv_units.
This data set is in R available as antivirals, after you
load the AMR package.
It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set here.
Direct download links:
This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.
| atc | cid | name | atc_group | synonyms | oral_ddd | oral_units | iv_ddd | iv_units |
|---|---|---|---|---|---|---|---|---|
| J05AF06 | 441300 | Abacavir | Nucleoside and nucleotide reverse transcriptase inhibitors | Abacavir, Abacavir sulfate, Ziagen | 0.6 | g | ||
| J05AB01 | 135398513 | Aciclovir | Nucleosides and nucleotides excl. reverse transcriptase inhibitors | Acicloftal, Aciclovier, Aciclovir, … | 4.0 | g | 4 | g |
| J05AF08 | 60871 | Adefovir dipivoxil | Nucleoside and nucleotide reverse transcriptase inhibitors | Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, … | 10.0 | mg | ||
| J05AE05 | 65016 | Amprenavir | Protease inhibitors | Agenerase, Amprenavir, Amprenavirum, … | 1.2 | g | ||
| J05AP06 | 16076883 | Asunaprevir | Antivirals for treatment of HCV infections | Asunaprevir, Sunvepra | ||||
| J05AE08 | 148192 | Atazanavir | Protease inhibitors | Atazanavir, Atazanavir Base, Latazanavir, … | 0.3 | g |
A data set with 20,369 rows and 11 columns, containing the following
column names:
guideline, method, site, mo,
rank_index, ab, ref_tbl, disk_dose,
breakpoint_S, breakpoint_R and uti.
This data set is in R available as rsi_translation,
after you load the AMR package.
It was last updated on 10 May 2022 19:42:39 UTC. Find more info about the structure of this data set here.
Direct download links:
This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST (2011-2022).
| guideline | method | site | mo | mo_name | rank_index | ab | ab_name | ref_tbl | disk_dose | breakpoint_S | breakpoint_R | uti |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EUCAST 2022 | MIC | F_ASPRG_MGTS | Aspergillus fumigatus | 2 | AMB | Amphotericin B | Aspergillus | 1 | 1 | FALSE | ||
| EUCAST 2022 | MIC | F_ASPRG_NIGR | Aspergillus niger | 2 | AMB | Amphotericin B | Aspergillus | 1 | 1 | FALSE | ||
| EUCAST 2022 | MIC | F_CANDD | Candida | 3 | AMB | Amphotericin B | Candida | 1 | 1 | FALSE | ||
| EUCAST 2022 | MIC | F_CANDD_ALBC | Candida albicans | 2 | AMB | Amphotericin B | Candida | 1 | 1 | FALSE | ||
| EUCAST 2022 | MIC | F_CANDD_DBLN | Candida dubliniensis | 2 | AMB | Amphotericin B | Candida | 1 | 1 | FALSE | ||
| EUCAST 2022 | MIC | F_CANDD_KRUS | Candida krusei | 2 | AMB | Amphotericin B | Candida | 1 | 1 | FALSE |
A data set with 134,956 rows and 2 columns, containing the following
column names:
mo and ab.
This data set is in R available as intrinsic_resistant,
after you load the AMR package.
It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set here.
Direct download links:
This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3 (2021).
Example rows when filtering on Enterobacter cloacae:
| microorganism | antibiotic |
|---|---|
| Enterobacter cloacae | Acetylmidecamycin |
| Enterobacter cloacae | Acetylspiramycin |
| Enterobacter cloacae | Amoxicillin |
| Enterobacter cloacae | Amoxicillin/clavulanic acid |
| Enterobacter cloacae | Ampicillin |
| Enterobacter cloacae | Ampicillin/sulbactam |
| Enterobacter cloacae | Avoparcin |
| Enterobacter cloacae | Azithromycin |
| Enterobacter cloacae | Benzylpenicillin |
| Enterobacter cloacae | Cadazolid |
| Enterobacter cloacae | Cefadroxil |
| Enterobacter cloacae | Cefazolin |
| Enterobacter cloacae | Cefoxitin |
| Enterobacter cloacae | Cephalexin |
| Enterobacter cloacae | Cephalothin |
| Enterobacter cloacae | Clarithromycin |
| Enterobacter cloacae | Clindamycin |
| Enterobacter cloacae | Cycloserine |
| Enterobacter cloacae | Dalbavancin |
| Enterobacter cloacae | Dirithromycin |
| Enterobacter cloacae | Erythromycin |
| Enterobacter cloacae | Flurithromycin |
| Enterobacter cloacae | Fusidic acid |
| Enterobacter cloacae | Gamithromycin |
| Enterobacter cloacae | Josamycin |
| Enterobacter cloacae | Kitasamycin |
| Enterobacter cloacae | Lincomycin |
| Enterobacter cloacae | Linezolid |
| Enterobacter cloacae | Meleumycin |
| Enterobacter cloacae | Midecamycin |
| Enterobacter cloacae | Miocamycin |
| Enterobacter cloacae | Nafithromycin |
| Enterobacter cloacae | Norvancomycin |
| Enterobacter cloacae | Oleandomycin |
| Enterobacter cloacae | Oritavancin |
| Enterobacter cloacae | Pirlimycin |
| Enterobacter cloacae | Primycin |
| Enterobacter cloacae | Pristinamycin |
| Enterobacter cloacae | Quinupristin/dalfopristin |
| Enterobacter cloacae | Ramoplanin |
| Enterobacter cloacae | Rifampicin |
| Enterobacter cloacae | Rokitamycin |
| Enterobacter cloacae | Roxithromycin |
| Enterobacter cloacae | Solithromycin |
| Enterobacter cloacae | Spiramycin |
| Enterobacter cloacae | Tedizolid |
| Enterobacter cloacae | Teicoplanin |
| Enterobacter cloacae | Telavancin |
| Enterobacter cloacae | Telithromycin |
| Enterobacter cloacae | Thiacetazone |
| Enterobacter cloacae | Tildipirosin |
| Enterobacter cloacae | Tilmicosin |
| Enterobacter cloacae | Troleandomycin |
| Enterobacter cloacae | Tulathromycin |
| Enterobacter cloacae | Tylosin |
| Enterobacter cloacae | Tylvalosin |
| Enterobacter cloacae | Vancomycin |
A data set with 169 rows and 9 columns, containing the following
column names:
ab, name, type, dose,
dose_times, administration, notes,
original_txt and eucast_version.
This data set is in R available as dosage, after you
load the AMR package.
It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set here.
Direct download links:
EUCAST breakpoints used in this package are based on the dosages in this data set.
Currently included dosages in the data set are meant for: ‘EUCAST Clinical Breakpoint Tables’ v11.0 (2021).
| ab | name | type | dose | dose_times | administration | notes | original_txt | eucast_version |
|---|---|---|---|---|---|---|---|---|
| AMK | Amikacin | standard_dosage | 25-30 mg/kg | 1 | iv | 25-30 mg/kg x 1 iv | 11 | |
| AMX | Amoxicillin | high_dosage | 2 g | 6 | iv | 2 g x 6 iv | 11 | |
| AMX | Amoxicillin | standard_dosage | 1 g | 3 | iv | 1 g x 3-4 iv | 11 | |
| AMX | Amoxicillin | high_dosage | 0.75-1 g | 3 | oral | 0.75-1 g x 3 oral | 11 | |
| AMX | Amoxicillin | standard_dosage | 0.5 g | 3 | oral | 0.5 g x 3 oral | 11 | |
| AMX | Amoxicillin | uncomplicated_uti | 0.5 g | 3 | oral | 0.5 g x 3 oral | 11 |