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 6 October 2021 09:31:11 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 | bc4fdde6867d5ecfc728000b0bfb49a3 | CoL | 1 | 64735005 | |||
| B_ESCHR_ALBR | Escherichia albertii | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | albertii | species | Huys et al., 2003 | 36618b1ed3b8b7e5a61f40eb9386e63c | CoL | 1 | 419388003 | |
| B_ESCHR_COLI | Escherichia coli | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | species | Castellani et al., 1919 | 3254b3db31bf16fdde669ac57bf8c4fe | CoL | 1 | 1095001000112106, 715307006, 737528008, … | |
| B_ESCHR_FRGS | Escherichia fergusonii | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | fergusonii | species | Farmer et al., 1985 | 82d98b10c456ce5f4c8c515f4e1567e2 | CoL | 1 | 72461005 | |
| B_ESCHR_HRMN | Escherichia hermannii | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | hermannii | species | Brenner et al., 1983 | b16086aee36e3b46b565510083ab4b65 | CoL | 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 5 October 2021 13:12:28 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:
Example rows when filtering on Escherichia:
| fullname | fullname_new | ref | prevalence |
|---|---|---|---|
| Escherichia adecarboxylata | Leclercia adecarboxylata | Leclerc, 1962 | 1 |
| Escherichia blattae | Shimwellia blattae | Burgess et al., 1973 | 1 |
| Escherichia vulneris | Pseudescherichia vulneris | Brenner et al., 1983 | 1 |
A data set with 456 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 2 September 2021 11:50:06 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 93,892 rows and 2 columns, containing the following column names:
microorganism and antibiotic.
This data set is in R available as intrinsic_resistant, after you load the AMR package.
It was last updated on 6 October 2021 08:29:50 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’ v3.2 (2020).
Example rows when filtering on Enterobacter cloacae:
| microorganism | antibiotic |
|---|---|
| Enterobacter cloacae | Amoxicillin |
| Enterobacter cloacae | Amoxicillin/clavulanic acid |
| Enterobacter cloacae | Ampicillin |
| Enterobacter cloacae | Ampicillin/sulbactam |
| Enterobacter cloacae | Avoparcin |
| Enterobacter cloacae | Azithromycin |
| 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 | Josamycin |
| Enterobacter cloacae | Lincomycin |
| Enterobacter cloacae | Linezolid |
| Enterobacter cloacae | Midecamycin |
| Enterobacter cloacae | Miocamycin |
| Enterobacter cloacae | Norvancomycin |
| Enterobacter cloacae | Oleandomycin |
| Enterobacter cloacae | Oritavancin |
| Enterobacter cloacae | Benzylpenicillin |
| Enterobacter cloacae | Pirlimycin |
| Enterobacter cloacae | Pristinamycin |
| Enterobacter cloacae | Quinupristin/dalfopristin |
| Enterobacter cloacae | Ramoplanin |
| Enterobacter cloacae | Rifampicin |
| Enterobacter cloacae | Rokitamycin |
| Enterobacter cloacae | Roxithromycin |
| Enterobacter cloacae | Spiramycin |
| Enterobacter cloacae | Tedizolid |
| Enterobacter cloacae | Teicoplanin |
| Enterobacter cloacae | Teicoplanin-macromethod |
| Enterobacter cloacae | Telavancin |
| Enterobacter cloacae | Telithromycin |
| Enterobacter cloacae | Thiacetazone |
| Enterobacter cloacae | Troleandomycin |
| Enterobacter cloacae | Vancomycin |
A data set with 22,000 rows and 10 columns, containing the following column names:
guideline, method, site, mo, 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 5 October 2021 13:13:41 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 (2010-2020) and EUCAST (2011-2021).
| guideline | method | site | mo | ab | ref_tbl | disk_dose | breakpoint_S | breakpoint_R | uti |
|---|---|---|---|---|---|---|---|---|---|
| EUCAST 2021 | DISK | Enterobacterales | Amoxicillin/clavulanic acid | Enterobacterales | 20-10ug | 19 | 19 | FALSE | |
| EUCAST 2021 | DISK | UTI | Enterobacterales | Amoxicillin/clavulanic acid | Enterobacterales | 20-10ug | 16 | 16 | TRUE |
| EUCAST 2021 | MIC | Enterobacterales | Amoxicillin/clavulanic acid | Enterobacterales | 8 | 8 | FALSE | ||
| EUCAST 2021 | MIC | UTI | Enterobacterales | Amoxicillin/clavulanic acid | Enterobacterales | 32 | 32 | TRUE | |
| EUCAST 2021 | MIC | Actinomyces | Amoxicillin/clavulanic acid | Anaerobes, Grampositive | 4 | 8 | FALSE | ||
| EUCAST 2021 | MIC | Bacteroides | Amoxicillin/clavulanic acid | Anaerobes, Gramnegative | 4 | 8 | FALSE |
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 |