All reference data (about microorganisms, antimicrobials, SIR
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, MS Excel, Apache Feather, Apache
Parquet, SPSS, and Stata. We also provide tab-separated text files that
are machine-readable and suitable for input in any software program,
such as laboratory information systems.
If you are working in Python, be sure to use our AMR for Python package. It allows all relevant AMR data sets to be natively available in Python.
microorganisms: Full Microbial Taxonomy
A data set with 78 679 rows and 26 columns, containing the following
column names:
mo, fullname, status, kingdom,
phylum, class, order, family,
genus, species, subspecies, rank,
ref, oxygen_tolerance, source, lpsn,
lpsn_parent, lpsn_renamed_to, mycobank,
mycobank_parent, mycobank_renamed_to, gbif,
gbif_parent, gbif_renamed_to, prevalence, and
snomed.
This data set is in R available as microorganisms, after
you load the AMR package.
It was last updated on 26 March 2025 16:19:17 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (1.8 MB)
- Download as tab-separated
text file (17.7 MB)
- Download as Microsoft
Excel workbook (8.7 MB)
- Download as Apache
Feather file (8.3 MB)
- Download as Apache
Parquet file (3.8 MB)
- Download as IBM
SPSS Statistics data file (28.4 MB)
- Download as Stata DTA file (89.5 MB)
NOTE: The exported files for SPSS and Stata contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub. Their file structures and compression techniques are very inefficient. Advice? Use R instead. It’s free and much better in many ways.
The tab-separated text file and Microsoft Excel workbook both contain all SNOMED codes as comma separated values.
Example content
Included (sub)species per taxonomic kingdom:
| Kingdom | Number of (sub)species |
|---|---|
| (unknown kingdom) | 1 |
| Animalia | 1 628 |
| Archaea | 1 419 |
| Bacteria | 39 249 |
| Chromista | 178 |
| Fungi | 28 137 |
First 6 rows when filtering on genus Escherichia:
| mo | fullname | status | kingdom | phylum | class | order | family | genus | species | subspecies | rank | ref | oxygen_tolerance | source | lpsn | lpsn_parent | lpsn_renamed_to | mycobank | mycobank_parent | mycobank_renamed_to | gbif | gbif_parent | gbif_renamed_to | prevalence | snomed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B_ESCHR | Escherichia | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | genus | Castellani et al., 1919 | facultative anaerobe | LPSN | 515602 | 482 | 11158430 | 1 | 407310004, 407251000, 407281008, … | ||||||||
| B_ESCHR_ADCR | Escherichia adecarboxylata | synonym | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | adecarboxylata | species | Leclerc, 1962 | likely facultative anaerobe | LPSN | 776052 | 515602 | 777447 | 1 | ||||||||
| B_ESCHR_ALBR | Escherichia albertii | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | albertii | species | Huys et al., 2003 | facultative anaerobe | LPSN | 776053 | 515602 | 5427575 | 1 | 419388003 | |||||||
| B_ESCHR_BLTT | Escherichia blattae | synonym | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | blattae | species | Burgess et al., 1973 | likely facultative anaerobe | LPSN | 776056 | 515602 | 788468 | 1 | ||||||||
| B_ESCHR_COLI | Escherichia coli | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | species | Castellani et al., 1919 | facultative anaerobe | LPSN | 776057 | 515602 | 11286021 | 1 | 1095001000112106, 715307006, 737528008, … | |||||||
| B_ESCHR_COLI_COLI | Escherichia coli coli | accepted | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Escherichia | coli | coli | subspecies | GBIF | 776057 | 12233256 | 11286021 | 1 |
antimicrobials: Antibiotic and Antifungal Drugs
A data set with 496 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 antimicrobials, after
you load the AMR package.
It was last updated on 19 March 2025 15:05:24 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (44 kB)
- Download as tab-separated
text file (0.1 MB)
- Download as Microsoft
Excel workbook (75 kB)
- Download as Apache
Feather file (0.1 MB)
- Download as Apache
Parquet file (0.1 MB)
- Download as IBM
SPSS Statistics data file (0.3 MB)
- Download as Stata DTA file (10 kB)
The tab-separated text, Microsoft Excel, SPSS, and Stata files all contain the ATC codes, common abbreviations, trade names and LOINC codes as comma separated values.
Example content
| 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, amikacina, … | 1.0 | g | 101493-5, 11-7, 12-5, … | ||
| AMX | 33613 | Amoxicillin | Beta-lactams/penicillins | J01CA04 | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | ac, amox, amx | acuotricina, alfamox, alfida, … | 1.5 | g | 3.0 | g | 101498-4, 15-8, 16-6, … |
| 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, alpen, … | 2.0 | g | 6.0 | g | 101477-8, 101478-6, 18864-9, … |
| AZM | 447043 | Azithromycin | Macrolides/lincosamides | J01FA10, S01AA26 | Macrolides, lincosamides and streptogramins | Macrolides | az, azi, azit, … | aritromicina, aruzilina, azasite, … | 0.3 | g | 0.5 | g | 100043-9, 16420-2, 16421-0, … |
| PEN | 5904 | Benzylpenicillin | Beta-lactams/penicillins | J01CE01, S01AA14 | Combinations of antibacterials | Combinations of antibacterials | bepe, pen, peni, … | bencilpenicilina, benzopenicillin, benzylpenicilline, … | 3.6 | g |
clinical_breakpoints: Interpretation from MIC values
& disk diameters to SIR
A data set with 34 376 rows and 14 columns, containing the following
column names:
guideline, type, host, method,
site, mo, rank_index, ab,
ref_tbl, disk_dose, breakpoint_S,
breakpoint_R, uti, and is_SDD.
This data set is in R available as clinical_breakpoints,
after you load the AMR package.
It was last updated on 13 March 2025 14:38:39 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (76 kB)
- Download as tab-separated
text file (3.1 MB)
- Download as Microsoft
Excel workbook (2 MB)
- Download as Apache
Feather file (1.5 MB)
- Download as Apache
Parquet file (0.1 MB)
- Download as IBM
SPSS Statistics data file (5.6 MB)
- Download as Stata DTA file (9.6 MB)
Example content
| guideline | type | host | method | site | mo | mo_name | rank_index | ab | ab_name | ref_tbl | disk_dose | breakpoint_S | breakpoint_R | uti | is_SDD |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EUCAST 2024 | human | human | DISK | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | 10 mcg | 26.000 | 20.000 | FALSE | FALSE | |
| EUCAST 2024 | human | human | MIC | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | MEM | Meropenem | A. xylosoxidans | 1.000 | 4.000 | FALSE | FALSE | ||
| EUCAST 2024 | human | human | DISK | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | 1.25 mcg/23.75 mcg | 26.000 | 26.000 | FALSE | FALSE | |
| EUCAST 2024 | human | human | MIC | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | SXT | Trimethoprim/sulfamethoxazole | A. xylosoxidans | 0.125 | 0.125 | FALSE | FALSE | ||
| EUCAST 2024 | human | human | DISK | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | 30 mcg/6 mcg | 26.000 | 26.000 | FALSE | FALSE | |
| EUCAST 2024 | human | human | MIC | B_ACHRMB_XYLS | Achromobacter xylosoxidans | 2 | TZP | Piperacillin/tazobactam | A. xylosoxidans | 4.000 | 4.000 | FALSE | FALSE |
microorganisms.groups: Species Groups and
Microbiological Complexes
A data set with 534 rows and 4 columns, containing the following
column names:
mo_group, mo, mo_group_name, and
mo_name.
This data set is in R available as
microorganisms.groups, after you load the AMR
package.
It was last updated on 26 March 2025 16:19:17 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (6 kB)
- Download as tab-separated
text file (50 kB)
- Download as Microsoft
Excel workbook (20 kB)
- Download as Apache
Feather file (19 kB)
- Download as Apache
Parquet file (13 kB)
- Download as IBM
SPSS Statistics data file (65 kB)
- Download as Stata DTA file (83 kB)
Example content
| mo_group | mo | mo_group_name | mo_name |
|---|---|---|---|
| B_ACNTB_BMNN-C | B_ACNTB_BMNN | Acinetobacter baumannii complex | Acinetobacter baumannii |
| B_ACNTB_BMNN-C | B_ACNTB_CLCC | Acinetobacter baumannii complex | Acinetobacter calcoaceticus |
| B_ACNTB_BMNN-C | B_ACNTB_LCTC | Acinetobacter baumannii complex | Acinetobacter dijkshoorniae |
| B_ACNTB_BMNN-C | B_ACNTB_NSCM | Acinetobacter baumannii complex | Acinetobacter nosocomialis |
| B_ACNTB_BMNN-C | B_ACNTB_PITT | Acinetobacter baumannii complex | Acinetobacter pittii |
| B_ACNTB_BMNN-C | B_ACNTB_SFRT | Acinetobacter baumannii complex | Acinetobacter seifertii |
intrinsic_resistant: Intrinsic Bacterial
Resistance
A data set with 271 905 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 28 March 2025 10:17:49 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (0.1 MB)
- Download as tab-separated
text file (10.1 MB)
- Download as Microsoft
Excel workbook (2.9 MB)
- Download as Apache
Feather file (2.3 MB)
- Download as Apache
Parquet file (0.3 MB)
- Download as IBM
SPSS Statistics data file (14.8 MB)
- Download as Stata DTA file (22.6 MB)
Example content
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 | Bleomycin |
| Enterobacter cloacae | Cadazolid |
| Enterobacter cloacae | Cefadroxil |
| Enterobacter cloacae | Cefalexin |
| Enterobacter cloacae | Cefalotin |
| Enterobacter cloacae | Cefazolin |
| Enterobacter cloacae | Cefoxitin |
| 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 | 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 |
dosage: Dosage Guidelines from EUCAST
A data set with 503 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 22 June 2023 13:10:59 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (3 kB)
- Download as tab-separated
text file (43 kB)
- Download as Microsoft
Excel workbook (25 kB)
- Download as Apache
Feather file (21 kB)
- Download as Apache
Parquet file (9 kB)
- Download as IBM
SPSS Statistics data file (64 kB)
- Download as Stata DTA file (0.1 MB)
Example content
| 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 | 13 | |
| AMX | Amoxicillin | high_dosage | 2 g | 6 | iv | 2 g x 6 iv | 13 | |
| AMX | Amoxicillin | standard_dosage | 1 g | 3 | iv | 1 g x 3-4 iv | 13 | |
| AMX | Amoxicillin | high_dosage | 0.75-1 g | 3 | oral | 0.75-1 g x 3 oral | 13 | |
| AMX | Amoxicillin | standard_dosage | 0.5 g | 3 | oral | 0.5 g x 3 oral | 13 | |
| AMX | Amoxicillin | uncomplicated_uti | 0.5 g | 3 | oral | 0.5 g x 3 oral | 13 |
example_isolates: Example Data for Practice
A data set with 2 000 rows and 46 columns, containing the following
column names:
date, patient, age, gender,
ward, mo, PEN, OXA, FLC,
AMX, AMC, AMP, TZP, CZO,
FEP, CXM, FOX, CTX, CAZ,
CRO, GEN, TOB, AMK, KAN,
TMP, SXT, NIT, FOS, LNZ,
CIP, MFX, VAN, TEC, TCY,
TGC, DOX, ERY, CLI, AZM,
IPM, MEM, MTR, CHL, COL,
MUP, and RIF.
This data set is in R available as example_isolates,
after you load the AMR package.
It was last updated on 15 June 2024 13:33:49 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Example content
| date | patient | age | gender | ward | mo | PEN | OXA | FLC | AMX | AMC | AMP | TZP | CZO | FEP | CXM | FOX | CTX | CAZ | CRO | GEN | TOB | AMK | KAN | TMP | SXT | NIT | FOS | LNZ | CIP | MFX | VAN | TEC | TCY | TGC | DOX | ERY | CLI | AZM | IPM | MEM | MTR | CHL | COL | MUP | RIF |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2002-01-02 | A77334 | 65 | F | Clinical | B_ESCHR_COLI | R | I | I | R | R | R | R | R | R | R | R | R | R | |||||||||||||||||||||||||||
| 2002-01-03 | A77334 | 65 | F | Clinical | B_ESCHR_COLI | R | I | I | R | R | R | R | R | R | R | R | R | R | |||||||||||||||||||||||||||
| 2002-01-07 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R | R | R | R | S | S | S | S | S | S | R | R | R | |||||||||||||||||||||||||||
| 2002-01-07 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R | R | R | R | S | S | S | S | S | S | R | R | R | |||||||||||||||||||||||||||
| 2002-01-13 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R | R | R | R | R | S | S | S | S | R | R | R | ||||||||||||||||||||||||||||
| 2002-01-13 | 067927 | 45 | F | ICU | B_STPHY_EPDR | R | R | R | R | R | S | S | S | S | R | R | R | R |
example_isolates_unclean: Example Data for
Practice
A data set with 3 000 rows and 8 columns, containing the following
column names:
patient_id, hospital, date,
bacteria, AMX, AMC, CIP, and
GEN.
This data set is in R available as
example_isolates_unclean, after you load the
AMR package.
It was last updated on 27 August 2022 18:49:37 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Example content
| patient_id | hospital | date | bacteria | AMX | AMC | CIP | GEN |
|---|---|---|---|---|---|---|---|
| J3 | A | 2012-11-21 | E. coli | R | I | S | S |
| R7 | A | 2018-04-03 | K. pneumoniae | R | I | S | S |
| P3 | A | 2014-09-19 | E. coli | R | S | S | S |
| P10 | A | 2015-12-10 | E. coli | S | I | S | S |
| B7 | A | 2015-03-02 | E. coli | S | S | S | S |
| W3 | A | 2018-03-31 | S. aureus | R | S | R | S |
microorganisms.codes: Common Laboratory Codes
A data set with 4 971 rows and 2 columns, containing the following
column names:
code and mo.
This data set is in R available as microorganisms.codes,
after you load the AMR package.
It was last updated on 29 September 2024 20:17:56 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (22 kB)
- Download as tab-separated
text file (0.1 MB)
- Download as Microsoft
Excel workbook (82 kB)
- Download as Apache
Feather file (85 kB)
- Download as Apache
Parquet file (56 kB)
- Download as IBM
SPSS Statistics data file (0.1 MB)
- Download as Stata DTA file (0.1 MB)
Example content
| code | mo |
|---|---|
| 1011 | B_GRAMP |
| 1012 | B_GRAMP |
| 1013 | B_GRAMN |
| 1014 | B_GRAMN |
| 1015 | F_YEAST |
| 103 | B_ESCHR_COLI |
antivirals: Antiviral Drugs
A data set with 120 rows and 11 columns, containing the following
column names:
av, name, atc, cid,
atc_group, synonyms, oral_ddd,
oral_units, iv_ddd, iv_units, and
loinc.
This data set is in R available as antivirals, after you
load the AMR package.
It was last updated on 20 October 2023 12:51:48 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.
Direct download links:
- Download as original
R Data Structure (RDS) file (6 kB)
- Download as tab-separated
text file (17 kB)
- Download as Microsoft
Excel workbook (16 kB)
- Download as Apache
Feather file (16 kB)
- Download as Apache
Parquet file (13 kB)
- Download as IBM
SPSS Statistics data file (32 kB)
- Download as Stata DTA file (78 kB)
The tab-separated text, Microsoft Excel, SPSS, and Stata files all contain the trade names and LOINC codes as comma separated values.
Example content
| av | name | atc | cid | atc_group | synonyms | oral_ddd | oral_units | iv_ddd | iv_units | loinc |
|---|---|---|---|---|---|---|---|---|---|---|
| ABA | Abacavir | J05AF06 | 441300 | Nucleoside and nucleotide reverse transcriptase inhibitors | abacavir sulfate, avacavir, ziagen | 0.6 | g | 29113-8, 30273-7, 30287-7, … | ||
| ACI | Aciclovir | J05AB01 | 135398513 | Nucleosides and nucleotides excl. reverse transcriptase inhibitors | acicloftal, aciclovier, aciclovirum, … | 4.0 | g | 4 | g | |
| ADD | Adefovir dipivoxil | J05AF08 | 60871 | Nucleoside and nucleotide reverse transcriptase inhibitors | adefovir di, adefovir di ester, adefovir dipivoxyl, … | 10.0 | mg | |||
| AME | Amenamevir | J05AX26 | 11397521 | Other antivirals | amenalief | 0.4 | g | |||
| AMP | Amprenavir | J05AE05 | 65016 | Protease inhibitors | agenerase, carbamate, prozei | 1.2 | g | 29114-6, 30296-8, 30297-6, … | ||
| ASU | Asunaprevir | J05AP06 | 16076883 | Antivirals for treatment of HCV infections | sunvepra, sunvepratrade | 0.2 | g |