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Download data sets for download / own use

14 October 2026

Source: vignettes/datasets.Rmd
datasets.Rmd

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 103 222 rows and 28 columns, containing the following column names:
mo, fullname, status, domain, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, oxygen_tolerance, morphology, 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 7 October 2026 10:55:12 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

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
20
(unknown kingdom) 222
Animalia 2 528
Archaea 142
Bacillati 24 122
Bacteria 138

First 6 rows when filtering on genus Escherichia:

mo fullname status domain kingdom phylum class order family genus species subspecies rank ref oxygen_tolerance morphology 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 Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia genus Castellani et al., 1919 facultative anaerobe rods LPSN 515602 482 CS33H CRYWR 1 407310004, 407251000, 407281008, …
B_ESCHR_ADCR Escherichia adecarboxylata synonym Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia adecarboxylata species Leclerc, 1962 likely facultative anaerobe rods LPSN 776052 515602 777447 CS33J CS33H 3SVX6 1
B_ESCHR_ALBR Escherichia albertii accepted Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia albertii species Huys et al., 2003 facultative anaerobe rods LPSN 776053 515602 3BGTB CS33H 1 419388003
B_ESCHR_BLTT Escherichia blattae synonym Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia blattae species Burgess et al., 1973 likely facultative anaerobe rods LPSN 776056 515602 788468 CS33K CS33H 4X4P7 1
B_ESCHR_COLI Escherichia coli accepted Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli species Castellani et al., 1919 facultative anaerobe rods LPSN 776057 515602 CS33N CS33H 1 1095001000112106, 715307006, 737528008, …
B_ESCHR_COLI_COLI Escherichia coli coli accepted Bacteria Pseudomonadati Pseudomonadota Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia coli coli subspecies GBIF 776057 12233256 CS33N 1

antimicrobials: Antibiotic and Antifungal Drugs

A data set with 506 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 10 October 2026 07:42:25 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

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, QD06AX12, … Aminoglycoside antibacterials Other aminoglycosides ak, ami, amik, … amikacillin, amikacina, amikacine, … 1.0 g 101493-5, 11-7, 12-5, …
AMX 33613 Amoxicillin Aminopenicillins, Penicillins, Beta-lactams J01CA04, QG51AA03, QJ01CA04 Beta-lactam antibacterials, penicillins Penicillins with extended spectrum ac, amox, amoxic, … acuotricina, alfamox, alfida, … 1.5 g 3.0 g 101498-4, 15-8, 16-6, …
AMC 23665637 Amoxicillin/clavulanic acid Aminopenicillins, Penicillins, Beta-lactams, … J01CR02, QJ01CR02 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 Aminopenicillins, Penicillins, Beta-lactams J01CA01, QJ01CA01, QJ51CA01, … Beta-lactam antibacterials, penicillins Penicillins with extended spectrum am, amp, amp100, … adobacillin, alpen, amblosin, … 2.0 g 6.0 g 101477-8, 101478-6, 18864-9, …
AZM 447043 Azithromycin Macrolides J01FA10, QJ01FA10, QS01AA26, … 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 Penicillins, Beta-lactams J01CE01, QJ01CE01, QJ51CE01, … 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 60 237 rows and 15 columns, containing the following column names:
guideline, type, host, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti, is_SDD, and note.

This data set is in R available as clinical_breakpoints, after you load the AMR package.

It was last updated on 10 October 2026 07:42:25 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

Example content

guideline type host method mo_name rank_index ab_name disk_dose breakpoint_S breakpoint_R uti is_SDD note
EUCAST 2026 human human DISK Achromobacter xylosoxidans 2.1 Cefiderocol FALSE FALSE [No breakpoint] EUCAST gives Note (see note) | [A] The in vitro activity of cefiderocol against Achromobacter xylosoxidans is comparable to the activity of the agent against Enterobacterales and there is animal data to suggest efficacy. However, there is insufficient clinical data to determine a clinical breakpoint. Isolates with MIC values <=0.5 mg/L (zone diameter >=26 mm) are mostly devoid of resistance mechanisms and are likely to be a target for treatment with this agent. Isolates with MICs 1-2 mg/L have some acquired resistance mechanisms. Little clinical data exists regarding clinical outcome for these isolates, however, they may still be a target for treatment with this agent if there are limited treatment options. Isolates with MIC values >2 mg/L (zone diameter <22 mm) have acquired resistance mechanisms and are likely to be resistant to this agent. | [1] Broth microdilution MIC determination must be performed in iron-depleted Mueller-Hinton broth and specific reading instructions must be followed. For testing conditions and reading instructions, see https://www.eucast.org/eucastguidancedocuments/.
EUCAST 2026 human human MIC Achromobacter xylosoxidans 2.1 Cefiderocol FALSE FALSE [No breakpoint] EUCAST gives Note (see note) | [2] The in vitro activity of cefiderocol against Achromobacter xylosoxidans is comparable to the activity of the agent against Enterobacterales and there is animal data to suggest efficacy. However, there is insufficient clinical data to determine a clinical breakpoint. Isolates with MIC values <=0.5 mg/L (zone diameter >=26 mm) are mostly devoid of resistance mechanisms and are likely to be a target for treatment with this agent. Isolates with MICs 1-2 mg/L have some acquired resistance mechanisms. Little clinical data exists regarding clinical outcome for these isolates, however, they may still be a target for treatment with this agent if there are limited treatment options. Isolates with MIC values >2 mg/L (zone diameter <22 mm) have acquired resistance mechanisms and are likely to be resistant to this agent. | [1] Broth microdilution MIC determination must be performed in iron-depleted Mueller-Hinton broth and specific reading instructions must be followed. For testing conditions and reading instructions, see https://www.eucast.org/eucastguidancedocuments/.
EUCAST 2026 human human DISK Achromobacter xylosoxidans 2.0 Meropenem 10 mcg 26.000 20.000 FALSE FALSE
EUCAST 2026 human human MIC Achromobacter xylosoxidans 2.0 Meropenem 1.000 4.000 FALSE FALSE
EUCAST 2026 human human DISK Achromobacter xylosoxidans 2.0 Trimethoprim/sulfamethoxazole 1.25/23.75 mcg 26.000 26.000 FALSE FALSE [A] There may be growth within the inhibition zone. The density of growth may vary from a fine haze to substantial growth (see pictures below). If any zone edge can be seen, ignore growth within the inhibition zone and read the zone diameter. | [1] Trimethoprim:sulfamethoxazole in the ratio 1:19. Breakpoints are expressed as the trimethoprim concentration.
EUCAST 2026 human human MIC Achromobacter xylosoxidans 2.0 Trimethoprim/sulfamethoxazole 0.125 0.125 FALSE FALSE [1] Trimethoprim:sulfamethoxazole in the ratio 1:19. Breakpoints are expressed as the trimethoprim concentration.

microorganisms.groups: Species Groups and Microbiological Complexes

A data set with 466 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 7 October 2026 10:55:12 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

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 lactucae
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 307 684 rows and 3 columns, containing the following column names:
mo, ab, and version.

This data set is in R available as intrinsic_resistant, after you load the AMR package.

It was last updated on 7 October 2026 10:55:12 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

Example content

Example rows when filtering on Enterobacter cloacae:

microorganism antibiotic
Enterobacter cloacae Acetylmidecamycin
Enterobacter cloacae Acetylmidecamycin
Enterobacter cloacae Acetylspiramycin
Enterobacter cloacae Acetylspiramycin
Enterobacter cloacae Amoxicillin
Enterobacter cloacae Amoxicillin
Enterobacter cloacae Amoxicillin/clavulanic acid
Enterobacter cloacae Amoxicillin/clavulanic acid
Enterobacter cloacae Ampicillin
Enterobacter cloacae Ampicillin
Enterobacter cloacae Ampicillin/sulbactam
Enterobacter cloacae Ampicillin/sulbactam
Enterobacter cloacae Avoparcin
Enterobacter cloacae Avoparcin
Enterobacter cloacae Azithromycin
Enterobacter cloacae Azithromycin
Enterobacter cloacae Benzylpenicillin
Enterobacter cloacae Benzylpenicillin
Enterobacter cloacae Bleomycin
Enterobacter cloacae Bleomycin
Enterobacter cloacae Cadazolid
Enterobacter cloacae Cadazolid
Enterobacter cloacae Cefadroxil
Enterobacter cloacae Cefadroxil
Enterobacter cloacae Cefalexin
Enterobacter cloacae Cefalexin
Enterobacter cloacae Cefalotin
Enterobacter cloacae Cefalotin
Enterobacter cloacae Cefazolin
Enterobacter cloacae Cefazolin
Enterobacter cloacae Cefoxitin
Enterobacter cloacae Cefoxitin
Enterobacter cloacae Clarithromycin
Enterobacter cloacae Clarithromycin
Enterobacter cloacae Clindamycin
Enterobacter cloacae Clindamycin
Enterobacter cloacae Cycloserine
Enterobacter cloacae Cycloserine
Enterobacter cloacae Dalbavancin
Enterobacter cloacae Dalbavancin
Enterobacter cloacae Dirithromycin
Enterobacter cloacae Dirithromycin
Enterobacter cloacae Erythromycin
Enterobacter cloacae Erythromycin
Enterobacter cloacae Flurithromycin
Enterobacter cloacae Flurithromycin
Enterobacter cloacae Fusidic acid
Enterobacter cloacae Fusidic acid
Enterobacter cloacae Gamithromycin
Enterobacter cloacae Gamithromycin
Enterobacter cloacae Josamycin
Enterobacter cloacae Josamycin
Enterobacter cloacae Kitasamycin
Enterobacter cloacae Kitasamycin
Enterobacter cloacae Lincomycin
Enterobacter cloacae Lincomycin
Enterobacter cloacae Linezolid
Enterobacter cloacae Linezolid
Enterobacter cloacae Meleumycin
Enterobacter cloacae Meleumycin
Enterobacter cloacae Midecamycin
Enterobacter cloacae Midecamycin
Enterobacter cloacae Miocamycin
Enterobacter cloacae Miocamycin
Enterobacter cloacae Nafithromycin
Enterobacter cloacae Nafithromycin
Enterobacter cloacae Norvancomycin
Enterobacter cloacae Norvancomycin
Enterobacter cloacae Oleandomycin
Enterobacter cloacae Oleandomycin
Enterobacter cloacae Oritavancin
Enterobacter cloacae Oritavancin
Enterobacter cloacae Ostreogrycin
Enterobacter cloacae Ostreogrycin
Enterobacter cloacae Pirlimycin
Enterobacter cloacae Pirlimycin
Enterobacter cloacae Primycin
Enterobacter cloacae Primycin
Enterobacter cloacae Pristinamycin
Enterobacter cloacae Pristinamycin
Enterobacter cloacae Quinupristin/dalfopristin
Enterobacter cloacae Quinupristin/dalfopristin
Enterobacter cloacae Ramoplanin
Enterobacter cloacae Ramoplanin
Enterobacter cloacae Rifampicin
Enterobacter cloacae Rifampicin
Enterobacter cloacae Rokitamycin
Enterobacter cloacae Rokitamycin
Enterobacter cloacae Roxithromycin
Enterobacter cloacae Roxithromycin
Enterobacter cloacae Solithromycin
Enterobacter cloacae Solithromycin
Enterobacter cloacae Spiramycin
Enterobacter cloacae Spiramycin
Enterobacter cloacae Tedizolid
Enterobacter cloacae Tedizolid
Enterobacter cloacae Teicoplanin
Enterobacter cloacae Teicoplanin
Enterobacter cloacae Telavancin
Enterobacter cloacae Telavancin
Enterobacter cloacae Telithromycin
Enterobacter cloacae Telithromycin
Enterobacter cloacae Thiacetazone
Enterobacter cloacae Thiacetazone
Enterobacter cloacae Tildipirosin
Enterobacter cloacae Tildipirosin
Enterobacter cloacae Tilmicosin
Enterobacter cloacae Tilmicosin
Enterobacter cloacae Troleandomycin
Enterobacter cloacae Troleandomycin
Enterobacter cloacae Tulathromycin
Enterobacter cloacae Tulathromycin
Enterobacter cloacae Tylosin
Enterobacter cloacae Tylosin
Enterobacter cloacae Tylvalosin
Enterobacter cloacae Tylvalosin
Enterobacter cloacae Vancomycin
Enterobacter cloacae Vancomycin
Enterobacter cloacae Virginiamycine
Enterobacter cloacae Virginiamycine
Enterobacter cloacae Zorbamycin
Enterobacter cloacae Zorbamycin

dosage: Dosage Guidelines from EUCAST

A data set with 759 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 20 April 2025 10:55:31 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

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 15
AMX Amoxicillin high_dosage 2 g 6 iv 2 g x 6 iv 15
AMX Amoxicillin standard_dosage 1 g 3 iv 1 g x 3-4 iv 15
AMX Amoxicillin high_dosage 0.75-1 g 3 oral 0.75-1 g x 3 oral 15
AMX Amoxicillin standard_dosage 0.5 g 3 oral 0.5 g x 3 oral 15
AMX Amoxicillin uncomplicated_uti 0.5 g 3 oral 0.5 g x 3 oral 15

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 24 June 2026 16:36:47 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 6 022 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 7 October 2026 10:55:12 UTC. Find more info about the contents, (scientific) source, and structure of this data set here.

Direct download links:

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:

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