Data sets for download / own use

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.

Microorganisms (currently accepted names)

A data set with 67,151 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’, ‘snomed’.

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

It was last updated on 3 September 2020 20:59:45 CEST. Find more info about the structure of this data set here.

Direct download links:

Source

Our full taxonomy of microorganisms is based on the authoritative and comprehensive:

Example content

Included (sub)species per taxonomic kingdom:

Kingdom Number of (sub)species
(unknown kingdom) 1
Animalia 2,153
Archaea 697
Bacteria 19,244
Chromista 32,164
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 112283007
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 DSMZ 1

Microorganisms (previously accepted names)

A data set with 12,708 rows and 4 columns, containing the following column names:
‘fullname’, ‘fullname_new’, ‘ref’, ‘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 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set here.

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Source

This data set contains old, previously accepted taxonomic names. The data sources are the same as the microorganisms data set:

Example content

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

Antibiotic agents

A data set with 455 rows and 14 columns, containing the following column names:
‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘loinc’.

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

It was last updated on 24 September 2020 00:50:35 CEST. Find more info about the structure of this data set here.

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Source

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.

Example content

ab atc cid name group atc_group1 atc_group2 abbreviations synonyms oral_ddd oral_units iv_ddd iv_units loinc
AMK J01GB06 37768 Amikacin Aminoglycosides Aminoglycoside antibacterials Other aminoglycosides ak, ami, amik, … amicacin, amikacillin, amikacin, … 1.0 g 13546-7, 15098-7, 17798-0, …
AMX J01CA04 33613 Amoxicillin Beta-lactams/penicillins 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 J01CR02 23665637 Amoxicillin/clavulanic acid Beta-lactams/penicillins 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 J01CA01 6249 Ampicillin Beta-lactams/penicillins 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 J01FA10 447043 Azithromycin Macrolides/lincosamides Macrolides, lincosamides and streptogramins Macrolides az, azi, azit, … aritromicina, azasite, azenil, … 0.3 g 0.5 g 16420-2, 25233-8
CZO J01DB04 33255 Cefazolin Cephalosporins (1st gen.) Other beta-lactam antibacterials First-generation cephalosporins cfz, cfzl, cz, … atirin, cefamezin, cefamezine, … 3.0 g 16566-2, 25235-3, 3442-1, …

Antiviral agents

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’, ‘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 21:53:07 CEST. Find more info about the structure of this data set here.

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Source

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.

Example content

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

Intrinsic bacterial resistance

A data set with 93,892 rows and 2 columns, containing the following column names:
‘microorganism’, ‘antibiotic’.

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

It was last updated on 24 September 2020 00:50:35 CEST. Find more info about the structure of this data set here.

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Source

This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes’, v3.2 from 2020.

Example content

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

Interpretation from MIC values / disk diameters to R/SI

A data set with 18,650 rows and 10 columns, containing the following column names:
‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘uti’.

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

It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set here.

Direct download links:

Source

This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020).

Example content

guideline method site mo ab ref_tbl disk_dose breakpoint_S breakpoint_R uti
EUCAST 2020 DISK Enterobacterales Amoxicillin/clavulanic acid Enterobacterales 20-10ug 19 19 FALSE
EUCAST 2020 DISK UTI Enterobacterales Amoxicillin/clavulanic acid Enterobacterales 20-10ug 16 16 TRUE
EUCAST 2020 MIC Enterobacterales Amoxicillin/clavulanic acid Enterobacterales 8 8 FALSE
EUCAST 2020 MIC UTI Enterobacterales Amoxicillin/clavulanic acid Enterobacterales 32 32 TRUE
EUCAST 2020 MIC Actinomyces Amoxicillin/clavulanic acid Anaerobes, Grampositive 4 8 FALSE
EUCAST 2020 MIC Bacteroides Amoxicillin/clavulanic acid Anaerobes, Gramnegative 4 8 FALSE