Data sets for download • AMR (for R)

This package contains a lot of reference data sets that are all reliable, up-to-date and free to download. You can even use them outside of R, for example to train your laboratory information system (LIS) about intrinsic resistance!

We included them in our AMR package, but also automatically ‘mirror’ them to our public repository in different software formats. On this page, we explain how to download them and how the structure of the data sets look like. The tab separated files allow for machine reading taxonomic data and EUCAST and CLSI interpretation guidelines, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI.

Note: Years and dates of updates mentioned on this page, are from on AMR package version 1.3.0.9004, online released on 16 August 2020. If you are reading this page from within R, please visit our website for the latest update.

Microorganisms

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

Source

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

Catalogue of Life (included version: 2019)
List of Prokaryotic names with Standing in Nomenclature (LPSN, included version: May 2020)

Structure

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.

Included 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

Download

Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 28 July 2020 20:52:40 CEST.

R file (.rds): from GitHub, from GitLab (file size: 2.7 MB)
Excel workbook (.xlsx): from GitHub, from GitLab (file size: 6.1 MB)
SPSS file (.sav): from GitHub, from GitLab (file size: 28.2 MB)
Stata file (.dta): from GitHub, from GitLab (file size: 28.2 MB)
SAS file (.sas): from GitHub, from GitLab (file size: 25.2 MB)
Tab separated file (.txt): from GitHub, from GitLab (file size: 13.3 MB)

Example

Example rows when filtering on genus Escherichia:

mo	fullname	kingdom	phylum	class	order	family	genus	species	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

Antibiotic agents

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

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.

ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)
PubChem by the US National Library of Medicine
WHONET software 2019

Structure

A data set with 456 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.

Download

Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 31 July 2020 12:12:13 CEST.

R file (.rds): from GitHub, from GitLab (file size: 37.3 kB)
Excel workbook (.xlsx): from GitHub, from GitLab (file size: 64.5 kB)
SPSS file (.sav): from GitHub, from GitLab (file size: 1.3 MB)
Stata file (.dta): from GitHub, from GitLab (file size: 1.3 MB)
SAS file (.sas): from GitHub, from GitLab (file size: 321.8 kB)
Tab separated file (.txt): from GitHub, from GitLab (file size: 146.1 kB)

Example

Example rows:

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, …	1.0	g	1.0	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, …	1.0	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	2.0	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

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

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.

ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)
PubChem by the US National Library of Medicine

Structure

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.

Download

Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 23 November 2019 19:03:43 CET.

R file (.rds): from GitHub, from GitLab (file size: 4.6 kB)
Excel workbook (.xlsx): from GitHub, from GitLab (file size: 13.6 kB)
SPSS file (.sav): from GitHub, from GitLab (file size: 67.7 kB)
Stata file (.dta): from GitHub, from GitLab (file size: 67.7 kB)
SAS file (.sas): from GitHub, from GitLab (file size: 67.2 kB)
Tab separated file (.txt): from GitHub, from GitLab (file size: 16.2 kB)

Example

Example rows:

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

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

Source

This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations.

The data set is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.

Structure

A data set with 49,462 rows and 2 columns, containing the following column names:

microorganism, antibiotic.

Download

Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 14 August 2020 14:18:20 CEST.

R file (.rds): from GitHub, from GitLab (file size: 96.6 kB)
Excel workbook (.xlsx): from GitHub, from GitLab (file size: 0.5 MB)
SPSS file (.sav): from GitHub, from GitLab (file size: 4.2 MB)
Stata file (.dta): from GitHub, from GitLab (file size: 4.2 MB)
SAS file (.sas): from GitHub, from GitLab (file size: 3.7 MB)
Tab separated file (.txt): from GitHub, from GitLab (file size: 1.8 MB)

Example

Example rows:

microorganism	antibiotic
Klebsiella	Amoxicillin
Klebsiella	Ampicillin
Klebsiella	Azithromycin
Klebsiella	Clarithromycin
Klebsiella	Daptomycin
Klebsiella	Erythromycin

Interpretation from MIC values / disk diameters to R/SI

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

Source

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

Structure

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.

Download

Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 29 July 2020 13:12:34 CEST.

R file (.rds): from GitHub, from GitLab (file size: 55.1 kB)
Excel workbook (.xlsx): from GitHub, from GitLab (file size: 0.6 MB)
SPSS file (.sav): from GitHub, from GitLab (file size: 3.4 MB)
Stata file (.dta): from GitHub, from GitLab (file size: 3.4 MB)
SAS file (.sas): from GitHub, from GitLab (file size: 3 MB)
Tab separated file (.txt): from GitHub, from GitLab (file size: 1.5 MB)

Example

Example rows:

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