Data sets for download / own use

11 mei 2022

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 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 9 mei 2022 20:57:33 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (1.3 MB)
  
• Download as Excel file (6.4 MB)
  
• Download as plain text file (13.1 MB)
  
• Download as SAS file (30.7 MB)
  
• Download as SPSS file (16.3 MB)
  
• Download as Stata file (27.5 MB)

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.

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, last updated: 5 October 2021)
• US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12

Example content

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		515602	LPSN	1	64735005
B_ESCHR_ALBR	Escherichia albertii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	albertii		species	Huys et al., 2003	776053	LPSN	1	419388003
B_ESCHR_COLI	Escherichia coli	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	coli		species	Castellani et al., 1919	776057	LPSN	1	1095001000112106, 715307006, 737528008, …
B_ESCHR_FRGS	Escherichia fergusonii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	fergusonii		species	Farmer et al., 1985	776059	LPSN	1	72461005
B_ESCHR_HRMN	Escherichia hermannii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	hermannii		species	Brenner et al., 1983	776060	LPSN	1	85786000
B_ESCHR_MRMT	Escherichia marmotae	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacterales	Enterobacteriaceae	Escherichia	marmotae		species	Liu et al., 2015	792928	LPSN	1	14961000146107

Microorganisms (previously accepted names)

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 9 mei 2022 20:57:33 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (0.2 MB)
  
• Download as Excel file (0.5 MB)
  
• Download as plain text file (1 MB)
  
• Download as SAS file (2.1 MB)
  
• Download as SPSS file (1.3 MB)
  
• Download as Stata file (2 MB)

Source

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

• Catalogue of Life (included version: 2019)
• List of Prokaryotic names with Standing in Nomenclature (LPSN, last updated: 5 October 2021)

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 464 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 9 mei 2022 20:57:33 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (33 kB)
  
• Download as Excel file (65 kB)
  
• Download as plain text file (0.1 MB)
  
• Download as SAS file (1.8 MB)
  
• Download as SPSS file (0.3 MB)
  
• Download as Stata file (0.3 MB)

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 freely available from the WHO CC website for personal use)
• PubChem by the US National Library of Medicine
• WHONET software 2019

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, 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

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 and iv_units.

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

It was last updated on 9 mei 2022 20:57:33 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (5 kB)
  
• Download as Excel file (14 kB)
  
• Download as plain text file (16 kB)
  
• Download as SAS file (80 kB)
  
• Download as SPSS file (68 kB)
  
• Download as Stata file (67 kB)

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 freely available from the WHO CC website for personal use)
• PubChem by the US National Library of Medicine

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 134,956 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 9 mei 2022 20:57:33 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (78 kB)
  
• Download as Excel file (1.3 MB)
  
• Download as plain text file (5.1 MB)
  
• Download as SAS file (10.4 MB)
  
• Download as SPSS file (7.5 MB)
  
• Download as Stata file (10.2 MB)

Source

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’ v3.3 (2021).

Example content

Example rows when filtering on Enterobacter cloacae:

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

Interpretation from MIC values / disk diameters to R/SI

A data set with 20,318 rows and 11 columns, containing the following column names:
guideline, method, site, mo, rank_index, 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 11 mei 2022 08:01:12 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (40 kB)
  
• Download as Excel file (0.7 MB)
  
• Download as plain text file (1.7 MB)
  
• Download as SAS file (3.6 MB)
  
• Download as SPSS file (2.2 MB)
  
• Download as Stata file (3.4 MB)

Source

This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2021) and EUCAST (2011-2021).

Example content

guideline	method	site	mo	rank_index	ab	ref_tbl	disk_dose	breakpoint_S	breakpoint_R	uti
EUCAST 2021	MIC		Aspergillus fumigatus	2	Amphotericin B	Aspergillus		1	4	FALSE
EUCAST 2021	MIC		Aspergillus niger	2	Amphotericin B	Aspergillus		1	4	FALSE
EUCAST 2021	MIC		Candida	3	Amphotericin B	Candida		1	2	FALSE
EUCAST 2021	MIC		Candida albicans	2	Amphotericin B	Candida		1	2	FALSE
EUCAST 2021	MIC		Candida krusei	2	Amphotericin B	Candida		1	2	FALSE
EUCAST 2021	MIC		Candida parapsilosis	2	Amphotericin B	Candida		1	2	FALSE

Dosage guidelines from EUCAST

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 9 mei 2022 20:57:33 UTC. Find more info about the structure of this data set here.

Direct download links:

• Download as R file (3 kB)
  
• Download as Excel file (14 kB)
  
• Download as plain text file (15 kB)
  
• Download as SAS file (52 kB)
  
• Download as SPSS file (45 kB)
  
• Download as Stata file (44 kB)

Source

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).

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	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