Data sets for download / own use

Source: vignettes/datasets.Rmd

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 teach 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. We also offer all data sets in formats for R, SPSS, SAS, Stata and Excel.

Note: Years and dates of updates mentioned on this page, are from on AMR package version 1.3.0.9005, online released on 17 August 2020. If you are reading this page from within R, please visit our website for the latest update.

Microorganisms (currently accepted names)

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

It was last updated on 28 July 2020 20:52:40 CEST.

Direct download links:
R file (.rds), 2.7 MB – Excel workbook (.xlsx), 6.1 MB – SPSS file (.sav), 28.2 MB – Stata file (.dta), 28.2 MB – SAS file (.sas), 25.2 MB – Tab separated file (.txt), 13.3 MB.

Source

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

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 (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)

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.

Direct download links:
R file (.rds), 0.3 MB – Excel workbook (.xlsx), 0.4 MB – SPSS file (.sav), 1.9 MB – Stata file (.dta), 1.9 MB – SAS file (.sas), 1.8 MB – Tab separated file (.txt), 0.8 MB.

Source

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

Structure

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.

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

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

It was last updated on 31 July 2020 12:12:13 CEST.

Direct download links:
R file (.rds), 37 kB – Excel workbook (.xlsx), 65 kB – SPSS file (.sav), 1.3 MB – Stata file (.dta), 1.3 MB – SAS file (.sas), 0.3 MB – Tab separated file (.txt), 0.1 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.

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.

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.

It was last updated on 23 November 2019 19:03:43 CET.

Direct download links:
R file (.rds), 5 kB – Excel workbook (.xlsx), 14 kB – SPSS file (.sav), 68 kB – Stata file (.dta), 68 kB – SAS file (.sas), 67 kB – Tab separated file (.txt), 16 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.

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.

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.

It was last updated on 14 August 2020 14:18:20 CEST.

Direct download links:
R file (.rds), 97 kB – Excel workbook (.xlsx), 0.5 MB – SPSS file (.sav), 4.2 MB – Stata file (.dta), 4.2 MB – SAS file (.sas), 3.7 MB – Tab separated file (.txt), 1.8 MB.

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.

Example rows when filtering on Klebsiella:

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.

It was last updated on 29 July 2020 13:12:34 CEST.

Direct download links:
R file (.rds), 55 kB – Excel workbook (.xlsx), 0.6 MB – SPSS file (.sav), 3.4 MB – Stata file (.dta), 3.4 MB – SAS file (.sas), 3 MB – Tab separated file (.txt), 1.5 MB.

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.

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