Antimicrobial Resistance Data Analysis • AMR (for R)

Works on Windows, macOS and Linux with all versions of R since R-3.0
Provides the full microbiological taxonomy and data on all antimicrobial drugs
Applies all recent CLSI and EUCAST clinical breakpoints for MICs and disk zones
Corrects for duplicate isolates, calculates and predicts AMR per antibiotic class
Integrates with WHONET, ATC, EARS-Net, PubChem, LOINC and SNOMED CT
Completely dependency-free, highly suitable for places with limited resources

https://msberends.github.io/AMR

https://doi.org/10.18637/jss.v104.i03

Introduction

The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.

This work was published in the Journal of Statistical Software (Volume 104(3); DOI 10.18637/jss.v104.i03) and formed the basis of two PhD theses (DOI 10.33612/diss.177417131 and DOI 10.33612/diss.192486375).

After installing this package, R knows ~49,000 distinct microbial species and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen, and is being actively and durably maintained by two public healthcare organisations in the Netherlands.

Used in 175 countries, translated to 16 languages

Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.

The AMR package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.

Practical examples

Filtering and selecting data

# AMR works great with dplyr, but it's not required or neccesary
library(AMR)
library(dplyr)

example_isolates %>%
  mutate(bacteria = mo_fullname()) %>%
  filter(mo_is_gram_negative(),
         mo_is_intrinsic_resistant(ab = "cefotax")) %>%
  select(bacteria,
         aminoglycosides(),
         carbapenems())

With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (mo_is_gram_negative() and mo_is_intrinsic_resistant()) and a column selection on two antibiotic groups (aminoglycosides() and carbapenems()), the reference data about all microorganisms and all antibiotics in the AMR package make sure you get what you meant:

bacteria	GEN	TOB	AMK	KAN	IPM	MEM
Pseudomonas aeruginosa	I	S		R	S
Pseudomonas aeruginosa	I	S		R	S
Pseudomonas aeruginosa	I	S		R	S
Pseudomonas aeruginosa	S	S	S	R		S
Pseudomonas aeruginosa	S	S	S	R	S	S
Pseudomonas aeruginosa	S	S	S	R	S	S
Stenotrophomonas maltophilia	R	R	R	R	R	R
Pseudomonas aeruginosa	S	S	S	R		S
Pseudomonas aeruginosa	S	S	S	R		S
Pseudomonas aeruginosa	S	S	S	R	S	S

A base R equivalent would be:

example_isolates$bacteria <- mo_fullname(example_isolates$mo)
example_isolates[which(mo_is_gram_negative() &
                         mo_is_intrinsic_resistant(ab = "cefotax")),
                 c("bacteria", aminoglycosides(), carbapenems())]

This base R snippet will work in any version of R since April 2013 (R-3.0).

Calculating resistance per group

library(AMR)
library(dplyr)

out <- example_isolates %>%
  # group by ward:
  group_by(ward) %>%
  # calculate AMR using resistance(), over all aminoglycosides
  # and polymyxins:
  summarise(across(c(aminoglycosides(), polymyxins()),
            resistance))
out

ward	GEN	TOB	AMK	KAN	COL
Clinical	0.229	0.315	0.626	1	0.780
ICU	0.290	0.400	0.662	1	0.857
Outpatient	0.200	0.368	0.605	NA	0.889

# transform the antibiotic columns to names:
out %>% set_ab_names()

ward	gentamicin	tobramycin	amikacin	kanamycin	colistin
Clinical	0.229	0.315	0.626	1	0.780
ICU	0.290	0.400	0.662	1	0.857
Outpatient	0.200	0.368	0.605	NA	0.889

# transform the antibiotic column to ATC codes:
out %>% set_ab_names(property = "atc")

ward	J01GB03	J01GB01	J01GB06	J01GB04	J01XB01
Clinical	0.229	0.315	0.626	1	0.780
ICU	0.290	0.400	0.662	1	0.857
Outpatient	0.200	0.368	0.605	NA	0.889

What else can you do with this package?

This package was intended as a comprehensive toolbox for integrated AMR data analysis. This package can be used for:

Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (manual)
Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline from the last 10 years (manual)
Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (manual)
Determining first isolates to be used for AMR data analysis (manual)
Calculating antimicrobial resistance (tutorial)
Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (tutorial)
Calculating (empirical) susceptibility of both mono therapy and combination therapies (tutorial)
Predicting future antimicrobial resistance using regression models (tutorial)
Getting properties for any microorganism (like Gram stain, species, genus or family) (manual)
Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (manual)
Plotting antimicrobial resistance (tutorial)
Applying EUCAST expert rules (manual)
Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (manual)
Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (manual)
Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to R/SI (link)
Principal component analysis for AMR (tutorial)

Get this package

Latest official version

This package is available here on the official R network (CRAN). Install this package in R from CRAN by using the command:

install.packages("AMR")

It will be downloaded and installed automatically. For RStudio, click on the menu Tools > Install Packages… and then type in “AMR” and press Install.

Note: Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.

Latest development version

Please read our Developer Guideline here.

The latest and unpublished development version can be installed from GitHub in two ways:

Manually, using:

install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")

Automatically, using the rOpenSci R-universe platform, by adding our R-universe address to your list of repositories (‘repos’):
```
options(repos = c(getOption("repos"),
                  msberends = "https://msberends.r-universe.dev"))
```
After this, you can install and update this AMR package like any official release (e.g., using install.packages("AMR") or in RStudio via Tools > Check for Package Updates…).

Get started

To find out how to conduct AMR data analysis, please continue reading here to get started or click a link in the ‘How to’ menu.

Partners

The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:

Copyright

This R package is free, open-source software and licensed under the GNU General Public License v2.0 (GPL-2). In a nutshell, this means that this package:

May be used for commercial purposes
May be used for private purposes
May not be used for patent purposes
May be modified, although:
- Modifications must be released under the same license when distributing the package
- Changes made to the code must be documented
May be distributed, although:
- Source code must be made available when the package is distributed
- A copy of the license and copyright notice must be included with the package.
Comes with a LIMITATION of liability
Comes with NO warranty

The AMR Package for R