Overview
AMRgen is an open-source R package designed to bridge the gap between genotypic and phenotypic antimicrobial resistance (AMR) data. Developed as an extension to the AMR R package, it provides tools to interpret AMR genes, integrate these findings with antimicrobial susceptibility test (AST) data, and calculate genotype-phenotype associations.
This package is developed in collaboration with the ESGEM-AMR Working Group and is tailored for researchers and healthcare professionals tackling AMR globally.
The AMRgen website has full function documentation and a Vignette working through analysing geno/pheno data using key functions.
Key Features
- Import Genotype and Phenotype Data: Import from common formats (NCBI or EBI antibiogram format for phenotypes; AMRFinderPlus and hAMRonization for genotypes
- Genotype-Phenotype Integration: Links AMR gene presence with phenotypic resistance profiles, enabling deeper insights into resistance mechanisms.
- Automated EUCAST MIC Distribution Integration: Fetch MIC distribution data directly from EUCAST for seamless comparison with local susceptibility data.
- Visualisation: Generate powerful UpSet plots to identify intersections of AMR gene presence and phenotypic resistance, highlighting multidrug resistance patterns.
- Modular and Extensible: Leverages the robust foundation of the AMR package, including antibiotic selectors and clinical breakpoint interpretations.
Planned for development:
- NCBI-Compliant Export: Export phenotype data to NCBI-compliant antibiogram format.
- Expanded Data Import: Import and parse phenotype data from other tools (e.g. CARD, ResFinder).
Getting Started
To install and explore the package, follow the instructions below:
Installation
Install the latest version of this package with:
install.packages("remotes") # if you haven't already
remotes::install_github("AMRverse/AMRgen")All required packages, including the AMR package, will be installed automatically.
It might be best to restart R before running the installation to prevent issues with running the examples below.
Quick Usage Examples
Investigate ciprofloxacin resistance vs quinolone genotype markers, via solo PPV and upset plots
# Example public E. coli AST data from NCBI
# (already imported via import_ncbi_ast() and re-interpreted with as.sir())
ecoli_ast
# Import matching E. coli AMRFinderPlus data from AllTheBacteria
ecoli_geno <- import_amrfp(ecoli_geno_raw, "Name")
# Calculate positive predictive value for ciprofloxacin resistance
# (for all quinolone-associated genotype markers)
soloPPV_cipro <- solo_ppv_analysis(ecoli_geno, ecoli_ast, antibiotic="Ciprofloxacin", drug_class_list=c("Quinolones"), sir_col="pheno_clsi")
# Do upset plot of ciprofloxacin MIC vs quinolone genotype marker combinations
# (for combinations observed at least 5 times)
cip_upset <- amr_upset(soloPPV_cipro$amr_binary, min_set_size=5, assay="mic", order="value")
# Do logistic regression of ciprofloxacin resistance as a function of presence/absence of quinolone-associated markers
# (for markers observed at least 10 times)
models <- amr_logistic(geno_table = import_amrfp(ecoli_geno_raw, "Name"),
pheno_table = ecoli_ast, sir_col="pheno_clsi",
antibiotic = "Ciprofloxacin", drug_class_list = c("Quinolones"), maf=10)Download reference MIC distribution from eucast.org and compare to example data
# Get MIC reference distribution for ciprofloxacin in E. coli
ecoli_cip_mic_data <- get_eucast_mic_distribution("cipro", "E. coli")
# Plot the reference distribution
mics <- rep(ecoli_cip_mic_data$mic, ecoli_cip_mic_data$count)
ggplot2::autoplot(mics, ab = "cipro", mo = "E. coli", title = "E. coli cipro reference distribution")
# Compare reference distribution to example E. coli data
ecoli_cip <- ecoli_ast$mic[ecoli_ast$drug_agent=="CIP"]
comparison <- compare_mic_with_eucast(ecoli_cip, ab = "cipro", mo = "E. coli")
comparison
ggplot2::autoplot(comparison)For more see the Vignette.