DOI: 10.5281/zenodo.14924033
title: AMRProfiler: A Comprehensive Tool for Identifying Antimicrobial Resistance Genes and Mutations Across Species

description: Antimicrobial resistance (AMR) remains a critical challenge in public health and research. AmrProfiler is a comprehensive tool with three specialized modules: identifying acquired AMR genes, resistance-associated point mutations, and rRNA gene mutations across nearly 18,000 bacterial species. By integrating and refining data from established databases, it provides a robust framework for AMR analysis. AmrProfiler is the first to systematically report mutations in rRNA genes, offering in-depth analysis of rRNA copy numbers and mutations—key for identifying potential rRNA-associated resistance mechanisms. Its curated database includes 7,600 unique AMR gene entries, 245 resistance-related genes, and over 4,300 mutations, alongside a detailed catalog of rRNA gene copy numbers and mutations. Supporting genome assemblies in multiple formats, AmrProfiler allows users to customize detection thresholds for AMR genes, mutations, and rRNA analysis. Validation with Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Staphylococcus epidermidis demonstrated that AmrProfiler accurately identified all AMR genes and mutations reported by other tools while also detecting additional resistance markers and mutations not previously recognized. By bridging AMR genotypes and phenotypes, AmrProfiler provides actionable insights that advance both research and clinical applications in antimicrobial resistance. AmrProfiler is freely available as an open-access web server without login at https://dianalab.e-ce.uth.gr/amrprofiler .

 

The uploaded files are :

1) amrprofiler-main.zip which is the repo from githup page (https://github.com/dianalabgr/amrprofiler)

2) three folders in zip format (databases.zip, db.zip, refseq.zip)  to be unzipped inside the folder amrprofiler-main. These folders are needed for AmrProfiler to run locally. The file Readme.txt on the GitHub page explains how to run AmrProfiler locally.

This dataset contains the curated databases used by AMRProfiler and the source code. AmrProfiler integrates non-redundant AMR gene sequences and mutation records derived from multiple publicly available sources, including CARD, Reference Gene Catalog, and ResFinder.

Contents of this dataset:

✅ Source Code of AmrProfiler ✅ Curated AMRProfiler databases with non-redundant AMR gene entries.✅ Processed metadata and annotations from various AMR databases.

Important Licensing Information:

📌 Included third-party data sources and their licenses:



Reference Gene Catalog (NCBI) – Public domain, freely available for unrestricted use.

ResFinder & PointFinder – Apache License 2.0, allowing free use, modification, and distribution.

AMRProfiler Curation & Metadata – MIT License, allowing free use, modification, and redistribution under its terms.


By using this dataset, users acknowledge that they must comply with the respective licenses of each third-party database.

⚠ This dataset does NOT include raw CARD data. CARD is available for non-commercial academic research only and must be downloaded separately from its official source (https://card.mcmaster.ca/download). Users are responsible for complying with its terms of use.

The full licence of AmrProfiler can be found here (https://github.com/dianalabgr/amrprofiler/blob/main/Licence)