AmrProfiler
AmrProfiler is an advanced tool designed to detect antimicrobial resistance (AMR) genes, identify mutations in species-specific core genes linked to AMR, and analyze rRNA genes for potential mutations. It provides a comprehensive approach to understanding the genetic basis of antimicrobial resistance. AmrProfiler is free and open to all users without registration or login requirements.
Antimicrobial resistance Genes
Point Mutations in Core Genes
To ensure correct operation, please select the assembly's most phylogenetically close species before running Point Mutations.
Mutations in rRNA Genes
To ensure correct operation, please select the assembly's most phylogenetically close species before running Mutations in rRNA Genes.
Species and input data type:
Upload and submit job:
Citations
If you have utilized as reference databases the database ResFinder+ReferenceGeneCatalog in your work, it is essential to appropriately cite the original publications associated with these resources. Below are the recommended citations:
- AmrProfiler
Skoulakis, A., Kostoula, V., Daniilidis, K., Gkountinoudis, C. G., Petinaki, E., & Hatzigeorgiou, A. G. (2025). AmrProfiler: a comprehensive tool for identifying antimicrobial resistance genes and mutations across species. Nucleic Acids Research, gkaf400. - ResFinder
Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640-2644. doi:10.1093/jac/dks261 - AMRFinderPlus
Feldgarden, M., Brover, V., Haft, D. H., et al. (2019). Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrobial Agents and Chemotherapy, 63(11), e00483-19. https://doi.org/10.1128/AAC.00483-19 - Blast+
Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. Published 2009 Dec 15. doi:10.1186/1471-2105-10-421
If you have used the following reference database: ResFinder+ReferenceGeneCatalog+CARD or You have used Tool2 and/or Tool3. Below are the recommended citations:
- AmrProfiler
Skoulakis, A., Kostoula, V., Daniilidis, K., Gkountinoudis, C. G., Petinaki, E., & Hatzigeorgiou, A. G. (2025). AmrProfiler: a comprehensive tool for identifying antimicrobial resistance genes and mutations across species. Nucleic Acids Research, gkaf400. - ResFinder
Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640-2644. doi:10.1093/jac/dks261 - AMRFinderPlus
Feldgarden, M., Brover, V., Haft, D. H., et al. (2019). Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrobial Agents and Chemotherapy, 63(11), e00483-19. https://doi.org/10.1128/AAC.00483-19 - CARD (Comprehensive Antibiotic Resistance Database)
Alcock BP, Huynh W, Chalil R, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023;51(D1):D690-D699. doi:10.1093/nar/gkac920 - Blast+
Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. Published 2009 Dec 15. doi:10.1186/1471-2105-10-421
Please ensure you include these citations in your work to acknowledge the contributions of these tools and databases.
License
AmrProfiler is released under the MIT License. Users should be aware that third-party databases are integrated into AmrProfiler, including CARD, Reference Gene Catalog, and ResFinder, each governed by its respective licensing terms:
- CARD data is available for non-commercial academic research under its terms of use (https://card.mcmaster.ca/about)
- ResFinder is licensed under the Apache License 2.0.
- Reference Gene Catalog is in the public domain.
The Antimicrobial Resistance Genes module depends on the selected gene database, and its use corresponds to the respective databases's license.
