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NCBI Antimicrobial Resistance Gene Finder Plus (AMRFinderPlus)

See Version 1 documentation for the old AMRFinder version 1 software

Overview for AMRFinderPlus 3.8

This software and the accompanying database are designed to find acquired antimicrobial resistance genes in bacterial protein or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we have added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.

By default the results returned by AMRFinderPlus will be similar to those returned by the original AMRFinder with some additional data on function. See Running AMRFinderPlus for information on how to get the additional hit types.

New in version 3.8 (AMRFinderPlus)

This release is incompatible with previous versions of the database. Run amrfinder -u to get the most recent release version of the database before using.

Fix for Bioconda MacOS installation bug that made the default database location not work
Update to --mutation_all output format to more clearly report all differences from reference sequence
Changed to using accessions as the primary sequence identifier

See New in AMRFinderPlus for more information.

Installation

AMRFinder requires BLAST and HMMER. We provide instructions using BioConda to install the prerequisites.

Installation Instructions

Methods

AMRFinder can be run in multiple modes with protein sequence as input and/or with DNA sequence as input. To get maximum information it should be run with both protein and nucleotide. When run with protein sequence it uses both BLASTP and HMMER to search protein sequences for AMR genes along with a hierarchical tree of gene families to classify and name novel sequences. With nucleotide sequences it uses BLASTX translated searches and the hierarchical tree of gene families. Adding the --organism option enables screening for point mutations in select organisms and suppresses the reporting of some that are extremely common in those organisms.

Running AMRFinderPlus
Methods
AMRFinderPlus database
Interpreting results

Related Resources

Pathogen Detection AMR resources - The Pathogen Detection team at NCBI has a page describing the AMR Resources we provide.
Pathogen Detection Reference Gene Catalog - Proteins used by AMRFinder in table form with query, filtering, and additional metadata are available in the Reference Gene Catalog. The above information is also included in a tab-delimited file Reference Gene Catalog on FTP.
Pathogen Detection Isolates Browser - NCBI runs AMRFinderPlus on all microbial genome assemblies in the Pathogen Detection system (over 600,000 isolate assemblies). Gene symbols from AMRFinderPlus runs, along with other metadata for the isolates are visible in the Isolates Browser
MicroBIGG-E - Detailed AMRFinderPlus results for individual elements, links to sequence, and additional metadata are included in the Pathogen Detection Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E)

amrfinder-announce mailing list

Subscribe to the amrfinder-announce mailing list to get updates when we release new versions of the software or database. This is a low-traffic list.

Help

Note that this version of AMRFinderPlus is an alpha version. If you have any questions about or experience problems running AMRFinderPlus, please contact [email protected].

License / Public Domain Notice

Publication

See our our AMRFinder paper for more details.

Citation

Feldgarden, M., Brover, V., Haft, D.H., Prasad, A.B., Slotta, D.J., Tolstoy, I., Tyson, G.H., Zhao, S., Hsu, C.-H., McDermott, P.F., Tadesse, D.A., Morales, C., Simmons, M., Tillman, G., Wasilenko, J., Folster, J.P., Klimke, W., 2019. Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrob. Agents Chemother. 63 no. 11 (November 1, 2019): e00483-19 https://doi.org/10.1128/AAC.00483-19.