AMRFinderPlus
NCBI has developed AMRFinderPlus, a tool that identifies AMR genes, resistance-associated point mutations, and select other classes of genes using protein annotations and/or assembled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data are displayed in NCBI’s Isolate Browser. AMRFinderPlus relies on NCBI’s curated Reference Gene Database and curated collection of Hidden Markov Models. For more information on how AMRFinderPlus operates, please see the Methods section of the AMRFinderPlus documentation. See our documentation for a description of all our NCBI antimicrobial resistance resources.
NCBI has made AMRFinderPlus software and databases open source and freely available
- Documentation
- Installation instructions
- Software releases
- Source code
- Pathogen Detecton Reference Gene Catalog Includes web interface for AMR genes, point mutations, and other classes of genes
- Pathogen Detecton Reference HMM Catalog Includes web interface for carefully curated HMMs used by AMRFinderPlus to identify AMR genes, and some stress and virulence proteins
- Bacterial Antimicrobial Resistance Reference Gene Database Bioproject containing curated AMR gene reference sequences only
- NCBIfam-AMRFinder Curated AMRFinderPlus HMM library
NCBI runs AMRFinderPlus on hundreds of thousands of isolates as part of the Pathogen Detection pipeline and makes the results publically available
- Pathogen Detection Isolates Browser Includes genes found by AMRFinderPlus in the AMR genotypes, Stress genotypes, and Virulence genotypes columns
- Pathogen Detection Isolates Browser documentation
- MicroBIGG-E (Microbial Browser for Identification of Genetic and Genomic Elements) contains detailed AMRFinderPlus results and associated metadata for individual AMRFinderPlus hits. Note that there may be a delay between when isolates appear in the isolates browser and when MicroBIGG-E results appear because MicroBIGG-E results are only available for isolates that have public assembly accessions.
- MicroBIGG-E documentation
A note about ABRicate
Many people are using ABRicate with the default "ncbi" database, and it has come to our attention that at least some users are confused that they are getting the same or similar results to what they would get from AMRFinderPlus. ABRicate uses a subset of the AMRFinderPlus database to do AMR gene detection and different methods so the results are not the same as those you get by running AMRFinderPlus. To identify AMR genes from assembled sequence we recommend using AMRFinderPlus to get the full value out of the NCBI compiled database, including correct allele and gene symbols, named allele vs. novel allele determination, protein-based search/naming, curated cutoffs, HMM searches, etc.
If you have questions about the database or software, or experience problems with AMRFinderPlus please contact pd-help@ncbi.nlm.nih.gov
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