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AMRFinderPlus
NCBI has developed AMRFinderPlus. AMRFinderPlus can identify acquired antimicrobial resistance genes in either protein datasets or nucleotide data, including genomic data. AMRFinderPlus relies on NCBI’s curated AMR, virulence, and stress response gene database which includes a curated collection of genes, proteins, and point mutations that are represented at the Pathogen Detection Reference Gene Catalog. The tools also uses a set of curated Hidden Markov Models (HMMs). NCBI also assigns alleles for novel beta-lactamase, Qnr, and MCR proteins which are incorporated into the reference set at release time. The 2019-10-31 release consists of 5,609 AMR genes (5,278 which are AMR genes, and 331 which are point mutations), 211 stress response genes (incuding biocides, metal, heat, and acid resistance), and 623 virulence genes.

The results of the tool are incorporated into the Pathogen Detection Isolates Browser effectively identifying the antimicrobial resistance genes of over 400, 000 pathogen isolates. These results have been used to analyze antimicrobial resistance in Shigella spp. in Israel.