q2-amrfinderplus wraps the functionalities of the AMRFinderPlus software. AMRFinderPlus is a tool developed by NCBI, together with the accompanying database it identifies acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. The database also includes select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.
AMRFinderPlus focuses primarily on clinically relevant resistance genes, emphasizing core AMR genes that directly confer resistance.
Installation¶
q2-amrfinderplus isn’t part of the MOSHPIT distribution and has to be installed separately. Please follow the steps described in the QIIME2 installation instructions for the pathogenome distribution.
- Feldgarden, M., Brover, V., Gonzalez-Escalona, N., Frye, J. G., Haendiges, J., Haft, D. H., Hoffmann, M., Pettengill, J. B., Prasad, A. B., Tillman, G. E., Tyson, G. H., & Klimke, W. (2021). AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports, 11(1). 10.1038/s41598-021-91456-0