Antimicrobial resistance (AMR) gene annotation describes the identification of known resistance genes and mutations in microbial genomes. Detecting these resistance markers helps researchers track the spread of AMR and assess potential public health risks.
In QIIME2 there are two plugins that facilitate AMR gene annotation. q2-amrfinderplus that wraps the functionalities of AMRFinderPlus and q2-rgi that uses the RGI tool.
Data¶
To run this tutorial you will need the reads, contigs and MAGs created in the end-to-end MAG reconstruction tutorial.
- 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
- Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M. A., Edalatmand, A., Petkau, A., Syed, S. A., Tsang, K. K., Baker, S. J. C., Dave, M., McCarthy, M. C., Mukiri, K. M., Nasir, J. A., Golbon, B., Imtiaz, H., Jiang, X., Kaur, K., … McArthur, A. G. (2022). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D690–D699. 10.1093/nar/gkac920