Kept on Wikipedia:AMRFinderPlus
AMRFinderPlus is software and an accompanying database developed by NCBI primarily to identify acquired antimicrobial resistance (AMR) genes in assembled bacterial genome and/or protein sequence.[1][2]. AMRFinderPlus also identifies select resistance associated point mutations, virulence factor genes, and stress response genes. The database was created by and is maintained by NCBI and is represented at the Pathogen Detection Reference Gene Catalog.[3] The tools also uses a set of NCBI curated Hidden Markov Models (HMMs) and combines the sequence similarity results to report on the evidence for a particular gene/protein as well the functional name and categorization of the genes and proteins. Because NCBI also assigns alleles for novel beta-lactamase, Qnr, and MCR proteins the definitions of these genes are authoritative and are incorporated into the reference set at release time. The 2020-03-20.1 release consists of 6,108 AMR genes (5,464 which are AMR genes, and 644 which are point mutations), 210 stress response genes (including biocides, metal, heat, and acid resistance), and 628 virulence genes.
The results of the tool are incorporated into the Pathogen Detection Isolates Browser[4] effectively identifying the antimicrobial resistance genes of over 500,000 pathogen genomes. The tool and database are free and open and have been included in many open analysis pipelines[5][6][7] and commercial packages[8]. AMRFinderPlus has been used to analyze AMR genes in Shigella spp. in Israel,[9] in Campylobacter spp.[10] from clusters of isolates in Washington State and Montreal, and Eschericha coli isolates from retail meat surveillance as part of the National Antimicrobial Resistance Monitoring System (NARMS)[11]
See also
References
- ↑ Feldgarden, Michael; Brover, Vyacheslav; Haft, Daniel H.; Prasad, Arjun B.; Slotta, Douglas J.; Tolstoy, Igor; Tyson, Gregory H.; Zhao, Shaohua; Hsu, Chih-Hao; McDermott, Patrick F.; Tadesse, Daniel A. (November 2019). "Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates". Antimicrobial Agents and Chemotherapy. 63 (11). doi:10.1128/AAC.00483-19. ISSN 1098-6596. PMC 6811410 Check
|pmc=value (help). PMID 31427293. - ↑ https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
- ↑ https://www.ncbi.nlm.nih.gov/pathogens/isolates#/refgene/
- ↑ https://www.ncbi.nlm.nih.gov/pathogens/isolates#/search/
- ↑ Horan, Kristy, abritamr: Running AMRFinderPlus for MDU, retrieved 2020-05-07
- ↑ Seemann, Torsten (2020-04-21), tseemann/abricate, retrieved 2020-05-07
- ↑ Corey, Brendan, mrsn-might: MIGHT: MRSN Integrated Genome Handling Tool for bacterial clinical isolates, retrieved 2020-05-07
- ↑ "Ridom SeqSphere+". www.ridom.com. Retrieved 2020-05-07. Unknown parameter
|url-status=ignored (help) - ↑ Ezernitchi, Analía V.; Sirotkin, Elizabeta; Danino, Dana; Agmon, Vered; Valinsky, Lea; Rokney, Assaf (2019). "Azithromycin non-susceptible Shigella circulating in Israel, 2014-2016". PLOS One. 14 (10): e0221458. doi:10.1371/journal.pone.0221458. ISSN 1932-6203. PMC 6799884 Check
|pmc=value (help). PMID 31626667. - ↑ Greninger, Alex; Addetia, Amin; Starr, Kimberly; Cybulski, Robert J.; Stewart, Mary K.; Salipante, Stephen J.; Bryan, Andrew B.; Cookson, Brad; Gaudreau, Christiane; Bekal, Sadjia; Fang, Ferric (2019-09-08). "International Spread of Multidrug-Resistant Campylobacter coli in Men Who Have Sex with Men in Washington State and Quebec, 2015-2018". Rochester, NY. SSRN 3436286.
- ↑ Tyson, Gregory H.; Li, Cong; Hsu, Chih-Hao; Bodeis-Jones, Sonya; McDermott, Patrick F. (2019). "Diverse Fluoroquinolone Resistance Plasmids From Retail Meat E. coli in the United States". Frontiers in Microbiology. 10: 2826. doi:10.3389/fmicb.2019.02826. ISSN 1664-302X. PMC 6906146 Check
|pmc=value (help). PMID 31866986.
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