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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Scientific reports, 2021-06, Vol.11 (1), p.12728-12728, Article 12728 [Peer Reviewed Journal]

This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021 ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/s41598-021-91456-0 ;PMID: 34135355

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  • Title:
    AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
  • Author: Feldgarden, Michael ; Brover, Vyacheslav ; Gonzalez-Escalona, Narjol ; Frye, Jonathan G ; Haendiges, Julie ; Haft, Daniel H ; Hoffmann, Maria ; Pettengill, James B ; Prasad, Arjun B ; Tillman, Glenn E ; Tyson, Gregory H ; Klimke, William
  • Subjects: Amino acid sequence ; Antimicrobial agents ; Antimicrobial resistance ; Drug resistance ; Genes ; Genotypes ; Mutation ; Nucleotide sequence ; Phenotypes ; Public health ; Stop codon ; Virulence ; Whole genome sequencing
  • Is Part Of: Scientific reports, 2021-06, Vol.11 (1), p.12728-12728, Article 12728
  • Description: Abstract Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used to detect known resistance mechanisms and potentially identify novel mechanisms. To enable accurate assessment of AMR gene content, as part of a multi-agency collaboration, NCBI developed a comprehensive AMR gene database, the Bacterial Antimicrobial Resistance Reference Gene Database and the AMR gene detection tool AMRFinder. Here, we describe the expansion of the Reference Gene Database, now called the Reference Gene Catalog, to include putative acid, biocide, metal, stress resistance genes, in addition to virulence genes and species-specific point mutations. Genes and point mutations are classified by broad functions, as well as more detailed functions. As we have expanded both the functional repertoire of identified genes and functionality, NCBI released a new version of AMRFinder, known as AMRFinderPlus. This new tool allows users the option to utilize only the core set of AMR elements, or include stress response and virulence genes, too. AMRFinderPlus can detect acquired genes and point mutations in both protein and nucleotide sequence. In addition, the evidence used to identify the gene has been expanded to include whether nucleotide or protein sequence was used, its location in the contig, and presence of an internal stop codon. These database improvements and functional expansions will enable increased precision in identifying AMR genes, linking AMR genotypes and phenotypes, and determining possible relationships between AMR, virulence, and stress response.
  • Publisher: London: Nature Publishing Group
  • Language: English
  • Identifier: ISSN: 2045-2322
    EISSN: 2045-2322
    DOI: 10.1038/s41598-021-91456-0
    PMID: 34135355
  • Source: PubMed Central
    ProQuest Central
    DOAJ Directory of Open Access Journals
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