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

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...

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Veröffentlicht in:	Scientific reports Jg. 11; H. 1; S. 12728 - 9
Hauptverfasser:	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
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	London Nature Publishing Group UK 16.06.2021 Nature Publishing Group Nature Portfolio
Schlagworte:	631/114 631/114/129 631/114/2785 631/326 631/326/22/1434 Amino acid sequence Antimicrobial agents Antimicrobial resistance Biocides Drug resistance Genes Genotypes Health risks Humanities and Social Sciences multidisciplinary Mutation Nucleotide sequence Phenotypes Public health Science Science (multidisciplinary) Stop codon Virulence Whole genome sequencing
ISSN:	2045-2322, 2045-2322
Online-Zugang:	Volltext
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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.
AbstractList	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.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. 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. 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.
ArticleNumber	12728
Author	Brover, Vyacheslav Pettengill, James B. Klimke, William Tyson, Gregory H. Haft, Daniel H. Hoffmann, Maria Haendiges, Julie Frye, Jonathan G. Feldgarden, Michael Tillman, Glenn E. Gonzalez-Escalona, Narjol Prasad, Arjun B.
Author_xml	– sequence: 1 givenname: Michael surname: Feldgarden fullname: Feldgarden, Michael email: michael.feldgarden@nih.gov organization: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health – sequence: 2 givenname: Vyacheslav surname: Brover fullname: Brover, Vyacheslav organization: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health – sequence: 3 givenname: Narjol surname: Gonzalez-Escalona fullname: Gonzalez-Escalona, Narjol organization: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration – sequence: 4 givenname: Jonathan G. surname: Frye fullname: Frye, Jonathan G. organization: Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture – sequence: 5 givenname: Julie surname: Haendiges fullname: Haendiges, Julie organization: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration – sequence: 6 givenname: Daniel H. surname: Haft fullname: Haft, Daniel H. organization: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health – sequence: 7 givenname: Maria surname: Hoffmann fullname: Hoffmann, Maria organization: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration – sequence: 8 givenname: James B. surname: Pettengill fullname: Pettengill, James B. organization: Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration – sequence: 9 givenname: Arjun B. surname: Prasad fullname: Prasad, Arjun B. organization: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health – sequence: 10 givenname: Glenn E. surname: Tillman fullname: Tillman, Glenn E. organization: Food Safety and Inspection Service, U.S. Department of Agriculture – sequence: 11 givenname: Gregory H. surname: Tyson fullname: Tyson, Gregory H. organization: Center for Veterinary Medicine, U.S. Food and Drug Administration – sequence: 12 givenname: William surname: Klimke fullname: Klimke, William organization: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
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Snippet	Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing... Abstract Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to...
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SubjectTerms	631/114 631/114/129 631/114/2785 631/326 631/326/22/1434 Amino acid sequence Antimicrobial agents Antimicrobial resistance Biocides Drug resistance Genes Genotypes Health risks Humanities and Social Sciences multidisciplinary Mutation Nucleotide sequence Phenotypes Public health Science Science (multidisciplinary) Stop codon Virulence Whole genome sequencing
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Title	AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
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