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

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 asses...

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Autores principales:	Michael Feldgarden, Vyacheslav Brover, Narjol Gonzalez-Escalona, Jonathan G. Frye, Julie Haendiges, Daniel H. Haft, Maria Hoffmann, James B. Pettengill, Arjun B. Prasad, Glenn E. Tillman, Gregory H. Tyson, William Klimke
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a74a376a5af442ffaa166193f704c31e
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spelling	oai:doaj.org-article:a74a376a5af442ffaa166193f704c31e2021-12-02T17:39:49ZAMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence10.1038/s41598-021-91456-02045-2322https://doaj.org/article/a74a376a5af442ffaa166193f704c31e2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91456-0https://doaj.org/toc/2045-2322Abstract 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.Michael FeldgardenVyacheslav BroverNarjol Gonzalez-EscalonaJonathan G. FryeJulie HaendigesDaniel H. HaftMaria HoffmannJames B. PettengillArjun B. PrasadGlenn E. TillmanGregory H. TysonWilliam KlimkeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michael Feldgarden Vyacheslav Brover Narjol Gonzalez-Escalona Jonathan G. Frye Julie Haendiges Daniel H. Haft Maria Hoffmann James B. Pettengill Arjun B. Prasad Glenn E. Tillman Gregory H. Tyson William Klimke AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
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.
format	article
author	Michael Feldgarden Vyacheslav Brover Narjol Gonzalez-Escalona Jonathan G. Frye Julie Haendiges Daniel H. Haft Maria Hoffmann James B. Pettengill Arjun B. Prasad Glenn E. Tillman Gregory H. Tyson William Klimke
author_facet	Michael Feldgarden Vyacheslav Brover Narjol Gonzalez-Escalona Jonathan G. Frye Julie Haendiges Daniel H. Haft Maria Hoffmann James B. Pettengill Arjun B. Prasad Glenn E. Tillman Gregory H. Tyson William Klimke
author_sort	Michael Feldgarden
title	AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
title_short	AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
title_full	AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
title_fullStr	AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
title_full_unstemmed	AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
title_sort	amrfinderplus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/a74a376a5af442ffaa166193f704c31e
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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

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