Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates

Antimicrobial Agents and Chemotherapy
Michael FeldgardenWilliam Klimke


Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole-genome sequences, the National Center for Biotechnology Information (NCBI) has produced AMRFinder, a tool that identifies AMR genes using a high-quality curated AMR gene reference database. The Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, it contains 4,579 antimicrobial resistance proteins and more than 560 HMMs. Here, we describe AMRFinder and its associated database. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli isolates phenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions. To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version ...Continue Reading


Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 31, 2001·Microbiology and Molecular Biology Reviews : MMBR·I Chopra, M Roberts
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 26, 2005·International Journal of Antimicrobial Agents·Katie L HopkinsE John Threlfall
Apr 29, 2005·BMC Bioinformatics·Erik L L Sonnhammer, Volker Hollich
May 23, 2006·Microbes and Infection·Sophie PayotQijing Zhang
Jun 29, 2006·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Kathryn GayDavid C Hooper
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Apr 18, 2008·Omics : a Journal of Integrative Biology·Samuel V AngiuoliOwen White
Feb 21, 2009·Bioinformatics·Alexandra MouraAntónio Correia
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Sep 24, 2009·The Journal of Antimicrobial Chemotherapy·Belén GutierrezBruno Gonzalez-Zorn
Dec 10, 2009·Antimicrobial Agents and Chemotherapy·Karen Bush, George A Jacoby
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Dec 6, 2011·Database : the Journal of Biological Databases and Curation·Guy TsafnatSally R Partridge
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jun 26, 2012·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·E Marti, J L Balcázar
Jun 27, 2012·Antimicrobial Agents and Chemotherapy·Thierry NaasPatrice Nordmann
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
May 8, 2013·Antimicrobial Agents and Chemotherapy·Andrew G McArthurGerard D Wright
Jun 5, 2013·Frontiers in Microbiology·María S RamirezMarcelo E Tolmasky
Oct 23, 2013·Antimicrobial Agents and Chemotherapy·Sushim Kumar GuptaJean-Marc Rolain
Jun 20, 2014·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·M OviañoG Bou
Jul 5, 2015·The Journal of Antimicrobial Chemotherapy·Gregory H TysonShaohua Zhao
Dec 20, 2015·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Kwai Lin ThongCindy Shuan Ju Teh
Jan 29, 2016·Journal of Clinical Microbiology·Basil Britto XavierSurbhi Malhotra-Kumar
May 27, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Emil P Lesho, Robert J Clifford
Jun 16, 2016·Journal of Medical Microbiology·Timothy J DallmanClaire Jenkins
Jul 2, 2016·The Journal of Antimicrobial Chemotherapy·Philip T L C ClausenOle Lund
Jul 7, 2016·Antimicrobial Agents and Chemotherapy·Patrick F McDermottShaohua Zhao
Aug 26, 2016·Journal of Clinical Microbiology·Alexander MellmannDag Harmsen
Aug 26, 2016·Microbial Drug Resistance : MDR : Mechanisms, Epidemiology, and Disease·Fábio CampioniJuliana Pfrimer Falcão
Oct 30, 2016·Nucleic Acids Research·Baofeng JiaAndrew G McArthur
Dec 21, 2016·Antimicrobial Agents and Chemotherapy·Gregory H TysonPatrick F McDermott

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