Automated antimicrobial susceptibility testing and antimicrobial resistance genotyping using Illumina and Oxford Nanopore Technologies sequencing data among
WGS-AST
antimicrobial susceptibility testing
carbapenem-resistant Enterobacteriaceae
molecular diagnostics
nanopore sequencing
point-of-care testing
whole-genome sequencing
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2022
2022
Historique:
received:
20
06
2022
accepted:
08
07
2022
entrez:
25
8
2022
pubmed:
26
8
2022
medline:
26
8
2022
Statut:
epublish
Résumé
Whole-genome sequencing (WGS) enables the molecular characterization of bacterial pathogens. We compared the accuracy of the Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for the determination of AMR classes and antimicrobial susceptibility testing (AST) among 181 clinical
Identifiants
pubmed: 36003946
doi: 10.3389/fmicb.2022.973605
pmc: PMC9393496
doi:
Types de publication
Journal Article
Langues
eng
Pagination
973605Informations de copyright
Copyright © 2022 Conzemius, Bergman, Májek, Beisken, Lewis, Jacobs, Tamma and Simner.
Déclaration de conflit d'intérêts
RC, PM, and SB are employees of Ares Genetics GmbH. PS has received grants and personal fees from Accelerate Diagnostics, OpGen Inc., and BD Diagnostics; grants from bioMérieux, Inc., Affinity Biosensors, and Hardy Diagnostics; and personal fees from Roche Diagnostics, GeneCapture, and Shionogi Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
J Antimicrob Chemother. 2017 Jan;72(1):104-114
pubmed: 27667325
Curr Protoc Bioinformatics. 2020 Jun;70(1):e102
pubmed: 32559359
Genome Res. 2017 May;27(5):737-746
pubmed: 28100585
J Clin Microbiol. 2020 Jun 24;58(7):
pubmed: 32295890
Nature. 2016 Feb 11;530(7589):228-232
pubmed: 26840485
Microb Drug Resist. 2003 Fall;9(3):265-71
pubmed: 12959405
Biomedicines. 2021 Jul 29;9(8):
pubmed: 34440114
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Bioinformatics. 2018 Jul 1;34(13):i142-i150
pubmed: 29949969
Antimicrob Agents Chemother. 2018 Dec 21;63(1):
pubmed: 30373801
Genome Biol. 2018 Jul 13;19(1):90
pubmed: 30005597
Nat Commun. 2018 Nov 30;9(1):5114
pubmed: 30504855
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
BMC Infect Dis. 2013 Jan 07;13:8
pubmed: 23295059
J Bacteriol. 2016 Nov 4;198(23):3200-3208
pubmed: 27645385
Antimicrob Agents Chemother. 2004 Jan;48(1):1-14
pubmed: 14693512
Nat Methods. 2015 Apr;12(4):351-6
pubmed: 25686389
Mol Biol Evol. 2021 Sep 27;38(10):4647-4654
pubmed: 34320186
Antimicrob Agents Chemother. 2012 Jul;56(7):3960-2
pubmed: 22547620
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Genome Biol. 2014 Mar 03;15(3):R46
pubmed: 24580807
Nat Biotechnol. 2021 Nov;39(11):1348-1365
pubmed: 34750572
Genome Med. 2015 Sep 29;7:99
pubmed: 26416663
Nat Biotechnol. 2019 Jul;37(7):783-792
pubmed: 31235920
Bioinformatics. 2018 Aug 1;34(15):2666-2669
pubmed: 29547981
Lancet. 2018 May 19;391(10134):1976-1978
pubmed: 29864011
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Int J Mol Sci. 2021 Dec 02;22(23):
pubmed: 34884852
Front Microbiol. 2016 Sep 05;7:1374
pubmed: 27656166
Microb Genom. 2021 Aug;7(8):
pubmed: 34431763
J Antimicrob Chemother. 2009 Apr;63(4):659-67
pubmed: 19233898
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Clin Microbiol Infect. 2004 Nov;10 Suppl 4:1-9
pubmed: 15522034
Front Cell Infect Microbiol. 2021 Feb 15;11:610348
pubmed: 33659219