Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies.
Flongle
SNP analysis
STEC
food surveillance
metagenomics
nanopore
outbreak
strain-level
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2021
2021
Historique:
received:
08
07
2021
accepted:
13
10
2021
entrez:
22
11
2021
pubmed:
23
11
2021
medline:
23
11
2021
Statut:
epublish
Résumé
The current routine laboratory practices to investigate food samples in case of foodborne outbreaks still rely on attempts to isolate the pathogen in order to characterize it. We present in this study a proof of concept using Shiga toxin-producing
Identifiants
pubmed: 34803953
doi: 10.3389/fmicb.2021.738284
pmc: PMC8602914
doi:
Types de publication
Journal Article
Langues
eng
Pagination
738284Informations de copyright
Copyright © 2021 Buytaers, Saltykova, Denayer, Verhaegen, Vanneste, Roosens, Piérard, Marchal and De Keersmaecker.
Déclaration de conflit d'intérêts
The 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
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
EFSA J. 2019 Dec 03;17(12):e05898
pubmed: 32626197
Comput Struct Biotechnol J. 2018 Feb 27;16:108-120
pubmed: 30026887
EFSA J. 2021 Feb 27;19(2):e06406
pubmed: 33680134
Front Microbiol. 2019 Mar 06;10:362
pubmed: 30894839
Foods. 2020 Aug 01;9(8):
pubmed: 32752159
EFSA J. 2018 Dec 12;16(12):e05500
pubmed: 32625785
Nat Methods. 2015 Aug;12(8):733-5
pubmed: 26076426
Int J Mol Sci. 2020 Aug 08;21(16):
pubmed: 32784459
Front Microbiol. 2017 Jul 04;8:1069
pubmed: 28725217
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
PLoS One. 2018 Feb 6;13(2):e0192504
pubmed: 29408896
J Antimicrob Chemother. 2017 Jan;72(1):104-114
pubmed: 27667325
Arch Public Health. 2014 Dec 15;72(1):44
pubmed: 25810911
Microorganisms. 2020 Aug 05;8(8):
pubmed: 32764329
Microb Genom. 2021 Apr;7(4):
pubmed: 33826490
Genome Biol. 2015 May 30;16:114
pubmed: 26025440
Appl Environ Microbiol. 2018 Jan 31;84(4):
pubmed: 29196295
Sci Rep. 2020 Sep 4;10(1):14649
pubmed: 32887913
Gigascience. 2019 Aug 1;8(8):
pubmed: 31433830
J Clin Microbiol. 2015 Aug;53(8):2410-26
pubmed: 25972421
Nat Microbiol. 2020 Mar;5(3):430-442
pubmed: 31844297
Nat Commun. 2019 Jul 11;10(1):3066
pubmed: 31296857
PLoS One. 2016 Dec 8;11(12):e0167870
pubmed: 27930729
Nat Biotechnol. 2019 Jul;37(7):783-792
pubmed: 31235920
EFSA J. 2019 Dec 11;17(12):e05926
pubmed: 32626211
J Clin Microbiol. 2014 May;52(5):1501-10
pubmed: 24574290
Appl Environ Microbiol. 2020 Jun 17;86(13):
pubmed: 32358002
Clin Chem. 2014 Apr;60(4):586-8
pubmed: 24398073
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Nat Rev Genet. 2018 Jan;19(1):9-20
pubmed: 29129921