Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study.
foodborne outbreak investigation
public health
strain-level metagenomics
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
08 Aug 2020
08 Aug 2020
Historique:
received:
13
07
2020
revised:
04
08
2020
accepted:
06
08
2020
entrez:
14
8
2020
pubmed:
14
8
2020
medline:
20
2
2021
Statut:
epublish
Résumé
Culture-independent diagnostics, such as metagenomic shotgun sequencing of food samples, could not only reduce the turnaround time of samples in an outbreak investigation, but also allow the detection of multi-species and multi-strain outbreaks. For successful foodborne outbreak investigation using a metagenomic approach, it is, however, necessary to bioinformatically separate the genomes of individual strains, including strains belonging to the same species, present in a microbial community, which has up until now not been demonstrated for this application. The current work shows the feasibility of strain-level metagenomics of enriched food matrix samples making use of data analysis tools that classify reads against a sequence database. It includes a brief comparison of two database-based read classification tools, Sigma and Sparse, using a mock community obtained by in vitro spiking minced meat with a Shiga toxin-producing
Identifiants
pubmed: 32784459
pii: ijms21165688
doi: 10.3390/ijms21165688
pmc: PMC7460976
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Belgian Federal Public Service of Health, Food Chain Safety and Environment
ID : RF 17/6316 StEQIDEMIC.be
Organisme : Sciensano
ID : contract RP NeXSplorer.iph and .Be READY
Références
Arch Public Health. 2014 Dec 15;72(1):44
pubmed: 25810911
Infect Genet Evol. 2016 Jun;40:389-397
pubmed: 26391184
BMC Microbiol. 2016 Nov 16;16(1):275
pubmed: 27852235
Genetics. 2014 Jul;197(3):925-37
pubmed: 24793089
Appl Microbiol Biotechnol. 2018 Apr;102(7):3267-3285
pubmed: 29460001
PLoS One. 2016 Dec 8;11(12):e0167870
pubmed: 27930729
Implement Sci. 2019 Aug 13;14(1):79
pubmed: 31409417
Nat Commun. 2017 Dec 22;8(1):2260
pubmed: 29273717
N Engl J Med. 2011 Aug 25;365(8):709-17
pubmed: 21793740
J Appl Microbiol. 2008 Nov;105(5):1259-65
pubmed: 18713293
Bioinformatics. 2017 Jul 15;33(14):i124-i132
pubmed: 28881972
Front Microbiol. 2017 May 01;8:777
pubmed: 28507541
Euro Surveill. 2011 Jun 16;16(24):
pubmed: 21699770
EFSA J. 2019 Dec 03;17(12):e05898
pubmed: 32626197
Genome Med. 2014 Nov 20;6(11):90
pubmed: 25422674
BMC Microbiol. 2015 Aug 12;15:160
pubmed: 26264042
Genome Announc. 2018 Jan 11;6(2):
pubmed: 29326203
Genome Biol. 2017 Sep 21;18(1):181
pubmed: 28934976
PLoS One. 2013 Sep 09;8(9):e73079
pubmed: 24039862
Microbiome. 2014 Sep 05;2:33
pubmed: 25225611
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Clin Microbiol Rev. 2013 Oct;26(4):822-80
pubmed: 24092857
Bioinformatics. 2016 Jan 15;32(2):292-4
pubmed: 26428292
BMC Bioinformatics. 2011 Apr 26;12:119
pubmed: 21521499
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
BMC Bioinformatics. 2012 Aug 21;13:209
pubmed: 22909249
Microb Genom. 2016 Apr 29;2(4):e000056
pubmed: 28348851
Front Microbiol. 2019 Aug 06;10:1805
pubmed: 31447815
Microbiome. 2018 Mar 20;6(1):50
pubmed: 29554948
Appl Environ Microbiol. 2017 Aug 1;83(16):
pubmed: 28625983
Nat Biotechnol. 2015 Oct;33(10):1045-52
pubmed: 26344404
Int J Food Microbiol. 2018 Dec 20;287:3-9
pubmed: 29246458
BMC Genomics. 2017 May 8;18(1):359
pubmed: 28482799
Food Microbiol. 2019 Jun;79:96-115
pubmed: 30621881
Nat Methods. 2016 May;13(5):435-8
pubmed: 26999001
Nucleic Acids Res. 2015 Sep 18;43(16):e105
pubmed: 25990729
BMC Genomics. 2018 Dec 27;19(1):968
pubmed: 30587114
J Clin Microbiol. 2015 Aug;53(8):2410-26
pubmed: 25972421
Genome Announc. 2015 Mar 26;3(2):
pubmed: 25814601
Nucleic Acids Res. 2017 Jan 25;45(2):e7
pubmed: 27651451
Microbiol Spectr. 2014 Dec;2(6):
pubmed: 26104460
J Clin Microbiol. 2014 Jul;52(7):2365-70
pubmed: 24759713
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Genome Res. 2017 Apr;27(4):626-638
pubmed: 28167665
Bioinformatics. 2015 Jan 15;31(2):170-7
pubmed: 25266224
Front Microbiol. 2017 Oct 20;8:2029
pubmed: 29104564
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
pubmed: 19855009
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Appl Environ Microbiol. 2015 Dec;81(23):8183-91
pubmed: 26386062
Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5
pubmed: 29447696
Front Microbiol. 2017 Jul 04;8:1069
pubmed: 28725217
J Clin Microbiol. 2014 May;52(5):1501-10
pubmed: 24574290
BMC Genomics. 2018 Aug 31;19(1):647
pubmed: 30170539
PLoS One. 2014 May 20;9(5):e98103
pubmed: 24844597
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842