Transforming Shiga toxin-producing
Shiga toxin-producing Escherichia coli
food safety
implementation
surveillance
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:
2023
2023
Historique:
received:
12
04
2023
accepted:
22
06
2023
medline:
31
7
2023
pubmed:
31
7
2023
entrez:
31
7
2023
Statut:
epublish
Résumé
Shiga toxin-producing In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed. We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated. This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.
Identifiants
pubmed: 37520372
doi: 10.3389/fmicb.2023.1204630
pmc: PMC10381951
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1204630Informations de copyright
Copyright © 2023 Nouws, Verhaegen, Denayer, Crombé, Piérard, Bogaerts, Vanneste, Marchal, Roosens 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
N Engl J Med. 2011 Nov 10;365(19):1771-80
pubmed: 21696328
Foodborne Pathog Dis. 2017 Feb;14(2):59-73
pubmed: 27992253
Infect Immun. 2011 Mar;79(3):1329-37
pubmed: 21199911
FEMS Microbiol Lett. 2013 Jan;338(1):18-23
pubmed: 23066907
Genome Res. 2018 Sep;28(9):1395-1404
pubmed: 30049790
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Epidemiol Infect. 2014 Aug;142(8):1599-608
pubmed: 24168860
Zoonoses Public Health. 2007;54(9-10):358-65
pubmed: 18035974
Appl Environ Microbiol. 2010 Jan;76(1):203-11
pubmed: 19880649
Euro Surveill. 2011 Jun 16;16(24):
pubmed: 21699770
EFSA J. 2019 Dec 03;17(12):e05898
pubmed: 32626197
J Med Microbiol. 2018 Jun;67(6):775-782
pubmed: 29687765
J Appl Microbiol. 2003;95(1):92-101
pubmed: 12807458
Int J Environ Res Public Health. 2020 Jul 16;17(14):
pubmed: 32708640
J Antimicrob Chemother. 2015 Sep;70(9):2440-6
pubmed: 26093376
Microb Genom. 2018 Mar;4(3):
pubmed: 29488865
Int J Med Microbiol. 2018 Jul;308(5):534-538
pubmed: 29884331
Eur J Clin Microbiol Infect Dis. 2017 Sep;36(9):1613-1620
pubmed: 28391537
Annu Rev Microbiol. 2011;65:189-213
pubmed: 21639793
Int J Food Microbiol. 2010 Sep 1;142(3):318-29
pubmed: 20675003
Genome Med. 2014 Nov 20;6(11):90
pubmed: 25422674
J Food Prot. 2017 May 1;80(5):829-836
pubmed: 28402187
Epidemiol Infect. 2015 Dec;143(16):3475-87
pubmed: 25920912
Int J Hyg Environ Health. 2017 Jan;220(1):57-67
pubmed: 27842895
PLoS One. 2016 Jan 29;11(1):e0147434
pubmed: 26824864
Arch Public Health. 2014 Dec 15;72(1):44
pubmed: 25810911
Cell Commun Signal. 2020 Sep 9;18(1):145
pubmed: 32907610
Gut Pathog. 2021 Feb 5;13(1):8
pubmed: 33546735
Eur J Clin Microbiol Infect Dis. 2017 Aug;36(8):1433-1441
pubmed: 28421309
Foodborne Pathog Dis. 2012 Jun;9(6):530-5
pubmed: 22545959
Microorganisms. 2022 Mar 07;10(3):
pubmed: 35336157
Foodborne Pathog Dis. 2019 Jul;16(7):441-450
pubmed: 31194586
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Lett Appl Microbiol. 2001 Feb;32(2):114-7
pubmed: 11169054
Emerg Microbes Infect. 2020 Dec;9(1):2562-2570
pubmed: 33179570
Nat Microbiol. 2016 Oct 10;2:16185
pubmed: 27723724
Clin Microbiol Infect. 2018 Apr;24(4):335-341
pubmed: 29074157
Front Microbiol. 2016 May 23;7:766
pubmed: 27242777
Clin Infect Dis. 2017 Feb 1;64(3):371-376
pubmed: 27986670
BMC Infect Dis. 2011 Sep 08;11:238
pubmed: 21902833
Ann Clin Microbiol Antimicrob. 2021 Apr 15;20(1):24
pubmed: 33858427
Appl Environ Microbiol. 2016 Jul 29;82(16):5049-56
pubmed: 27342555
Bull World Health Organ. 1963;29:387-400
pubmed: 14058230
Epidemiol Infect. 2019 Sep 27;147:e281
pubmed: 34596012
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
J Infect Dis. 2005 Oct 15;192(8):1422-9
pubmed: 16170761
Epidemiol Infect. 2016 May;144(7):1394-405
pubmed: 26584572
Epidemiol Infect. 2016 Jul;144(9):1983-90
pubmed: 26838291
J Clin Microbiol. 2012 Apr;50(4):1336-45
pubmed: 22238434
Epidemiol Infect. 2018 Sep 05;147:e6
pubmed: 30182864
Appl Environ Microbiol. 2002 Feb;68(2):576-81
pubmed: 11823193
Sci Rep. 2020 Sep 4;10(1):14649
pubmed: 32887913
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Appl Environ Microbiol. 2000 Feb;66(2):632-7
pubmed: 10653728
BMC Genomics. 2018 Dec 4;19(1):870
pubmed: 30514209
Nephrol Dial Transplant. 2012 Jul;27(7):2673-85
pubmed: 22802583
J Food Prot. 1998 Nov;61(11):1511-4
pubmed: 9829195
PLoS One. 2019 Feb 28;14(2):e0213039
pubmed: 30818354
Antimicrob Resist Infect Control. 2018 Apr 16;7:53
pubmed: 29686859
Annu Rev Food Sci Technol. 2016;7:353-74
pubmed: 26772415
J Med Microbiol. 2021 Dec;70(12):
pubmed: 34870582
Genome Res. 2020 Jan;30(1):138-152
pubmed: 31809257
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
J Med Microbiol. 2021 Jul;70(7):
pubmed: 34309502
Int J Microbiol. 2021 Dec 15;2021:1978952
pubmed: 34956368
J Clin Microbiol. 1998 Apr;36(4):878-82
pubmed: 9542902
Int J Med Microbiol. 2018 Jun;308(4):438-446
pubmed: 29574061
Front Public Health. 2017 Dec 18;5:347
pubmed: 29326921
Microb Genom. 2021 Mar;7(3):
pubmed: 33656437
J Clin Microbiol. 2015 Aug;53(8):2410-26
pubmed: 25972421
Emerg Infect Dis. 2004 May;10(5):842-7
pubmed: 15200817
Rev Argent Microbiol. 2019 Jan - Mar;51(1):32-38
pubmed: 29937134
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Epidemiol Infect. 2016 Oct;144(13):2812-23
pubmed: 27338677
EFSA J. 2022 Dec 13;20(12):e07666
pubmed: 36524203
EFSA J. 2021 Feb 27;19(2):e06406
pubmed: 33680134
EFSA J. 2021 Dec 13;19(12):e06971
pubmed: 36329690
Antimicrob Agents Chemother. 2021 Oct 18;65(11):e0118921
pubmed: 34424041
J Clin Microbiol. 2018 Feb 22;56(3):
pubmed: 29263202
Food Res Int. 2019 Feb;116:802-809
pubmed: 30717011
Clin Infect Dis. 2016 Jul 1;63(1):64-70
pubmed: 27025820
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Int J Food Microbiol. 2015 Jan 16;193:68-73
pubmed: 25462925
Bacteriophage. 2014 Jan 1;4(1):e27943
pubmed: 24575358
PLoS One. 2021 Oct 6;16(10):e0258262
pubmed: 34614029
EFSA J. 2019 Dec 11;17(12):e05926
pubmed: 32626211
Emerg Infect Dis. 2017 Sep;23(9):1609-1611
pubmed: 28820370
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Zoonoses Public Health. 2019 Feb;66(1):1-13
pubmed: 30375197
PLoS One. 2015 Mar 19;10(3):e0120353
pubmed: 25789994
Zoonoses Public Health. 2015 Nov;62(7):518-24
pubmed: 25571907
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Can J Infect Dis. 2002 May;13(3):175-81
pubmed: 18159389
Foods. 2020 Aug 01;9(8):
pubmed: 32752159
Food Microbiol. 2018 May;71:60-67
pubmed: 29366470
Front Microbiol. 2016 Mar 03;7:258
pubmed: 26973632
Int J Med Microbiol. 2018 Oct;308(7):927-932
pubmed: 30257809
Sci Rep. 2018 Jun 18;8(1):9305
pubmed: 29915208
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
J Infect Dis. 2000 May;181(5):1825-9
pubmed: 10823794
Zoonoses Public Health. 2018 Feb;65(1):e8-e22
pubmed: 28921940
Foodborne Pathog Dis. 2009 May;6(4):417-24
pubmed: 19415971
J Med Microbiol. 2004 Nov;53(Pt 11):1145-1149
pubmed: 15496394
Antimicrob Resist Infect Control. 2016 Jan 05;5:1
pubmed: 26734130
Epidemiol Infect. 2019 Sep 09;147:e264
pubmed: 31496452
Animals (Basel). 2021 Jun 22;11(7):
pubmed: 34206206
J Clin Microbiol. 2019 Sep 24;57(10):
pubmed: 31366691
J Food Sci Technol. 2022 Jun;59(6):2150-2159
pubmed: 35602458
Clin Infect Dis. 2016 May 15;62(10):1251-1258
pubmed: 26917812
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
PLoS One. 2018 Jul 2;13(7):e0199968
pubmed: 29965972
Jpn J Infect Dis. 2012;65(2):117-21
pubmed: 22446117
Mol Biol Rep. 2022 Jan;49(1):539-565
pubmed: 34822069
J Clin Microbiol. 2014 May;52(5):1501-10
pubmed: 24574290
Vet Rec. 2000 Sep 2;147(10):259-64
pubmed: 11030226
Clin Microbiol Infect. 2018 Apr;24(4):350-354
pubmed: 29309930
PLoS One. 2018 Nov 12;13(11):e0207492
pubmed: 30419067
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
Pediatr Nephrol. 2017 Jul;32(7):1263-1268
pubmed: 28343354
J Clin Microbiol. 2016 Aug;54(8):1975-83
pubmed: 27008877
J Food Prot. 2019 Aug;82(8):1398-1404
pubmed: 31335182
Microb Drug Resist. 2017 Sep;23(6):781-790
pubmed: 28304216
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
J Clin Microbiol. 2013 Jul;51(7):2082-8
pubmed: 23616449
J Clin Microbiol. 2015 May;53(5):1588-98
pubmed: 25740764
Front Microbiol. 2018 Sep 03;9:1983
pubmed: 30233509
J Antimicrob Chemother. 2019 Sep 1;74(9):2480-2496
pubmed: 31002332
Front Microbiol. 2021 Feb 05;12:627861
pubmed: 33613494