Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.
antimicrobial resistance
food‐borne outbreak investigation
metagenomics
microbial risk assessment
source attribution
typing of food‐borne pathogens
whole genome sequencing
Journal
EFSA journal. European Food Safety Authority
ISSN: 1831-4732
Titre abrégé: EFSA J
Pays: United States
ID NLM: 101642076
Informations de publication
Date de publication:
Dec 2019
Dec 2019
Historique:
entrez:
7
7
2020
pubmed:
7
7
2020
medline:
7
7
2020
Statut:
epublish
Résumé
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source-attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogen-host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for
Identifiants
pubmed: 32626197
doi: 10.2903/j.efsa.2019.5898
pii: EFS25898
pmc: PMC7008917
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e05898Informations de copyright
© 2019 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
Références
Nucleic Acids Res. 2017 Jan 4;45(D1):D535-D542
pubmed: 27899627
Clin Infect Dis. 2015 Nov 1;61 Suppl 4:S259-65
pubmed: 26449940
Nat Microbiol. 2018 Aug;3(8):898-908
pubmed: 30038308
Stat Biosci. 2017 Jun;9(1):13-27
pubmed: 28959368
Sci Rep. 2016 Apr 12;6:24175
pubmed: 27067514
Microb Genom. 2018 Feb;4(2):
pubmed: 29338812
J Clin Microbiol. 2015 Aug;53(8):2402-3
pubmed: 26085609
Nat Rev Microbiol. 2013 Oct;11(10):728-36
pubmed: 23979428
Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):6335-6340
pubmed: 30862737
Front Microbiol. 2018 Mar 27;9:592
pubmed: 29636749
Euro Surveill. 2018 May;23(18):
pubmed: 29741151
FEMS Microbiol Ecol. 2018 Feb 1;94(2):
pubmed: 29300934
J Clin Microbiol. 2014 Aug;52(8):2782-6
pubmed: 24850348
Microbiome. 2017 Dec 11;5(1):159
pubmed: 29228991
Clin Infect Dis. 2012 Apr;54(8):1046-52
pubmed: 22281845
Appl Environ Microbiol. 2011 Feb;77(4):1171-80
pubmed: 21169442
Front Microbiol. 2016 Jan 19;6:1573
pubmed: 26834722
Appl Environ Microbiol. 2017 Jan 17;83(3):
pubmed: 27881416
Nat Rev Genet. 2018 Sep;19(9):549-565
pubmed: 29973680
Microb Genom. 2016 Jul 11;2(7):e000064
pubmed: 28348859
J Clin Microbiol. 2012 Mar;50(3):788-97
pubmed: 22170908
Appl Environ Microbiol. 2018 Jun 18;84(13):
pubmed: 29728379
EMBO Rep. 2016 Nov;17(11):1499-1505
pubmed: 27644260
PLoS Genet. 2008 Sep 26;4(9):e1000203
pubmed: 18818764
Food Microbiol. 2018 Aug;73:122-128
pubmed: 29526197
EcoSal Plus. 2012 Nov;5(1):
pubmed: 26442824
PLoS Pathog. 2008 Sep 05;4(9):e1000146
pubmed: 18773117
Emerg Infect Dis. 2014 Sep;20(9):1481-9
pubmed: 25147968
Microb Genom. 2018 Mar;4(3):
pubmed: 29488865
Sci Adv. 2019 Mar 27;5(3):eaau9124
pubmed: 30944853
J Clin Microbiol. 2003 Nov;41(11):4930-40
pubmed: 14605120
mSphere. 2019 Apr 3;4(2):
pubmed: 30944215
Genome Med. 2014 Nov 20;6(11):90
pubmed: 25422674
Epidemiol Infect. 2015 Dec;143(16):3475-87
pubmed: 25920912
Sci Rep. 2018 Oct 15;8(1):15251
pubmed: 30323193
Emerg Infect Dis. 2019 Jan;25(1):82-91
pubmed: 30561314
J Antimicrob Chemother. 2017 Jan;72(1):145-152
pubmed: 27678285
Antimicrob Agents Chemother. 2001 May;45(5):1467-72
pubmed: 11302812
Nat Biotechnol. 2018 Jan;36(1):61-69
pubmed: 29227468
Epidemiol Infect. 2017 Apr;145(5):864-871
pubmed: 27964764
Genes Genet Syst. 2007 Feb;82(1):1-8
pubmed: 17396015
Microbiome. 2019 Mar 21;7(1):44
pubmed: 30898140
DNA Res. 2015 Feb;22(1):101-7
pubmed: 25428893
Food Microbiol. 2018 May;71:39-45
pubmed: 29366467
J Clin Microbiol. 2019 Feb 27;57(3):
pubmed: 30381421
Genomics Inform. 2019 Mar;17(1):e6
pubmed: 30929407
Genome Res. 2019 Feb;29(2):304-316
pubmed: 30679308
Microb Genom. 2019 Jan;5(1):
pubmed: 30648944
Int J Food Microbiol. 2019 Feb 16;291:181-188
pubmed: 30530095
PLoS Negl Trop Dis. 2013 Nov 14;7(11):e2557
pubmed: 24244782
Int J Food Microbiol. 2019 Mar 2;292:72-82
pubmed: 30579059
Clin Microbiol Infect. 2018 Apr;24(4):342-349
pubmed: 29309933
Front Microbiol. 2016 Jun 30;7:985
pubmed: 27446025
PLoS One. 2013;8(1):e55254
pubmed: 23383127
PeerJ. 2016 Apr 05;4:e1752
pubmed: 27069781
PLoS Negl Trop Dis. 2015 Mar 24;9(3):e0003611
pubmed: 25803844
Mol Biol Evol. 2013 May;30(5):1224-8
pubmed: 23408797
Int J Food Microbiol. 2018 Dec 20;287:18-27
pubmed: 29032838
J Bacteriol. 2003 May;185(9):2936-43
pubmed: 12700273
Nature. 2004 Mar 4;428(6978):37-43
pubmed: 14961025
Food Microbiol. 2018 May;71:32-38
pubmed: 29366466
Biotechniques. 2014 Feb 01;56(2):61-4, 66, 68, passim
pubmed: 24502796
Front Microbiol. 2017 May 09;8:808
pubmed: 28536563
mBio. 2013 Mar 05;4(2):
pubmed: 23462113
Foodborne Pathog Dis. 2016 Jun;13(6):296-302
pubmed: 27046731
Int J Food Microbiol. 2014 Sep 18;187:57-72
pubmed: 25051454
Clin Microbiol Infect. 2017 Jan;23(1):2-22
pubmed: 27890457
BMC Bioinformatics. 2008 Dec 16;9:539
pubmed: 19087322
Emerg Microbes Infect. 2019;8(1):486-502
pubmed: 30924410
Int J Food Microbiol. 2013 May 15;163(2-3):193-203
pubmed: 23562696
Nat Microbiol. 2016 Oct 10;2:16185
pubmed: 27723724
Clin Microbiol Infect. 2018 Apr;24(4):335-341
pubmed: 29074157
Appl Environ Microbiol. 2017 Aug 1;83(16):
pubmed: 28625983
J Antimicrob Chemother. 2015 Jan;70(1):75-80
pubmed: 25190723
Mob DNA. 2018 Dec 19;9:37
pubmed: 30574213
Anim Health Res Rev. 2018 Feb 22;:1-16
pubmed: 29467055
J Antimicrob Chemother. 2013 Apr;68(4):771-7
pubmed: 23233485
Science. 2018 Oct 26;362(6413):404-406
pubmed: 30361362
G3 (Bethesda). 2014 May 22;4(7):1339-46
pubmed: 24855317
Appl Environ Microbiol. 2015 Oct 30;82(2):459-66
pubmed: 26519386
Pediatr Res. 2017 Nov;82(5):829-838
pubmed: 28665922
BMC Microbiol. 2016 Nov 16;16(1):275
pubmed: 27852235
PeerJ. 2016 Aug 17;4:e2308
pubmed: 27602279
Risk Anal. 2019 Jun;39(6):1397-1413
pubmed: 30462833
J Clin Microbiol. 2007 Jun;45(6):2020-4
pubmed: 17446326
Emerg Infect Dis. 2017 Oct;23(10):1631-1639
pubmed: 28930002
Front Microbiol. 2017 Jun 26;8:1068
pubmed: 28694792
Risk Anal. 2018 Oct;38(10):2013-2028
pubmed: 29900563
J Clin Microbiol. 2015 May;53(5):1765-7
pubmed: 25788543
Bioinform Biol Insights. 2015 May 05;9:75-88
pubmed: 25983555
Nat Commun. 2018 Feb 28;9(1):870
pubmed: 29491419
PLoS One. 2014 Jan 17;9(1):e85901
pubmed: 24465775
Arch Microbiol. 2010 Apr;192(4):267-78
pubmed: 20174918
Int J Food Microbiol. 2018 Dec 20;287:3-9
pubmed: 29246458
Euro Surveill. 2018 Aug;23(35):
pubmed: 30180926
Front Public Health. 2019 Sep 04;7:242
pubmed: 31552211
Front Microbiol. 2017 Jun 09;8:1044
pubmed: 28649236
J Antimicrob Chemother. 2017 Oct 1;72(10):2764-2768
pubmed: 29091202
Epidemiol Infect. 2000 Oct;125(2):229-55
pubmed: 11117946
mSystems. 2016 Oct 18;1(5):
pubmed: 27822556
J Antimicrob Chemother. 2018 May 1;73(5):1121-1137
pubmed: 29370371
Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1325-1338
pubmed: 28285331
Gene. 2012 Oct 10;507(2):146-51
pubmed: 22850272
Microbiome. 2018 Jan 15;6(1):11
pubmed: 29335005
Nucleic Acids Res. 2019 Jun 20;47(11):5539-5549
pubmed: 31076776
Nat Rev Genet. 2016 May 17;17(6):333-51
pubmed: 27184599
J Food Prot. 2018 Nov;81(11):1815-1820
pubmed: 30307759
Genetics. 2003 Jan;163(1):367-74
pubmed: 12586722
Food Microbiol. 2019 Jun;79:96-115
pubmed: 30621881
Front Microbiol. 2018 May 17;9:891
pubmed: 29867804
Epidemiol Infect. 2014 May;142(5):1070-82
pubmed: 23920400
J Clin Microbiol. 2015 Aug;53(8):2410-26
pubmed: 25972421
Appl Environ Microbiol. 2008 Jan;74(1):172-81
pubmed: 17981942
Genes Genet Syst. 2004 Feb;79(1):1-8
pubmed: 15056931
J Food Prot. 2016 Jul;79(7):1161-8
pubmed: 27357035
J Hazard Mater. 2016 Dec 15;320:10-17
pubmed: 27505289
Euro Surveill. 2018 Mar;23(13):
pubmed: 29616614
Euro Surveill. 2019 Jan;24(4):
pubmed: 30696532
Anim Health Res Rev. 2011 Dec;12(2):169-85
pubmed: 22152292
Microb Genom. 2015 Sep 14;1(3):e000029
pubmed: 28348814
Nat Commun. 2019 Mar 8;10(1):1124
pubmed: 30850636
Int J Food Microbiol. 2018 Dec 20;287:28-39
pubmed: 29703417
Clin Microbiol Rev. 2016 Oct;29(4):837-57
pubmed: 27559074
Clin Microbiol Rev. 2018 Aug 1;31(4):
pubmed: 30068738
Int J Food Microbiol. 2018 Dec 20;287:10-17
pubmed: 29157743
Epidemiol Infect. 2018 Aug;146(11):1452-1460
pubmed: 29961436
Trends Microbiol. 2014 May;22(5):275-81
pubmed: 24572764
PLoS One. 2015 Jul 16;10(7):e0132783
pubmed: 26182345
J Food Prot. 2006 Feb;69(2):335-44
pubmed: 16496574
PLoS One. 2016 Jan 22;11(1):e0147101
pubmed: 26800248
Appl Environ Microbiol. 2017 Mar 17;83(7):
pubmed: 28115376
Nat Biotechnol. 2019 Jul;37(7):783-792
pubmed: 31235920
PLoS One. 2016 Dec 8;11(12):e0167870
pubmed: 27930729
Epidemiol Infect. 2018 Jan;146(2):187-196
pubmed: 29248018
Front Microbiol. 2018 Dec 13;9:2993
pubmed: 30619114
Pediatr Infect Dis J. 2006 Jan;25(1):2-7
pubmed: 16395094
Nat Genet. 2016 Mar;48(3):308-313
pubmed: 26829754
Int J Food Microbiol. 2019 Jan 16;289:115-126
pubmed: 30223195
Mol Ecol. 2006 Sep;15(10):2833-43
pubmed: 16911204
PLoS One. 2016 Feb 05;11(2):e0148028
pubmed: 26849217
Euro Surveill. 2018 Feb;23(6):
pubmed: 29439754
PeerJ. 2014 May 27;2:e415
pubmed: 24918035
Nat Biotechnol. 2017 Sep 12;35(9):833-844
pubmed: 28898207
Trends Microbiol. 2018 Sep;26(9):794-808
pubmed: 29525421
J Clin Microbiol. 2019 Jan 30;57(2):
pubmed: 30333126
Sci Rep. 2016 Apr 20;6:24645
pubmed: 27095377
Antimicrob Agents Chemother. 2019 May 24;63(6):
pubmed: 30910897
Int J Food Microbiol. 2018 Jun 2;274:1-11
pubmed: 29574242
Microb Genom. 2018 Aug;4(8):
pubmed: 30052170
PLoS Genet. 2018 Apr 5;14(4):e1007261
pubmed: 29621240
Euro Surveill. 2019 Jan;24(3):
pubmed: 30670140
Food Microbiol. 2018 May;71:60-67
pubmed: 29366470
Clin Microbiol Infect. 2016 Jul;22(7):620-4
pubmed: 27145209
Front Microbiol. 2016 Mar 03;7:258
pubmed: 26973632
Food Microbiol. 2018 May;71:46-54
pubmed: 29366468
Sci Rep. 2018 Jun 18;8(1):9305
pubmed: 29915208
Res Microbiol. 2014 Sep;165(7):526-30
pubmed: 25049166
Nat Genet. 2014 Dec;46(12):1321-6
pubmed: 25383970
PLoS Pathog. 2012;8(6):e1002776
pubmed: 22737074
Microbiol Spectr. 2018 May;6(3):
pubmed: 29916343
JAMA. 2013 Apr 10;309(14):1502-10
pubmed: 23571589
Genetics. 2014 Jun;197(2):573-89
pubmed: 24700103
Cell. 2019 Jan 24;176(3):649-662.e20
pubmed: 30661755
Risk Anal. 2004 Feb;24(1):255-69
pubmed: 15028016
Foodborne Pathog Dis. 2009 May;6(4):417-24
pubmed: 19415971
BMC Genomics. 2014 Sep 08;15:768
pubmed: 25196593
J Clin Microbiol. 2018 Aug 27;56(9):
pubmed: 29925638
PLoS One. 2018 May 2;13(5):e0195885
pubmed: 29718947
PLoS Pathog. 2019 Apr 24;15(4):e1007700
pubmed: 31017982
Nat Rev Microbiol. 2015 Feb;13(2):116-23
pubmed: 25534811
BMC Genomics. 2011 Aug 22;12:425
pubmed: 21859443
J Antimicrob Chemother. 2017 Dec 1;72(12):3317-3324
pubmed: 28962028
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Int J Food Microbiol. 2015 Nov 20;213:130-8
pubmed: 25910947
J Antimicrob Chemother. 2017 Feb;72(2):385-392
pubmed: 28115502
Emerg Infect Dis. 2018 Dec;24(12):2303-2308
pubmed: 30457532
Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11312-11317
pubmed: 27647883
Microorganisms. 2019 Feb 19;7(2):
pubmed: 30791454
Appl Environ Microbiol. 2015 Dec;81(23):8183-91
pubmed: 26386062
Emerg Infect Dis. 2016 Dec;22(12):2078-2086
pubmed: 27584691
Trends Microbiol. 2016 Apr;24(4):241-245
pubmed: 26875619
J Clin Microbiol. 2014 Apr;52(4):1182-91
pubmed: 24501024
J Antimicrob Chemother. 2016 Aug;71(8):2300-5
pubmed: 27090630
J Antimicrob Chemother. 2017 Dec 1;72(12):3288-3297
pubmed: 28961934
Euro Surveill. 2019 Jan;24(4):
pubmed: 30696528
BMC Microbiol. 2017 Jun 8;17(1):133
pubmed: 28595575
Lancet Planet Health. 2019 Aug;3(8):e357-e369
pubmed: 31439317
Front Microbiol. 2017 May 23;8:909
pubmed: 28588568
Emerg Infect Dis. 2013 Aug;19(8):1302-4
pubmed: 23877005
Clin Microbiol Infect. 2018 Apr;24(4):350-354
pubmed: 29309930
Appl Environ Microbiol. 2016 Apr 04;82(8):2433-2443
pubmed: 26873315
Nat Commun. 2019 Jun 6;10(1):2488
pubmed: 31171794
Int J Food Microbiol. 2016 Jul 2;228:1-9
pubmed: 27077825
Genes (Basel). 2018 May 22;9(5):
pubmed: 29789467
Nature. 2019 Apr;568(7753):505-510
pubmed: 30867587
Euro Surveill. 2017 Jun 8;22(23):
pubmed: 28662764
Genome Biol. 2016 Dec 16;17(1):260
pubmed: 27986083
J Clin Microbiol. 2016 Aug;54(8):1975-83
pubmed: 27008877
Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):863-8
pubmed: 25535353
Lancet Infect Dis. 2016 Feb;16(2):161-8
pubmed: 26603172
Risk Anal. 2016 Mar;36(3):571-88
pubmed: 27002674
Genetics. 2003 Aug;164(4):1567-87
pubmed: 12930761
Front Microbiol. 2019 May 21;10:1107
pubmed: 31231317
BMC Genomics. 2010 Feb 18;11:120
pubmed: 20167121
Risk Anal. 2009 Jul;29(7):970-84
pubmed: 19486473
Front Microbiol. 2018 Sep 03;9:1983
pubmed: 30233509
BMC Biol. 2014 Nov 12;12:87
pubmed: 25387460
Emerg Infect Dis. 2017 Oct;23(10):1680-1683
pubmed: 28930013
Microbiome. 2019 Aug 29;7(1):123
pubmed: 31466530
Ann N Y Acad Sci. 2017 Jan;1388(1):108-120
pubmed: 28134443
PLoS One. 2015 Jun 05;10(6):e0128797
pubmed: 26047499
Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11923-7
pubmed: 23818615