Whole Genome Sequencing (WGS): How significant is it for food safety?
Transcript of Whole Genome Sequencing (WGS): How significant is it for food safety?
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WholeGenomeSequencing:Howsignificant isit
for foodsafety?
TechnicalMeetingontheimpactofWholeGenomeSequencingonfoodsafetymanagementwithinaOneHealthframework
GMI9
23May2016CelineNadon,PhD
PublicHealthAgencyofCanada
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ThePaperExpertWorkshop,December2015,Rome
FrankMøllerAarestrup(Chair,Denmark)MarcAllard(USA)JohnBesser(USA)SabahBidawid(Canada)TimDallman(UK)StephanieDefibaugh-Chávez(USA)
JohnN.Kiiru(Kenya)AnaMariaMaquieira(Uruguay)PaulaMussio(Uruguay)CelineNadon(Vice-Chair,Canada)EvaMøllerNielsen(Denmark)SophieRoussel(France)
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OutlineBackground
Examples
BenePits&DrawbacksRegulatorychallenge
ResourceConsiderations
Discussion
Conclusions&Summary
WhyWGSforfoodsafety?TechnicalPapersec.on2
Real-lifeapplicaEonsTechnicalPaperSec.on3
TechnicalPaperSec.on4
ApplyingWGSwithinregulatoryframeworksTechnicalPaperSec.on5
Countrieswithlimitedcapacity&resourcesTechnicalPaperSec.on6
OneHealthandneededglobalacEonsTechnicalPaperSec.on7
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Background
600000000
WHO,2015
420000
foodborneillnesses
deaths
31majorfoodsafetyhazards
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Background
WGSwillimpactfoodsafetyworldwide
DISEASESURVEILLANCEFOODINSPECTION
OUTBREAKINVESTIGATION
ATTRIBUTION FOODTECHNOLOGY
CentreImage:SmithsonianInsEtuEon
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Background
test$1$
test$2$
test$3$
test$4$
test$5$
purpose$1$$
purpose$2$$
purpose$3$$
purpose$4$
purpose$5$
$
$
lab$1$
lab$2$
lab$3$
lab$4$
lab$5$
CourtesyofAleishaReimer
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Background
Sample collection
Bacterial Growth
DNA Extraction
Fragment
Sequencing Raw Sequence Reads
Prep DNA Library
DATA
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Background
Laboratorysubtypingmethodsaffectoutbreakdetectionandresponse
AdaptedfromJohnBesser,2006
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Background
offoodsafetyproblems
fromimpreciseorincorrectproductimplicaEons
IdentiPication,mitigationandprevention
Reducedeconomiclossesandwaste
foodsecurity
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Examples
WGSisalreadybeingusedforfoodsafetywhatcanwelearn?
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Examples
Availableatcdc.gov
HIGHERRESOLUTIONListeriosisoutbreak,UnitedStates2014
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Examples
PFGECLUSTER1
PFGECLUSTER2
PFGECLUSTER3
Seasonalfoodproduct
Seasonalfoodproduct&other*
WGSCLUSTER
WGSCLUSTER
Seasonalfoodproduct
Season
alfo
odprodu
ct
notoutbreak-associated
*ready-to-eatfoodproductcommonlyassociatedwithL.monocytogenes
AdaptedfromBesser,2015
HIGHERRESOLUTIONListeriosisoutbreak,UnitedStates2014
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Examples
WGSCLUSTER
WGSCLUSTER Se
ason
alfo
odprodu
ct
notoutbreak-associated
Confirmedhypothesisquickly
Addedstrengthtoevidence
Resolvedambiguouslab-epidata
Acceleratedresponseduetodatasharing
FueledresearchforprevenEon
WhatdidWGSdo?
HIGHERRESOLUTIONListeriosisoutbreak,UnitedStates2014
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ExamplesREDEFINED“SPORADIC”Listeriosiscases,Denmark2014-2015
TOTA
LCA
SES
5-YEARMOVIN
G
AVERAGE
Sporadiccase:anyillnessesbelowexpectedlevels?
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ExamplesREDEFINED“SPORADIC”Listeriosiscases,Denmark2014-2015
10casesover24months
WGSCLUSTER
EnvironmentalsamplesfromCompanyX,supplierto
Supermarket
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ExamplesREDEFINED“SPORADIC”Listeriosiscases,Denmark2014-2015
WGSCLUSTER
Detectedandconfirmedsourceofillnessesthatwouldhaveotherwisebeen“sporadic”
WhatdidWGSdo?
Enabledstrongevidencefromenvironmentalandfoodsampling
Delineatedoutbreakscausedbythesameproducttypefromdifferentcompanies
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ExamplesUNCOVEREDROOTCAUSESalmonellaEnteriEdis,UK2014
EnteriEdisphagetype14b
Innsetal–Eurosurveillance2015
Associatedwithea^ngatrestaurants
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ExamplesUNCOVEREDROOTCAUSESalmonellaEnteriEdis,UK2014
Innsetal–Eurosurveillance2015
Restaurantassocia^onwasjustthebeginning:
WGSshowed• Outbreaksatdifferentrestaurants
werelinked• EggdistribuEonnetworkcorrelated
withdistribuEonofcases• Tracebackofeggstosinglesupplierin
anothercountry,andlinkedtocasesoutsideofUK
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ExamplesUNCOVEREDROOTCAUSESalmonellaEnteriEdis,UK2014
Revealedtheepidemiologybehindtheoutbreak
WhatdidWGSdo?
IdenEfiedtruesource–ratherthanimplicaEngrestaurantbusinessonly,astheinterfacewiththeconsumer
EnabledtargetedintervenEonfurtherupstreaminfoodproducEon
DemonstratedbenefitsofglobalWGSsharing
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ExamplesMOTIVATEACTIONKenyanExperience
VibrioSalmonellaCampylobacterE.coli
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ExamplesMOTIVATEACTIONKenyanExperience
Demonstratesvalueofmappingdiseasehotspots,idenEfyinghighriskfoods,revisingtreatment
WhatdidWGSdo?
IncreasesconsideraEontoinvestmentsinfoodsafety
FuelsinterestinregulatoryintervenEons,foodtesEng,AMR
Illuminatesneedforadvocacy
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Examples
Whyweretheseapplicationssuccessful?
• FuncEoningnaEonalfoodcontrolsystem• Inter-sectoralinfrastructure&networks(includinglaboratory)• Adequatevolumeofisolates(costeffecEve)• Abilitytoisolatepathogensfromallmatrices• Technicalsupport:laboratory,bioinformaEcs• SufficientdatastorageandconnecEvity• InformaEcscapacityandinfrastructure
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BenePits
Image:ChrisRinke,availableatjgi.doe.gov
UNIVERSALITY
STRENGTH TO EVIDENCE
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Drawbacks
Image:ChrisRinke,availableatjgi.doe.gov
SURVEILLANCE REQUIRED
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GlobalDataSharing
Improvesfoodsafetysciences
Efficientuseofresources
Enablestrendanalysis&rapidresponse
MiEgateshealth,social,economicimpacts
InequiEesincapacity&resources
Dataownership&metadataaccess
Accountability&transparency
ValidaEon,standards&quality
Fearofbeing“scooped”
Technicaltradebarriers
Privacylaw
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RegulatoryChallenge
GUIDELINES AND BEST PRACTICES ROLE OF WGS IN EXISTING STREAMS OF EVIDENCE DATA ACCESS & TRANSPARENCY
Developedcountries:
FactorstoconsiderforusingWGSinregulatorydecisions
needtobesortedout
legal issues
trade impacts
quality control
training
communication
sustainability continuous improvement
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RegulatoryChallenge
ASSESS AND SENSITIZE
Developingcountries:
(YES)(NO)
STRENGTHEN NATIONAL FOOD SAFETY
DEVELOP AND EDUCATE
TRANSITION & FUND
Prepare policy makers, and assess: is your country’s infrastructure ready for WGS?
Build/enhance human health surveillance, food monitoring/testing, laboratories.
Decision-making guidance, rationale, cost-benefit, leverage other countries’ experiences. Educate & train.
Establish stakeholder engagement. Implement national coordination mechanisms. Harmonize SOPs. Sensitize. Sustainable funding.
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ResourceConsiderations
PERCEPTION
“WGSistooadvancedandtoodifficulttoimplement”
“WGSistheperfectsoluEon
toallourproblems”
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ResourceConsiderationsFeasibilityAssessment quesEonsforfact-basedanswers
PRIORITIES Isfoodsafetyhighpriority?Aremanypeopleaffected?Areindustry,tradeandeconomyaffected?WillWGShelpwiththeprioritypathogens?
PREREQUISITES NaEonalfoodsafetypolicyandintegratedfoodcontrolsysteminplace?FuncEonalnaEonalhealthsurveillance,withnaEonalclinicalreporEnganddatabases?FuncEonalnaEonalfoodmonitoringandtesEng?
READINESS WhereistheappropriateplacefornaEonalcoordinaEon?Howwillthesystemwork?Canotherresourcesbeleveraged,e.g.WHO,FAO,PulseNetInternaEonal,GlobalMicrobialIdenEfier?
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OneHealth
Image:NagasakiUniversity
WGScanhelpbridgeinter-sectoralapproachesthroughatrulyglobalcommondataset
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GlobalAction-Needs
FORUMSFORDISCUSSION
ASSISTANCEFORDEVELOPING
COUNTRYCAPACITY
INTERNATIONALOUTBREAK
INVESTIGATIONS
TECHNICALGUIDANCEANDBESTPRACTICES
COORDINATIONOFGLOBALONE
HEALTHACTIVITIES
LINKCOUNTRIESWITHEXTERNAL
PARTNERS
HARMONIZEDGUIDANCETOTRADEISSUES
PUBLIC-PRIVATEPARTNERSHIPFACILITATION
Opportunityforinternationalorganizations
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ConclusionCountrieswithexistingeffectivefoodsafety&healthsystems wellposiEonedforadopEngWGS
OthersmayneedtodeveloporstrengthenthebasicsPirst competentauthoriEes,labs,foodmonitoring,humanhealthsurveillance
WGSwillbecomestandardmethodologyinfoodsafety Expectedtobebeneficialforallcountries,withsomechallengesremaining
Greaterroleforinternationalorganizations Neutralandtransparentbrokers?
WGSwillnotsupplantepidemiologyandbasicgoodpractices WGSalonewillnotfixlackingorbrokensystems
GlobalsustainedcommitmentandcollaborationEnsuretechnologyadvancesdonotcontributetofurtherinequiEes
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AcknowledgementsMasamiTakeuchi(FAO,DocumentDevelopmentCoordinator)
MarkusLipp(FAO),RenataClarke(FAO)
DocumentPeer-Reviewers:SaoudAlHabsi(Oman),GenevieveBaah-Mante(Ghana),ChrisBraden(USA),JosefinaCampos(ArgenEna),IsabelChinen(ArgenEna),AlmuedaC.David(Philippines),JoanneEdge(UK),MariamEid(Lebanon),DinaEl-Khishin(Egypt),JeffFarber(Canada),AgabaFriday(Uganda),PeterGerner-Smidt(USA),MoragGraham(Canada),KaiManKam(China),KarenKeddy(SouthAfrica),ErnestoLiebana(EFSA),VirachneeLohachoompol(Thailand),KinleyPelden(Bhutan),JenniferRonholm(Canada),JorgenShlundt(Denmark),MarEnWiedmann(USA),SeyoumWolde(Ethiopia),andMayrenZamora(Mexico)
VanessaJones,SarahCahill(FAO),AmyLouiseCawthorne(WHO),GwenalaelleDauphin(FAO),FranciscoLopez(FAO)
EditingandTechnicalContributions: