whole genome sequencing (wgs): how significant is it for food safety?

WholeGenomeSequencing:Howsignificant isit

for foodsafety?

TechnicalMeetingontheimpactofWholeGenomeSequencingonfoodsafetymanagementwithinaOneHealthframework

GMI9

23May2016CelineNadon,PhD

PublicHealthAgencyofCanada

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)

OutlineBackground

Examples

BenePits&DrawbacksRegulatorychallenge

ResourceConsiderations

Discussion

Conclusions&Summary

WhyWGSforfoodsafety?TechnicalPapersec.on2

Real-lifeapplicaEonsTechnicalPaperSec.on3

TechnicalPaperSec.on4

ApplyingWGSwithinregulatoryframeworksTechnicalPaperSec.on5

Countrieswithlimitedcapacity&resourcesTechnicalPaperSec.on6

OneHealthandneededglobalacEonsTechnicalPaperSec.on7

Background

600000000

WHO,2015

420000

foodborneillnesses

deaths

31majorfoodsafetyhazards

Background

WGSwillimpactfoodsafetyworldwide

DISEASESURVEILLANCEFOODINSPECTION

OUTBREAKINVESTIGATION

ATTRIBUTION FOODTECHNOLOGY

CentreImage:SmithsonianInsEtuEon

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

Background

Sample collection

Bacterial Growth

DNA Extraction

Fragment

Sequencing Raw Sequence Reads

Prep DNA Library

DATA

Background

Laboratorysubtypingmethodsaffectoutbreakdetectionandresponse

AdaptedfromJohnBesser,2006

Background

offoodsafetyproblems

fromimpreciseorincorrectproductimplicaEons

IdentiPication,mitigationandprevention

Reducedeconomiclossesandwaste

foodsecurity

Examples

WGSisalreadybeingusedforfoodsafetywhatcanwelearn?

Examples

Availableatcdc.gov

HIGHERRESOLUTIONListeriosisoutbreak,UnitedStates2014

Examples

PFGECLUSTER1

PFGECLUSTER2

PFGECLUSTER3

Seasonalfoodproduct

Seasonalfoodproduct&other*

WGSCLUSTER

WGSCLUSTER

Seasonalfoodproduct

Season

alfo

odprodu

ct

notoutbreak-associated

*ready-to-eatfoodproductcommonlyassociatedwithL.monocytogenes

AdaptedfromBesser,2015


Examples

WGSCLUSTER

WGSCLUSTER Se

ason

alfo

odprodu

ct

notoutbreak-associated

Confirmedhypothesisquickly

Addedstrengthtoevidence

Resolvedambiguouslab-epidata

Acceleratedresponseduetodatasharing

FueledresearchforprevenEon

WhatdidWGSdo?


ExamplesREDEFINED“SPORADIC”Listeriosiscases,Denmark2014-2015

TOTA

LCA

SES

5-YEARMOVIN

G

AVERAGE

Sporadiccase:anyillnessesbelowexpectedlevels?


10casesover24months

WGSCLUSTER

EnvironmentalsamplesfromCompanyX,supplierto

Supermarket


WGSCLUSTER

Detectedandconfirmedsourceofillnessesthatwouldhaveotherwisebeen“sporadic”

WhatdidWGSdo?

Enabledstrongevidencefromenvironmentalandfoodsampling

Delineatedoutbreakscausedbythesameproducttypefromdifferentcompanies

ExamplesUNCOVEREDROOTCAUSESalmonellaEnteriEdis,UK2014

EnteriEdisphagetype14b

Innsetal–Eurosurveillance2015

Associatedwithea^ngatrestaurants


Innsetal–Eurosurveillance2015

Restaurantassocia^onwasjustthebeginning:

WGSshowed•  Outbreaksatdifferentrestaurants

werelinked•  EggdistribuEonnetworkcorrelated

withdistribuEonofcases•  Tracebackofeggstosinglesupplierin

anothercountry,andlinkedtocasesoutsideofUK


Revealedtheepidemiologybehindtheoutbreak

WhatdidWGSdo?

IdenEfiedtruesource–ratherthanimplicaEngrestaurantbusinessonly,astheinterfacewiththeconsumer

EnabledtargetedintervenEonfurtherupstreaminfoodproducEon

DemonstratedbenefitsofglobalWGSsharing

ExamplesMOTIVATEACTIONKenyanExperience

VibrioSalmonellaCampylobacterE.coli

ExamplesMOTIVATEACTIONKenyanExperience

Demonstratesvalueofmappingdiseasehotspots,idenEfyinghighriskfoods,revisingtreatment

WhatdidWGSdo?

IncreasesconsideraEontoinvestmentsinfoodsafety

FuelsinterestinregulatoryintervenEons,foodtesEng,AMR

Illuminatesneedforadvocacy

Examples

Whyweretheseapplicationssuccessful?

•  FuncEoningnaEonalfoodcontrolsystem•  Inter-sectoralinfrastructure&networks(includinglaboratory)•  Adequatevolumeofisolates(costeffecEve)•  Abilitytoisolatepathogensfromallmatrices•  Technicalsupport:laboratory,bioinformaEcs•  SufficientdatastorageandconnecEvity•  InformaEcscapacityandinfrastructure

BenePits

Image:ChrisRinke,availableatjgi.doe.gov

UNIVERSALITY

STRENGTH TO EVIDENCE

Drawbacks

Image:ChrisRinke,availableatjgi.doe.gov

SURVEILLANCE REQUIRED

GlobalDataSharing

Improvesfoodsafetysciences

Efficientuseofresources

Enablestrendanalysis&rapidresponse

MiEgateshealth,social,economicimpacts

InequiEesincapacity&resources

Dataownership&metadataaccess

Accountability&transparency

ValidaEon,standards&quality

Fearofbeing“scooped”

Technicaltradebarriers

Privacylaw

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

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.

ResourceConsiderations

PERCEPTION

“WGSistooadvancedandtoodifficulttoimplement”

“WGSistheperfectsoluEon

toallourproblems”

ResourceConsiderationsFeasibilityAssessment quesEonsforfact-basedanswers

PRIORITIES Isfoodsafetyhighpriority?Aremanypeopleaffected?Areindustry,tradeandeconomyaffected?WillWGShelpwiththeprioritypathogens?

PREREQUISITES NaEonalfoodsafetypolicyandintegratedfoodcontrolsysteminplace?FuncEonalnaEonalhealthsurveillance,withnaEonalclinicalreporEnganddatabases?FuncEonalnaEonalfoodmonitoringandtesEng?

READINESS WhereistheappropriateplacefornaEonalcoordinaEon?Howwillthesystemwork?Canotherresourcesbeleveraged,e.g.WHO,FAO,PulseNetInternaEonal,GlobalMicrobialIdenEfier?

OneHealth

Image:NagasakiUniversity

WGScanhelpbridgeinter-sectoralapproachesthroughatrulyglobalcommondataset

GlobalAction-Needs

FORUMSFORDISCUSSION

ASSISTANCEFORDEVELOPING

COUNTRYCAPACITY

INTERNATIONALOUTBREAK

INVESTIGATIONS

TECHNICALGUIDANCEANDBESTPRACTICES

COORDINATIONOFGLOBALONE

HEALTHACTIVITIES

LINKCOUNTRIESWITHEXTERNAL

PARTNERS

HARMONIZEDGUIDANCETOTRADEISSUES

PUBLIC-PRIVATEPARTNERSHIPFACILITATION

Opportunityforinternationalorganizations

ConclusionCountrieswithexistingeffectivefoodsafety&healthsystems wellposiEonedforadopEngWGS

OthersmayneedtodeveloporstrengthenthebasicsPirst competentauthoriEes,labs,foodmonitoring,humanhealthsurveillance

WGSwillbecomestandardmethodologyinfoodsafety Expectedtobebeneficialforallcountries,withsomechallengesremaining

Greaterroleforinternationalorganizations Neutralandtransparentbrokers?

WGSwillnotsupplantepidemiologyandbasicgoodpractices WGSalonewillnotfixlackingorbrokensystems

GlobalsustainedcommitmentandcollaborationEnsuretechnologyadvancesdonotcontributetofurtherinequiEes

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:

whole genome sequencing (wgs): how significant is it for food safety?

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