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Food Microbiology and Food Safety Jeff rey M. Farber Rozita Dara Jennifer Ronholm Editors Harnessing Big Data in Food Safety Food Microbiology and Food Safety The Food Microbiology and Food Safety series is published in conjunction with the International Association for Food Protection, a non-profit association for food safety professionals. Dedicated to the life-long educational needs of its Members,IAFPprovidesaninformationnetworkthroughitstwoscientificjournals (Food Protection Trends and Journal of Food Protection), its educational Annual Meeting,internationalmeetingsandsymposia,andinteractionbetweenfoodsafety professionals. Jeffrey M. Farber • Rozita Dara • Jennifer Ronholm Editors Harnessing Big Data in Food Safety Editors JeffreyM.Farber RozitaDara JMFarberGlobalFoodSafety SchoolofComputerScience UniversityofGuelph UniversityofGuelph Guelph,ON,Canada Guelph,ON,Canada JenniferRonholm FacultyofAgriculturalandEnvironmental Science McGillUniversity Montreal,QC,Canada ISSN2629-1010 ISSN2629-1029 (electronic) FoodMicrobiologyandFoodSafety ISBN978-3-031-07178-2 ISBN978-3-031-07179-9 (eBook) https://doi.org/10.1007/978-3-031-07179-9 ©SpringerNatureSwitzerlandAG2023 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof thematerialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressedorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface Bigdatatechnologieshavethepotentialtorevolutionizetheagriculturesectorand improve food safety and quality. The goal of this book is to share information and insights related to the current and future uses of big data in the food supply chainandtohighlightthemanyadvantages,drawattentiontopotentialpitfalls,and outlineareasripefordevelopment.Thisbookisdesignedtoprovideafoundational understandingofthevariousapplicationsofbigdatainfoodqualityandsafety. Big data requires the use of sophisticated approaches for cleaning, processing, andextractingusefulinformationtoimprovedecision-making.Foodsafety–related data are being generated in large volumes and from a variety of sources such as farms, processors, retailers, and government organizations. This book includes concrete examples of how data sources are aggregated and used in food quality and safety applications, such as decreasing food spoilage and helping to mitigate foodbornediseaseoutbreaks. Thebookalsoaddressesstandardization,datatraceability,datainteroperability, andotherdatagovernance,aswellasdata-relatedtechnicalchallenges.Theability toextractvaluefrombigdatawhileensuringtheinteroperabilityofdifferentsources toassurefoodsafetyandqualityisanexistingandcurrentchallenge. The first part of this book addresses (i) the application of machine learning techniquestothefoodsupplychain;(ii)theusesofwholegenomesequencingand bioinformatictoolsandtechnologiesforsolvingbacterialfoodborneoutbreaks;(iii) thecurrentstateofthescienceregardingthemethodologiesusedforthegeneration of big data for foodborne viruses; and (iv) the history of classical methodologies andtheadvancesinbigdatamolecular/omictechnologiesusedforfoodbornefungi. Thesecondhalfofthebookcovers(v)theroleofindicators,sensors,anddigital stakeholder interactions as relevant sources of big data in food spoilage; (vi) how blockchain-basedledgersarenowbeingusedtoimprovefoodtraceability;(vii)the advantages of big data standardization, for example, how data standardization is a criticalfoundationforaddressingdatainteroperabilitychallenges;(viii)insightsinto thedigitaltransformationthathashappenedinDubai,withaparticularemphasison how data is enabling better decision-making in food safety; and (ix) how greater advancements in the collection and use of big data in the food safety area depend v vi Preface on the organization and execution of high-level standard specifications and the developmentofincreasedprivacyprotection. The applications of big data are numerous, and in the food quality and safety area,bigdatacanbe,andoftenis,collectedalongallstepsofthefoodsupplychain. The application of big data technologies in food quality and safety control is well placed to have a tremendous impact and to drive continuous improvements in the foodindustry,nowandintothefuture. We would like to thank our respected authors for sharing their expertise and taking the time during the pandemic to write what they are passionate about. The pandemichasbeenastruggleformany,andithasreallybeenanhonortoworkwith somanydedicatedauthorswhohaveworkedthroughthepandemictogiveusgreat insightintotheirworldofbigdata,asrelatedtofood. Finally, the authors would like to give a big thanks to both Susan Safren and DeepakRaviforstickingwithusandguidingusthroughsomedifficulttimesduring thewritingandeditingofthisbook. Guelph,ON,Canada JeffreyM.Farber Guelph,ON,Canada RozitaDara Montreal,QC,Canada JenniferRonholm Contents 1 MachineLearningApplicationinFoodSafety,Production, andQuality ................................................................... 1 MitraKaviani,RozitaDara,andJeffreyM.Farber 2 FoodborneBacterialPathogen BigData–GenomicAnalysis............................................... 23 JessikaMarquis-Hrabe,DongyunJung,SoyounPark,AnitaBoray, andJenniferRonholm 3 FoodborneViralPathogenBigData:GenomicAnalysis................ 47 MatthewDallnerandNedaNasheri 4 TheUseofBigDataintheFieldofFoodMycologyandMycotoxins .. 65 MartaH.Taniwaki,JosuéJ.Silva,andLudwigNiessen 5 BigDataanditsRoleinMitigatingFoodSpoilageandQuality DeteriorationalongtheSupplyChain..................................... 93 MaleekaSinghandMariaG.Corradini 6 AlgorithmstoLocalizeFoodContaminationEvents..................... 113 HuozhiZhou,AshishJagmohan,andLavR.Varshney 7 TheNeedforDataStandardizationintheFoodSupplyChain......... 125 MitraKaviani,RozitaDara,andJeffreyM.Farber 8 BigDataDigitalTransformationinFoodSafety:ADubai Experience.................................................................... 141 T. M.BobbyKrishna 9 TheRoleofPolicyandRegulationsintheAdoptionofBig DataTechnologiesinFoodSafetyandQuality ........................... 151 ValeriaR.ParreiraandJeffreyM.Farber Index............................................................................... 161 vii Chapter 1 Machine Learning Application in Food Safety, Production, and Quality MitraKaviani,RozitaDara,andJeffreyM.Farber 1.1 Introduction Statistics indicate that the world population increased about 4.25 times (4250%) from 1920 to 2020 (Worldometer, 2021), with about 2.7 times of this growth occurringinabouthalfofacentury,from1960.Suchgrowthisaresultofimprove- mentsinmedicine,technology,andhumanlifestyle.However,itisundeniablethat supportingthepopulationisimpossiblewithoutasafeandsecurenetworkoffood productionanddelivery. The food supply chain is a complex system that comes with many challenges fromtheearlystagesof foodproduction, processing,qualitycontrol,and thefinal stagesofpackagingandtransportation.Thedemandforhigh-qualityfoodandlow- cost production has increased the need to automate and optimize supply chain processes. The recent trends in emerging artificial intelligence technologies offer new solutions for many of the agri-food problems. In the last two decades, many studiesontheapplicationofmachinelearninghavesuccessfullyimprovedthespeed and/oraccuracyofmanyprocessesinthefoodsupplychain. M.Kaviani·R.Dara((cid:2)) SchoolofComputerScience,UniversityofGuelph,Guelph,ON,Canada e-mail:[email protected] J.M.Farber SchoolofFoodScience,UniversityofGuelph,Guelph,ON,Canada ©SpringerNatureSwitzerlandAG2023 1 J.M.Farberetal.(eds.),HarnessingBigDatainFoodSafety,FoodMicrobiologyand FoodSafety,https://doi.org/10.1007/978-3-031-07179-9_1 2 M.Kavianietal. 1.2 AnIntroductiontoFoodSupply Chain Foodsupplychaincouldbedefinedastheprocessofsorting,storing,anddelivering until it is reached to the final customers (Navickas & Gružauskas, 2016). Food supplychaintasksincludefoodmanufacturing,foodcomposition,foodprocessing systems, and food safety, just to name a few. The flow of production in the food supplychainneedstobeanalyzedtocontroltheefficiencyoftheproductionprocess andfoodsafetyandmaintainqualitystandards. Thefoodsupplychainisoneoftheworld’smostcomplexandcriticallogistics systems that rapidly requires accurate traceability, food safety, and quality stan- dards. Moreover, operating a food supply chain entails several significant costs, includingtransportation,energy,logistics,humanresources,andinvestmentinnew technology.Thesupplychainbecamemorecomplexthaneverbythesechallenges. 1.2.1 FoodSafety Foodsafetyisadisciplinethatdefineshowfoodistreated,prepared,andstoredto ensurethatfoodwillnotcauseharmtotheconsumer.Foodsafetyrequiresvarious procedurestobeobservedtopreventpossiblehealthhazards(Macaskill,2009).This definition should not be confused with food security, which requires all people to accessenoughfoodtomeettheirnutritionalrequirements(Nunoetal.,2016). However, food safety also overlaps with food security to prevent harm to consumers. Safety between business and market and then between company and customers are the tracks in this line of thought. This study focused on three main typesoffoodsafety,includingfoodborneillness,foodbornediseaseoutbreaks,and foodcontamination. 1.2.1.1 FoodborneIllness Foodborne illnesses usually include any disease caused by the consumption of foodcontaminatedwithpathogensand/ortheirtoxins,includingfoodbornebacteria, viruses, protozoan parasites, as well as fungal and algal toxins. It is important to understandwhatpreventivestepscanbetakentokeepfoodsafeandavoidfoodborne illness. In addition to biological hazards, there are also chemical hazards such as natural toxins and chemical contaminants. Some environmental contaminants are intrinsically involved with the food itself (i.e., some mushrooms). In contrast, othersareproducedinfoodbypathogenswhenthereistime/temperatureabuse(i.e., the formation of histamine in certain seafood species). Food allergens are another form of chemical hazard. Meat, milk, seafood, shellfish (lobster, crab, shrimp), wheat,rice,peanuts,andnutsarethemostcommonfoodallergens.However,food sensitivity differs from people to people and food to food (Moy & Todd, 2014).