One Health through new methodology Joergen Schlundt Professor Food Science JIFSAN Conference November 2019 1 One Health Action One Health refers to the collaborative efforts of multiple disciplines working locally nationally and globally to attain optimal health for people anim ID: 1045142
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1. Quid pro Quo: How Whole Genome Sequencing will enable international connection of food-, water- and human microbiology – One Health through new methodology Joergen SchlundtProfessor Food Science JIFSAN ConferenceNovember, 20191
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3. One Health Action?One Health refers to “the collaborative efforts of multiple disciplines working locally, nationally and globally to attain optimal health for people, animals and our environment.”(from World Bank: PEOPLE, PATHOGENS AND OUR PLANET, Vol. 2: The Economics of One Health, 2012)
4. One Health: the interface in Infectious Disease SurveillanceAnimal Infection and DiseaseSurvillance(including wildlife)Human DiseasesurveillanceEcosystems - WaterOne Health
5. One Health – Cost-Benefit – rel. to FoodIntegrated SurveillanceGaining understanding of Human disease attributionImproving upstream prevention of human diseaseGaining understanding of pathogens in animal populationsControlling / EliminatingImportant Human pathogensIn animal populationsImproving national Disease prevention and Animal/Food export Decrease in health costsIncrease in export earning= Economic DevelopmentOne Health Win-Win
6. One Health sharing data and isolatesWe need to find mechanisms to share data and actual microorganisms (human/animal)There needs to be clear benefit for all countries involved (industrialized countries -> help developing countries – as per SPS/WTO agreement)In future, systems will provide dramatically different potential for pathogen characterization and pathogen tracking (global interactive database of total DNA sequencing data)
7. History197720031953Watson & Crick1970Frederick SangerWalter GilbertAlan Maxam198019902004454 starts the next generation sequencing eraNew Opportunities ?15.10.2014DTU Management Engineering7
8. Leeuwenhook – 1676 – Bacteria/MicroscopyPasteur– 1861– Proves Germ TheoryInvents pure culture technique (+ Koch)Schwann– 1839– Cell TheoryFleming– 1928– Discovers AntibioticsNOTEWORTHY MILESTONES IN MICROBIOLOGY 2005 – Next Generation Sequencing (NGS) of microorganismsWhole Genome Sequencing (WGS) - The next MilestoneWhat about Gram ??
9. Some see new technologies and ask: ”Why?”We see dramatic technological improvement, and ask: ”Why not?” (paraphrased from Robert Kennedy)
10. Global Microbial Identifier: GMIA global system will enable two major lines of action:Simple identification of all microorganisms in clinical (or other) settings, making redundant existing systems, and enabling reduction of total time for characterization down to typical time needed to obtain the original isolateA total database of unique sequences of all relevant microbiological strains globally, enabling real-time global surveillance of disease and pathogen developments
11. Growing networkI----Cloud computingAll DNA sequencesDiagnosis Antimicrobial Resistance DNA SequencingPatient – or Food , Food & DiseaseSurveillance FUTURE Global Microbial Identifier: GMI1st global tool to identify Microorganisms and Antimicrobial ResistanceIndependent experts from 57 countriesStill:Just an Idea !
12. Virus – Bacteria – ParasitesSame - Samewww.globalmicrobialidentifier.org
13. The most important One Health issue:AMR - A global emerging threat World Bank Group, March 2017, Drug-resistant Infections – A threat to our economic future/Review on AMR, Dec. 2014
14. Real-time sharing of data on occurrences of all infectious agents including AMR dataBioinformatic tools for automatically detections of related clusters in time and spacePossibilities to observe trends in clones and species as well as resistance, virulence, and other epidemiological markersAbility to rapidly compare between all types of data; genomic, epi, explanatory variablesWhat is needed!
15. Now – we all know USA is the greatest !(GenomeTrakr and Pulsenet just a few examples)But sometimes other countries can contribute alsoEspecially - if you can get them to share their … SEWAGE And although the idea is not from Norway – its close You guessed it – its from Denmark 15
16. Monitoring large healthy populationsusing a metagenomic approach
17. Metagenomic sequencingMetagenomics – One technology that takes all Metagenomics is defined as the sequencing-based analysis of genomes contained within an environmental sample
18. WHO - NNF - EU/COMPARE -Global Sewage Surveillance project 2016
19. Hiseq, Novoseq,MinIon, PlasmidBioinformatic workflowsSamples processing & sequencingGlobal, localUse, trade, travelSample anddata collectionData and information sharing platformactionableinformation Predictive models Epidemiological modellingMapping, binning, abundanceMulti-variante, Machine LearningGlobal input for analysisDissemination and interactionSupporting activitiesBarriers to open data sharingThe structure of the project
20. Global sewage surveillance – 2016AMR abundance per AMR class and gene Developed by Patrick Munk15 most common AMR genes – Resistance genes depended on bacterial species Hendriksen RS et al. Accepted NCOMMS
21. Predicting global AMR significance for persistence in metagenomics sewage samples by applying artificial intelligence using explanatory variables, social demographics Global sewage surveillance – 2016Applying artificial intelligenceDatabaseSourceAntimicrobial usageMIDAS, Xponent, ECDCHuman Development Index World BankHealth, Nutrition and Population World BankGEMS/Food consumption database World Health OrganizationFAOSTAT Food security and agriculture Food and Agriculture Organization UNGlobal Livestock Production and Health Atlas Food and Agriculture Organization UNAntimicrobial resistanceSewers, ECDCFlight dataLabor dataInternational Labor organizationEnvironmentCDIAC (Carbon Dioxide Information Analysis Center)
22. Global sewage surveillance – 2016Predicting resistanceMap showing predicted prevalence of AMRDeveloped by Frank AarestrupHendriksen RS et al. Accepted NCOMMS
23. Predictors of higher AMRMortality rateInformal employmentTime to importDeath, by communicable diseases and maternal, prenatal and nutrition conditionsRisk of maternal deathOpen defecationDiarrhoea prevalence in childrenRisk of impoverishing expenditure for surgical care Predictors of lower AMRInvestment in water and sanitationCompleteness of death reportingGrace period on external debtEducational attainmentNumber of surgical proceduresLife expectancy at birthNumber of PhysiciansBirths attended by skilled health staff 23Global sewage surveillance – 2016Important predictors Developed by Patrick NjageHendriksen RS et al. Accepted NCOMMS
24. Global sewage surveillance –2017 - 2018On average 85 countries and 160 cities per round620 samples in totalApp 100 countriesCollected by Rene Hendriksen / Jette Kjeldsen
25. Metagenomic sequencing is potential superior to conventional and other genomic methods for quantification of AMR and pathogensPowerful way to determine prevalence and differences of all genesA realistic alternative to conventional surveillanceurban sewage is a proxy for clinical or individual human samples for population based surveillance?Potential to use the same data for other surveillance topicsSome challenges still to overcomeSanitation and health seems to be the main drivers of resistance in healthy humans / usage in animals but other explanatory variables might also explain the occurrence of AMR Sustainability!Conclusions – sewage studies
26. Tine HaldTimo RöderSaria OtaniMark Woolhouse Bram Van BunnikLuke McNallyMilou G. M. van de Schans Simon RasmussenBent Petersen Clara AmidGuy CochraneThomas Sicheritz-PontenAna Maria de Roda HusmanHeike Schmitt Tina ZuidemaDavid NieuwenhuijseHeike SchmittJorge Raul Matheu AlvarezAwa Aidara-KaneMarion Koopmansthe Global Sewage Surveillance project consortium and many many more…..Acknowledgement (for global sewage study)Frank M. Aarestrup (PI)Patrick Munk Patrick M. K. Njage Thomas Nordahl Petersen Pimlapas Leekitcharoenphon Håkan VigreJette Sejer KjeldgaardOle LundPhilip ClausenRolf S. KaasJudit SzarvasMarie Louise JespersenJolene PedersenMarkus JohanssonSünje Johanna PampDerya AytanOksana LukjancenkoLukasz Dariusz DynowskiCamilla Hundahl JohnsenChristian BrinchJolene PedersenFunding and Support
27. http://cge.cbs.dtu.dk/services/all.phpBuilding Global Capacity Center for Genomic Epidemiology – DTU: Technical University of Denmark
28. Future of Infectious Disease Control:International – and NationalHuman - Animal“Microbial molecular data are essential information for effective surveillance and proportional response to international Public Health Emergencies” (EU/GESTURE Expert Meeting, 2009)But we need same systems for:Animal and Human strainsEnvironmental, Food and Water strains National and International eventsDeveloping and Richer countries
29. So, Why is WHO not driving this revolutionary potential for change: too many players ??29Food SafetyAMRTBEmergenciesFluPolioEnvironment/WaterSexual and reproductive healthNagoya Protocol ?However: at World Health Assembly May 2020 There will be a Food Safety ResolutionHopefully Member States will include strong statements about the global use of NGS
30. It’s all:One Health
31. Continuous improvementScience IndependenceResolveDare to change: One Health!