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Standards for public health genomic epidemiology to improve
infec7ous disease outbreak detec7on and inves7ga7on
Simon Fraser University and BC Public Health Microbiology and Research Laboratory
8th Interna*onal Biocura*on Conference, April 26th 2015
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Mélanie Courtot, Ph.D. [email protected]
@mcourtot
h$p://www.slideshare.net/mcourtot
3
Each year, one in eight Canadians (or four million people)
get sick with a domes7cally acquired food-‐borne illness.
Current Methods of Characterizing Foodborne Pathogens in a Public
Health Laboratory
8
• Growth characterisKcs • Phenotypic panels • AggluKnaKon reacKons • Enzyme immuno assays (EIAs) • PCR • DNA arrays (hybridizaKon) • Sanger sequencing • DNA restricKon • Electrophoresis (PFGE, capillary) Each pathogen is characterized by methods that are specific to that pathogen in mulKple workflows (separate workflows for each pathogen) TAT: 5 min – weeks (months)
Source: Rebecca Lindsey
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2011 E. coli O104:H4 German outbreak
-‐ 53 deaths, 3950 ill -‐ Farmers compensated €210 million by EU
Germany
Egypt
Source: Fiona Brinkman
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NationalPublic Health Agency
Provincial Public Health Agency Academic/Public
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The IRIDA pla^orm (Integrated Rapid InfecKous
Disease Analysis) fills in selected key
bioinformaKcs gaps, to support real-‐Kme infecKous
disease outbreak invesKgaKons in Canada
Open source, standards compliant, resource for public health agencies that can interact with, and complement, other ini-a-ves
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BC CDC Epi
NML
BC PHMRL
Doctor Private or Hospital Lab MHO LHA Pa7ent
Local HA
Public HA
Na7onal HA (NESP, PulseNet -‐ Canada)
Sunquest
CNPHI
PANORAMA PHRDWMart Sunquest (Crystal Reports)
Strain sent to BC CDC
paper
Various ReporKng Systems
PLIS PLIS
paper
paper
PFGE Pa$erns AR, Biochemical Tests
Phagetyping MLVA CGF PFGE
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Source: Emma Griffiths
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Datastorage
Dataprocessing
Data Sources
Clinical data
Epidemiology data
Laboratory data
IRIDA modules
Epi-analysis Ready Data
Epidemiologist
Interactive Genome Browser
Discovery Platform
Researcher
End Users
Lab-analysis Ready Data
Med-MicrobiologistLab Technologist
Quality Control
API
Analysis
Visualization
Value added
Activities and
Analyses
Alert from Laboratory/
Health Authority
OUTBREAKINVESTIGATION
OUTBREAK CONCLUSION & REPORTING
Dataexport
IRIDA PLATFORM
ONTOLOGY & DATA STANDARDS
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Laboratory(information( (TypON& The(Typing(ontology( Designed(with(the(goal(of(having(a(machine9readable(
language(that(describes(the(field(of(microbial(typing(OBI& Ontology(for(Biomedical(
Investigations(OBI(is(an(ontology(of(investigations,(the(protocols(and(instrumentation(used,(the(material(used,(the(data(generated(and(the(types(of(analysis(performed(on(it.(
Next(Generation(Sequencing( (NGSOnto& Next(Generation(Sequencing(
Ontology(An(ontology(to(describe(workflows(in(a(Whole(Genome(Sequencing(experiment.(Fairly(recent(effort(which(needs(to(be(expanded.(
NIAID0GSC0BRC&
NIAID,(GSCID(and(BRC(Core(metadata(
A(standard(to(annotate(core(metadata(for(those(consortia.(Very(high(level,(and(extends(OBI.(
MIxS&ontology&
An(ontological(representation(of(the(MIxS(standard(
Work(in(progress(with(the(GSC.(
Epidemiology( (TRANS& Pathogen(Transmission(
Ontology(Describes(a(process(that(is(the(means(of(how(a(pathogen(is(transmitted(from(one(host,(reservoir,(or(source(to(another(host.(
ExO& Exposure(ontology( Exposure(information(for(toxicology,(epidemiology,(disease(surveillance,(and(epigenetics(
EPO& Epidemiology(Ontology( Designed(to(support(the(semantic(annotation(of(epidemiology(resources.(A(translation(of(the(Porta(Dictionary(of(Epidemiology.(
IDO& Infectious(Disease(Ontology( A(small(middle9level(resource(aimed(at(representing(terms(common(for(infectious(diseases,(such(as(pathogen.(
Food(USDA& USDA(Nutrient(Database( Nutrient information on over 8,000 foods. Very
detailed, but not very categorized.(EFSA& European(Food(Safety(Authority(
Comprehensive(Food(Consumption(Database(
Huge resource, available via browsing tool and PDF documentation.
!
Review exisKng resources
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Metadata category Example
Sample collec7on metadata
Geographical loca-on, date, collector
Sample source metadata Host, host body site, disease status
Environmental metadata Temperature, pH, turbidity
Lab analy7c PFGE paTern, MLST, CGF
Sequencing metadata PlaWorm, Read length, Sequencing kit
Assembly process/QC Coverage, nb of con-gs
Pa7ent demographic Name, age, sex, physician
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DATA VALIDATION Validate ontology and pla^orm
• Load exis7ng datasets on the first version of IRIDA
• Annotate and integrate the data
• Validate the ontology content and its implementa7on
27 h$p://pathogenomics.sfu.ca/islandviewer
IslandViewer Dhillon and Laird et al. 2015, Nucleic Acids Research
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IRIDA SNVPhyl pipeline output in GenGis, unpublished
h$p://kiwi.cs.dal.ca/GenGIS/Main_Page
IRIDA SNVPhyl pipeline
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#1. Genomic epidemiology can help detect infecKous disease outbreak earlier #2. Integrated Rapid Infec7ous Disease Analysis plaaorm deployed in Canada, supported by a set of ontologies and standards #3. IRIDA capitalizes on exis7ng resources to make genomic epidemiology a pracKcal reality
Acknowledgements Project Leaders
Fiona Brinkman – SFU Will Hsiao – PHMRL Gary Van Domselaar – NML University of Lisbon Joᾶo Carriҫo Na7onal Microbiology Laboratory (NML) Franklin Bristow Aaron Petkau Thomas Ma$hews Josh Adam Adam Olsen Tara Lynch Shaun Tyler Philip Mabon Philip Au Celine Nadon Ma$hew Stuart-‐Edwards Morag Graham Chrystal Berry Lorelee Tsche$er Laboratory for Foodborne Zoonoses (LFZ) Eduardo Toboada Peter Kruczkiewicz Chad Laing Vic Gannon Ma$hew Whiteside Ross Duncan Steven Mutschall
Simon Fraser University (SFU) Melanie Courtot Emma Griffiths Geoff Winsor Julie Shay Ma$hew Laird Bhav Dhillon Raymond Lo BC Public Health Microbiology & Reference Laboratory (PHMRL) and BC Centre for Disease Control (BCCDC) Judy Isaac-‐Renton Patrick Tang Natalie Prystajecky Jennifer Gardy Damion Dooley Linda Hoang Kim MacDonald Yin Chang Eleni Galanis Marsha Taylor Cletus D’Souza Ana Paccagnella University of Maryland Lynn Schriml Canadian Food Inspec7on Agency (CFIA) Burton Blais Catherine Carrillo Dominic Lambert Dalhousie University Rob Beiko Alex Keddy
30
McMaster University Andrew McArthur Daim Sardar European Nucleo7de Archive Guy Cochrane Petra ten Hoopen Clara Amid European Food Safety Agency Leibana Criado Ernesto Vernazza Francesco Rizzi ValenKna