Standards for public health genomic epidemiology - Biocuration 2015

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  

  1  

Mélanie  Courtot,  Ph.D.  [email protected]  

@mcourtot  

h$p://www.slideshare.net/mcourtot    

2  Source:  Interna-onal  Associa-on  for  Food  Protec-on  

3  

Each  year,  one  in  eight  Canadians  (or  four  million  people)  

get  sick  with  a  domes7cally  acquired    food-­‐borne  illness.  

4  Source:  Peter  Gleick,  Scienceblogs.com  

5  

6  

7  

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  

9  

10  

Epidemiology Case centric

Clinical Patient centric

Laboratory Test centric

11  Source:  Jennifer  Gardy  

12  

   2011  E.  coli  O104:H4    German  outbreak    

       -­‐  53  deaths,  3950  ill            -­‐  Farmers  compensated                €210  million  by  EU      

Germany    

Egypt    

Source:  Fiona  Brinkman  

13  

NationalPublic Health Agency

Provincial Public Health Agency Academic/Public

13  

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    

14  14  

IRIDA  Annual  General  Mee7ng  Winnipeg,  April  8-­‐9,  2015    

15  

16  

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  

16  

Source:  Emma  Griffiths  

17  

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

How  do  we  build  those  standards?    

18  

Interviews  with  key  personnel  

19  

20  

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  

21  

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  

22  

23  Source:  h$p://learn.geneKcs.utah.edu/content/gsl/diversity/  

What’s  next?  

24  

25  

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  

26  Source:  Damion  Dooley  

INTERFACE  SUPPORT  Enable  flexible  user-­‐specific  interface  

27  h$p://pathogenomics.sfu.ca/islandviewer  

IslandViewer  Dhillon  and  Laird  et  al.  2015,  Nucleic  Acids  Research  

28  

IRIDA  SNVPhyl  pipeline  output  in  GenGis,  unpublished  

h$p://kiwi.cs.dal.ca/GenGIS/Main_Page    

IRIDA  SNVPhyl  pipeline    

29  

#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        

31  

Lisbon,  Portugal  July  28th  2015  

 hfp://purl.org/net/mcourtot/2015genomics.html