A presentation introducing genomic epidemiology and its application in public health. It also explains the need for standards to support the Canadian Integrated Rapid Infectious Disease Analysis platform which implements genomic epidemiology analyses for detection and investigation of infectious disease outbreaks caused by food-borne pathogens.

1. 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.
mcourtot@gmail.com
@mcourtot
h$p://www.slideshare.net/mcourtot

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

3. 3
Each
year,
one
in
eight
Canadians
(or
four
million
people)
get
sick
with
a
domes7cally
acquired
food-­‐borne
illness.

4. 4
Source:
Peter
Gleick,
Scienceblogs.com

5. 5

6. 6

7. 7

8. 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. 9

10. 10
Epidemiology
Case centric
Clinical
Patient centric
Laboratory
Test centric

11. 11
Source:
Jennifer
Gardy

12. 12
2011
E.
coli
O104:H4
German
outbreak
-­‐
53
deaths,
3950
ill
-­‐
Farmers
compensated
€210
million
by
EU
Germany
Egypt
Source:
Fiona
Brinkman

13. 13
National
Public 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
14
IRIDA
Annual
General
Mee7ng
Winnipeg,
April
8-­‐9,
2015

15. 15

16. 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. 17
Data
storage
Data
processing
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-Microbiologist
Lab Technologist
Quality
Control
API
Analysis
Visualization
Value
added
Activities
and
Analyses
Alert from
Laboratory/
Health
Authority
OUTBREAK
INVESTIGATION
OUTBREAK
CONCLUSION & REPORTING
Data
export
IRIDA PLATFORM
ONTOLOGY & DATA STANDARDS

18. How
do
we
build
those
standards?
18

19. Interviews
with
key
personnel
19

20. 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.(
NIAID0GSC0
BRC&
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. 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. 22

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

24. What’s
next?
24

25. 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. 26
Source:
Damion
Dooley
INTERFACE
SUPPORT
Enable
flexible
user-­‐specific
interface

27. 27
h$p://pathogenomics.sfu.ca/islandviewer
IslandViewer
Dhillon
and
Laird
et
al.
2015,
Nucleic
Acids
Research

28. 28
IRIDA
SNVPhyl
pipeline
output
in
GenGis,
unpublished
h$p://kiwi.cs.dal.ca/GenGIS/Main_Page
IRIDA
SNVPhyl
pipeline

29. 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

30. 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. 31
Lisbon,
Portugal
July
28th
2015
hfp://purl.org/net/mcourtot/2015genomics.html