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OPEN-SOURCE
THE
OUTBREAK01010111 01001000 01000101 01010010 01000101 00100000
01000100 01000001 01010100 01000001 00100000 01001101
01000101 01000101 01010100 01010011 00100000 01000100
01001001 01010011 01000101 01000001 01010011 01000101
where data meets disease
dr. jennifer gardy, bc centre for disease control
canada research chair in public health genomics
@jennifergardy
BOSC 2016 - The Open-Source Outbreak
BSL-4 BSL-4
BSL-3 BSL-3
BSL-1BSL-1
FLU
EBOLA
COL D
RABIES
WE DON’T KNOW a lot
about infectious DISEASES
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
56 MILLION1/3 FROM INFECTIOUS DISEASE GLOBALLY
DEATH RATE$ARE LOWER IN HIGH-INCOME REGIONS 5X
LUNG FROM AN EGYPTIAN MUMMY, 2050BC,
showing evidence of tb infection.
e·merg·ing in·fec·tious dis·ease (n): a disease that
has appeared in a population for the first time, or
that may have existed previously but is rapidly
increasing in incidence or geographic range.
OLD FOES
new forms
Lyme Disease incidence, 2001
DATA COURTESY CDC
Lyme Disease incidence, 2013
DATA COURTESY CDC
BOSC 2016 - The Open-Source Outbreak
22
34
42
57
93
87
1940S 1950S 1960S 1970S 1980S 1990S
335new infectious diseases
emerged from 1940–2004
K.Jonesetal,Nature,2008
ADAPTED FROM K. Jones et al, Nature, 2008
WE’RE NOT
LOOKING
DECEMBER 6: DEATH OF PATIENT ZERO, GUINEA
MARCH 22 : FIRST PRO-MED MAIL ALERT
MARCH 25 : SUSPECT CASE IN CANADA
JUNE 23 : MSF - “EBOLA OUT OF CONTROL”
JUNE 26 : FIRST WHO PRESS RELEASE
AUGUST 8: WHO DECLARES PUBLIC HEALTH EMERGENCY
28,616
11,310
BOSC 2016 - The Open-Source Outbreak
HOTSPOT SURVEILLANCE
VIRAL CENSUS-BY-SEQUENCING
SURVEY POOP-ULATION HEALTH
BOSC 2016 - The Open-Source Outbreak
IT CAN BE AS
SIMPLE
ASA
phone
@daanensen
epihack.org
BOSC 2016 - The Open-Source Outbreak
@johnbrownstein
DECEMBER 6: DEATH OF PATIENT ZERO, GUINEA
MARCH 22 : FIRST PRO-MED MAIL ALERT
MARCH 25 : SUSPECT CASE IN CANADA
JUNE 23 : MSF - “EBOLA OUT OF CONTROL”
JUNE 26 : FIRST WHO PRESS RELEASE
AUGUST 8: WHO DECLARES PUBLIC HEALTH EMERGENCY
MARCH 14: FIRST HEALTH MAP ALERT
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
nEmesisAdam Sadilek
Bioinformatics opportunities - disease detection
rapid ID of pathogens from metagenomic surveillance data
computing in the (under-resourced) field
applying our algorithms to new data types
leading by open-source example
http://zibraproject.github.io
@zibraproject
BOSC 2016 - The Open-Source Outbreak
01000100 01100001 01110100 01100001
00100000 01100011 01100001 01101110
00100000 01101000 01100101 01101100
01110000 00100000 01110101 01110011
00100000 01110100 01110010 01100001
01100011 01101011 00100000 01100101
01101101 01100101 01110010 01100111
01101001 01101110 01100111 00100000
01101001 01101110 01100110 01100101
01100011 01110100 01101001 01101111
01110101 01110011 00100000 01100100
01101001 01110011 01100101 01100001
01110011 01100101 01110011
HOWDODISEASESSPREAD
WITHINPOPULATIONS
BOSC 2016 - The Open-Source Outbreak
socialcontacts
BOSC 2016 - The Open-Source Outbreak
SURVEILLANCE IDENTIFIES A POTENTIAL OUTBREAK
MOLECULAR EPIDEMIOLOGY IDENTIFIES
CLUSTERED ISOLATES
EPIDEMIOLOGICAL INVESTIGATION IDENTIFIES
PUTATIVE TRANSMISSIONS
L I M I TAT I O N S O F C U R R E N T M E T H O D S
• Genotyping methods only tell you a cluster of cases
exists, not the order/direction of transmission
• Size/membership of the cluster varies with the
molecular typing method(s) used
• Epidemiological investigation is required to derive
the links between cases, and may not be available
or of sufficient quality
GENOMICS TO THE RESCUE
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
ge·no·mic ep·i·de·mi·ol·o·gy (jē
ˈnōmik ˌepiˌdēmēˈäləjē/)
n. reading whole genome
sequences from outbreak isolates
to track person-to-person spread
of an infectious disease.
AAAAAA
AAAAAA
AAAAAA
AACAAA
AAAAAA
AAAAAA
AACAAA
AACAAA
GACAAA
AAAATA
AAAAAA
AAAAAA AACAAA
AACAAA
AACTAA AACTAA
AACAAG
TELEPHONE
ARTBYDEVIANTARTUSERSCUMMY
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
TRANSPHYLO INTERPRETS A
BAYESIAN PHYLOGENY IN THE
CONTEXT OF WITHIN-HOST
GENETIC DIVERSITY .
with Xavier Didelot & Caroline Colijn
(Imperial College London)
Can we infer a transmission tree T
given a phylogenetic tree G?
A
B
C
D A
B
C
D
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
HATHERELL ET AL, 2016. microbial genomics.
An updated model to better infer time of infection
BOSC 2016 - The Open-Source Outbreak
MEMO
Bus: (250) 868-7818 Fax: (250) 868-7826 Kelowna Health Centre
Email: sue.pollock@interiorhealth.ca 1340 Ellis Street
www.interiorhealth.ca Kelowna, BC V1Y 9N1
Quality Integrity Respect Trust
In 2008, an outbreak of Mycobacterium Tuberculosis (TB) was declared after a higher-than-expected number of
TB cases were identified in the Central Okanagan. Between 2008 and 2014, 52 outbreak-related active TB cases
were identified. Most cases were homeless and/or street-involved persons in Kelowna with a small linked
cluster in Penticton, and several cases in Salmon Arm.
Interior Health’s TB Outbreak Management Team, in partnership with community organizations and the BC
Centre for Disease Control have used numerous strategies to identify and treat new cases and to minimize the
public health risk. Epidemiological and genomics (genetic fingerprinting) data demonstrate that the peak of the
outbreak occurred in late 2010/early 2011. There is currently no evidence of ongoing transmission and
incidence of new TB cases has returned to baseline (pre-outbreak) levels.
The Central Okanagan TB outbreak is declared over as of January 29, 2015.
We expect to see sporadic new TB diagnoses connected to the outbreak in the coming years; early detection of
these cases will be critical to preventing another outbreak. The CD Unit will disseminate further information
about next steps as the outbreak response is de-escalated.
Outbreaks of TB among homeless persons are strongly related to social determinants of health such as
employment, income, safe housing, and access to health care. Preventing and controlling future outbreaks
requires continued attention to these inequities through comprehensive policies and programs that aim to
reduce health disparities in our community.
On behalf of the Office of the Medical Health Officers, we thank each of you for your hard work and
collaboration in controlling this outbreak and for your continued dedication to TB prevention and control.
If you have any questions, please contact the Communicable Disease Unit at 1-866-778-7736 or by email
CDUnit@interiorhealth.ca.
To:
CIHS Promotion & Prevention; Infection Control, Workplace Health & Safety, KGH Administrators, PRH
Administrators, Senior Executive Team, CD Unit
From: Dr. Sue Pollock, Medical Health Officer & Medical Director, Communicable Disease
Date: February 4, 2015
RE: Central Okanagan TB Outbreak Declared Over
STEPHEN GIRE ET AL.
99 EBOLA GENOMES
55 MUTATIONS
1 SUPER-SPREADER
SPREAD via funeral
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
2009SWINE FLU
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
virological.org (@arambaut)
@trvrb & @richardneher
BOSC 2016 - The Open-Source Outbreak
BOSC 2016 - The Open-Source Outbreak
microreact.org @daanensen
ASSOCIATED PRESS
JUNE 2
THE TWEET
JUNE 2
THE BLOG
JUNE
THE WIKI
JUNE
THE WIKI
JULY
A PAPER
“Our rapid open-source
analysis of an outbreak-
associated bacterial
pathogen was characterized
by a propitious confluence of
high-throughput genomics,
crowd-sourced analyses,
and a liberal approach to
data release”
Bioinformatics opportunities - disease TRACKING
bridge the evolutionary-maths-bioinformatics gap
leverage the power of information visualization
get on twitter!
@jennifergardy
jennifer.gardy@bccdc.ca
thanks Canada Research Chairs program & the
Michael Smith Foundation for Health Research

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BOSC 2016 - The Open-Source Outbreak

  • 1. OPEN-SOURCE THE OUTBREAK01010111 01001000 01000101 01010010 01000101 00100000 01000100 01000001 01010100 01000001 00100000 01001101 01000101 01000101 01010100 01010011 00100000 01000100 01001001 01010011 01000101 01000001 01010011 01000101 where data meets disease dr. jennifer gardy, bc centre for disease control canada research chair in public health genomics @jennifergardy
  • 3. BSL-4 BSL-4 BSL-3 BSL-3 BSL-1BSL-1 FLU EBOLA COL D RABIES WE DON’T KNOW a lot about infectious DISEASES
  • 7. 56 MILLION1/3 FROM INFECTIOUS DISEASE GLOBALLY DEATH RATE$ARE LOWER IN HIGH-INCOME REGIONS 5X
  • 8. LUNG FROM AN EGYPTIAN MUMMY, 2050BC, showing evidence of tb infection.
  • 9. e·merg·ing in·fec·tious dis·ease (n): a disease that has appeared in a population for the first time, or that may have existed previously but is rapidly increasing in incidence or geographic range.
  • 11. Lyme Disease incidence, 2001 DATA COURTESY CDC
  • 12. Lyme Disease incidence, 2013 DATA COURTESY CDC
  • 14. 22 34 42 57 93 87 1940S 1950S 1960S 1970S 1980S 1990S 335new infectious diseases emerged from 1940–2004 K.Jonesetal,Nature,2008
  • 15. ADAPTED FROM K. Jones et al, Nature, 2008
  • 17. DECEMBER 6: DEATH OF PATIENT ZERO, GUINEA MARCH 22 : FIRST PRO-MED MAIL ALERT MARCH 25 : SUSPECT CASE IN CANADA JUNE 23 : MSF - “EBOLA OUT OF CONTROL” JUNE 26 : FIRST WHO PRESS RELEASE AUGUST 8: WHO DECLARES PUBLIC HEALTH EMERGENCY
  • 24. IT CAN BE AS SIMPLE ASA phone
  • 29. DECEMBER 6: DEATH OF PATIENT ZERO, GUINEA MARCH 22 : FIRST PRO-MED MAIL ALERT MARCH 25 : SUSPECT CASE IN CANADA JUNE 23 : MSF - “EBOLA OUT OF CONTROL” JUNE 26 : FIRST WHO PRESS RELEASE AUGUST 8: WHO DECLARES PUBLIC HEALTH EMERGENCY MARCH 14: FIRST HEALTH MAP ALERT
  • 36. Bioinformatics opportunities - disease detection rapid ID of pathogens from metagenomic surveillance data computing in the (under-resourced) field applying our algorithms to new data types leading by open-source example
  • 39. 01000100 01100001 01110100 01100001 00100000 01100011 01100001 01101110 00100000 01101000 01100101 01101100 01110000 00100000 01110101 01110011 00100000 01110100 01110010 01100001 01100011 01101011 00100000 01100101 01101101 01100101 01110010 01100111 01101001 01101110 01100111 00100000 01101001 01101110 01100110 01100101 01100011 01110100 01101001 01101111 01110101 01110011 00100000 01100100 01101001 01110011 01100101 01100001 01110011 01100101 01110011
  • 44. SURVEILLANCE IDENTIFIES A POTENTIAL OUTBREAK
  • 47. L I M I TAT I O N S O F C U R R E N T M E T H O D S • Genotyping methods only tell you a cluster of cases exists, not the order/direction of transmission • Size/membership of the cluster varies with the molecular typing method(s) used • Epidemiological investigation is required to derive the links between cases, and may not be available or of sufficient quality
  • 48. GENOMICS TO THE RESCUE
  • 52. ge·no·mic ep·i·de·mi·ol·o·gy (jē ˈnōmik ˌepiˌdēmēˈäləjē/) n. reading whole genome sequences from outbreak isolates to track person-to-person spread of an infectious disease.
  • 62. TRANSPHYLO INTERPRETS A BAYESIAN PHYLOGENY IN THE CONTEXT OF WITHIN-HOST GENETIC DIVERSITY . with Xavier Didelot & Caroline Colijn (Imperial College London)
  • 63. Can we infer a transmission tree T given a phylogenetic tree G? A B C D A B C D
  • 67. HATHERELL ET AL, 2016. microbial genomics. An updated model to better infer time of infection
  • 69. MEMO Bus: (250) 868-7818 Fax: (250) 868-7826 Kelowna Health Centre Email: sue.pollock@interiorhealth.ca 1340 Ellis Street www.interiorhealth.ca Kelowna, BC V1Y 9N1 Quality Integrity Respect Trust In 2008, an outbreak of Mycobacterium Tuberculosis (TB) was declared after a higher-than-expected number of TB cases were identified in the Central Okanagan. Between 2008 and 2014, 52 outbreak-related active TB cases were identified. Most cases were homeless and/or street-involved persons in Kelowna with a small linked cluster in Penticton, and several cases in Salmon Arm. Interior Health’s TB Outbreak Management Team, in partnership with community organizations and the BC Centre for Disease Control have used numerous strategies to identify and treat new cases and to minimize the public health risk. Epidemiological and genomics (genetic fingerprinting) data demonstrate that the peak of the outbreak occurred in late 2010/early 2011. There is currently no evidence of ongoing transmission and incidence of new TB cases has returned to baseline (pre-outbreak) levels. The Central Okanagan TB outbreak is declared over as of January 29, 2015. We expect to see sporadic new TB diagnoses connected to the outbreak in the coming years; early detection of these cases will be critical to preventing another outbreak. The CD Unit will disseminate further information about next steps as the outbreak response is de-escalated. Outbreaks of TB among homeless persons are strongly related to social determinants of health such as employment, income, safe housing, and access to health care. Preventing and controlling future outbreaks requires continued attention to these inequities through comprehensive policies and programs that aim to reduce health disparities in our community. On behalf of the Office of the Medical Health Officers, we thank each of you for your hard work and collaboration in controlling this outbreak and for your continued dedication to TB prevention and control. If you have any questions, please contact the Communicable Disease Unit at 1-866-778-7736 or by email CDUnit@interiorhealth.ca. To: CIHS Promotion & Prevention; Infection Control, Workplace Health & Safety, KGH Administrators, PRH Administrators, Senior Executive Team, CD Unit From: Dr. Sue Pollock, Medical Health Officer & Medical Director, Communicable Disease Date: February 4, 2015 RE: Central Okanagan TB Outbreak Declared Over
  • 70. STEPHEN GIRE ET AL. 99 EBOLA GENOMES 55 MUTATIONS 1 SUPER-SPREADER SPREAD via funeral
  • 86. JULY A PAPER “Our rapid open-source analysis of an outbreak- associated bacterial pathogen was characterized by a propitious confluence of high-throughput genomics, crowd-sourced analyses, and a liberal approach to data release”
  • 87. Bioinformatics opportunities - disease TRACKING bridge the evolutionary-maths-bioinformatics gap leverage the power of information visualization get on twitter!
  • 88. @jennifergardy jennifer.gardy@bccdc.ca thanks Canada Research Chairs program & the Michael Smith Foundation for Health Research