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
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.
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
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
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
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
64.
65.
66.
67. HATHERELL ET AL, 2016. microbial genomics.
An updated model to better infer time of infection
68.
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!