BOSC 2016 - The Open-Source Outbreak

OPEN-SOURCETHE

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 diseasedr. jennifer gardy, bc centre for disease control canada research chair in public health genomics

@jennifergardy

BSL-4 BSL-4

BSL-3 BSL-3

BSL-1BSL-1FLU

EBOLA

COLD

RABIES

WE DON’T KNOW a lot about infectious DISEASES

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 FOESnew forms

Lyme Disease incidence, 2001

DATA COURTESY CDC

Lyme Disease incidence, 2013

DATA COURTESY CDC

22

3442

57

93

87

1940S 1950S 1960S 1970S 1980S 1990S

335new infectious diseases emerged from 1940–2004

K. Jo

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ADAPTED FROM K. Jones et al, Nature, 2008

WE’RE NOTLOOKING

DECEMBER 6: DEATH OF PATIENT ZERO, GUINEA

MARCH 22 : FIRST PRO-MED MAIL ALERTMARCH 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

HOTSPOT SURVEILLANCE

VIRAL CENSUS-BY-SEQUENCING

SURVEY POOP-ULATION HEALTH

IT CAN BE ASSIMPLE AS

A

phone

@daanensen

epihack.org

@johnbrownstein

DECEMBER 6: DEATH OF PATIENT ZERO, GUINEA

MARCH 22 : FIRST PRO-MED MAIL ALERTMARCH 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

nEmesisAdam Sadilek

Bioinformatics opportunities - disease detectionrapid 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

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

HOW DO DISEASES SPREADWITHIN POPULATIONS

social contacts

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

ge·no·mic ep·i·de·mi·ol·o·gy (jēˈnōmik ˌepiˌdēmēˈäləjē/) n. reading whole genome sequences from outbreak isolates to track person-to-person spread of an infectious disease.

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AACAAG

TELEPHONE

ART B

Y DE

VIAN

TART

USE

R SC

UMMY

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

BC

D

HATHERELL ET AL, 2016. microbial genomics.

An updated model to better infer time of infection

MEMO

Bus: (250) 868-7818 Fax: (250) 868-7826 Kelowna Health Centre Email: [email protected] 1340 Ellis Street www.interiorhealth.ca Kelowna, BC V1Y 9N1

Quality y Integrity y Respect y 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 [email protected].

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

2009 SWINE FLU

virological.org (@arambaut)

@trvrb & @richardneher

microreact.org @daanensen

ASSOCIATED PRESS

JUNE 2THE TWEET

JUNE 2THE BLOG

JUNETHE WIKI

JULYA 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 TRACKINGbridge the evolutionary-maths-bioinformatics gap leverage the power of information visualization

get on twitter!

@[email protected]

thanks Canada Research Chairs program & the Michael Smith Foundation for Health Research

BOSC 2016 - The Open-Source Outbreak

Science

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