genomics in public health

genomics in public healthTracking & treating disease with DNA sequencing

Dr. Jennifer Gardy, BC Centre for Disease Control @jennifergardy [email protected]

HelLO!

Senior Scientist (Genomics), BCCDC Asst. Professor, UBC SPPH

Canada Research Chair in Public Health Genomics

agenda of funWhere does microbiology fit in public health? What are we doing now? Diagnostics & outbreaks The genomics revolution Current genomics approaches in public health microbiology Future directions

Goal: show you a very cool domain where interesting genomics is maybe going to prevent

us all from dying of something awful

microbiology in public health

public health (noun, \ˈpə-blik ˈhelth\): the organized efforts of society to keep people healthy and prevent injury, illness and premature death, combining programs, services and policies that protect and promote people’s health.

our health is governed by a number of factors

health protection

surveillance prevention

health assessmenthealth

promotion

emergency

preparedness

the public health lab

patient sample for diagnosis

study sample for surveillance

environmental sample

patient sample for diagnosis what does this patient have? how should I treat them?

study sample for surveillance what is circulating in our population? what does this mean for PH?

environmental sample what is circulating in our water, food? what does this mean for PH?

What are we doing now?

1. What does this patient have? Culture-based diagnostics.

2. What does this patient have? serology

3. What does this patient have? nucleic acid amplification testing.

a representative example: mycobacterial diagnostics

1

Clinician suspects TB

DAY 0

1 2

Sample collected, submitted

DAY 0

Sample collected, submitted

Courtesy Mabel Rodrigues

1 2 3

AFB smear microscopy

DAY 1-2

Slides are prepped


Smears are read


AFB smear microscopy

1 2 3

Nucleic Acid Amplification Testing (NAAT)

3*

DAY 2-3

Prelim report issued

1 2 3 4

Inoculate into culture

DAY 1

Solid culture on LJ


Liquid culture on Bactec MGIT


2nd report issued with culture results

Success! I have diagnosed my patient. Now what do I treat them with?

AMR occurs through multiple routes

1. what do i treat this patient with? phenotypic dst.

2. What do i treat this patient with? molecular testing.

a representative example: mycobacterial dst

Liquid culture on Bactec MGIT


Third report issued after DST results

Cool. Thanks. I’m done. Over to you, public health.

Public health: what’s going around and why?

communicable disease surveillance

• multiple data streams: lab positives, other reports, physician billing codes, alert healthcare workers

• what is out there? • is there more than usual? • are blips due to an outbreak?

?How do we investigate an

SURVEILLANCE IDENTIFIES CASES

MOLECULAR EPIDEMIOLOGY IDENTIFIES POTENTIALLY RELATED CASES

Restriction digest (RFLP) Multilocus sequence typing (MLST) Multilocus variable number

tandem repeat analysis (MLVA/VNTR)

RFLP MLST/MLVA

Enzymes cleave chromosome into large fragments

PCR primers amplify specific regions of the chromosome

RFLP MLST/MLVA

The whole chromosome, broken into a few pieces

A few short fragments of the chromosome

RFLP MLST/MLVA

The whole chromosome, broken into a few pieces

Run on a gel

A few short fragments of the chromosome

Compare against database

Size S

tanda

rd

Size S

tanda

rd

Size S

tanda

rd

FIELD EPIDEMIOLOGY SUGGESTS TRANSMISSIONS

Basic Principles of Field Epidemiology • Identify cases and controls • Structured or semi-structured interview • Data collated into a line list • Combined with clinical data to infer likely exposures and

transmissions

BUT WAIT. WE HAVE A PROBLEM. • Genotyping methods only tell you a cluster of cases exists, not the order/

direction of transmission • Size/membership of the cluster varies with the typing method(s) used • Epidemiological investigation is required to derive the links between cases,

and may not be available or of sufficient qualitY

a representative example: mycobacterial GENOTYPING

Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat

A map of all MIRU-VNTR TB genotypes in BC, 2005-2014

a summary of our roadblocks

diagnostics: time-consuming, require suspicion, variable performance, still many “unknown” samples phenotypic dst: sloooooooooooooooooow surveillance: low-resolution typing techniques, heavily reliant on field epidemiological data the whole process: multiple parallel steps, reporting at various stages throughout the process

our chainsaw: genomics

THE FIRST SEQUENCED GENOME1995. 1 GENOME, 13 MONTHS, $600,000, ROOM FULL OF MACHINES

with the current technology800-1000 GENOMEs, 5 days, <$100 each, one single machine

with the current technology20 GENOMEs, 8 hours, <$150 each, one single machine

the future?

STARTING MATERIAL:

~weeks immediate

genomics is revolutionizing public health microbiology

pathogen genomes contain nearly everything we need for diagnosis, phenotyping, and surveillance

are these roadblocks any more?

diagnostics: time-consuming, require suspicion, variable performance, still many “unknown” samples phenotypic dst: sloooooooooooooooooow surveillance: low-resolution typing techniques, heavily reliant on field epidemiological data the whole process: multiple parallel steps, reporting at various stages throughout the process

agenda of funWhere does microbiology fit in public health? What are we doing now? The genomics revolution Current genomics approaches in public health microbiology Future directions

Story #1: Rapid WGS-based diagnosis

“Joshua Osborn, 14, lay in a coma at American Family Children’s Hospital in Madison, Wis. For

weeks his brain had been swelling with fluid, and a battery of tests had failed to reveal the cause.”

–Carl Zimmer, New York Times, June 2014

Culture? Serology? NAAT? Other assay? Bacteria? Virus? Parasite? Fungus? Autoimmunity?

Charles Chiu, UCSF

“Joshua’s cerebrospinal fluid contained DNA from a potentially lethal type of bacteria called Leptospira…readily treated with penicillin…

That afternoon, Joshua started getting large doses of penicillin. The swelling in his brain almost immediately started subsiding, and two

weeks after the first test results, Joshua was walking.”

genomics for diagnostics

• FROM CULTURE OR DIRECT FROM SPECIMEN

• SEQUENCE SAMPLE, REMOVE HUMAN READS, COMPARE TO DATABASE OF KNOWN SEQUENCES (BUT WHO’S WHO?)

• FASTER THAN NAAT IN SOME CASES, BUT NOT ALL

Clinical metagenomics toolbox: • Nanopore for near-patient sequencing • Illumina for slightly longer turnaround • Metagenomics pipeline for binning reads (e.g. SURPI) • ID physician to make the call on commensal vs pathogen

Story #2: WGS-based tailored therapy

SPECIMEN

SPECIMEN

DIAGNOSIS

SPECIMEN STANDARD THERAPY

DIAGNOSIS


DIAGNOSIS DRUG SENSITIVITY TESTING



PERSONALIZED THERAPY

SPECIMEN

DIAGNOSIS

SPECIMEN

DIAGNOSIS

ACGTACGATCG

ACGTACGATCGACGTACGATCG

ACGTACGATCG

ACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACG

ATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACG

TACGATCGACGTACGATCGACGTACGATCGACGTACGATCGCGCCGGACGTACGATCGACGTACGATCGACGT

ACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCG

ACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACGATCGACGTACG

ATCGACGTACGATCGACGTACGATCG

SPECIMEN

ACGTACGATCG


ACGTACGATCG

SPECIMEN

diagnosis

& dst


1-day positive MGIT

BATCH & SEQUENCE

UPLOAD & ANALYSE

speciation via metagenomic analysis

M. tuberculosis H. sapiens R. randombacterium

resistotyping via mutation catalogue

Personalized therapy toolbox: • Illumina sequencing at reference lab • Rapid resistance prediction from genomic data (e.g. Mykrobe) • Growing catalogue of resistance-associated mutations

Story #3: Tracking outbreaks with WGS

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.

AAAAAA

AAAAAA

AAAAAA

AACAAA

AAAAAA

AAAAAA

AACAAA

AACAAA

GACAAA

AAAATA

AAAAAA

AAAAAA AACAAA

AACAAA

AACTAA AACTAA

AACAAG

TELEPHONE

ART B

Y DE

VIAN

TART

USE

R SC

UMMY

TB TRANSMISSION IN BC IS CONCENTRATED IN OUR MOST

VULNERABLE POPULATIONS

December 2010: a phone call

May 2008 - person with afb4+ pulmonary tb visits shelter

december 2008 - shelter screening identifies six further cases

december 2010 - outbreak has grown to 30 cases, largely within a few blocks

are the outbreak management activities directed at the right

persons and locations?

TELEPHONE

ART B

Y DE

VIAN

TART

USE

R SC

UMMY

index case

second case

WE FORGOT ABOUT WITHIN-HOST GENETIC DIVERSITY

detour: reconstructing a transmission network in the

light of within-host diversity

With xavier didelot & caroline colijn

¯\_( )_/¯direct observation of within-host diversity may not be possible

due to the nature of infection and specimen collection

math modelling

start by making loads of these coloured “infection” trees

create a transmission social network from the suite of infection trees

combine with your epidemiological data to arrive at a final reconstruction

miner MINOR

variants

how did the shelter contribute to infection?

With ANAMARIA CRISAN

INDEX CASE ACTIVE TB LATENT TB

UNINFECTED NO DATA

VISIT 1: DECEMBER 2007

VISIT 2: MAY 2008

TIME IN THE SHELTER WAS ASSOCIATED WITH INCREASED RISK OF INFECTION (OR 1.26), ESPECIALLY STAYS OF 5+ NIGHTS (OR 4.97)

September 2014: another phone call

by 2014, the outbreak had grown to 52 cases and 2310 screened clients.

COULD THE OUTBREAK BE DECLARED OVER?

2008 2009 2010 2011 2012 2013

7 7

11 12

86

1

can we truly say that the outbreak is over?

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

BUT WAIT!there’s more!

1. understand epidemic dynamics

Group A Streptococcus PMID: 20142485

1. Sequence & assemble genomes of pathogens sampled from an epidemic (an outbreak spanning a large region)

2. Build a phylogeny to identify clades - “subclones” 3. Plot the prevalence of subclones across space and/or time

to understand why/how the epidemic is happening

2. discover a brand-new pathogen

Bas-Congo virus PMID: 23028323

1. Do metagenomics on a sample from a patient with an unknown disease

2. BLAST reads against a database of all known organisms

3. Look in the set of reads that didn’t match to any known organisms

4. Try some lab tricks to sequence the whole virus

3. describe a novel pathogen

German outbreak E. coli O104:H4 PMID: 21793740

1. Sequence & assemble genome(s) of novel pathogen 2. Build a phylogeny to see how it relates to other members of

its genus 3. Do comparative genomics to identify genes/elements

present or absent in new pathogen relative to other species

PMC4556809

PMC4587932

4. understand the drivers and

evolution of within-host and

population-level evolution

of resistance.

5. date the time of a viral infection

HIV PMID: 218322936

1. Sequence all the viruses found in a patient (the viral “quasispecies”)

2. Build a phylogenetic tree where branch lengths correspond to calendar time

3. Identify the time of the TMRCA - this is the infection time

6. therapeutic monitoring of DRUG resistance

HIV PMID: 20628644

1. Sequence all the viruses found in a patient (“quasispecies”) at multiple times throughout their ART treatment

2. Scan the sequences for known mutations that confer drug resistance - if you see them, change the treatment plan

PMID: 27150362 (OA)

7. understand pathogen population structure

DIAGN

OSIS

1. Sensitivity in sequencing directly from a clinical sample

2. Clinical metagenomics - who’s the pathogen, who’s a commensal, who’s a contaminant?

3. Building lab capacity

RESIS

TANC

E PRE

DICTIO

N1. What’s a resistance-determining mutation versus a

compensatory or other mutation? 2. What is the effect of rare variants on resistance

phenotype? 3. What’s in the databases? Who is maintaining the

databases? 4. How the @#$% are we supposed to identify

resistance associated with different modes, levels of gene expression?

EPIDE

MIOL

OGY

1. How can we infer transmission from genomic data alone?

2. How can we infer transmission when it’s not just a strain but an MGE that’s moving?

3. Do we have enough spatial and temporal coverage of annotated genomes to make useful inferences about population dynamics?

@jennifergardy

genomics in public health

Health & Medicine