WGS as a starting point to understand AMR Jennifer Gardy, Canada Research Chair in Public Health Genomics, University of British Columbia & BC Centre for Disease Control @jennifergardy

with Laura Piddock, Professor of Microbiology, University of Birmingham @LauraPiddock

http://www.slideshare.net/jennifergardy

The 37,000 foot view

The 37,000 foot view

PMC4525730PMC4156311

1995-20042005 2014

14,000

12,000

10,000

8,000

6,000

4,000

2,000

0 Adap

ted

from

Land

et al

., PM

C436

1730

There are over 70,000 prokaryotic genomes in NCBI

We sequenced 36 TB genomes!

We sequenced 1400 TB genomes!

WGS is now POC

or point-of-smartphone!

From proof-of-concept to clinical implementation

academic clinical

understand diagnose characterize track

PMC4698465

356 samples, 8 sites

Speciation - 93%

Resistance - 93%

Faster Cheaper

What does WGS mean for AMR: diagnosis?

Clinicians want to know what a bug is and what

to treat it with. Fast.

Is WGS faster than NAATs or LPAs for

diagnosis/speciation? Not really.

1. WGS will impact AMR diagnostics by offering new insights and new targets

PMC3989053

• 2007 S. aureus isolate, phenotypically MRSA but no mecA • WGS at Sanger revealed mecA homolog with 69% identity - named mecC • mecC detected all over the place after its discovery • Diagnostic PCRs and Vitek protocols changed to capture this new gene

What does WGS mean for AMR: resistance prediction?

2. WGS couples diagnosis and resistance prediction

PMC4703848 http://www.mykrobe.com

3. WGS identifies and queries a larger set of resistance determinants

Walker et al, Lancet ID, PMC4579482

3651 Mtb isolates sequenced, 232 resistance determinants found

PMC4295408

PMID 15591164 (OA)

Sequenced 3 isolates after BDQ tx

4. WGS enables the discovery of new antimicrobial mechanisms of action

PMC4556809

PMC4587932

5. WGS reveals the drivers and

evolution of within-host and population-level

evolution of resistance.

What does WGS mean for AMR: transmission & epidemiology?

PMC4203314

6. WGS can reconstruct AMR outbreaks and

inform infection control.

6. WGS can differentiate

between mutational and plasmid-

mediated resistance.PMID: 23543608 (OA)

PMID: 27150362 (OA)

7. WGS can describe the emergence and spread

of AMR lineages.

8. WGS reveals inherent mutational capacityFord et al, Nat Genet, PMC3777616

Roadblocks

DIAGN

OSIS

1. Sensitivity in sequencing from a clinical sample

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

RESIS

TANC

E PRE

DICTIO

N 1. 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?

5. Are people releasing enough well-annotated genomes to enable comparative genomics efforts?

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?

Laura Piddock, Canada Research Chairs program, Michael Smith Foundation for

Health Research Scholar program. @jennifergardy