WHOLE GENOME SEQUENCING FOR FOOD SAFETY INITIATIVE

Obstacles, Opportunities and an Outlook

Behzad Imanian: Project Leader, IFSH WGS Initiative

WGS is not a perfect tool

It is new

Whole ≠ Complete

Genome ≠ Organism

Data intensive

Hard to analyze

Hard to interpret

It is expensive

It takes too long

WGS is the new ‘gold standard’

‘Genotype’ vs ‘Phenotype’

Genome ≈ Organism

Data intensive More informative

Broad view

Better resolution

Reproducible

More applications

Becoming faster, cheaper

Advancing fast

Adopted and applied widely

WGS: data up; costs down

http://www.ncbi.nlm.nih.gov/genbank/statistics/

https://www.genome.gov/27565109/the-cost-of-sequencing-a-human-genome/

2015-2016

2014

WGS

Massively parallel signature sequencing (MPSS)

Polony sequencing

454 pyrosequencing

Illumina (Solexa) sequencing

Ion Torrent semiconductor sequencing

DNA nanoball sequencing

Heliscope single molecule sequencing

Single molecule real time (SMRT) sequencing (PacBio)

Nanopore DNA sequencing

(Oxford Nanopore Tech)

Tunneling currents DNA sequencing

Sequencing with mass spectrometry

Microfluidic Sanger sequencing

Main article: Sanger sequencing

Microscopy-based techniques

RNAP sequencing

In vitro virus high-throughput sequencing

Developed In Development

Courtesy of Wikipedia

IFSH WGS Project

Proposal and a preliminary charter (March/April 2015)

Start date: (Oct 01 2015)

Objectives: - Collaboration with food companies

- Research and laboratory services

- Pathogens and GenomeTrakr

IFSH WGS ‘Consortium’

IFSH/Industry ‘Steering Committee’ Several members of industry

Several members of IFSH officials/scientists

‘Steering Committee’ Conference call, (July 2015)

Advising instead of Steering

Concerns about WGS data interpretation

Obstacles: legal repercussions

IFSH WGS Initiative

A new Industry Advisory Committee (July 2016)

15 companies invited, 14 accepted

Advisory Committee Conference Call (August 2016)

Interpretation of WGS data

Concerns about regulatory policies

Concerns about traceability, privacy, metadata

IFSH WGS Initiative: What’s done so far?

Infrastructure Laboratory

IFSH WGS Initiative: What’s done so far?

Infrastructure Laboratory

Equipment

IFSH WGS Initiative: What’s done so far?

Infrastructure Laboratory

Equipment

HPC

Data transfer

IFSH WGS Initiative: What’s done so far?

Outreach IFSH WGS Symposium for Food Safety

Industry Advisory Committee

Collaborations IFSH/FDA Scientists (Moffett Campus)

IIT Scientists (Main Campus)

External Scientists

Consulting and Analytical Companies

IFSH WGS Initiative: What’s being done?

Charter Has been revised (September 2016)

Spoilage, allergenic and toxin producing microorganisms

Collaboration with industry, academia and consulting/analytical companies

Extra staff A postdoctoral fellow (November 2016)

Students (January 2017)

IFSH WGS Initiative: What’s being done?

Cost estimates Are being done (October 2016)

Business plan Is being developed (October 2016)

A note: We are not a for-profit organization! Collaboration

Competition

IFSH WGS Initiative: Services

WGS sequencing Genomic

Pathogens (all FDA-defined zones)

Spoilage

Allergenic substance and toxin producing bacteria

Viruses (January 2017?)

Metagenomic 16S

Shotgun

Environmental samples

Transcriptomic (March 2017?)

RNA-seq

IFSH WGS Initiative: Services

Data analysis & bioinformatics Filtering data (read trimming and contaminant removal)

Genome assembly

Whole genome annotation

SNP analysis

Phylogenetic analysis (SNP, gene, multi-genes, genome wide, source tracking …)

Specific analysis (pathogenicity, antibiotic or heat/cold resistance …)

IFSH WGS Initiative: Workflow

Sample submission (directly or through 3rd party)

Re-labelling

DNA extraction

Library preparation Sequencing (MiSeq)bacterial isolates

IFSH WGS system

DNA

Strain confirmation

Quantification

Metadata

Metadata minimum requirements

bioproject ID

Sample type (clinical, environmental, food, etc.)

If clinical specific host host disease

Collection

collector, year, source

Location

country State

Obstacles

WGS regulatory policies Not legislated yet Not spoken of officially Not fully communicated

Confusion

Privacy and liability concerns Metadata Traceability of isolates Matches with past and present outbreaks ….

Not enough dialogues

Realities

WGS is providing superior power to Identify

Differentiate

Track sources

Monitor environments

Government has embraced WGS and is promoting it

Despite reservations, industry is interested

We are in a transitional period

Opportunities

Dialogues

Collaborations

Better policies

Faster implementation of WGS & its growing apps

Preventing outbreaks, recalls, loss of money

Preventing suffering and loss of and life

WGS Initiative: An outlook and our plans

Infrastructure Local database (IFSH WGS data) Third party submission of isolates? An extra HPC Other high throughput sequencing equipment

Training Wet lab, data submission & analysis

Promoting the dialogues between the government & industry

Expand collaborations with Industry Academia Analytical/consulting companies Government

Acknowledgements

Kristin M. Schill

Richard E. McDonald, Mary Lou Tortorello, Glen Black

Wei Zhang, Armand Paradis, Alvin Lee, Jason Wan, Robert Brackett

Cindy Koschetz, Haley Tomlinson, Barbara Neuman, Andrew Ehn, Ellen Spiewak, David Griesemer, KaipingDeng, Yingshu He

Jean-Francois Pombert

The Industry Advisory Committee

Eric Brown, Marc Allard, Ruth Timme, Hugh Rand, Errol strain and the rest of the WGS team in College Park

George Atkinson, Tim Jackson, Mickey Parish, Chris Braden, Palmer Orlandi, Peter Gerner-Smidt

Our fantastic speakers

Consulting/Analytical Companies who have reached us and our sponsors

FDA/IFSH/IIT Others