Integrating Modern Genomic Sciences into Practical

Microbiology: WGS and The Case for Food Safety

Eric W. BrownDirector, Division of Microbiology

Office of Regulatory Science

Center for Food Safety and Applied Nutrition,

US Food and Drug Administration

Food Safety & High-Throughput Sequencing

Symposium May 30-31, 2018

Genomics Brings the World of Food Safety into a More Manageable Light

Tracking contamination down…and FAST!

Finished Product Processing Facility Farm

Ecologic ReservoirsImport LinesGlobal Point Source

SAVES LIVES

STAR-GAZING

LIGHT-

TELESCOPE

MODERN

REFRACTION

TELESCOPE

RADIO

TELESCOPE HUBBLE

PATHOGEN

PLATING

BIOTYPING

SPECIATION

SEROTYPING

PFGE WGS

time

The Complex and Global Etiology of Foods

Shrimp – India

Cilantro – Mexico

Romaine – Salinas, CA

Cheddar – Wisconsin

Carrots – Idaho

Gruyere – Switzerland

Pecans – Georgia

Sprouts – Chicago

Red Cabbage - NY

Shrimp – Indonesia

Imitation Crab – Alaska

Tuna Scrape – India

Fish Roe – Seychelles

Salmon – Puget Sound

Soy Sauce – China

Rice – Thailand

Seaweed Wrap – CA

Avocado – Mexico

Cucumber – Maryland

Wasabi – Japan

Pepper – Vietnam

Watermelon – Delaware

Blackberries – Guatemala

Blueberries – New Jersey

Pineapple – Guam

Grapes – California

Kiwi – New Zealand

Apples – New York

Pears – Oregon

Cantaloupe – Costa Rica

Honeydew – Arizona

Papaya – Mexico

Banana – Costa Rica

Salad Sushi Fruit platter

Salmonella reveals extensive

phylogeographic structure

Romaine #1

Pistachio #3

Pistachio #2

Pistachio #1

Why is environmental sampling important.1)The GenomeTrakr database relies on a reference set of isolates from known foods and known geographic localities.2)A match of an unknown clinical to a known food or known geographic location provides an investigational clue for sourcetracking where the contamination has occurred.3)Knowledge of where a contaminant is coming from allows industry to fix the problem based on scientific evidence. This is research supporting preventative controls.4)If the root cause of the problem is left unresolved then it is likely to occur again at a later date.

Environmental sampling combined with WGS can help point to root cause

of the contamination

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Field 1

Field 2

Processing facility

Scenario 1 (pass through)

Field 1

Field 2

Processing facility

Scenario 2 (harborage and persistence)

Earlier intervention means:

• Reduced amount of recalled product

• Fewer sick patients and fewer lawsuits

• Less impact overall and minimal damage to brand recognition

Immediate impacts of WGS to industry,

growers, and distributers, countries,

states

Why Develop a WGS Based Network?

• Tracking and Tracing of food pathogens• Insufficient resolution of current tools

-matching clinical to environmental

• Faster identification of the food involved in the outbreak

• Limited number of investigators vs. facilities and import lines

• Global travel

• Global food supply

GenomeTrakr

• First distributed sequencing based network (2012)

• State and Federal laboratory network collecting and

sharing genomic data from foodborne pathogens

• Partnered with NIH/NCBI for storage and serving data

• Partnered with CDC for human real-time surveillance

• Partnered with FSIS/USDA to better cover the food supply

• Partnered with the food industry to expand use to industry

• Partnered with international organizations to expand use

worldwide (GMI, WHO, FAO)

• Open-access genomic reference database

FDA’s GenomeTrakr

• First distributed network of labs to use WGS:

- 25 US State health and university labs

- 15 federal labs

- 1 US hospital lab

- 10 international labs

• Focuses on environmental and food isolates to be a large complementary reference database for clinical samples

• Each genomic sequence has associated metadata

- Species

- Geographic location (within US has states, outside US has countries)

- Date of isolation and Collector

- Isolation source (food product, environmental swab)

www.fda.gov

Importance of a Balanced Approach

Clinical

Samples

Food and

Environmental

Samples

Maximum

WGS Benefit

~206,000 pathogens as of end of May 2018

Putting it all together

• Focus on collecting environmental and food isolates to be a large reference database for clinical samples

• Each genomic sequence has associated metadata

• Data made public so that:• Everyone can benefit

from using this technology

• Transparency of methods/data for regulatory decisions

www.fda.gov

www.fda.gov

Improving Food Safety

1. Stop Contamination

• Food Safety Modernization Act (2010) –Preventive Controls, Improve Industry Practices

2. Identify Source of Foodborne Outbreaks More Quickly

• Whole-Genome Sequencing (WGS) surveillance of bacterial pathogens, environmental testing

3. Resolve Sporadic Illnesses

• Low level contamination events, Whole-Genome Sequencing (WGS) surveillance of bacterial pathogens, environmental testing

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Reference number of working document:

ISO/TC 34/SC 9 N 2133

Date: 2018-01-29

Reference number of document:

Committee identification: ISO/TC 34

Secretariat: ANSI

Document type: International standard

Document subtype: if applicable

Document stage: (19) Preparation

Document language: E

Chair: Errol Strain, Ph.D. (US FDA)

MINIMAL STANDARDS FOR:

Coverage/Data Quality/Chemistry/Alignment Parameters/Data Translation

(SNP or Allele Calling)/Clustering Tools/Data Interpretation and Linkage

THUS, Very important to ensure complete and open access to the WGS data

Applications of WGS in the

Food Safety EnvironmentDelimiting scope and traceback of food

contamination events (Track-N-Trace)

Quality control for FDA testing and surveillance

(Confidence in Regulatory Actions)

Preventive control monitoring for compliance

standards (the “repeat offender” project)

ID, geno/pheno typing schemes (AST,Serotyping,

VP) (CVM,CDRH,CFSAN) – risk assessment and

adaptive change in Salmonella and Listeria

From WGS to Antibiotic Resistance Genotype

DNA from

Single colony

Sequencing

With Illumina Miseq

Assembly

CLC Genomics

Workbench

Local Blast AR

Gene Database

BLAST ®

Sequences alignment

gyrA gene

23S rRNA gene

Acquired AR genes

AR Genotype

Point mutations related

to AR

aac(3)-IIa, aadA1,

aph(3')-Ia

catA1, tetO …

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GOAL = <5 years have first 25 mapped and rapid detection assay developed

Adaptations of particular interest to food safety specialists:

(1) Thermal tolerance

(2) Dessication resistance

(3) Osmotic/Ionic tolerance

(4) Quat resistance

(5) Chlorine resistance

(6) Biofilm persistence

(7) Surface adherence

(8) Antibiotic resistance

(9) Antimicrobial resistance

(10) Ecological fitness

(11) Heavy metal resistance

(12) Metabolic persistence

(13) Enhanced hydrophobic fitness

(14) Produce invasiveness

(15) Flower invasiveness

(16) Root system invasiveness

(17) Acid resistance

(18) Surface water fitness

(19) In vivo plant migratory fitness

(20) Soil fitness

(21) Capsaicin resistance

(22) Swarming

(23) Trans-ovarian poultry colonization

(24) Fecal persistence (poultry)

(25) Yolk content invasion

(26) Multidrug resistance

(27) External amoeba harborage

(28) Internal amoeba harborage

(29) Acyl-homoserine lactone (AHL)

(30) KatE stationary-phase catalase

(31) In vivo migratory fitness

(32) RDAR phenotype

(33) The ‘Weltevreden’ type

(34) Persistence within the tomato**

F

A

En

P

Ev

*

Computational/Big Data Challenges

-multiple platforms

-cost and availability

-partnering/collaboration

-centers of excellence

Data Sharing is too Risky

-Use WGS internally then

-”anonymizing clearinghouses”

-other non-pathogen applications

A New Way Forward for Testing

-WGS is NOT a first line solution yet

-It’s also not the only solution

-its utiity in food safety is undisputed

-connects the dots