WGS Challenges and Opportunities

Tim Jackson, Ph.D.

VP Food Safety, Regulatory Compliance, Worker Welfare

Driscoll’s of the Americas

2

3

Should Industry use WGS?

Isolate

Internal investigation

Cracked floor

Traffic

Database

Penalty

Control measures – cooling and packing

• Protection and handling of primary and secondary

packaging

• Hygienic design and cleanliness of cooling tunnels and storage areas

• Movement of people and materials

• Cleanliness of transport

equipment

• Facility pest control

A

61

2

8

11 12

19

21

22

23

24

2526

27

28 30 31

32 34

40

39

41

53

545557

56

58

16

33

17

Sample “59” was not received

13 14 15

203736 38 46

43 44 45 47

48 49

50 51

52 60

35

5

3729

18

62

64

65

63

30b 30c

30d

28c

28d

28b

31b31c

Numbers correspond to location places indicated by the factory

31d

33b

35b

54b

Resident or Repeat Transient?

Resident in

orchard,

transient in

facility

Resident in facility-what is the true ubiquity of

sequences?

Direct benefits of WGS / metagenomics for industry

• Characterizing relatedness of strains to assist with investigations

• Understanding factors that contribute to distribution / movement in the

environment

• Understanding strain virulence to refine targets of control measures

• Understand mechanisms of entry into plants to design

• Understanding factors that impact persistence

• Resistance to sanitizing agents

• Strategies for hygienic design

• Factors that impact survival, biofilm formation

• Development and validation of control measures

Direct benefits of WGS / metagenomics for industry

• Determine root cause of spoilage

• Improve detection methods and enrichment protocols

• Determine appropriate surrogates for challenge studies

• Further characterize environmental microorganisms to determine most appropriate hygiene indicators

• Assist with detection of food fraud

• Determine health / disease state of plants for agricultural operations

Blueberry mosaic virus

ww

w.v

iralz

on

e.e

xpa

sy.

co

m

• Characterizing relatedness of strains to assist with source attribution

• Understanding factors that contribute to distribution / movement in the environment

• Understand mechanisms of entry into food plants

• Determine role of microbial populations in nutrition / chronic illness

• Provide inputs for risk assessors to answer specific risk management questions

• Establishment of FSO, PO, PC

Indirect benefits of WGS / metagenomics for industry

E. coli O157:H7 in lettuce

13

14

Cyclospora outbreak

592 Cyclospora cases not

associated with foreign travel

WGS – Food Safety Management -Considerations

Quality assurance –Standards

P- Test

WGS is not just another typing tool –

Robust Underpinning

Science

Protocol Harmonization

Stakeholder Guidelines on

Decision-making

/Interpretation

Technical competence: authorities,

industry, labs, academia

WGS is ONE tool:

epidemiology must also be

used

Sharing of data: legal, political,

psychological constraints

Food safety is global – WGS will be a global tool

Slide: John Donaghy Nestec, SA

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

17

WGS – It Requires Technical Competencies Beyond TraditionalMicrobiology

‘Traditional’ Microbiology

Molecular Microbiology

Bio-Informatics

‘Wet’ ProcessingWGS

‘Dry’ ProcessingWGS

Slide: John Donaghy Nestec, SA

ILSI Europe: The use of Next Generation Sequencing (NGS): Translation into practice

Application of WGS

WGS is infallible (and

we won’t need epi

anymore).

WGS match

between a food

and clinical

isolate doesn’t

mean food

caused illness.

Epi and traceback

critical

Current CDC,

FDA, FSIS

What industry heard a

few years ago

Challenges for Industry (& others) for Public WGS Databases

Meta Data Required (Confidentiality)

Data Accessibility (Security)

Data Sharing & Implications (Legal/Regulatory))

Legacy data & Technical Interpretations

20

Hurdles and challenges

• GenomeTrakr: Access to metadata

• Availability / capacity of sequencing equipment / bio informatics expertise

• Training and awareness

• Cost vs benefit of technology

• Culture-independent testing?

Opportunities for collaboration

• Specific, targeted studies to answer persistent questions

• Sharing data from facility assessments in a timely manner

• Ecological studies to provide context to sequence data

• Provide awareness, training, support to smaller industry players.

Photos: nih.nbi.gov; medimoon.com