An Industrial Lab s Experience of NGS. Dr Greg Jones

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1 An Industrial Lab s Experience of NGS Dr Greg Jones

2 Campden BRI The partner of choice for the development and application of technical knowledge and commercially relevant solutions for the food and drink supply chain

3 Practical science, technology and knowledge services for the food and drinks industry We ve been around for almost 100 years 400 staff across 5 sites

4 An extension of your in-house technical team... 3,500 sq m pilot plant 1,000 days of industry attendance each year at our interest groups 3,000sq m laboratories

5 We work with industry worldwide 2,400 members 75 countries The top 8 UK retailers 8 of the 10 top global manufacturers Many of the world s biggest brands

6 Some of our North American Members

7 Campden BRI Offices Hungary Korea Leamington Spa Chipping Campden Nutfield

8 The UK and WGS Currently used by Public Health England (PHE) for strain tracking. Anyone can submit an isolate to PHE to have it run through their pipeline. PHE submit data to Genome Trakr (NCBI BioProject PRJNA248042).

9 What does PHE give you? SNP address The first number indicates which 250 SNP threshold group the isolate is in and so on until the last number which represents the 0 SNP cluster that the isolate is in. SNP address (1) SNP address (2) SNP address (3) SNP threshold

10 The Due Diligence Defence If a UK company is found to be linked to an outbreak, they can avoid prosecution if it can be shown that they have done everything reasonably possible to prevent contamination.

11 Carrots and sticks pressuring adoption of WGS in the UK PHE are doing it. WGS may be considered part of Due Diligence (not yet tested). Better strain tracking internally. Early warning of links to outbreaks = better brand protection.

12 Is UK industry adopting WGS comprehensively? NO

13 Why not?.. Concern over implicating oneself. Concern over links to historical outbreaks. Concern regarding data ownership.

14 Solutions? Private databases? Only really useful for larger companies with supply and manufacture handled within the company. Smaller companies are the source of most outbreaks.

15 A possible system Large public database of all sequences with accompanying relationships between each other (e.g. Genome Trakr) Update as appropriate Small database of sequences linked to current outbreaks as a collection of.fastq files Local download Local download Local download Local analysis, with companies retaining ownership of sequence under investigation.

16 Pros and Cons Pro Local analysis will speed up time to dealing with source. Many more outbreaks will be investigated. Fewer people will become ill during identified outbreaks. Many more sequences will be generated. Con Regulator may not become involved in source detection. The investigation results are unlikely to be shared publically. N/A Ownership of those sequences for epidemiological purposes.

17 Metagenomics We are currently looking at 16S rdna amplicons sequenced using Illumina technology. Challenge: Link challenges in the food industry to solutions provided by metagenomics.

18 Pathogen Challenge Testing

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21 Order

22 Family

23 Genus

24 Species

25 Final Thoughts WGS is Nearly There in terms of industrial uptake. Can regulators help to tip the balance? Metagenomics has seen a more enthusiastic uptake, particularly when linked to standard tests.

26 Thank You