Whole Genome Sequencing for food safety FSA Chief Scientific Advisor Report and 2013 Listeria pilot study

Transcription

1 Whole Genome Sequencing for food safety FSA Chief Scientific Advisor Report and 2013 Listeria pilot study Dr Edward Hayes Date: July 2016, Version 1

2 Foodborne Pathogens 280,000 cases of Campylobacter, 30,000 cases of Salmonella in UK p.a. Listeria monocytogenes another FSA priority pathogen case fatality rates 20 to 40% Food industry has additional concerns brand, reputation, litigation etc.

3 Ways to ID bacteria MALDI-TOF rapid method for identifying species Serotyping identifies subtypes based on surface antigens MLST more discriminatory, but many common STs PFGE highly discriminatory, but labour intensive

4 Whole Genome Sequencing (WGS) Conceptually very simple Extract total DNA from bacterial culture, sequence this in a massively parallel manner, interpret bioinformatically Coverage to sequence L. monocytogenes at 20x coverage (to correct for sequencing errors) would require generation of 58,000,000 bases of DNA sequence. Bacterial genome sizes vary: Campylobacter jejuni = 1,600,000 base pairs (1.6 Mb) Listeria monocytogenes = 2.9 Mb Salmonella Enteritidis = 4.7 Mb

5 DNA Sequencing Technology Capillary based DNA sequencing (Life Tech) (<2007?) GS-FLX-Titanium + (454) ( ) MiSeq (Illumina) (2013) Oxford Nanopore MinIon (2014) 96x750bp 750bp x 1 million 300bp x 2 x 25 million 4-50 kb x thousands Long reads, Individual clones / barcodes First out, Long reads, time consuming, expensive, phased out 2016 Simple work flow, relatively cheap, shorter reads, high quality data (worse at end) Small, cheap, very long reads, high error rate (15%, but will improve)

6 Analysis Rapid clustering algorithms e.g. k-mers De novo assembly vs reference mapping SNP analysis vs MLST MLST < ribosomal MLST < core genome MLST < whole genome MLST Additional information virulence factors, antimicrobial resistance genes

7 FSA CSA Report FSA driving application of WGS to food safety problems Provides the ultimate level of discrimination Basic data is highly portable and globally comparable Cost per base of sequencing has reduced phenomenally

8 Listeria pilot project FSA-funded project at Fera to demonstrate the capacity for rapid WGS, analysis and upload to the global Sequence Read Archive database Sequenced 18 isolates of Listeria spp. from Red Meat Survey, and analysed along with 100 other genomes Identified clusters from different outlets of same retailer, and same farm Reconstructed metabolic pathways Identified genes which may promote evolution of antimicrobial resistance

9 GenomeTrakr Run by US Food and Drug Administration (FDA) More than 51,000 isolates sequenced and uploaded to public database PHE has uploaded thousands of Salmonella genomes and hundreds of STEC genomes

10 Roos Cheese Eight people infected August to November 2013 Foods from Roos Foods found to be L. monocytogenes positive Feb 2014 Extensive hygiene violations found at processing facility - February-March WGS showed that strains from Roos facilities were highly related to those from all outbreak cases. February 2015 company charged with distribution of adulterated cheese in interstate commerce.

11 Salmonella in tuna - USA Large, multistate outbreak of Salmonella Bareilly and Salmonella Nchanga. 425 cases, in 28 states, between 1 January and 7 July were Salmonella Bareilly. CDC 2012

12 Benefits to industry Identify multiple types vs continuous contamination with a resident strain Monitor trends over time For broader applications of high throughput sequencing, see Next Generation Sequencing in the Food Industry, Food Analysis Supplement 2016, New Food. Potential to implicate processes or equipment Reduce risk of recalls/demonstrate due diligence Suggest external sources of contamination would require sharing anonymised data

13 Source Tracking Service - OriGen Fera will be releasing a service to the food industry to use WGS to better understand contamination issues Regain Market Share Regain Consumer Confidence OriGen Regain Customers Keen for discussions with industry to shape the product as it evolves Regain Control

14 The Future Rapid, in field genomics, for example: +