Annual Science Symposium Whole Genome Sequencing - A New Approach for Tracking Pathogens Back to Their Source. Co-Sponsored by:

Transcription

1 Annual Science Symposium Whole Genome Sequencing - A New Approach for Tracking Pathogens Back to Their Source Co-Sponsored by:

2 Whole Genome Sequencing - A New Approach for Tracking Pathogens Back to Their Source Ruth E. Timme, PhD Research Microbiologist

3 Some perspective on the food supply Tracking and Tracing of food pathogens ~200,000 registered food facilities (2/14) 81,574 Domestic and 115,753 Foreign > 300 ports of entry > 130,000 importers and more than 11 million import lines/yr > 2 million US farms

4 Recent FDA Related Recalls, Withdrawals, and Alerts 05/02/2014 Chili powder Salmonella 04/23/2014 Ground Annato Salmonella 04/10/2014 Chile Molido Puro Salmonella 04/09/2014 Sweet basil Salmonella 03/14/2014 Organic basil Salmonella 03/13/2014 Sliced Fruit Salmonella 02/11/2014 Curly Parsley Salmonella 02/07/2014 Tomatoes Salmonella 01/22/2014 Cheese Salmonella 12/31/2013 cashew cheese Salmonella 12/27/2013 Cheese Salmonella 11/26/2013 Blue cheese Salmonella 05/09/2013 Sesame Paste Salmonella 03/18/2013 Chocolate Bars Salmonella 03/18/2013 Pet Food Salmonella 11/21/2012 Cherry tomatoes Salmonella 11/13/2012 Tahineh Salmonella 11/12/2012 Ice Cream and Gelato Salmonella 11/08/2012 Choc olate Salmonella 11/08/2012 Spinach Salmonella 11/01/2012 Carrots Salmonella 10/29/2012 Peanut Butter Candy Salmonella 10/16/2012 Peanut Butter Salmonella 10/15/2012 Candy Salmonella 10/15/2012 Salad Kit Salmonella 10/12/2012 Red Pepper Salmonella 10/12/2012 Nut Butter Salmonella 10/12/2012 Peanuts Salmonella 10/10/2012 Hot Peppers Salmonella 10/08/2012 pb fudge Salmonella 10/02/2012 Chicken Spring Rolls Salmonella 10/17/2012 Ice Cream Salmonella 9/28/2012 Crackers Salmonella

5 Current method for pathogen identification 1. antigens are screened to identify serovar 2. PFGE: genome is cut into pieces. Sizes of these pieces and the banding patterns theydetermine discrimination within serovar. PulseNet 4

6 Outline The whole genome sequencing (WGS) program at FDA-CFSAN Reference database and pathogen detection pipeline Benefits to industry, growers, distributers and public/private health labs and the FDA. 5

7 Outline The whole genome sequencing (WGS) program at FDA-CFSAN Reference database and pathogen detection pipeline Benefits to industry, growers, distributers and public/private health labs and the FDA. 6

8 Next-Generation Sequencing A high-throughput sequencing method that parallelizes the sequencing process, producing millions of sequences at once. Over the past six years, Next-Generation sequencing technologies have collected data capable of answering questions fundamental to our understanding of life and the factors that govern human health. The combination of the vast increase in data generated, coupled with plummeting costs required to generate these data, has rendered this technology a tractable, general purpose tool for a variety of applications. 7

9 2008 Next-Generation Sequencing (NGS) provides support for other technologies and fosters novel targets and assay design for rapid diagnostics. Biomarker Assays MLVA and CRISPR loci Microarray Targets NGS SNP Discovery Outbreak response

10 Whole genome sequencing is becoming a standard tool in microbiology biocomicals.blogspot.com

11 Next-generation sequencing can be used to address different facets of outbreak response: Have we seen this isolate before? (Compare it to reference isolates) Do these isolates form a cluster? (i.e. is it outbreak or background) (Compare them to reference and other outbreak isolates) Is there a similarity between food/environmental and clinical isolates? (Compare them to reference, clinical, and food/environmental isolates) Can we do this?

12 Is WGS a viable solution? Cost Increasing ease of operation Database longevity Comparable times to conventional pipelines Sample prep Identical for all pathogens Cost savings Resistance, subtyping, virulence factors, more New applications Source-tracking, internal controls/validation, historical trends, more $3,500 $3,000 $2,500 $2,000 $1,500 $1,000 $500 Cost per bacterial genome 454 Illumina Miseq $ $90/genome in 2014 $50/genome in 2015

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14 Salmonella enterica evolutionary tree 156 genomes 78 serovars ~119,000 SNPs Timme et. al. Gen. Biol. Evol. 2013

15 Clonal outbreak of Salmonella Bareilly Same PFGE but not part of the outbreak 25 SNPs Outbreak Isolates 5 SNPs

16 This from 1859, Darwin's, On the Origin of Species It is obvious that the Galapagos Islands would be likely to receive colonists, whether by occasional means of transport or by formerly continuous land, from America; and the Cape de Verde Islands from Africa; and that such colonists would be liable to modification; the principle of inheritance still betraying their original birthplace" With WGS, we now have the potential to discern those birthplaces

17 Can WGS fill a Public Health role? If yes, then... Initiate pilot study Develop collaborations and partnerships NCBI, States, CDC and other Federal partners What infrastructure would be needed? How would data be accessed and stored? Public vs. private No data hoarding Metadata

18 Outline The whole genome sequencing program at FDA-CFSAN Reference database and pathogen detection pipeline Benefits to industry, growers, distributers and public/private health labs and the FDA. 17

19 PRL-NW State Federal WEAC SAN-DO PRL-SW DEN ARL FCC NRL MOD1 CPK-1 SRL 6 state health depts. (WA, AZ, NY, FL, MN, VA) + 12 FDA-ORA labs

20 GenomeTrakr Database: tracking foodborne contamination events. Requirements: High-resolution genomic database Open access for viewing data Functions in real-time Samples have a minimum set of metadata (sensitive metadata remains in PulseNet) Future: Open access for PHL submitters

21 Partners with sequencers United Kingdom* Denmark Italy Argentina Brazil Germany Canada Mexico* Argentina* Partners with isolates Ireland* Mexico Turkey Argentina Columbia

22 Pilot Phase: Building a pathogen reference database at NCBI Data Generation 18 State and Federal Health labs Data transfer Data QC and Submission at FDA Register strains with NCBI Illumina MiSeq Data Generation Data transfer to FDA Batch QC of data Conversion to SRA format Upload to SRA CFSAN Genomic Information Management System (GIMS) integration Automated WGS accessions Genome assembly + PGAP annotation Hybrid k-mer and reference-based SNP calling analysis NCBI pathogen detection pipeline BioProject:

23 Salmonella GenomeTrakr BioProject 5269 BioSamples 3900 genome submissions

24 BioSamples / metadata

25 Database diversity collected in the first year Spatial diversity Genetic diversity Temporal diversity

26 Global Diversity 63 countries Global Region Count Africa 45 Asia 185 Australia 6 Central America 56 Europe 20 Middle East 102 North America 4316 Russia 1 SE Asia 492 South America 28

27 3904 US strains across 43 states AK AL AR AZ CA CO CT FL GA HI IA ID IL IN KS KY LA MA MD ME MI MN MO MT NC ND NE NH NJ NM NV NY OH OR PA RI SD TN TX UT VA WA WI

28 Genetic Diversity: Salmonella enterica subsp. indica, 1 salamae, arizonae, 8 21 diarizonae, 23 houtenae, 27 missing, 1007 enterica, 4179

29 Serovar Diversity 436 total, top 56 serovars Serovar count Serovar count Typhimurium 716 Typhimurium var Enteritidis 433 Virchow 26 Newport 339 Bareilly 22 Kentucky 191 Poona 21 Heidelberg 175 Typhimurium var. O 5 - (Copenhagen) 21 Senftenberg 115 Havana 20 Weltevreden 103 Ohio 20 Montevideo 92 Brandenburg 19 Saintpaul 86 Paratyphi B var. L(+) tartrate + (Java) 17 Mbandaka 82 Albany 16 Anatum 80 Braenderup 16 Meleagridis 70 Choleraesuis var. Kunzendorf 16 Tennessee 69 Inverness 16 Agona 57 Uganda 16 Hadar 51 Brunei 15 Infantis 50 Nchanga 15 Muenchen 50 Worthington 15 Derby 43 Berta 14 Dublin 43 Muenster 14 Cerro 40 Sandiego 14 Oranienburg 40 Litchfield 12 Give 37 Paratyphi B 11 Thompson 37 Hvittingfoss 10 Schwarzengrund 35 I 4,5,12:i:- 10 Bredeney 33 Lexington 10 Reading 31 Minnesota 10 Javiana 30 Cubana 9 Rubislaw 29 Gaminara 9

30 Temporal Diversity

31 Distributed sequencing for other foodborne pathogens Listeria monocytogenes CDC-lead effort: sequence every Lm collected in the US (Aug 2013-July 2014) E.coli 658 clinical food/env. isolates 239 food/env. isolates Vibrio parahaemolyticus coming soon 30

32 Salmonella enterica Kmer phylogeny 31

33 Listeria monocytogenes Kmer phylogeny 32

34 0.02 Roos cheese outbreak PNUSAL NY-NYAG12B PNUSAL VA-WGS VA-WGS PNUSAL CFSAN VA-WGS PNUSAL CFSAN CFSAN VA-WGS PNUSAL VA-WGS CFSAN VA-WGS CFSAN CFSAN CFSAN VA-WGS VA-WGS CFSAN CFSAN VA-WGS VA-WGS VA-WGS CFSAN Same PFGE pattern SNPs 2014 outbreak 5 SNPs 33

35 Whole-genome sequencing (WGS) of Listeria monocytogenes strains isolated from Roos Foods cheese products has been performed by the FDA and Virginia s Division of Consolidated Laboratory Services. These strains were found to be highly related by WGS to the Listeria strains isolated from patients in this outbreak, adding further confidence that cheese products produced by Roos Foods were a likely source of the outbreak. WGS provides genetic information that allows investigators to rapidly identify differences among isolates. Compared with pulsed-field gel electrophoresis (PFGE), WGS provides clearer distinction between cases and foods that are likely part of a given outbreak and those that are not.

36 Real-time Integration of WGS into FDA regulatory workflow

37 Next-Generation sequencing faces several large challenges as it deploys to a global public health tool: Will all share data? Who pays? Who owns the IP? 2016 W G S 2017 Quality concerns and curation? Industry participation? Administration, coordination, and oversight? 2020 How much metadata?

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39 Global Microbial Identifier Make novel genomic technologies and informatics tools available for improved global patient diagnostics, surveillance, research and public health response. Develop a global system to aggregate, share, mine and use microbiological genomic data to address global public health and clinical challenges, a high impact area in need of focused effort. 500 members in 30 countries Work groups 1.Political challenges, outreach and building a global network 2.Repository and storage of sequence and meta-data 3.Analytical approaches 4.Ring trials and quality assurance 5.Pilot project

40 Outline The whole genome sequencing program at FDA-CFSAN Reference database and pathogen detection pipeline Benefits to industry, growers, distributers and public/private health labs and the FDA. 39

41 The Fresh-cut Tomato Supply Chain

42 The Fresh-cut Tomato Supply Chain

43 Genome precision benefits industry Contamination of common PFGE pattern can falsely implicate a large swath of the distribution chain. WGS can pinpoint a specific source, exonerating the remaining network supply chain. Multi-ingredient processing plants can distinguish between endemic vs. incoming ingredient contamination. Public reference database and real-time analysis of pathogen genomes. 42

44 Future Directions for FDA WGS Continue WGS analysis for support of investigations into contamination events to enhance our understanding of Salmonella and other organisms (i.e. Listeria) Expand GenomeTrakr internationally Support state health labs with technical and bioinformatic support and training as needed Provide path for industry participation ASM stand alone meeting September 2015 on public health and WGS in Wash DC

45 The power of open data (Slide courtesy of J. Ostell, NCBI) FDA_2010_142_Pistachio-3

46 FDA/CFSAN Steven Musser Marc Allard Peter Evans Eric Brown Justin Payne Charlie Wang Rebecca Bell Christine Keys Errol Strain Yan Luo James Pettengill Hugh Rand Darcy Hanes Gopal Gopinathrao Chis Grim Palmer Orlandi CDC John Besser Eija Trees Patti Fields Lee Katz Duncan MacCannell National Institutes of health (NCBI) David Lipman Jim Ostell William Klimke Martin Shumway State Health Labs Bill Wolfgang (NY) Dave Boxrud (MN) Anita Wright (FL) Elizabeth Driebe (AZ) Angela Fritzinger (VA) Ailyn Perez-Osorio (WA) Illumina Susan Knowles Omayma Al-Awar Kelly Hoon

47 Genomic triaging is now possible for surveillance, testing, and traceability of foodborne contamination Subtyping ID Source tracking PCR/RT-PCR X-Map Serotyping Mass Codes PFGE MLST SNP panels* MLVA Optical Mapping GSS technology Microarray/Genotyping Whole Genome Sequencing