MPH, MS, PhD · 2017-06-15 · Uday Dessai MPH, MS, PhD Senior Public Health Advisor Office of Public Health Science, FSIS, USDA USDA, Food Safety and Inspection Service IFSH WHOLE

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Uday Dessai MPH, MS, PhD

Senior Public Health Advisor

Office of Public Health Science, FSIS, USDA

USDA, Food Safety and Inspection Service

IFSHWHOLE GENOME SEQUENCING

FOR FOOD INDUSTRY SYMPOSIUMMay 22-23, 2017

Chicago Marriott Southwest at Burr Ridge1200 Burr Ridge Parkway, Burr Ridge, IL 60527

Food Safety and Inspection Service

FSIS Update: Whole Genome Sequencing (WGS) - Presentation Outline

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Mission and Strategic Plan Whole Genome Sequencing WGS Highlights Current Status Application

Investigative Process Harborage AMR

Interagency Collaboration Gen-FS WGS Public Meeting Concluding Remarks


FSIS Update

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Mission and Strategic Plan

FSIS Challenge


FSIS Mission, Strategic Planning and Public Health

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Inspection and Testing About 6000 Establishments 7350 Inspection Personnel Over 100 K Samples 3.4 million Scientific Analysis Over 233K Micro Analysis

FSIS is the public health agency in the U.S. Department of Agriculture responsible for ensuring that the nation's commercial supply of meat, poultry, and egg products is safe, wholesome, and correctly labeled and

packaged.

Our Authority Federal Meat Inspection Act (FMIA), 1906 Agricultural Marketing Act (AMA), 1946 Poultry Products Inspection Act (PPIA), 1957 Humane Methods of Slaughter Act (HMSA),

1958 Egg Products Inspection Act (EPIA), 1970

Projected FSIS Timelines

2014 2015 2016 2017 2018 2019 2020 2021 2022 2023

Application of Science, Technology and Innovation Continues

FSIS Strategic Plan 2012 - 2016

Healthy People Goals and Targets: 2020

Implementation of WGS

← External validation

Strategic Plan 2017-2021Goal 2: Modernize Inspection Systems , Policies and the Use of Scientific Approaches

Strategic Plan 2012-2016Goal 5: Effectively Use Science to Understand Foodborne Illness and Emerging Trends

Strategic Plan 2017 - 2021

Strategic Plan 2022- 2026

HP: 2030

WGS/NGS/other applications in routine use at FSIS

Upgrade Infrastructure

Decreased reliance on non-WGS technologiesTrad

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Continue to develop criteria for the application of WGS in regulatory decision making

Explore Utilization of In-Field Real-time Technologies

• Fit-For-Purpose -Detection system

• Partner collaborations• Pilot studies• Large Scale

implementation • In-field detection, data-

analysis and decision making capability

• FSIS set of Reference Genomes• Unique analytic capability

• Community/Microbiome• Resistome, Virulome etc.

• FSIS WGS data analysis pipelines• Pan-genome (core + variable)

type of analysis• Less dependence on culture

enrichment and isolates (!)• Complement CID

2011

2012

Food Safety and Inspection Service:

FSIS Mission, Strategic Planning and Public Health

Serotyping, PFGEs, AST and other ...

SNP (Kmer, hqSNP) and wgMLST and new tools

FSIS WG

S

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FSIS Mission, Strategic Planning and Public Health: Strategic Plan (2017-2021) - Goals

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FSIS Mission, Strategic Planning and Public Health: Strategic Plan (2017-2021) – Objectives and Outcomes

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While FSIS reported overall declines in the total number of Salmonella, Lm, and E. coli 0157:H7 illnesses attributed to FSIS-regulated products from FY 2012 to FY 2015, it did not meet the associated FY2016 target, both because the targets, which were anchored toHealthy People 2020 pathogen-specific goals, were highly ambitious and because the manner in which attribution was estimated washighly influenced by year-to-year variations in outbreaks, causing major changes in illness estimates.

FSIS has changed this approach for FY 2017 forward, given the limitations

FSIS All-Illness Measure estimates the total number of foodborne illnesses from Salmonella, Lm, and E. coli O157:H7 from FSIS-regulated products. Objectives were produced using attribution estimates from 2005-2007 FDOSS data, quarterly FoodNet data, Scallan et al. scaling factors, and U.S. Census data with annual objectives tied to Healthy People 2020 pathogen-specific goals.


FSIS Mission, Strategic Planning and Public Health: Pathogen Reduction Goals and Progress

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Reporting Period

Baseline 2007-2009

FY 2011 FY 2012 FY 2013 FY2014 FY2015 FY 2016 Change Since

Baseline

ExpectedChangeBy 2020

All IllnessObjective 415,586 405,178 394,770 384,362 373,955 363,547 321,916Measure 436,401 491,353 479,621 427,171 386,265 382,123

SalmonellaObjective 395,148 385,740 376,331 366,923 357,515 348,107 310,473Measure 413,965 472,591 458,359 393,381 360,747 374,671

LmObjective 856 836 816 795 775 754Measure 897 748 897 0 55 0 0 -100.0%

E. coli O157:H7

Objective 19,581 18,602 17,623 16,644 15,665 14,686

Measure 21,540 18,015 20,365 33,790 25,464 7,451 7,682 -64.3%


FSIS Update

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Whole Genome Sequencing (WGS)

WGS application in FSIS Outbreak investigations Harborage and more NARMS/Novel AMR gene

------------- FSIS is interested in looking at - virulence, adaptation

(heat, pH, biofilms, resistance to biocides ...), mobilome, resistome etc.

---------------- Note: In its investigative decision making process FSIS

utilizes WGS findings/interpretations as a part of the totality available evidence

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FSIS Update: WGS Applications

FSIS continues to build capacity for WGS of isolates obtained from FSIS sampling programs At full capacity we will have 10 + sequencers Goal is to sequence all FSIS isolates (around 10,000 per year)

To further understand the relationship between clinical and food isolates -in collaboration with our public health and regulatory partners, FSIS currently considers available WGS analyses in addition to PFGE and epidemiological information

FSIS works with National Antimicrobial Resistance Monitoring System (NARMS) partners (FDA, CDC) to understand the occurrence or introduction of antimicrobial resistance genes in pathogens of interest

FSIS is part of an interagency collaboration with CDC, FDA, and NCBI (Gen-FS) to harmonize efforts for implementation of WGS for food safety purposes within the US

WGS Public Meeting

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FSIS Update: WGS - Highlights

In FY2017 we began sequencing regulatory FSIS isolates in addition to NARMS cecal isolates (Salmonella, Campylobacter) in real-time

NARMS AMR E. coli and Enterococcuswill also be sequenced in-house

----------------WGS Public Meeting

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FSIS Update: FY 2017

Metadata and sequence data is immediately available for upload to NCBI

---------------------Product/Source type (Ready to eat product, raw

meat/poultry, environmental swab, etc.)Year sample was collectedState where sample was collectedSubtyping information when availableSalmonella – serovarAdulterant STECs – O-group Campylobacter – species

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FSIS Update: WGS - Metadata


FSIS WGS Update: WGS Milestones and NCBI Uploads

• July 2014: Salmonella and Listeria monocytogenes

• December 2014: STECs • February 2015: Campylobacter• May 2015: Capability to directly upload

WGS files to NCBI

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Isolates Sequenced Milestone Dates

As of 1/01/2017: 5,490 FSIS isolates have been sequenced and uploaded to NCBI

Listeria monocytogenes STEC Salmonella Campylobacter Total

Routine/Special Projects 337 420 1226 369 2352

NARMS Cecal Sampling 1499 1639 3138

Total 337 420 2725 2008 5490

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FSIS Update: WGS Application– Potential Use in Outbreak Investigation (Ex-1)

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FSIS Update: WGS Application– Potential Use in Outbreak Investigation (Ex-1)

FSIS is also currently exploring use of WGS as a tool to understand potential harborage or reoccurrence of contamination in establishments

FSIS works collaboratively with FDA in dual-jurisdiction establishments that produce both FDA and FSIS-regulated productsWhen one agency identifies potential harborage

through bacterial characterization of Lm isolates (PFGE and/or WGS), information is shared to inform a collaborative regulatory response within the establishment

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Applications of WGS at FSIS: Lm HarborageFood Safety and Inspection Service

FSIS Update: WGS Application– Potential Use in Harborage

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Applications of WGS at FSIS: Lm HarborageFood Safety and Inspection Service

FSIS Update: Harborage ‘WGS and PFGE’ – Lm Experience (Ex-1)

Lm harborage: WGS and PFGE comparison

High quality SNPs wgMLST

Same PFGE pattern: WGS agreement 0-2 SNPs 0-7 allele differences

Same PFGE pattern: WGS exclusion 34-45 SNPs 29-33 allele differences

Different PFGE: WGS inclusion 0-3 SNPs 0-5 allele differences

WGS and PFGE results are generally in agreement WGS can sometimes exclude isolates from a group

with the same PFGE pattern or include isolates in a group with different PFGE patterns

In the examples below inclusion or exclusion considered all information including sample metadata (establishment, isolation date, etc.)

Note the trend between the SNP and wgMLST approaches

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FSIS Update: WGS Applications to AMR

Ability to rapidly identify new genes of concern Work with NARMS and other partners in a real-time to identify the

presence, magnitude and impact of undesirable gene(s) Proactively work with stakeholders to start taking the necessary

actions Examples of WGS application to novel gene detection and actions

ESBL blaCTX-M-65

Colistin Resistance Quinolone Resistance Linezolid Resistance Daptomycine Resistance

In 2015, FDA isolated Salmonella with extended spectrum beta-lactamase (ESBL) resistance from a NARMS retail poultry product purchased in December 2014Contained bla CTX-M … plasmid based resistance gene Never-before reported in Salmonella from food items in the US

Patients with Salmonella infection expressing this resistance pattern have few treatment options

FSIS actionsDetermined bla CTX-M-65 ESBL resistance in FSIS isolates

Phenotype and genotype (ResFinder)

Isolates with a match were investigated for their sources/origin and possible connections to human casesNo human illnesses were found connected to FSIS-regulated products

FSIS promptly notified all corporations with ESBL matches21


FSIS Update: WGS Application to AMR– Use in Determination of Unique AMR Gene (Ex-1)

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WGS at FSIS: Interagency Collaboration – Gen-FS

Interagency Group Name: Interagency Collaboration on Genomics and Food Safety (Gen-FS)

Federal partners: CDC, FDA, NCBI and FSIS Agencies with public health and regulatory focus Discussions is ongoing to include USDA-ARS and USDA-APHIS in Gen-FS

Nature of Work: WGS technology is rapidly evolving and Gen-FS provides the participating

agencies a governance structure for collaborative decision making Gen-FS will focus on the development and implementation of WGS tools, data

analysis pipelines and methods for the in-depth analyses of pathogens from food, feed, environmental, clinical, and animal sources

Gen-FS will harmonize the planning and implementation of WGS activities including surveillance, detection, investigation and research activities

Gen-FS will further strengthen outbreak cluster detection and response, and the detection/transmission of antimicrobial resistance

Charter and Signatories: Agency Heads/Leaders Director/Commissioner/Administrator Charter to be signed very soon and anticipated to become effective in FY 2017


FSIS Update: WGS – Gen-FS Activities

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WGS at FSIS: Interagency Collaboration – Gen-FSFood Safety and Inspection Service

FSIS Updates: WGS – Gen-FS Activities

Gen-FS Workgroups, Goals/Objectives and Activities

Workgroup Main goals/objectives

1 Data/analytic standards,

comparisons,

interpretations,

interagency working group

Conduct cross validation studies between SNP calling (important to FDA), and cluster methods, i.e., wg MLST (important to CDC)

Put together validation sets to test SNP calling and clustering methods Standards for whole genome sequencing for outbreak investigation

2 Interagency Training Working Group

Plan and coordinate WGS training activities for state health departments and other partners in order to avoid duplication and make sure the training offered is relevant for our partners

3 Communications Work Group

Standardize interpretation and communication of sequence data for different target audiences (e.g., regulatory staff in FDA and FSIS, public health partners (state, local health and agricultural food safety agencies; CSTE, APHL, ASTHO, NASDA, AFDO, other)

4 Genome-Trakr – PulseNet

Workflow Harmonization

Workgroup

Harmonize wet lab procedures, where feasible (laboratory worksheets, recommendations for QA steps and appropriate stopping points, run and file naming)

Harmonize raw data upload to NCBI Harmonize data tracking so that both sides know what is being sequenced to

avoid duplicate requests Harmonize certification and Proficiency Testing


FSIS Update: WGS Public Meeting Announcement

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The overall goal of the WGS public meeting is to discuss most current information and seek public inputWGS application in a regulatory context

Expected participationGen-FS and NARMS partners

Industry, Academia and other stakeholders

International partners


FSIS Update: Concluding Remarks

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FSIS is committed its Healthy People 2020 Pathogen Reduction Goals and beyond To accomplish the pathogen reduction goals, FSIS works closely with its public

health partners FSIS utilizes the best available science to understand the sources of food

pathogens and their prevention and control

FSIS is fully committed to utilizing the analytic power and resolution of WGS in its ‘pathogen reduction – public health protection’ pursuit FSIS is rapidly developing WGS capacity and intends to conduct real-time WGS

on all the FSIS isolates FSIS continues to collaborate with the CDC, FDA and NCBI to further understand

the ‘scope and applicability’ of WGS findings in FSIS’s regulatory context

FSIS intends to conduct a public meeting on WGS in this Fiscal year The overall goal of the meeting is to discuss the most current information

related to WGS and seek public input on - WGS application in a regulatory context

In its investigative decision making process FSIS utilizes WGS findings/interpretations as a part of the totality available evidence


FSIS Update:

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Discussion

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MPH, MS, PhD · 2017-06-15 · Uday Dessai MPH, MS, PhD Senior Public Health Advisor Office of Public Health Science, FSIS, USDA USDA, Food Safety and Inspection Service IFSH WHOLE

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