National Center for Emerging and Zoonotic Infectious Diseases FSIS - - PowerPoint PPT Presentation

National Center for Emerging and Zoonotic Infectious Diseases FSIS & CDC Working Together for Rapid Response and Action: The Transformation of Surveillance and Outbreak Investigation for Foodborne and Enteric Pathogens

Ian Williams, PhD, MS Chief, Outbreak Response and Prevention Branch Division of Foodborne, Waterborne and Environmental Diseases National Center for Emerging Zoonotic and Infectious Diseases

FSIS Seminar March 22, 2017

InterAgency Agreement (IAA) Background

• Established in FY07
• Three goals listed in FY16

– National outbreak detection and response will be fully coordinated between the responding federal, state, and local agencies – Implement metrics, performance measures, and best practices for foodborne outbreak response – Provide assistance to state and local health departments for outbreak response

2

Overall Impact of IAA on National Outbreak Response Activities

• Ensured close collaboration between CDC and FSIS
• Ensured that Foodborne Outbreak Response and Management

(InFORM) meetings and PulseNet/OutbreakNet Regional Meetings were held

• Helped continue the Foodborne Diseases Centers for Outbreak

Response Enhancement (FoodCORE) and OutbreakNet Enhanced projects

• Helped develop approaches to detection and investigation of

multistate foodborne disease outbreaks

• Ensured successful investigations of FSIS regulated products

3

Targeted CDC Programs to Address Gaps in Foodborne Disease Outbreak Response Capacity

• OutbreakNet
• OutbreakNet Enhanced
• Foodborne Diseases Centers for Outbreak Response

Enhancement (FoodCORE)

• Integrated Food Safety Centers of Excellence

FoodCORE Centers of Excellence

Building Capacity in Participating Health Departments ~ Collaborations among: Laboratorians Epidemiologists Environmental Health Specialists Providing Support for Other Health Departments ~ Collaborations across: Health Departments Academia

OutbreakNet Enhanced

Additional Funding for Participating Health Departments ~ Collaborations with CoEs

OutbreakNet/NORS

Epi Support

Model Practices Technical Assistance

Improve Lab, Epi, and EH Capacity Share Lessons Learned as Model Practices Measure Success through Metrics

FoodCORE

• Started in late 2009
• 10 participating sites

• Started in 2015
• 18 participating sites

Partner with a Center

• f Excellence

Expanding to Additional Sites

Build on FoodCORE Successes – Focus on Epi Capacity

OutbreakNet Enhanced

Measure Success through Metrics

Collaboration and Integration

 InFORM Conference - tenth annual OutbreakNet meeting

• Joint national conference with Lab, Epi, and EH
• November 17-20, 2015 in Phoenix, AZ

 Joint PulseNet/OutbreakNet Regional Meetings during FY17

• Regional meeting with Lab, Epi, and EH

 OutbreakNet Quarterly Calls

• All-state partner calls with range of topics
• OWL calls – wise persons cal on selected topics

Impact of IAA on National Outbreak Response Activities

 Critical in making OutbreakNet and FoodCORE fully functional  Paved the way for the implementation of the 11 OutbreakNet

Enhanced sites during FY15 and expansion to 18 sites in FY16.

 Working together during 2016 we investigated over 200 multistate

clusters

• > 6,500 culture-confirmed enteric illnesses, resulting in over 900 hospitalizations and

approximately 25 deaths

• In any given week, we were investigating an average of 41 clusters with a range of 21

to 57 clusters per week

 Fifteen major foodborne and zoonotic outbreak investigations (13

foodborne and 2 enteric zoonotic)

• FSIS-regulated products mplicated and recalled included pork and beef products
• 35 individual web postings which were viewed over 2.5 million times

 The investigations of these outbreaks led to important short-term and

long-term preventive measures that are making the food supply safer

WHOLE GENOME SEQUENCING (WGS): TRANSFORMING SURVEILLANCE AND OUTBREAK INVESTIGATION FOR FOODBORNE AND ENTERIC PATHOGENS

Foodborne Diseases in the United States: A Changing Landscape

• Food production and distribution has changed

substantially over the last several decades

• Fewer food producers, but with wider

distribution

• On average, food comes from farther away
• More “ready-to-eat” and industrially produced

foods

Foodborne Diseases in the United States: A Changing Landscape

“Classic” Foodborne Outbreak Disseminated Foodborne Outbreak

Detecting Outbreaks with PulseNet

• Subtyping enteric bacteria is essential to identifying highly

disseminated outbreaks

• PulseNet laboratory network established in 1996
• Bacteria collected from ill people undergo DNA

“fingerprinting” using pulse-field gel electrophoresis (PFGE)

=

Bacteria with the same “fingerprint” are more likely to come from a common source

PulseNet Groups Together Cases Most Likely To Share a Cause for Their Illnesses

14

PulseNet In Transition

PFGE WGS

2005 1996 2010

Modified from Carleton and Gerner-Smidt (ASM Microbe July 2016)

PFGE WGS

In Preparation: PulseNet International Vision for the Implementation

• f WGS for Global Foodborne disease Surveillance

MLVA

2018  PulseNet is transitioning from PFGE to WGS

Conceptual Framework for PFGE Subtyping

Bacterial Genome Genome “Fragments” PFGE Patterns

Analogous to comparing two books based on the number of words in each chapter

“Cut” Sites

Strengths and Limitations of PFGE-Based Subtyping

• Successful over the last 20 years in detecting

highly disseminated outbreaks

– Would not have otherwise been detected – Would have been detected later

• Limitations to PFGE-based subtyping

– Some PFGE patterns common, limiting utility – PFGE patterns are indirectly reflective of underlying genetic relatedness of bacteria – Related bacteria can appear different by PFGE and vice versa

2010 Outbreak of Salmonella Enteritidis Infections Linked to Shell Eggs

• Most common PFGE pattern in the

PulseNet database

• 3,578 illnesses reported during the
• utbreak period
• 1,639 presumed to be unrelated

“baseline” cases

• Complicated investigation into the

source

WGS Provides a Higher Resolution View of the Bacterial Genome

“Cut” Sites All Positions PFGE only gives information at a “cut” site via the banding pattern WGS has the ability to give us information at every position in the bacterial genome

Analogous to comparing two books based on all the words in the book

Incorporation of Whole Genome Sequencing Techniques into Multistate Foodborne Outbreaks

• In September 2013, CDC began prospectively sequencing all clinical

isolates from listeriosis cases – Collaboration between numerous federal and state agencies – Near real-time results (<1 week for patient isolates)

• WGS also being performed on selected Salmonella and E. coli isolates

– Consensus process between lab and epi on what to sequence/analyze – To answer specific investigation questions

Public Health Impact of WGS on Listeriosis Outbreak Investigations

14 2 6 13 19 6 5 4 20 21 6 9 3 103 17 8 5 4 42

20 40 60 80 100 120

• No. of clusters

detected

• No. of clusters

detected sooner

• r only by WGS*
• No. of outbreaks

solved (food source identified) Median no. of cases per cluster

• r outbreak
• No. of cases

linked to food source

Pre-WGS (Sept 2012–Aug 2013) WGS Year 1 (Sept 2013–Aug 2014) WGS Year 2 (Sept 2014–Aug 2015) WGS Year 3 (Sept 2015-Aug 2016)

WGS Impact on Outbreak Investigations

• Grouped isolates with different PFGE patterns into single clusters
• Blue Bell listeriosis outbreak
• Determined the source of older unsolved illnesses/clusters
• Karoun Dairies Cheese listeriosis outbreak
• Demonstrated that some PFGE-defined clusters did not consist of

highly related isolates

• Salmonella Typhimurium pseudo-cluster with high mortality
• Refined outbreak case definitions
• Multidrug-Resistant Salmonella I 4,[5],12:i:- and Salmonella

Infantis Infections Linked to Pork

• Linked sporadic illnesses to contaminated food
• Two listeriosis cases linked to raw milk
• Identified outbreaks following product testing
• Listeriosis illnesses linked to bagged salad
• Helped understand the ecology of pathogen reservoirs
• Multidrug-Resistant Salmonella Heidelberg Infections Linked to

Foster Farms Brand Chicken

What Is an Outbreak?

• PFGE model has focuses on illnesses “exceeding baseline”

– More cases than expected over a specified time period – Interpretation affected by how common the PFGE pattern is – Many “background” cases may be included in an investigation

• WGS model throws out the idea of a baseline?

– Groups isolates that are highly likely to share a common source – More analogous to seeing an outbreak with a novel PFGE pattern

Changing Notion of Sporadic Illness

Listeriosis linked to frozen vegetables

• 9 cases in 3 years

Listeriosis linked to ice cream

• 10 cases in 5 years

These illnesses are not sporadic, but are endemic disease that previously appeared sporadic because of limitations in investigation tools

How Will Cluster Detection Change with WGS?

• Clusters will be detected sooner, smaller, and with few “background”

illnesses included

• Currently cluster detection with WGS is relatively manual

– No statistical algorithms to detect clusters

• Nomenclature will provide a way forward

– Scheme similar to PFGE pattern names, but based on WGS – Easily query closely related isolates – Create genomically-based detection algorithms like CODA

• Can other data points be used to detect anomalies?

– Food/animal exposure data from interviews – Demographics – Contemporaneous non-human isolates

What Do All These Changes Mean?

• Identify more outbreaks and solve them faster, many that might never

have been solved in the past – Implementation of WGS – Improving sharing, compiling, and analyzing epi data (e.g., SEDRIC, Enterics Direct, STEC Initiative)

• Know resistance and virulence factors in near real time when uploaded

to PulseNet

• Start chipping away at “sporadic” illness (and maybe even reduce the

population incidence of some of these pathogens)

ATTENTION SEMINAR ATTENDEES:

Data and information presented in this seminar are strictly for informational purposes. The contents of the slides or the information discussed during the seminar may be privileged, proprietary or confidential in nature and a sole property of the presenting entity. Hence, any recipient of the information or material from FSIS seminars should not share it further with a third party without an explicit consent of the presenter and/or the entity responsible for such information.

FOR ADDITIONAL INFORMATION, PLEASE CONTACT JUDE SMEDRA, FSIS SEMINAR COORDINATOR AT FSISSEMINARCOORDINATOR@FSIS.USDA.GOV.

For more information please contact Centers for Disease Control and Prevention 1600 Clifton Road NE, Atlanta, GA 30333 Telephone: 1-800-CDC-INFO (232-4636)/TTY: 1-888-232-6348 Visit: www.cdc.gov | Contact CDC at: 1-800-CDC-INFO or www.cdc.gov/info

The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.

National Center for Emerging and Zoonotic Infectious Diseases Division Name in this space