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PulseNet on the High Wire
16th Annual PulseNet Update Meeting8th Annual OutbreakNet Meeting
Atlanta, Georgia
National Center for Emerging and Zoonotic Infectious Diseases
Division of Foodborne, Waterborne, and Environmental Diseases
Efrain M. Ribot, Ph.D.
PulseNet USA
Centers for Disease Control and Prevention
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Disclaimers
National Center for Emerging and Zoonotic Infectious Diseases
Division of Foodborne, Waterborne and Environmental Disease
The findings and conclusions in this presentation have not
been formally disseminated by the Centers for Disease
Control and Prevention and should not be construed to
represent any agency determination or policy
Use of trade names is for identification only and does not
imply endorsement by the Centers for Disease Control and
Prevention or by the U.S. Department of Health and Human
Services
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825’
Carving = 3 acres or ~12,000m2
Stone Mountain
Pres. Jefferson Davis
Gen. Robert E. Lee
Gen. T. J. “Stonewall “Jackson
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Objectives
After this talk, participants will:
Understand the challenges posed by emerging diagnostic
techniques for foodborne laboratory-based surveillance
Know about new subtyping approaches being pursued by
PulseNet
Describe possible scenarios for the future structure and
functionality of PulseNet
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Outline
No Matter Where You Go, There You Are
To Culture or Not to Culture; Is that the
Question?
Ability Will Never Catch Up with its Demand
The Present is Now!
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No Matter Where You Go,
There You Are
Confucius / Buckaroo Banzai
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So, Where Is PulseNet Now?
• >85 PulseNet participating
laboratories in the US
• ~87 PulseNet International
laboratories in six regions around
the world
Nine standardized
PFGE protocols
Three standardized
MLVA protocols
PulseNet National Database 2011
• “Isolates” uploaded to database: 60,234
• Total PFGE patterns submitted: 74,817
Long-term investment in next generation subtyping methods
E. coli O157, S. Typhimurium,
and S. Enteritidis
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Dice (Opt:1.50%) (Tol 1.5%-1.5%) (H>0.0% S>0.0%) [0.0%-100.0%]
PFGE-AscI
100
90
80
70
60
PFGE-AscI
CT___140711001
USDA_201044022
FCF__626923 53-2
FCF__676031 101-2
FCF__704399 60
MA___11EN2031
CDC__11026231
CDC__2011032385
CDC__2011032988-1
CDC__2011032988-2
CDC__2011033047
CDC__2011033182
CDC__30126429
CDC__30144000
CDC__30240775
CDC__M11-178
CO___ENV-201101.
CO___HUM-201102.
CO___HUM-201102.
CO___HUM-201102.
CO___HUM-201102.
CO___HUM-201102.
CO___HUM-201102.
CO___HUM-201102.
CO___HUM-201102.
IN___12REF0033
TX___TXACB11026.
TX___TXACB11027.
TX___TXACB11027.
TX___TXACB11027.
TX___TXACB11028.
NYC__nyc11-10124.
FCF__704399 62
OH___2011053167
MI___CL11-200449
FCF__688919 35
SDC__12-007552
CO___HUM-201102.
FCF__300717-02A
FCF__668274 87-16
FCF__694241-91
FCF__623013 59-6
FCF__662081 10-1
VA___R110930005
MA___11EN1911
NY___IDR11000312.
FCF__610697 27-1
MI___CL11-200501
Cluster analysis
Trends, Burden, and Attribution
Outbreak Detection
Outbreak Investigation
Control
PulseNet
• 245 Clusters Identified in CY2011
• 187 in FY2012 (as of 7/31/2012)
FoodNet
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Where Were We Headed?
Next generation subtyping efforts
CRISPR Analysis
MLVA
SNP Analysis
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Trends, Burden, and Attribution
Outbreak Detection
Outbreak Investigation
Control
FoodNet
Next Generation
Subtyping Approach
Perform “Next Gen”
Subtyping Locally
• Distill Data
• Cluster analysis
• Correlate ‘next gen” data
with historical profiles
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1944
Saturn V
1903
1800s
2.5 million years ago
Clothes
170,000 years ago
Sun Dial 800 BC
1500 BC
1895
1900s
Mechanical Computer
1946
“Digital Computer”
1908 Model T
312 BC
William Gilbert
Electricity
1600
Benjamin Franklin
1750s
Atomic Clock
Tesla
Fisker Karma
1.5 million years ago
15,000 BC
Domestication
of animals
8,500 BC
Farming
1935
1981 “IBM PC”
Space Shuttle
2011Medieval
Times
8,000 B.C.
PCR
The World Wide Web
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Pacific Biosciences
1ST Generation Sequencing
(Sanger)
Whole Genome Mapping
OpGen
Genome Sequence Scanning
Pathogenetix
SNP Analysis
Array- and Luminex-based
Roche 454
Nanopore
Illumina (MiSeq)
LifeTech/Ion Torrent
Next (NOW) Generation Sequencing
Many Others…
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of PulseNet
Adapted from WIRED Magazine 2010
CIDT
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To Culture or Not to Culture,
Is that the Question?
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Vet/Ag
Labs
Pathogen Specific Surveillance
Lab Reports Lab Reports
Isolates
Public Health
Case Reports
Case Interviews
Prevention/Control
Clinical LabPhysician/Patient
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Vet/Ag
Labs
On a Need to Know Basis
Lab Reports Lab Reports
Isolates
Public HealthClinical Lab
“Private Health”
Diagnose illness
Guide therapy
Rapid test
Accurate test
Control cost
Outbreak detection Characterization
Subtyping
Susceptibility monitoring
Limit transmission
Control
Monitor trends
Informed policy
development
That is the question!
Academic
Knowledge
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Clinical Diagnostics Trending
Toward “Culture-Independent” Tests
Enzyme ImmunoassaysAmplification (molecular)
PCR:Hybridization
Isothermal DNA
Amplification (LAMP)
Mass SpectroscopyMALDI-TOF S. Typhimurium
(Proteins)
Sauer & Kliem, Nature Reviews Microbiology 8, 74-82 (January 2010)
Electro Spray Ionization
(nucleic acids/PCR)
Luminex
xTag GPP
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CIDT: Coping Mechanisms
Status quo not an option
Education/Awareness (a two-way street)
Culture-Independent Diagnostics Forum: Charting a Path
for Public Health
• First meeting held in April 2012 in Atlanta
• Coordinated by CDC, APHL, CSTE
• Attendees included regulatory, clinical, scientific, and industry
experts
• Outcomes
o Formation of several workgroups
o Relationships
o Publications
o Follow-up meetings
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Guidelines and Recommendations
Work with medical industry to make new tests
compatible with public health needs
Modify criteria for medical device licensure?
Make reflex culture reimbursable?
Modify State reporting rules
Develop isolate recovery capacity for PHLs
Sentinel culture-based surveillance?
CIDT: Coping Mechanisms
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Technology
Intermediate-term:
• Next generation” approaches adaptable to a
non-culture world
o Characterization and subtyping
Longer-term:
• Evaluate platforms that specifically address CIDT
issues
o Next Gen Whole Genome Sequence Analysis
o Metagenomics
CIDT: Coping Mechanisms
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CIDT: Opportunities
Faster results
Improved exposure recall
Faster intervention
More reported cases
Better understanding of disease causation
Outbreaks of unknown etiology
“Village” approach to adoption of new methods
Increase the speed of diagnosis and reporting to
public health
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Ability Will Never Catch Up
with its DemandConfucius
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Path to the Future
Lead to solutions that address
our ability to:
Enhance laboratory-base
surveillance
Loss of cultures/isolates to
“CIDT”
Long-term approach:
Next Generation Sequencing
of Whole/Partial Genomes
Metagenomics (“specimen
sequencing”)
Next gen subtyping tools must:
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Path to the Future
Next Gen Sequencing:
Complex
Infrastructure
Bioinformatics (bottleneck)
Expertise
Pipelines
Turn-key approaches
Data quality (standardization)
Data management, storage
and security issues
Data interpretation
Data accessibility
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It Takes a Village…
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The Present Is Now!
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Grater Genome Projects
250 STEC whole genome sequencing project
Reference of sequences
Diversity within and across STEC serotypes
Metagenomics project
Stool samples
Outbreak specific projects (V. cholerae, Listeria, E.
coli, others)
Collaborations with national and international groups
100K Foodborne Pathogen Genome Project
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Listeria Cantaloupe Outbreak
Eight Listeria Isolates sent to
Illumina and Life Tech/Ion Torrent
for genome sequencing
Strains represented four different
outbreak patterns
Results from sequence comparisons
(based on SNPs) correlate with
PFGE data
First of a series of collaborations
aimed at streamlining process
PHL friendly
Illumina MiSeq
Ion Torrent
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Trends, Burden, and Attribution
Outbreak Detection
Outbreak Investigation
Control
FoodNet
Next Gen
Whole Genome
Sequencing
• Distill Data
• Cluster analysis
• “Deep drilling” analysis
Specimen,
material or device
PulseNet In The Clouds
Public?
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Parallel Subtyping Universe
Gold Standard
Next Gen Subtyping
- Epidemiologic relevance
- Adaptable to a network like PulseNet
- Practical
- Cost effective
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Forecasting the Future is Hard…
Atlanta, 8/27/2012@8PM Atlanta, 8/28/2012 @8PM
Atlanta, 8/28/2012 @10PM
1 2
3 4 Atlanta, 8/29/2012 @6AM
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Technology, Next Generation or Otherwise, is Not a Substitute for Strong Epi
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Life is on the Wire!Karl Wallenda
Photo: Reuters
The Canadian Press, Nathan Denette / AP
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For more information please contact Centers for Disease Control and
Prevention1600 Clifton Road NE, Atlanta, GA 30333
Telephone, 1-800-CDC-INFO (232-4636)/TTY: 1-888-232-6348
E-mail: [email protected] Web: www.cdc.gov
Thank You!
National Center for Emerging and Zoonotic Infectious Diseases
Division of Foodborne, waterborne, and Emerging Diseases
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.