Infrastructure and Methods to Support Real Time Biosurveillance
Drs. Jeff Zimmerman & Rodger Main - Evolution of Biosurveillance
Transcript of Drs. Jeff Zimmerman & Rodger Main - Evolution of Biosurveillance
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Evolution of Biosurveillance
Rodger Main and Jeff ZimmermanIowa State University
Ames, Iowa
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Why talk about surveillance?
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2009 pH1N1 … "swine flu"
pH1N
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$2 b
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Surveillance = data based on testing.
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Serum Feces Tonsil0%
20%
40%
60%
80%
100%
18%36%
55%9%
18%
27%
Percentage of positive sows
Clinically affetcted Clinically normal
Sows: % Senecavirus A rRT-PCR-positive 11 sows with SVA lesions 11 clinically normal sows
Clinically affected Clinically normal
Serum Feces Tonsil
Courtesy of Dr. Pablo Piñeyro
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Serum Feces Tonsil0%
20%
40%
60%
80%
100%
33% 33% 33%
18%36% 27%
Percentage of positive piglets
Clinically affetcted Clinically normal
Courtesy of Dr. Pablo Piñeyro
Piglets: % Senecavirus A rRT-PCR-positive
Clinically affected Clinically normal
Serum Feces Tonsil
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How to make surveillance work? (fast, accurate, affordable, practical)
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How to make it work?
• Federal-State-Industry partnership– Long-recognized fact.
• GAO-15-664T (July 8, 2015)– Resources that constitute a national biosurveillance capability are
largely owned by nonfederal entities.– Strengthen and leverage nonfederal partners … to build and maintain
national biosurveillance capability.
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How to make surveillance work? (fast, accurate, affordable, practical)
… in a Fed-State-Industry partnership … ?
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"Start where you are, with what you have."George Washington Carver
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VDL 1 VDL 2 VDL 3 VDL 4
Centralized Database
"Start where you are, with what you have." GWC
Anticipate the need for testing capacity …UMN (FY 2012) 1,374,925 tests runSDSU (FY 2013) 400,292 tests runISU (2013) 1,128,455 tests run
VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS
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Shared Database
VDL 1 VDL 2 VDL 3 VDL 4
VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS
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VDL 1 VDL 2 VDL 3 VDL 4
Shared Database
Coordinated Emergency Response
VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS
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"Start where you are, with what you have."
• On the farm … – Vets know the producers, the pigs, the farms. – Vets know how to collect and deliver samples to
the VDLs quickly.• The VDLs …
– Know how to receive, process, and test massive numbers of specimens.
– Know how to manage huge databases & deliver results quickly.
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We have an unprecedented opportunity to create an effective surveillance system.
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Things to think about, bumps in the road, hurdles, etc. etc.
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• So who will collect the samples?– Federally-accredited, swine specialist vets (AASV) and others under their
supervision– "mission of the National Veterinary Accreditation Program is to ensure the health
of the … animal population and to protect the public health and well-being."`
Collecting samples in the U.S. classical swine fever eradication program ~1970
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What sample will they collect?
• The specimen "most fit for purpose"– Screening? For detection = oral fluids– Confirmation/follow-up? Individual pig samples – Pre-movement? Individual animal samples
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ISU - VDL - oral fluid tests:• 2010 - 10,231
• 2011 - 32,591
• 2012 - 60,034
• 2013 - 94,101 • 2014 - 146,831
• 2015 - ~175,000 TOTAL 518,788
Our vets & producers know oral fluids.
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Continual test assessment & improvement
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Oral fluids … sensitive screening sample for antibody- and nucleic acid-based assays
PRRSV Prevalence
Pigs(+/total)
ONE Oral Fluid SAMPLE probability of detection
Sample size to match OF probability of detection
4% 1/25 15% Bleed 4 pigs12% 3/25 45% Bleed 5 pigs20% 5/25 75% Bleed 7 pigs36% 9/25 95% Bleed 8 pigs
Olsen et al. 2013. Probability of detecting PRRSV infection using pen-based swine oral fluid specimens as a function of within-pen prevalence. J Vet Diagn Invest 25:328-335
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What tests will we run?
• For FADs, options very limited. PCRs on selected samples e.g., CSFV - tonsil, tonsil scrapings, nasal swabs.
• Repertoire of tests & samples must be expanded. • Fed-State-Industry partnership USDA retains
ownership of tests and test results
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What tests will we run?
• Commercial kits. (Fed-State-Industry)• High through-put.• Robust technology.• Reproducible/repeatable.• Accurate. Dx specific.
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CONTINUAL TEST ASSESSMENT/IMPROVEMENTPigs inoculated with ALD strain CSFV.Dr. Y Panyasing, Chulalongkorn University
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VDL 1 VDL 2 VDL 3 VDL 4
Centralized Database We have an unprecedented opportunity to create an effective surveillance system
VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS
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Evolution of Biosurveillance
Rodger Main and Jeff ZimmermanIowa State University
Ames, Iowa
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HPAI Spring 2015
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300ISU VDL AIV PCR Cases by Week
H5 Positive Cases
Negative Cases
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ISU VDL AIV H5 Positive Cases by Week
Diagnostic Case Submissions ≠ Number of Infected Premises {10 week HPAI Outbreak in IA}
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5
0100200300400500600700800900
1000110012001300
ISU VDL AIV PCR Tests by Week H5 Positive Tests
Negative Tests
{4 months sustained response at VDL}
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Summary HPAI Infected Premises• 35 Commercial Turkey Farms• 22 Commercial Table Egg Layer Farms• 13 Commercial Table Egg Pullet Farms• 1 Commercial Breeder Flock• 5 Backyard Producers• 1 Commercial Mail Order Breeder Operation
• Total = 77 HPAI Infected Premises
Data courtesy of:Dr. David Schmitt, State VeterinarianIowa Department of Agriculture and Land Stewardship
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2015 Iowa Affected Poultry
Data courtesy of:Dr. David Schmitt, State VeterinarianIowa Department of Agriculture and Land Stewardship
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Core Elements of FAD Preparedness at VDL(Remained same as identified during PEDV)
• Competent Personnel & Robust VDL Systems• Validated Assays• High-Throughput Testing Platforms• User Friendly & Effective Sample Types• PINs on VDL Records• Automated Electronic Messaging of Results
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What could VDL improve its role in support HPAI preparedness / response ?
Early Detection, Rapid Response, & Effective Communication (Seamless, Timely, Clear)
Competency of Personnel & VDL Systems Quality of Test & Results High-Throughput & Sensitive Assays User Friendly & Effective Sample Types Testing Capacity Turn-around Time Quality of Information in VDL Record
• Complete, Consistent, Traceable, Fit for Digital Transmission
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AIV Diagnostic Record Information Flow
Submitter(Producer)
VDL Receiving / Case Entry
State & FederalPrimary Points of Contact
VDL LIMSLab Information
Management System
USDALab Messaging Service
State & Federal OperationsEMERS
Emergency Management Emergency Response System
Human Readable Digital Code
5 W’s = Who, What, When, Where, and Why
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Observation at VDL• Manually Entered Premises Level Identifiers
(Farm Site Information) Are Not Compatible With Web-Based Data Management Applications
• Need To Transcend VDL Records Into Digital Era
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Manual Transcription of PINs Doesn’t Work!• O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0,
5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O,006DO17, D176S501, 001SD6S, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O71G6D0, 5S0D61O, O80DS6G
1 Day, 1 VDL, (Submitter and Case Entry Staff)≈ 350 Cases or 700 Transcriptions of PINs / Day
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Our Conclusion or “Litmus Test”
Can You “Scan It” or “Click On It” ?
If Yes = It Works (Repeatable, Connected, Automation)
If No = It Doesn’t Work (Inconsistent, Manual Data Transfer)
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Diagnostic Record Information Flow
SubmitterVDL Receiving /
Case Entry
Human Readable Digital Code
• Premises Level Data On VDL Submission Form Case Entry• Completeness• Consistency• Traceability• Connectivity
Katie WoodardClient Outreach/Education
Less More
X
Front-end of Diagnostic Process
ISU VDL IT Team
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Sustained Responses to Large-Scale Emerging Disease Events: “Real Life Is Not A Drill”
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Baseline Stakeholder Expectations of VDL’s
• Competent VDL Personnel & Infrastructure• Quality Assays & Test Results• Turn-Around-Time (Same Day/Next Day)• Electronic Distribution of Results• Cost Effective Service• Protect & Sustain Continuity Their Business (All consistent with the mission of the NAHLN)
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Serving Food Animal Agriculture Comprehensive Diagnostic Service, Teaching, and Discovery
(Iowa’s only Full-Service & Fully Accredited Veterinary Diagnostic Laboratory)
Processing > 70,000 cases/year from livestock producers for across USApplying world-class technology to solve real-world problems
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Network of Interdependent Relationships to Improve & Protect Food Animal Agriculture
Food
AnimalAgriculture Consumer
GeneticsFacilities / Environment
Nutrition
HealthManagement
Business / Finance
Practicing Veterinarian
VeterinaryDiagnostic
Labs
Production AnimalMedicine
SuppliersOf Health Products
Producer
Pathology Virology
Bacteriology Serology
ToxicologyPharmacolog
yEpidemiology Parasitology
State and Federal VeterinaryOfficials & Agencies Strategic Alliances → Service, Innovation, & Teaching
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1 Monitoring Health Status of Swine Farms Overtime(Operation, Production System, Clinic, or Area-Regional Level)2 Health Status = Qualitative, Quantitative, and/or “Strains” Active
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Highly Collaborative Journey
Southeast IA North AmericaMB-MO (Princeton)
Pilot Project Participants
Information Mgt Technology
Peer VDLs
B. Martinez, Z. WhedbeeA. Perez (UMN)
R Main, B. Crim, K. Mueller, K Woodard, J Bjustrom-KraftIT Team
D. Polson, E Lowe, E Mondaca
$
(HIMS) (HIMS) (NAHLN) (Data Standards)
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Objective• Link VDL submissions, corresponding
test results, attending veterinarian insight, and an interpreted health status of farm sites to a highly capable spatiotemporal disease management tool for use in area-regional, veterinary clinic, or production system swine health monitoring and control initiatives.
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Desired Outcome
• Provide User-Friendly System for Monitoring Health Status of Swine Herds Overtime– Individual Farm or Operation– Production System– Veterinary Practice – Area-Regional Project
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Working on Both Ends & Everywhere in Between
# 1
# 2
# 6
# 3
# 5
# 4
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Front End
• Transcend Quality of VDL Records into Digital Era
“Electronic transfer of premises level identifiers (PINs) on VDL submission form”
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VDL’s Efforts to Improve Quality of VDL Record(Completeness, Consistency, Traceability, Connectivity)
• Provide clients two options to transcend quality of VDL records in to digital era.
1. Web-Submissions2. Premises Specific Bar-Code Labels
Both options:* Result in electronic transfer of the full complement or premises or site level identifiers.
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Middle
• Diagnostic Data Standards (PRRS, PEDV, PDCoV, M hyo, SIV)• Rules Based Algorithms For Assigning Status / Classification • Web-Based Database Application (SAHDD)
• House Participant Premises Level Data (Pre-Populated)• Receive and Interpret (VDL Cases Results & Attending Vet)• Assign Status & Classification• Archive Data• Push to 3rd Party Database Application (BioPortal) for Analysis & Reporting
B Crim
K Mueller
J Bjustrom-Kraft
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Back End
• Web-Based Database Application (Disease BioPortal)• Spatiotemporal and Bionformatic Analysis and Reporting• Update Structure, Design, & Capabilities of Database• Create Reporting Functionality Applicable to Swine Health Monitoring
• Health Status & Classification of Herds Over Time• Sequencing Analysis ( Monitor Various Strains / Variants)
B Martinez Z Whedbee
D Polson E Lowe
E Mondaca
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Synergistic Collaborations
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Where We Are Today• Ensure VDL Record “Fit” for Digital Era
ISU VDL Web-Portal (last updated, 11/04/2015)– Web-Submissions (Electronic)– Site-Specific Bar-Codes (Paper)
• SAHDD (Secure Animal Health Diagnostic Database)– Receives Input (VDL Case Results & Veterinarian Input)– Interprets Case Results– Assigns Health Status to Case and Site (By Pathogen)– Assigns Health Classification to Site (By Pathogen)– Archives & Push to Disease BioPortal
• Disease Bioportal – Data Analysis & Summary
• Advanced Spatiotemporal & Bioinformatic Analysis Capabilities – User Group Defined Dashboards – Site Specific and/or Aggregate Data Capabilities
All Components Web-Based, Permissioned Access
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1 Monitoring Health Status of Swine Farms Overtime(Operation, Production System, Clinic, or Area-Regional Level)2 Health Status = Qualitative, Quantitative, and/or “Strains” Active
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Next Steps• Transition Development Service in 2016
– Initially offering & operating service as a “Bureau”• Deliver a “Viewable Product”
– Client Specific Dashboards (Disease BioPortal)– View Only Access to SAHDD
SAHDDAccount Manager
Vet Clinic“ABC”
Genetic Company
“XYZ”
ARC Project“SE IA”
Production System“DEF” Disease BioPortal
Client Specific Dashboards
SAHDDClient SpecificPremises Level
History
Permission Users(Clients)
View Only
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Summary – Evolution of Biosurveillance
• Risks, Gaps & Opportunities for Improvement• Systems of Surveillance Need to Evolve
– Federal, State, & Industry Partnerships
• Address the Obvious & Put into Routine Practice – Assays, High-Throughput Platforms, Traceability, & IT– Continuity of Business Programs
• Emergency Preparedness ?? → Routine Practices• Progress on New Tools For Private Sector Applications
* Early Stages - Dawn of New Age for Animal Health Information Management
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Evolution of Biosurveillance
Rodger Main and Jeff ZimmermanIowa State University
Ames, Iowa
Thank You ! Questions ?