Transcript CFSAN Chemical Signal Detection and Management System

GenomeTrakr: A Pathogen Databases to Build
a Global Genomic Network for Pathogen
Traceback and Outbreak Detection
Penn State
10 March, 2015
Marc W. Allard, PhD
SBRS officer
Co-authors: C. Wang, G. Kastanis, C. Pirone, Tim
Muruvanda, E. Strain, R. Timme, J. Payne, Y. Luo, Narjol
Gonzalez-Escalona, Magaly ToroIbaceta, A. Ottesen, D.
Melka, P. Evans, S. M. Musser and E. W. Brown.
Food and Drug Administration, College Park MD USA.
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Economic Burden of 15
Major Pathogens
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http://ers.usda.gov/data-products/cost-estimates-of-foodborne-illnesses.aspx#48443
Whole genome sequencing is changing
the science of infectious disease
WGS has to potential to serve as the single assay for microbial
surveillance/outbreak detection and supplant multiple methods
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2.
3.
4.
Classical serotyping
PFGE and other strain typing methods
In vivo antimicrobial susceptibility testing
Piecemeal PCR gene detection and plasmid typing
And to provide:
1.
2.
3.
4.
5.
6.
Genome/nucleotide surveillance
Virulence profiles
Molecular phage typing
Markers for source attribution
Better understanding of emerging trends
Costs savings
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DNA Sequencing
•
Bases of DNA (ATGC) are sequentially
identified from a DNA template strand
Cost per bacterial genome
$3,500
$3,000
•
Next Generation Sequencing (NGS)
extends this process across millions of
reactions in a massive parallel fashion
FDA 1st
$2,500
Desk-top
$2,000
$1,500
$1,000
•
NGS involves rapid sequencing of
large DNA stretches spanning entire
genomes
– Technology shift
– 3-5 million data points for each isolate
•
Increasing availability and affordability
of NGS is rapidly changing the face of
microbiology
$500
$0
2007
2008
2009
2010
$70/genome
in 2014
2011
2012
2013
$40/genome
in 2015 w/
Higher througput
Technology
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How FDA is Using WGS
• To differentiate sources of contamination, even within the same
outbreak
• To determine which ingredient in a multi-ingredient food harbored
the pathogen associated with an outbreak
• To narrow the search for the source of a contaminated ingredient,
even when the source may be half way around the world
• As a clue to the possible source of illness – even before a food
has been associated with illness using traditional epidemiological
methods
• To determine unexpected vectors for food contamination
• To develop rapid methods to identify/characterize resistant
bacteria
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Whole Genome Sequencing Program (WGS)
GenomeTrakr
• State and Federal laboratory network
collecting and sharing genomic data
from foodborne pathogens
• Distributed sequencing based network
• Partner with NIH
• Open-access genomic reference
database
•
http://www.ncbi.nlm.nih.gov/bioproject/183844
• Can be used to find the contamination
sources of current and future outbreaks
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http://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgramWGS/default.htm#trakr
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External labs
FDA labs
24 labs, historical strains and real time surveillance isolates
External Labs
Alaska
Hawaii
New Mexico
Arizona
Texas
Minnesota
New York
NY agriculture
Maryland
Virginia
W Carolina Univ.
USDA-FSIS
Florida
Florida agriculture
California
South Dakota
Argentina
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GenomeTrakr databases
Organism
isolate metadata genomes submitted
Salmonella enterica
15,508
10,518
Listeria monocytogenes
3,326
1,272 / 2,606
E.coli
428
332
Cronobacter
154
56
94
110
Campylobacter jujunii
Vibrio parahaemolyticus
10
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Salmonella database diversity:
Spatial:
• 65 countries
• 45 US states
Genetic:
• all 5 Salmonella subspecies
• over 400 Serovars of subsp. enterica
Temporal:
• sample collection dates span the past 25 years.
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WGS-surveillance approach to public health
clinical and environmental isolates
enter the database in real-time.
FDA, CDC, USDA, States
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Source of contamination
identified through WGS combined
database queries
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Number of cases
30
25
20
15
Food
enters
commerce
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5
0
4
8
12
16
20
24
28
32
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Days
40
44
48
52
56
60
64
68
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Current status
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WGS clearly defines foodborne
outbreaks – more than 24 different
examples
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NGS network is reliable, efficient and can
provide very good location specificity of
outbreaks
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We have sequenced more than 10,500
Salmonella, more than 2,500 Listeria,
and closed 100 genomes. Our current
rate is about 800 draft sequences a
month.
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The need for increased number of well
characterized environmental (food, water,
facility, etc.) sequences may outweigh
need for extensive clinical isolates
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Highly successful partnership with CDC
on real-time tracking of Listeria outbreaks
Salmonella
Listeria
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The power of open data
FDA_2010_142_Pistachio-3
(Slide courtesy of J. Ostell, NCBI)
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Program Chairs: Dag Harmsen (Univ. Münster, DE), Marc Allard and Eric Brown (both FDA, US)
ASM Conference Committee Liaison: Gary Procop (Cleveland Clinic Foundation, US)
ASM Conferences Program Manager: Lisa Nalker (Washington DC, US)
Keynote Speakers: Francis Collins (NIH Director, US), Stephen Ostroff (FDA Commissioner), Julian Parkhill
(Sanger, UK) & George Weinstock (Jackson Lab., US)
Invited Speakers: David Aanensen (Imperial, UK), Frank Aarestrup (DTU, DK), Marc Allard (FDA, US), Greg
Armstrong (?, CDC, US), Bruce Budowle (Unvi. Texas, US), Charles W. Chiu (Univ. San Francisco, US), Amy
Gargis (CDC, US), George Garrity (Michigan State Univ., US), Dag Harmsen (Univ. Münster, DE), Kathryn Holt
(Univ. Melbourne, AUS), Paul Keim (Northern Arizona Univ., US), W. Ian Lipkin (Colombia Univ., US), David
Lipman (NCBI Director, US), Martin Maiden (Univ. Oxford, UK), Alexander Mellmann (Univ. Münster, DE),
Stefan Niemann (FZB Borstel, DE), Pardis C. Sabeti (?, Harvard, US), Julie Segre (NIH, US), and MuhamedKheir Taha (?, Inst. Pasteur, FR).
Registration opens April 20th, 2015.
Twitter: #ASMNGS15
With Additional Thanks….
FDA
Steven Musser
Marc Allard
Justin Payne
Christine Keys
James Pettengill
Gopal Gopinathrao
David Melka
Maria Hoffman
Tim McGrath
Cong Li
Shaohua Zhao
Patrick McDermott
Peter Evans
Charlie Wang
Errol Strain
Hugh Rand
Chis Grim
Cary Pirone Davies
Eric Stevens
Don Burr
George Kastanis
National Institutes of health (NCBI)
David Lipman
Jim Ostell
Martin Shumway
Richa Agarwala
State Health Labs
Bill Wolfgang (NY)
Elizabeth Driebe (AZ)
Ailyn Perez-Osorio (WA)
CDC
Chris Braden
Cheryl Tarr
Marguerite Pappaioanou
USDA
David Goldman
And a Growing Cast of Colleagues….
Illumina
Susan Knowles
Ruth Timme
Eric Brown
Rebecca Bell
Yan Luo
Darcy Hanes
Palmer Orlandi
Justin Payne
Andrea Ottesen
Jie Zheng
Tim Muravunda
William Klimke
Dave Boxrud (MN)
Angela Fritzinger (VA)
More to come…….
Anita Wright (FL)
Duncan MacCannell
Eija Trees
John Besser
Peter Gerner-Smidt
Kristin Holt
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Omayma Al-Awar
Kelly Hoon