the listeria initiative in a new era of whole genome ... · the listeria initiative in a new era of...
TRANSCRIPT
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The Listeria Initiative in a New Era of Whole Genome Sequencing
Benjamin Silk, PhD, MPH John Besser, PhD
Rajal Mody, MD, MPH
Division of Foodborne, Waterborne, and Environmental Diseases
InFORM, San Antonio, Texas
November 21, 2013
National Center for Emerging and Zoonotic Infectious Diseases Division of Foodborne, Waterborne, and Environmental Diseases
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Outline
1. Overview of Listeria Initiative: Ben Silk, CDC
2. Overview of the new WGS Project: John Besser, CDC
3. Examples of how WGS has been of value in the first 3 months of the project: Ben Silk, CDC
4. Discussion of what can be done to make WGS even more effective: Raj Mody, CDC
5. Q&A
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Listeria Infect ion (Listeriosis) by Risk Group
Group Typical illness Elderly Bloodstream infection or
meningitis Persons with immunocompromising conditions
Bloodstream infection or meningitis
Pregnant women and their newborn infants
Pregnant women: Asymptomatic infection or “flu-like” illness with fever, then sometimes miscarriage or stillbirth Infants: Bloodstream infection or meningitis
Healthy persons Diarrhea with fever
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Listeria Infect ion (Listeriosis) by Risk Group
Group Typical illness Surveillance Elderly Bloodstream infection or
meningitis Yes
Persons with immunocompromising conditions
Bloodstream infection or meningitis
Yes
Pregnant women and their newborn infants
Pregnant women: Asymptomatic infection or “flu-like” illness with fever, then sometimes miscarriage or stillbirth Infants: Bloodstream infection or meningitis
Yes
Healthy persons Diarrhea with fever No
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Isolat ion of Listeria monocytogenes from a normally sterile site
(usually blood or cerebrospinal fluid) or products of conception
Surveillance Case Definit ion for Invasive Listeriosis
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PulseNet Data Analysis Involves Searching for Clusters
PulseNet teams at CDC and in states search for similar PFGE patterns
When a cluster is identified, they report it to epidemiologists
Each row is PFGE pattern from one isolate. Box shows cluster of 4 rows with same pattern
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Mult istate Outbreak of Listeriosis from Cantaloupe, July – October, 2011
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Rapid Invest igat ion of Cantaloupe Outbreak
Largest known U.S. outbreak of listeriosis (147 cases) deadliest U.S. foodborne outbreak in >90 years (33 deaths)
Rapid, coordinated identification of food source using PulseNet and the Listeria Initiative questionnaires prevented an estimated prevented ~36 illnesses and ~7 deaths
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Is it better to be lucky or good?
(Actually both are best.)
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Status of Listeriosis Control in 2004
Incidence Marked decline in 1990s, stable from 2001 through 2003
Outbreaks Marked increase in number of outbreaks detected Marked decrease in size of outbreaks Detecting clusters of patients with similar PFGE patterns for
which could not find source
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Challenges of Listeriosis Outbreaks
Cases are often geographically dispersed so detecting outbreaks is difficult
Gett ing food histories from ill persons is difficult incubation period may be weeks, so memories have faded elderly and ill patients may have poor food recall ill persons may die before interview
Controls are needed, but are difficult to find need to ask controls who are similar to cases about foods
consumed
Many clusters of cases are small which makes determining the source difficult
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State and local health depts Promptly interview all pat ients (whether or not part of an
outbreak) with a standard form that asks about foods Rapidly perform PFGE for all L. monocytogenes isolates upload
patterns to PulseNet
CDC Scans for clusters of similar isolates When cluster detected, epidemiologists analyze quest ionnaires
New Approach: Listeria Init iat ive, 2004
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• What: Statistical comparison of food exposure frequencies • How: Use of Listeria Initiative database
Outbreak cases: patients with outbreak-related listeriosis Sporadic cases: patients with listeriosis unrelated to any cluster
• Why: Generate hypothesis about outbreak source based on epidemiological measure of association (e.g., odds ratios and confidence intervals)
Listeria Init iat ive: Case-case Analysis
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Listeria Init iat ive (LI): Case-Case Analyses
Date Food Outbreak Cases LI Sporadic Cases* OR (95% CI)
September 9
Ham 7/11 (64) 360/774 (47) 2.0 (0.5–9.4)
Watermelon 5/10 (50) 49/82 (60) 0.7 (0.1–3.2)
Cantaloupe 11/11 (100) 54/85 (64) 8.5 (1.3–∞)
September 12 Cantaloupe 13/13 (100) 54/85 (64) 10.1 (1.6–∞)
September 14 Cantaloupe 19/19 (100) 54/85 (64) 14.9 (2.4–∞)
*In sporadic cases of listeriosis, 2004-2010, lim ited to adults ≥60 years of age and isolation dates in A ugust (m elons only)
No./total no. (%)
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Outline
1. Overview of Listeria Initiative: Ben Silk, CDC
2. Overview of the new WGS Project: John Besser, CDC
3. Examples of how WGS has been of value in the first 3 months of the project: Ben Silk, CDC
4. Discussion of what can be done to make WGS even more effective: Raj Mody, CDC
5. Q&A
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New York Times 11/20/2013
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U.S. Nationwide Real-Time Listeriosis Surveillance using Whole Genome
Sequencing: Proof-of-Concept Study U.S. collaborators State health
agencies NCBI FDA USDA CDC
Collaborating countries France UK Denmark Australia Canada
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Will the use of whole genome sequencing as part of real-time surveillance lead to a public health benefit?
Core Question
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“Real-time” whole genome sequencing (WGS) and analysis of isolates from all U.S. cases of Listeria monocytogenes and food/environmental isolates
Assess technological and interpretive challenges Develop a path to a WGS-based PulseNet
infrastructure Improve epidemiological follow-up of cases and
clusters Develop new epidemiological tools
Goals
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Budget
$139,000 (one year)
Timeline
July, 2013: Started planning, September 1, 2013: official start date
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What clustering markers have the strongest epidemiological concordance? (e.g. k-mer SNPS; hqSNPS; wgMLST) What sort of infrastructure is needed?
(sequencing capacity, platform compatibility, quality control, standardization, bioinformatic pipelines, bandwidth, storage, etc)
Technical Questions
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Continuous versus categorical data o Strain naming o Defining “closeness” o Defining clusters (in a real-time context)
Interpretive challenges o How much epidemiological inference
can we make from (agent) phylogenetic information?
Interpretive Challenges
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Parallel Workflow
State and Local Public health laboratories
State Departments of Agriculture
PFGE Case Definit ion
WGS Case Definit ion
?
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Real-Time WGS Surveillance
Shipment of isolate to CDC : 4 days WGS and analysis: 1 week
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CDC Labs FDA Genome Trackr Labs
State Health Laboratories
NCBI
isolates isolates
sequences sequences
Public Release
isolates
Patient-level metadata (PulseNet database)
Reduced metadata
sequences cluster analyses
Listeria Project Data Flow
Food / Environmental Monitoring Programs
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Number Real-time WGS program
350
100K Pathogen study
78 (7 serotypes)
Total 428
Strains Sequenced; 11/15/2013
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What Do We Hope To See: Outbreaks Solved
Faster, with fewer cases (e.g. 2-3) Strong hypotheses from
food/environmental findings Better determination of scope WGS findings lead to alternate
hypotheses
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Continuous versus categorical data o Strain naming o Defining “closeness” o Defining clusters (in a real-time context)
Interpretive challenges o How much epidemiological inference
can we make from (agent) phylogenetic information?
Interpretive Challenges
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Listeria Cluster September 19, 2013
PFGE: Categorical Data (strains indistinguishable or not)
Whole genome sequence differences
Whole Genome Sequences: Continuous Data
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control
A D C
B
OR AD CB =
exposed
not exposed
case
F
F F
F
T
T
T T
T
T T
T
Classification of Cases (by Agent)
PFGE Case Definition
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Whole Genome Sequence Case Definition (exact match)
F
F F
F
T
T
T T
T
T T
T
control
A
D C
B
OR Not significant
exposed
not exposed
case
Classification of Cases (by Agent)
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Cluster definitions
F
F F
F
T
T
T T
T
T T
T
Proper Classification of Cases Improves Measures of Association
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Whole Genome Sequencing of Listeria monocytogenes during the Crave Brothers Cheese outbreak High confidence core SNP
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excluded case retrospective controls Epi-related PFGE match- from outbreak period
Whole Genome Sequencing of Listeria monocytogenes during the Crave Brothers Cheese outbreak High confidence core SNP
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excluded case retrospective controls Epi-related PFGE match- from outbreak period
Whole Genome Sequencing of Listeria monocytogenes during the Crave Brothers Cheese outbreak High confidence core SNP
Most specific case definition
Most inclusive case definition
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Options for Defining Clusters
Use multiple case definitions Develop / test measures of clade
significance
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Sensit ivity
Specificity
Specific Case Definit ion
Inclusive Case Definit ion
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Station C Station B Station A
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Detect Cluster
Develop Hypothesis
Test Hypothesis
Determine Scope
Clinical Diagnoses
Food Monitoring
Trace- backs Targeted
Food/Env Testing
Key Steps in an Outbreak Investigation Use more specific case definition
Use more inclusive case definition to find additional cases
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Options for Defining Clusters
Use multiple case definitions Develop / test measures of clade
significance
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Statistical Options for Cluster Recognition?
Example: Fixation Index (measures strain consolidation above background rate)
Source: Wikipedia
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From Hannes Pouseele; Applied Maths
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From Hannes Pouseele; Applied Maths
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wgMLST pipeline
Nomenclature server
Calculation engine Trimming, mapping, de novo assembly, SNP detection, allele detection
SQL databases
BioNumerics client
BIGSDb Public nomenclature Isolate
database
Allele databases
External storage NCBI, ENA, BaseSpace
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Continuous versus categorical data o Strain naming o Defining “closeness” o Defining clusters (in a real-time context)
Interpretive challenges o How much epidemiological inference
can we make from (agent) phylogenetic information?
Interpretive Challenges
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Central Assumption
Phylogenetic similarity (and distance) between disease-causing organisms can be used to infer epidemiological associations (between people, animals, food, and the environment)
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Complex Ecology of Outbreaks
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Complex Transmission Mechanisms
Meaning of a “close match”: High likelihood of some connection between isolates (from cases, food, environment)
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Outline
1. Overview of Listeria Initiative: Ben Silk, CDC
2. Overview of the new WGS Project: John Besser, CDC
3. Examples of how WGS has been of value in the first 3 months of the project: Ben Silk, CDC
4. Discussion of what can be done to make WGS even more effective: Raj Mody, CDC
5. Q&A
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Listeria Outbreaks, 1983-2012
0
1
2
3
4
5
6
1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
Before PulseNet 1983-1997 (15 years) 5 outbreaks Median 69 cases/outbreak
PulseNet ’s first years 1998-2003 (6 years) 14 outbreaks Median 11 cases/outbreak
Listeria Init iat ive & PulseNet 2004-2012 (9 years) 28 outbreaks Median 5.5 cases/outbreak
No. outbreaks
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Listeria Outbreaks and Incidence, 1983-2012
0123456789
0
1
2
3
4
5
6
1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
Outbreak
Incidence
Before PulseNet 1983-1997 (15 years) 5 outbreaks Median 69 cases/outbreak
PulseNet ’s first years 1998-2003 (6 years) 14 outbreaks Median 11 cases/outbreak
Listeria Init iat ive & PulseNet 2004-2012 (9 years) 28 outbreaks Median 5.5 cases/outbreak
No. outbreaks Incidence (per million pop)
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You are here
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An Epidemiologist's Wish List for WGS
Epidemiological concordance
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Whole Genome Sequencing of Listeria monocytogenes during the Crave Brothers Cheese outbreak High confidence core SNP
Historical isolates from the plant environment added to the comparison (courtesy FDA/CFSAN) C
FSAN004365
CFSAN
004359 C
FSAN004361
CFSAN
004360 C
FSAN004358
CFSAN
004353 2010L-1790
CFSAN
004348 C
FSAN004363
2013L-5298 C
FSAN004355
CFSAN
004356 C
FSAN004352
CFSAN
004369 2013L-5214
2011L-2809 C
FSAN004377
CFSAN
004375 C
FSAN004374
CFSAN
004373 C
FSAN004349
CFSAN
004364 2013L-5275 2013L-5223
2013L-5337 C
FSAN004354
2013L-5357 C
FSAN004372
CFSAN
004370 C
FSAN004371
CFSAN
004368 C
FSAN004350
CFSAN
004357 2013L-5283
CFSAN
004366 C
FSAN004376
CFSAN
004362 C
FSAN004351
2012L-5487 2013L-5121
2013L-5284 2012L-5105
2012L-5274 2013L-5374
2013L-5301
100
100
100
100 100
100
100
100
0.005
Red= epi-related clinical isolates Blue= retrospective clinical controls or not outbreak related Green= historical environmental isolates from the plant
Isolates from cheese factory, 2010-2011 Isolates from patients in current outbreak Isolates from patients in past, exposure is not known
Whole genome sequencing data on isolates with 2-enzyme PFGE match
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excluded CO case retrospective controls Epi-related PFGE match- from outbreak period
NY – no soft cheese exposure
TX - no exposure info
Whole Genome Sequencing of Listeria monocytogenes during the Crave Brothers Cheese outbreak High confidence core SNP
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PFGE-ApaI+PFGE-AscI AscI_ApaI
100
99
98
97
PFGE-AscI PFGE-ApaI AscI_ApaI
State A State B State A State A State A State A
State C State B
.
.
.
.
.
.
.
.
GX6A16.0005 GX6A16.0164 GX6A16.0164 GX6A16.0005 GX6A16.0005 GX6A16.0005
GX6A16.1244 GX6A16.1244
GX6A12.0088 GX6A12.0088 GX6A12.0197 GX6A12.0088 GX6A12.0088 GX6A12.0088
GX6A12.0021 GX6A12.0021
SNP Ref 145 62 31 53 46 229 182
Cluster in Midwest State A
PA*, Mexican-style cheese (State A)
*PA=pregnancy-associated
PA*, Mexican-style cheese (State A)
PA*, No exposure info (State A) PA*, Mexican-style cheese (State A)
PA*, Mexican-style cheese (State A)
No info (State B) No info (State C)
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An Epidemiologist's Wish List for WGS
Epidemiological concordance Subtyping value added (beyond PFGE)
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Number of Pat ients by Date of Illness Onset and PFGE Pattern — United States, 2008–2011
0
10
20
30
40
50
60
70
80
90
100
J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D
2011
Date of Illness Onset
Pattern 4
Num
ber o
f Iso
late
s
2010 2009 2008
Pattern 3 Pattern 2 Pattern 1
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Company A
2013L-5289 M13010038 PNUSAL000037 6/7/2013 State A 1/2a GX6A16.0018 GX6A12.1394 2013L-5428 13MP007218 PNUSAL000166 7/13/2013 State B 1/2a GX6A16.0018 GX6A12.0022 2013L-5458 LM14-004 PNUSAL000195 8/12/2013 State C 1/2a GX6A16.0018 GX6A12.0222
AscI_ApaI
100
98
PFGE-AscI PFGE-ApaI
GX6A16.0018GX6A16.0018
GX6A12.0022GX6A12.1394
1111
x
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Clinical isolate for patient with exposure to Company A product
Clinical isolate for patient with exposure to Company B product Clinical isolate for patient with exposure to Company B product
Node A
Node B
Companies A and B
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2013L-5290|PNUSAL000038|6/12/2013|MI|CL13-200456|blood|4b|GX6A16.0596|GX6A12.0718
2013L-5445|PNUSAL000180|8/15/2013|FL|JBI13001093|CSF|4b|GX6A16.1244|GX6A12.0585
2013L-5396|PNUSAL000138|7/22/2013|MN|C2013015120|blood|4b|GX6A16.0022|GX6A12.0028|1309MLGX6-2WGS
2013L-5295|PNUSAL000043|6/22/2013|TN|N13B001231|blood|4b|GX6A16.0022|GX6A12.0028|1309MLGX6-2WGS
2013L-5493|PNUSAL000219|9/5/2013|TN|N13B001538|blood|4b|GX6A16.0022|GX6A12.0028|1309MLGX6-2WGS
2013L-5471|PNUSAL000204|8/6/2013|NC|MB090313-0056|blood|4b|GX6A16.0022|GX6A12.0028|1309MLGX6-2WGS
2013L-5286|PNUSAL000034|5/30/2013|TN|N13B001097|blood|4b|GX6A16.0022|GX6A12.0417|1309MLGX6-2WGS
2013L-5450|PNUSAL000185|8/17/2013|NY|101352425|blood|4b|GX6A16.0022|GX6A12.2083|1309MLGX6-2WGS
2013L-5380|PNUSAL000122|7/22/2013|NY|nyc13-101351112|blood|4b|GX6A16.0022|GX6A12.0028|1309MLGX6-2WGS
2013L-5549|PNUSAL000308|9/17/2013|WI|13MP008661|blood|4b|GX6A16.0044|GX6A12.2508
GCF_000258905.1
2013L-5293|PNUSAL000041|6/17/2013|FL|JBI13000757|CSF|4b|GX6A16.0601|GX6A12.2493
2013L-5281|PNUSAL000030|6/4/2013|WI|13MP005398|CSF|4b|GX6A16.0022|GX6A12.1336
2013L-5344|PNUSAL000089|5/7/2013|NY|101347115|CSF|4b|GX6A16.1244|GX6A12.0009|1307MLGX6-1
2013L-5414|PNUSAL000153|7/18/2013|CT|327091001|blood|4b|GX6A16.1244|GX6A12.0009|1307MLGX6-1
2013L-5385|PNUSAL000127|7/16/2013|NY|nyc13-101350491|blood|4b|GX6A16.0420|GX6A12.0009|1307MLGX6-1
GCF_000026705.1
GCF_000307085.1
2013L-5349|PNUSAL000094|6/30/2013|CT|324831001|blood|4b|GX6A16.1244|GX6A12.0021
2013L-5328|PNUSAL000075|6/21/2013|CA|M13X02836|blood|4b|GX6A16.1244|GX6A12.0021
2013L-5536|PNUSAL000287|9/12/2013|WA|5521|CSF|4b|GX6A16.1244|GX6A12.0794
2013L-5122|PNUSAL000015|3/1/2013|0|123719|placenta|4b|GX6A16.0164|GX6A12.0197|1308ILGX6-1
2013L-5413|PNUSAL000152|7/27/2013|CT|329847001|blood|4b|GX6A16.0164|GX6A12.0088|1308ILGX6-1
2013L-5224|PNUSAL000020|6/2/2013|0|125606|blood|4b|GX6A16.0005|GX6A12.0088|1308ILGX6-1
2013L-5225|PNUSAL000021|6/2/2013|0|125556|blood|4b|GX6A16.0005|GX6A12.0088|1308ILGX6-1
2013L-5405|PNUSAL000147|7/31/2013|IL|130756|amniotic fluid|4b|GX6A16.0005|GX6A12.0088|1308ILGX6-1
2013L-5421|PNUSAL000159|8/14/2013|IL|131063|blood|4b|GX6A16.0005|GX6A12.0088|1308ILGX6-1
2013L-5408|PNUSAL000146|7/30/2013|PA|M13013611001A|blood|4b|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5300|PNUSAL000055|6/28/2013|TN|N13B001250|blood|4b|GX6A16.0139|GX6A12.2245|1307MLGX6-2
2013L-5332|PNUSAL000079|6/3/2013|MA|13EN3910|blood|4b|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5280|PNUSAL000029|6/6/2013|NC|MB061213-0031|unknown|4b|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5427|PNUSAL000165|7/30/2013|WI|13MP007105|aspirate|4b|GX6A16.0139|GX6A12.2470|1307MLGX6-2
2013L-5515|PNUSAL000250|8/24/2013|WI|13MP008009|blood|4b|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5463|PNUSAL000200|8/19/2013|MA|MA 13EN6507|blood|4b|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5417|PNUSAL000156|8/10/2013|MN|C2013016116|blood|4b|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5550|PNUSAL000309|9/22/2013|WI|13MP008888|blood|1/2a|GX6A16.0139|GX6A12.0009|1307MLGX6-2
2013L-5498|PNUSAL000233|8/11/2013|CT|336604001|blood|4b|GX6A16.0134|GX6A12.0863
2013L-5534|PNUSAL000285|9/2/2013|WA|5500|CSF|4b|GX6A16.0395|GX6A12.0509
2013L-5333|PNUSAL000080|6/13/2013|SC|SC14-005|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1NOT
2013L-5314|PNUSAL000069|6/25/2013|SC|SC13-257|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5204|PNUSAL000320|5/17/2013|HI|N13-140|0|0|GX6A16.1244|GX6A12.0112|1307MLGX6-1
SAMN02381993_clinical/host-associated|Listeria monocytogenes|NULL|NULL|PNUSAL000270|FDA/CFSAN|NY|2013-09-13|clinical sample|USA:NY|Homo sapiens|Listeriosis|NULL|NULL
2013L-5308|PNUSAL000063|unknown|NY|IDR1300016274|blood|4b|GX6A16.0163|GX6A12.0199|1307MLGX6-1
2013L-5345|PNUSAL000090|5/26/2013|NY|101347849|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5540|PNUSAL000291|9/10/2013|MI|CL13-200753|blood|4b|GX6A16.1244|GX6A12.0655
2013L-5556|PNUSAL000315|9/19/2013|WA|REF135555|blood|1/2b|GX6A16.1244|GX6A12.0614|1307MLGX6-1
2013L-5545|PNUSAL000296|9/12/2013|CA|M13X04891|blood|4b|GX6A16.1244|GX6A12.1370
2013L-5439|PNUSAL000189|8/9/2013|OH|2013042642|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5527|PNUSAL000278|9/13/2013|MI|CL13-200750|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5473|PNUSAL000212|6/13/2013|MD|A13-096803|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5521|PNUSAL000256|8/15/2013|NY|IDR1300025739|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5297|PNUSAL000052|6/16/2013|SC|SC13-254|CSF|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5359|PNUSAL000104|7/13/2013|MI|CL13-200523|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5548|PNUSAL000307|#N/A|#N/A|#N/A|#N/A|#N/A|#N/A|#N/A|#N/A
2013L-5560|PNUSAL000319|9/25/2013|OH|2013063623|blood|0|GX6A16.1244|GX6A12.0112|1307MLGX6-1
0.00065
0.05425
0.00003
0.00004
0.00010
0.00006
0.00725
0.01004
0.01205
0.00113
0.00136
0.00074
0.00124
0.00120
0.00220
0.00796
0.01882
0.05664
0.03636
0.00049
0.00062
0.00073
0.00103
0.01436
0.01314
0.00261
0.04062
0.00027
0.00045
0.00096
0.00037
0.00067
0.00083
0.00146
0.00102
0.00931
0.01012
0.00354
0.01761
0.00659
0.01096
0.01121
0.02109
0.01036
0.00367
0.00592
0.01771
0.00147
0.00106
0.00079
0.00074
0.01340
0.01489
0.00391
0.01243
0.05768
0.00011
0.00327
0.00217
0.00995
0.00231
0.00067
0.00044
0.00311
0.000340.02648
0.00159
0.00112
0.00387
0.01199
0.00035
0.00033
0.00043
0.00248
0.03430
0.02100
0.00170
0.000180.00005
0.00023
0.000250.00025
0.00048
0.00144
0.00315
0.00069
0.005480.00333
0.00081
0.00031
0.00103
0.00067
0.05264
0.00120
0.00064
0.00269
0.000070.00086
0.00740
0.00336
0.03599
0.05318
0.00935
0.00325
0.01
Human| blood|141/112
Large, Multistate Cluster
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2013L-5439|PNUSAL000189|8/9/2013|OH|2013042642|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5527|PNUSAL000278|9/13/2013|MI|CL13-200750|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5473|PNUSAL000212|6/13/2013|MD|A13-096803|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5521|PNUSAL000256|8/15/2013|NY|IDR1300025739|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5297|PNUSAL000052|6/16/2013|SC|SC13-254|CSF|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5359|PNUSAL000104|7/13/2013|MI|CL13-200523|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5548|PNUSAL000307|#N/A|#N/A|#N/A|#N/A|#N/A|#N/A|#N/A|#N/A
2013L-5560|PNUSAL000319|9/25/2013|OH|2013063623|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5308|PNUSAL000063|unknown|NY|IDR1300016274|blood|4b|GX6A16.0163|GX6A12.0199|1307MLGX6-1
SAMN02381993|clinical/host-associated|Listeria monocytogenes|NULL|NULL|PNUSAL000270|FDA/CFSAN|NY|2013-09-13|clinical sample|USA:NY|Homo sapiens|L
2013L-5345|PNUSAL000090|5/26/2013|NY|101347849|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5540|PNUSAL000291|9/10/2013|MI|CL13-200753|blood|4b|GX6A16.1244|GX6A12.0655
2013L-5545|PNUSAL000296|9/12/2013|CA|M13X04891|blood|4b|GX6A16.1244|GX6A12.1370
2013L-5556|PNUSAL000315|9/19/2013|WA|REF135555|blood|1/2b|GX6A16.1244|GX6A12.0614|1307MLGX6-1
2013L-5204|PNUSAL000320|5/17/2013|HI|N13-140|blood|1/2a|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5314|PNUSAL000069|6/25/2013|SC|SC13-257|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5587|PNUSAL000348|10/11/2013|WA|REF135587|blood|1/2a|GX6A16.1244|GX6A12.0112|1307MLGX6-1
2013L-5333|PNUSAL000080|6/13/2013|SC|SC14-005|blood|4b|GX6A16.1244|GX6A12.0112|1307MLGX6-1NOT
0.00027
0.00045
0.00099
0.00033
0.00067
0.00083
0.00146
0.00104
0.01121
0.01166
0.02119
0.01027
0.00038
0.00028
0.01844
0.00894
0.00992
0.00951
0.00015
0.00008
0.00037
0.00025
0.00023
0.00034
0.00210
0.00014
0.00098
0.00073
0.00018
0.00242
0.00315
0.00352
0.00268
0.00068
0.002
Subcluster
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Epidemiological concordance Subtyping value added (beyond PFGE) Ease of interpretation? How close is close (phylogenetically)? What node on a tree is most meaningful?
An Epidemiologist's Wish List for WGS
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MAXIMIZING THE VALUE OF WGS TO IMPROVE IDENTIFICATION OF FOOD SOURCES OF LISTERIA OUTBREAKS
Timely WGS Timely &Thorough Exposure Data
Integrat ion
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Ways to Improve WGS-Epi Data Integrat ion to Better Detect and Solve Listeria Outbreaks
1. Now: CDC following-up with states To assure, on a regular basis, that Listeria Initiative (LI) data and
isolate data are linked as best as possible
2. Proposed: collect more exposure information Produce, specialty deli items, foods eaten at restaurants, recalled
products, others? Greater use of open-ended interviewing
3. Proposed: build better IT systems Web-based Listeria Initiative data entry Integrated Epi-WGS database that allows for point-and-click
assessment of exposures at different nodes in a phylogenetic tree
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58%
84%
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
2004 2005 2006 2007 2008 2009 2010 2011 2012
Isolate and Quest ionnaire Submission, 2004-2012
Denominator is Listeria cases reported to National Notifiable Disease Surveillance System
Isolates submitted to PulseNet
% of patients
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58%
84%
15%
77%
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
2004 2005 2006 2007 2008 2009 2010 2011 2012
Isolate and Quest ionnaire Submission, 2004-2012
Denominator is Listeria cases reported to National Notifiable Disease Surveillance System
Isolates submitted to PulseNet
Questionnaires submitted to Listeria Initiative
% of patients
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58%
84%
12%
56%
15%
77%
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
2004 2005 2006 2007 2008 2009 2010 2011 2012
Isolate and Quest ionnaire Submission, 2004-2012
Denominator is Listeria cases reported to National Notifiable Disease Surveillance System
Isolates submitted to PulseNet
Questionnaires submitted to Listeria Initiative
Isolates and questionnaires linked
% of patients
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Novel Data Closeout in 2013: Improved Linkage
Asked states to Review exist ing linkages between LI data and isolates
for any errors If possible, link any un-linked LI forms and isolates If any Listeria Init iat ive forms or isolates remain missing
or unlinked, explain why Findings 45 jurisdict ions respond Increased cases with linked LI data & isolate by 7% Isolates are often not sent to state laboratories Patients are often unable to be interviewed
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Ways to Improve WGS-Epi Data Integrat ion to Better Detect and Solve Listeria Outbreaks
1. Now: CDC following-up with states To assure, on a regular basis, that Listeria Initiative (LI) data and
isolate data are linked as best as possible
2. Proposed: collect more exposure information Produce, specialty deli items, foods eaten at restaurants, recalled
products, others? Greater use of open-ended interviewing
3. Proposed: build better IT systems Web-based Listeria Initiative data entry Integrated Epi-WGS database that allows for point-and-click
assessment of exposures at different nodes in a phylogenetic tree
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National Center for Emerging and Zoonotic Infectious Diseases Division Name in this space
For thoughts on strengthening the Listeria Init iat ive, please contact Raj Mody, [email protected]
The findings and conclusions in this presentation are those of the author and do not necessarily represent the
views of the Centers for Disease Control and Prevention
Questions?
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Causal Pathways in Outbreaks: Polyclonal Outbreaks
No molecular linkage (when an epidemiological linkage exists)
100
99989796
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Does a WGS “mis-match” rule out?
Does a WGS match prove association?
Molecular Markers for Outbreak Detection : Interpretation Issues
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Causal Pathways in Outbreaks: Direct
Molecular linkage = likely epidemiological linkage
100
99989796
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Causal Pathways in Outbreaks: Indirect (or cross-contamination)
no direct connection
NO ISOLATE
runoff
Molecular linkage….possibly misleading or not useful
100
99989796
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Causal Pathways in Outbreaks: Multiple Contamination Events; One 1 leads to Outbreak
NO ISOLATE
Molecular linkage….possibly incorrect conclusion
100
99989796
NO ISOLATE
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Causal Pathways in Outbreaks: Secondary and Tertiary Transmission
NO ISOLATE
Molecular linkage….incorrect conclusion, or no conclusion
100
99989796
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Meaning of a WGS “Match”
High likelihood of some connection between isolates (from cases, food, environment)*
* Everything else requires epidemiology
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Gett ing the Word Out
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Scallan E et al, Emerging Infectious Diseases, 2011
Pathogen Illnesses Deaths Case-fatality rate
Listeria 1,600 260 16%
Campylobacter 1,300,000 120 0.1%
Salmonella 1,230,000 450 0.5%
Estimated Annual Numbers of Illnesses and Deaths from Major Enteric Pathogens
(not just lab-confirmed)
Listeriosis is much less common, but much more deadly, than other major bacterial pathogens
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Silk BJ et al, CID 2012
Risk group Incidence (per million)
Persons >65 years old 12
Persons <65 years old (most immunocompromised; not pregnant) 1
Pregnant women and their newborns, non-Hispanic 23
Pregnant women and their newborns, Hispanic 89
Incidence of Listeriosis by Risk Group, United States, 2004-2009
(overall 2.7 per million persons)
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Silk BJ et al, CID 2012
Risk group Incidence (per million)
Proportion of Cases
Persons >65 years old 12 53%
Persons <65 years old (most immunocompromised; not pregnant) 1 31%
Pregnant women and their newborns, non-Hispanic 23 9%
Pregnant women and their newborns, Hispanic 89 6%
Incidence of Listeriosis by Risk Group, United States, 2004-2009
(overall 2.7 per million persons)
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Captures outbreak data on agents, foods, and sett ings responsible for illness
Foodborne Disease Outbreak Surveillance System
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Food Vehicle # of Outbreaks
Delicatessen meat (usually turkey)
5
Hot dogs 3 Cheese 2 Other 1
Data from Foodborne Disease Outbreak Surveillance System
Food Vehicles for Listeria Outbreaks, 1998-2003 (11 outbreaks with known vehicle)
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Food Vehicles for Listeria Outbreaks, 2004-2012 (9 years, 20 outbreaks with known vehicle)
Food Vehicle # of Outbreaks
Cheese 10 Produce (sprouts, celery, cantaloupe) 3 Deli meat 2 Other* 5
Data from Foodborne Disease Outbreak Surveillance System;
*milk, chicken, sushi rolls, taco salad, tuna salad
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Listeria Wake-up Call, 1985
Outbreak in California 142 ill
• 93 pregnancy-related • 40 not pregnancy -related
28 deaths, 20 miscarriages traced to Mexican-style
soft cheese (queso fresco) Began surveillance for
individual cases
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1989: Hot Dogs Detected as Source
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108 ill • 13 pregnancy-related • 95 not pregnancy-related
14 deaths, 4 miscarriages Patients in 24 states
isolates linked by PFGE pattern Hot dogs contaminated at one processing plant after cooking Outcome: industry efforts to make hot dogs safer
Hot Dog Outbreak, 1998
12 Death or miscarriage
6/27 8/2 9/6 10/11 11/15 12/20 1/24 2/27 4/3 0 1 2 3 4 5 6 7 8 9
10 11
1998-1999
hot dog recall Survived
plant construction
# pat ients
Mead et al, Epidemiol Infect 2006;134:744-751
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Hot Dog Outbreaks: A Regulatory and Industry Success
Cartwright E et al, Emerg Infect Dis 2013;19:1-9
No hot dog outbreak detected since 1999
Hot dogs probably an important source of illness before the 1998 outbreak PulseNet made hidden multistate
outbreaks detectable Following the 1998 outbreak, regulatory
agencies and industry improved safety
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Delicatessen Turkey Meat Outbreak, 2002
54 ill 12 pregnancy-related 42 not pregnancy-related
8 deaths, 3 miscarriages Patients in 9 states isolates linked by PFGE pattern
Gottlieb S, et. al. Clin Infec Dis 2006 42:29-36
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Deli Meat Outbreaks: A Regulatory and Industry Success
Cartwright E et al, Emerg Infect Dis 2013;19:1-9
Only 2 (small) deli meat outbreaks since 2002
Contaminat ion occurs in the processing plant, after meat cooked
After the 2002 outbreak US Department of Agriculture t ightened
regulat ions industry added growth inhibitors
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0123456789
0
1
2
3
4
5
6
1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
% processed meat positiveIncidence
Before PulseNet
PulseNet ’s first years
Listeria Init iat ive & PulseNet
% Processed Meat
Incidence (per million pop)
Listeria Incidence and Percentage of Ready-to-Eat Meats Posit ive for L. monocytogenes,
1983-2012
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0123456789
0
1
2
3
4
5
6
1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011
% processed meat positiveIncidence
Before PulseNet
PulseNet ’s first years
Listeria Init iat ive & PulseNet
Listeria Incidence and Percentage of Ready-to-Eat Meats Posit ive for L. monocytogenes,
1983-2012
% Processed Meat
Incidence (per million pop)
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Listeriosis Outbreak from Cantaloupe, July – October, 2011
Detected by Colorado state health department
notified CDC September 2 Rapid nationwide investigat ion using Listeria Init iat ive
cantaloupe from a single farm recalled September 14 147 ill
7 pregnancy-related 139 not pregnancy-related
33 deaths, 1 miscarriage Patients in 28 states
isolates linked by PFGE pattern • outbreak caused by strains with 5 patterns
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Environmental Assessment at Farm
Processing facility most likely source of contamination Listeria outbreak strains were found on cantaloupes and
surfaces at the facility Deficiencies
cantaloupes not cooled after harvest
equipment designed and used improperly
sanitation inadequate
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Characterist ics of Cheese Outbreaks, United States, 2004-2012
(n = 10 outbreaks) • Cheese type
– 60% Mexican-style, soft – 40% other, usually soft, often specialty
• 80% made with pasteurized milk – suggests environmental contamination during
or after cheese-making
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Outbreak from Imported Cheese that Cross-Contaminated Other Cheeses, 2012
Index patient • 68 year-old person in Pennsylvania with Listeria meningitis • consumed 2 cheeses purchased from a store (“Grocery Store A”)
Health department cultured the 2 cheeses in his refrigerator • both had the patient’s strain of Listeria
Blue l’Édel de Cléron
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Investigation of Index Patient, July 2012
Health department went to Grocery Store A • isolated outbreak strain from a wedge of l’Édel de Cléron cheese
that had been cut from a wheel of cheese and repackaged • did not isolate Listeria from Blue cheese
CDC checked PulseNet database • a few isolates with same rare PFGE pattern from patients in other
states in 2012
l’Édel de Cléron
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Investigation of Index Patient, July 2012
Health department went to Grocery Store A • isolated outbreak strain from a wedge of l’Édel de Cléron cheese
that had been cut from a wheel of cheese and repackaged • did not isolate Listeria from Blue cheese
CDC checked PulseNet database • a few isolates with same rare PFGE pattern from patients in other
states in 2012
l’Édel de Cléron
Was l’Édel de Cléron cheese the source of their illnesses?
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Initial Analysis of Listeria Initiative Data
Compared food exposures of • 10 patients with rare PFGE pattern • 204 other patients with listeriosis during 2008-2012
Result • 9 (90%) of patients whose isolates had the rare pattern,
but only 37% of control patients had recently consumed soft cheese (odds ratio 17, p-value <0.01)
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Epidemiologic Investigation
Designed a supplemental questionnaire to collect more information about cheese • types and brands, including l’Édel de Cléron • packaging information • where purchased
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Initial Analysis of Supplemental Questionnaire
Re-interviewed 9 patients with supplemental questionnaire
Patients consumed a variety of cheeses • none reported consuming l’Édel de Cléron! • no common brand of cheese named
6 had information about packaging • all 6 consumed cheese from a wedge that had been cut
from a wheel and repackaged
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Meanwhile, in California….
On a routine inspection at a distributor (“Distributor Z”), regulators cultured samples of cheese isolated outbreak strain from 2 other types of cheese
• Distributor Z did not supply cheese to Store A (index patient’s store) suggested that the cheeses at Distributor Z and Store A
were contaminated by another cheese (“Cheese X”) when they were cut and repackaged
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Finding Cheese X
CDC Identified 17 cheeses that were cut and repackaged at both • Distributor Z in California • Store A in Pennsylvania
FDA obtained intact wheels of cheese and began culturing On September 5, isolated outbreak strain from ricotta salata
(imported from Italy, made from pasteurized sheep milk )
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Summary of Ricotta Salata Outbreak, March-October 2012
22 ill • 9 pregnancy-related • 13 not pregnancy-related
4 deaths, 1 miscarriage Patients in 13 states
isolates linked by PFGE
• All 16 patients with complete food histories consumed cheese 7 ricotta salata 9 another cheese
• probably cross-contaminated by ricotta salata when cut and re-packaged
• Ricotta salata was recalled and WHO notified
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Reads are chopped up into sections of length=k
We hope/assume that k is long enough to be unique in the genome. However, the assumption will be wrong in repeat regions, like in 16S.
This read is 150 bp
K=25 or 35
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Each kmer is a sliding window. Not mutually exclusive
Many overlapping kmers
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AAAAAAAAAAAATAAAAAAAAAAAA
AAAAAAAAAAAACAAAAAAAAAAAA
The purpose of kmers in this project? To pattern-match quickly across the millions of base pairs in hundreds of genomes. To find differences between genomes.
Genome 1
Genome 2
[Genome 3] [Genome 4] ….. [and so on]
AAAAAAAAAAAATAAAAAAAAAAAA
K=25 (in this example)
AAAAAAAAAAAACAAAAAAAAAAAA
12 bp 12 bp
Check for variation
![Page 112: The Listeria Initiative in a New Era of Whole Genome ... · The Listeria Initiative in a New Era of Whole Genome Sequencing Benjamin Silk, PhD, MPH John Besser, PhD . Rajal Mody,](https://reader035.vdocuments.us/reader035/viewer/2022070708/5eb71614fb68fb7d626b2b4a/html5/thumbnails/112.jpg)
The purpose of kmers in this project?
Pos1 Pos2 Pos3 Pos4 Pos5 Pos6 … posXXX
Genome1 C A T T A C
Genome2 C A T T G C
Genome3 C A T C A C
Genome4 C A T C A C
Ultimately, find relatedness across all genomes. Find the common ancestor. Find support for which genomes might be in a cluster.
Most related
Sites of variation (SNPs)