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Whole Genome Sequencing of Listeria monocytogenes: A Public Health Revolution
National Center for Emerging and Zoonotic Infectious Diseases
Division of Foodborne, Waterborne, and Environmental Diseases
Peter Gerner-Smidt, MD ScD, ChiefEnteric Diseases Laboratory Branch
Workshop on Evaluation of Risk Factors for Foodborne Listeriosis Greenbelt, MD, June 16- 18, 2015
“Transforming Public Health Microbiology –PulseNet and Beyond”
Replacing traditional microbiology with WGS For Food Safety Reference Labs:
o Cost-efficient consolidation of multiple workflows: Identification –serotyping – virulence profiling – antimicrobial resistance characterization – subtyping
Listeria Outbreaks and Incidence, 1983-2014
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013
Outbreak
Incidence
Pre-PulseNet0.369
Early PulseNet2.311
Listeria Initiative2.95.5
No. outbreaksIncidence (per million pop)
EraOutbreaks per yearMedian cases per
outbreak
WGS94
Data are preliminary and subject to change
14
N/A1
6
19
6
4 4
16
4
7
3
0
2
4
6
8
10
12
14
16
18
20
No. of clustersdetected
No. of clustersdetected sooner or
only by WGS
No. of outbreakssolved
(food sourceidentified)
Median no. of casesper cluster
Pre-WGS (Sept 2012–Aug 2013)
WGS Year 1 (Sept 2013–Aug 2014)
WGS Year 2 (Sept 2014–May 2015; 8.5 months)
Listeria Cluster Metrics Before and After WGS
Data are preliminary and subject to change
Listeria and Caramel Apples
35 cases, 12 states Nov 20: Small multistate cluster detected
by Whole Genome Sequencing• Dec 19: First recalls, public warned• Investigation continues
Whole Genome Sequencing• Outbreak identified a week faster than
would have been by PFGE
Novel food vehicle• Food microbiology research needed to
find how best to prevent in future
wgMLST and PFGE in the 2014 Caramel Apples Listeria Outbreak
4 [1–6]
89 [89–89]
5 [1–114]
3 [0–10]
4 [0–44]
1,628 [0–1,694]
Allele differences at node: median [min–max](>5,800 loci analyzed by BioNumerics software)
Cluster 1 (≤6 allele differences)
Cluster 2 (≤10 allele differences)
PFGE
Unrelated isolates (hot dog and patient)
Unrelated patient isolate (Sept. 2014)
Highly-related patient isolate; different PFGE pattern
Not closely related
(minimum 1,628 allele differences)
PFGE Pattern 1
PFGE Pattern 2
PFGE Pattern 3
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2014L-6572
2014L-6716
2014L-6704
2014L-6707
2014L-6684
2014L-6710
2014L-6656
2014L-6724
2014L-6681
2014L-6695
2014L-6677
2014L-6679
2014L-6714
2014L-6723
2014L-6660
2014L-6713
2014L-6577 .
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PFGE Patterns Seen In The Blue Bell ( ) and Jeni’s ( ) Ice Cream Listeria Recalls
AscI_ApaI
100
90
80
70
60
PFGE-AscI PFGE-ApaI
Key
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SourceState
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PFGE-AscI-pattern
GX6A16.0061
GX6A16.0061
GX6A16.0061
GX6A16.0061
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0020
GX6A16.0207
GX6A16.0336
GX6A16.0336
GX6A16.0617
GX6A16.0416
GX6A16.0282
PFGE-AscI-status
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PFGE-ApaI-pattern
GX6A12.2358
GX6A12.1512
GX6A12.2551
GX6A12.0026
GX6A12.0094
GX6A12.0077
GX6A12.0227
GX6A12.0489
GX6A12.0227
GX6A12.0511
GX6A12.2255
GX6A12.1840
GX6A12.1840
GX6A12.2353
GX6A12.0355
PFGE-ApaI-status
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Outbreak
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
SourceCounty
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SourceCity
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SourceCountry
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SourceType
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SourceSite
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TypeDetailsPatientAge
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PatientSex
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IsolatDate
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ReceivedDate
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UploadDate
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Traveled_ToExposureAdditionalCommentUploadModifiedDate
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ListMember
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TEMP
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StatusNARMS-EBFoodNetListeriaActSurvAccuProbeRiboprinter DUP NumberRiboprinter DUP similarityPFGE-AscI-file
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PFGE-AscI-rundate
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PFGE-ApaI-file
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PFGE-ApaI-rundate
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PFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-status
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LabID
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Species
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OtherStateIsolate
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Serotype
not typed
not typed
not typed
not typed
not typed
not typed
1/2b
not typed
not typed
not typed
not typed
not typed
not typed
not typed
1/2a
N Serotype1 1/2b1 1/2b3 1/2b28 1/2b1 1/2b3 1/2b15 1/2b6 1/2b13 3b1 Not typed18 3b36 3b2 3b4 Not typed1 1/2a
****************
*
*
wgMLST (<All Characters>)
10
0
95
90
85
80
75
70
65
60
55
50
45
40
35
30
25
20
15
10
5
Key
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Modified date
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CalculationStatusRunIds
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cdc_id
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Id
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State ID
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PFGE-AscI-pattern
GX6A16.0720
GX6A16.0020
GX6A16.0061
GX6A16.0061
GX6A16.0061
GX6A16.0720
GX6A16.0061
GX6A16.0061
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0026
GX6A16.0061
GX6A16.0061
GX6A16.0061
GX6A16.0026
GX6A16.0720
GX6A16.0020
GX6A16.0020
GX6A16.0020
GX6A16.0020
GX6A16.0020
GX6A16.0020
GX6A16.0207
GX6A16.0336
GX6A16.0336
GX6A16.0336
GX6A16.0336
GX6A16.0336
GX6A16.0336
GX6A16.0336
GX6A16.0336
GX6A16.0416
GX6A16.0416
GX6A16.0416
GX6A16.0282
PFGE-ApaI-pattern
GX6A12.0026
GX6A12.0227
GX6A12.0026
GX6A12.0026
GX6A12.1512
GX6A12.0026
GX6A12.0026
GX6A12.0026
GX6A12.0227
GX6A12.0227
GX6A12.0227
GX6A12.0227
GX6A12.0077
GX6A12.0077
GX6A12.0489
GX6A12.2551
GX6A12.2551
GX6A12.2551
GX6A12.0227
GX6A12.0026
GX6A12.0227
GX6A12.0227
GX6A12.0227
GX6A12.0227
GX6A12.0227
GX6A12.0227
GX6A12.0511
GX6A12.2255
GX6A12.2255
GX6A12.1840
GX6A12.1840
GX6A12.1840
GX6A12.1840
GX6A12.2255
GX6A12.1840
GX6A12.2353
GX6A12.2353
GX6A12.2353
GX6A12.0355
Outbreak
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
1502KSGX6-1
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
1/2b
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
not typed
3b
3b
not typed
3b
not typed
not typed
not typed
not typed
1/2a
SourceCountry
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SourceState
TX
TX
TX
TX
SC
TX
TX
TX
KS
TX
TX
TX
SC
SC
TX
SC
SC
TX
TX
TX
TX
TX
TX
TX
AL
OK
OK
OK
OK
OK
OK
TX
OK
TX
TX
TX
KS
***************************************
wgMLST Tree Of Isolates From The Blue Bell ( ) and Jeni’s ( ) Ice Cream Listeria Recalls
*
*
14[0-25]
16[0-159]17[0-1891]
18[1-25]
146[0-2463]
216[0-2573]
WGS Of Listeria monocytogenes From The Crave Brothers Cheese outbreak (2013)
hqSNPHistorical isolates from the plant environment added to the comparison (courtesy FDA/CFSAN)
CF
SA
N0
04
36
5
CF
SA
N0
04
35
9
CF
SA
N0
04
36
1
CF
SA
N0
04
36
0
CF
SA
N0
04
35
8
CF
SA
N0
04
35
3
20
10
L-1
79
0
CF
SA
N0
04
34
8
CF
SA
N0
04
36
32
01
3L
-52
98
CF
SA
N0
04
35
5C
FS
AN
00
43
56
CF
SA
N0
04
35
2
CF
SA
N0
04
36
92
01
3L
-52
14
20
11
L-2
80
9
CF
SA
N0
04
37
7
CF
SA
N0
04
37
5
CF
SA
N0
04
37
4
CF
SA
N0
04
37
3
CF
SA
N0
04
34
9
CF
SA
N0
04
36
4
20
13
L-5
27
5
20
13
L-5
22
32
01
3L
-53
37
CF
SA
N0
04
35
4
20
13
L-5
35
7
CF
SA
N0
04
37
2
CF
SA
N0
04
37
0
CF
SA
N0
04
37
1
CF
SA
N0
04
36
8
CF
SA
N0
04
35
0
CF
SA
N0
04
35
7
20
13
L-5
28
3
CF
SA
N0
04
36
6
CF
SA
N0
04
37
6
CF
SA
N0
04
36
2
CF
SA
N0
04
35
1
20
12
L-5
48
7
20
13
L-5
12
1
20
13
L-5
28
4
20
12
L-5
10
5
20
12
L-5
27
4
20
13
L-5
37
4
20
13
L-5
30
1
100
100
100
100
100
100
100
100
0.0
05 Red= epi-related clinical isolates
Blue= retrospective clinical controls or not outbreak relatedGreen= historical environmental isolates from the plantBlack= unrelated isolate used as an outlier to root the tree
Listeria Initiative
Nationwide initiative to collect standardized exposure information from listeria patients (since 2005)
Coordinated by CDC
0.550.64
0.7
0.80.85 0.9
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
2011–2012 Baseline
2013Actual
2014Target
2015Target
2016Target
2017Target
Pro
po
rtio
n o
f ca
ses
lin
ke
d
Proportion of listeriosis cases* with epidemiological data reported to the Listeria Initiative linked to molecular
subtyping data, by CY
Target achieved
*Reported to the National Notifiable Disease Surveillance System (NNDSS)**Note: Data for 2014 will be available fall 2015 after NNDSS data available
Data are preliminary and subject to change
Click-of-a-Button Tool Linking Nodes in a WGS Tree to Exposure Information
ANI of Listeria
Average Nucleotide Identity (ANI) – similarity measure of the nucleotide content in homologous regions of two isolates
Suggested as a robust way to identify the species of an isolate with well characterized reference strains by WGS
Species identity ANI >0.95
Gladney, Huang, Kucerova, Katz, Roache, Carleton, Tarr: Validation of Whole Genome Average Nucleotide Identity for Identification of Listeria monocytogenes and related species, SFAF 2015
ANI of ListeriaBox-plots of ANI-values for different within and between Listeria species combinations
ANI of ListeriaL. monocytogenes~ L. monocytogenes~ L. non-monocytogenes
ANI of ListeriaL. monocytogenes lineages~ other L. monocytogenes lineages~ L. non-monocytogenes
Lineage I Lineage II
Lineage III & IV
Acknowledgements
National Center for Emerging and Zoonotic Infectious Diseases
Division of Foodborne, Waterborne, and Environmental Diseases
Disclaimers:
“The findings and conclusions in this presentation are those of the author and do not necessarily represent
the official position of the Centers for Disease Control and Prevention”
“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.”
Public Health Agency of Canada
Lab: Lori Gladney, Andrew Huang, Zuzana Kucerova, Lee Katz, Katie Roache, Heather Carleton, Cheryl Tarr, John Besser, Steven Stroika
Epi: Brendan Jackson, Raj Mody, Kelly Jackson, Amanda Conrad, Ben Silk, Katie Fullerton, Matthew Wise, Ian Williams, Patricia Griffin , Rob Tauxe, Chris Braden
36
