virginia - aphl · virginia katherine g. mccombs, mph foodborne disease epidemiology program...
TRANSCRIPT
VirginiaKatherine G. McCombs, MPH
Foodborne Disease Epidemiology Program Coordinator
Virginia Department of Health
And
Lauren Turner, Ph.D.
Foodborne and Advanced Pathogen Characterization Lead Scientist
Division of Consolidated Laboratory Services
Department of General Services
Country Ham vs. Deli Ham vs. Country Ham Sliced
Reported Listeriosis Cases by Year
Virginia, 2008-2018
0
5
10
15
20
25
30
35
40
2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018
Num
ber
of
Lis
teri
osi
sCase
s
Year
Patient Information
Patient 1 (2017)
• Onset 7/8/2017
• 70 years of age
• underlying illnesses
• hospitalized for illness
• survived illness
• died in July 2018
Patient 3 (2018)
• Onset 6/19/2018
• 70 years of age
• underlying illness and dementia
• survived
• died in August 2018
Patient 2 (2018)
• Onset 6/14/2018
• 81 years of age
• underlying illnesses
• living in an ALF
• Died in June 2018 from
the illness
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18:
P2 to ALF
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
6/18:
P2 Dies
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
6/18:
P2 Dies
6/19:
P3 Illness Onset
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
6/18:
P2 Dies
6/19:
P3 Illness Onset
6/22:
Interview at ALF for P2
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
6/18:
P2 Dies
6/19:
P3 Illness Onset
6/22:
Interview at ALF for P2
6/29-7/3:
Interviews with family of
P2
Timeline of Listeriosis Investigation, Virginia
7/7/17:
P1 Onset
4/28/18: P2 to ALF
6/14:
P2 Illness Onset
6/18:
P2 Dies
6/19:
P3 Illness Onset
6/22:
Interview at ALF for P2
6/29-7/3:
Interviews with family
of P2
7/2:
DCLS informs of
cluster
Requirement for
submission of Listeria
monocytogenes to DCLS
DCLS’ Laboratory Testing Algorithm for Listeria monocytogenes
Day 1: Purity checkPass for Molecular
Day 2 - 4 Pathogen Confirmatory Identification
Day 2 - 4 Molecular Subtyping by PFGE
Lab Team Day 0 Day 1 Day 2 Day 3 Day 4 Day 5 Day 6 Day 7/8
Micro Test Isolate Receipt and subculture
Purity check Confirmatory Identification
PFGE Test Plug Preparation Restriction Digestion
Gel Analysis
WGS Test DNA extraction Library Preparation/MiSeq Run Data Review and Analysis:• Run Metrics• Worksheets• BioNumericsReporting to VDH/CDC
1807VAGX6-1: Virginia Testing Timeline
2017
July
July
July
2018
VDH Epidemiologist Notification Format
1807VAGX6-1: August 13, 2018
Updated: 2018-08-13
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
4[1,7]
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
wgMLST (<All Characters>)
100 Key
USDA_853313749
VA___R180620742
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
FSIS31800263
PNUSAL004057
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
SourceSite
Pork
Blood
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
IsolatDate
2018-03-08
2018-06-19
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
Species
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
SequencerRun_id
.
.
commentsExposureLabID
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
PatientSex
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
SourceCountry
.
.
.
.
.
.
SourceCounty
.
.
.
SourceState
NC
VA
VA
NC
VA
NC
1807VAGX6-1: August 30, 2018wgMLST Analysis
Updated: 2018-08-30
3.0 [1, 7]
wgMLST (<All Characters>)
100 Key
NC___MB081518-0059
VA___R180620742
USDA_853313749
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
PNUSAL004247
PNUSAL004057
FSIS31800263
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
.
SourceSite
Blood
Blood
Pork
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
.
IsolatDate
2018-08-11
2018-06-19
2018-03-08
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
.
Species
.
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
.
SequencerRun_id
.
.
.
commentsExposureLabID
.
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
.
PatientSex
.
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
.
SourceCountry
.
.
.
.
.
.
.
SourceCounty
.
.
.
.
SourceState
NC
VA
NC
VA
NC
VA
NC
3.0 [1, 7]
wgMLST (<All Characters>)
100 Key
NC___MB081518-0059
VA___R180620742
USDA_853313749
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
PNUSAL004247
PNUSAL004057
FSIS31800263
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
.
SourceSite
Blood
Blood
Pork
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
.
IsolatDate
2018-08-11
2018-06-19
2018-03-08
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
.
Species
.
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
.
SequencerRun_id
.
.
.
commentsExposureLabID
.
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
.
PatientSex
.
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
.
SourceCountry
.
.
.
.
.
.
.
SourceCounty
.
.
.
.
SourceState
NC
VA
NC
VA
NC
VA
NC
3.0 [1, 7]
wgMLST (<All Characters>)
100 Key
NC___MB081518-0059
VA___R180620742
USDA_853313749
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
PNUSAL004247
PNUSAL004057
FSIS31800263
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
.
SourceSite
Blood
Blood
Pork
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
.
IsolatDate
2018-08-11
2018-06-19
2018-03-08
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
.
Species
.
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
.
SequencerRun_id
.
.
.
commentsExposureLabID
.
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
.
PatientSex
.
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
.
SourceCountry
.
.
.
.
.
.
.
SourceCounty
.
.
.
.
SourceState
NC
VA
NC
VA
NC
VA
NC
3.0 [1, 7]
wgMLST (<All Characters>)
100 Key
NC___MB081518-0059
VA___R180620742
USDA_853313749
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
PNUSAL004247
PNUSAL004057
FSIS31800263
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
.
SourceSite
Blood
Blood
Pork
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
.
IsolatDate
2018-08-11
2018-06-19
2018-03-08
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
.
Species
.
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
.
SequencerRun_id
.
.
.
commentsExposureLabID
.
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
.
PatientSex
.
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
.
SourceCountry
.
.
.
.
.
.
.
SourceCounty
.
.
.
.
SourceState
NC
VA
NC
VA
NC
VA
NC
3.0 [1, 7]
wgMLST (<All Characters>)
100 Key
NC___MB081518-0059
VA___R180620742
USDA_853313749
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
PNUSAL004247
PNUSAL004057
FSIS31800263
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
.
SourceSite
Blood
Blood
Pork
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
.
IsolatDate
2018-08-11
2018-06-19
2018-03-08
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
.
Species
.
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
.
SequencerRun_id
.
.
.
commentsExposureLabID
.
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
.
PatientSex
.
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
.
SourceCountry
.
.
.
.
.
.
.
SourceCounty
.
.
.
.
SourceState
NC
VA
NC
VA
NC
VA
NC
3.0 [1, 7]
wgMLST (<All Characters>)
100 Key
NC___MB081518-0059
VA___R180620742
USDA_853313749
VA___R180617588
USDA_590324576
VA___R170709909
USDA_210373329
Modified date
.
.
.
.
.
.
.
cdc_id
2018L-6276
2018L-6221
2017L-6294
WGS_id
PNUSAL004247
PNUSAL004057
FSIS31800263
PNUSAL004045
FSIS1606762
PNUSAL003187
FSIS11809104
NCBI_ACCESSION
.
.
.
.
.
.
.
SRR_ID
.
.
.
.
.
.
.
WGST
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20.
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
LMO1.0 - 106.1.1.1.20
Outbreak
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
1807VAGX6-1
SourceType
.
.
.
.
.
.
.
SourceSite
Blood
Blood
Pork
Blood
Pork
Blood
Pork
TypeDetails
.
PulseNet_UploadDate
.
.
.
.
.
.
.
IsolatDate
2018-08-11
2018-06-19
2018-03-08
2018-06-15
2016-05-12
2017-07-08
2018-03-28
ReceivedDate
.
.
.
.
.
.
.
UploadDate
.
.
.
.
.
.
.
PFGE-AscI-pattern
GX6A16.0048
GX6A16.0048
PFGE-AscI-status
.
.
PFGE-ApaI-pattern
GX6A12.0804
GX6A12.0804
PFGE-ApaI-status
.
.
Genus
.
.
.
.
.
.
.
Species
.
.
.
.
.
.
.
Lineage
.
.
.
.
.
.
.
Serotype
not typed
not typed
not typed
not typed
not typed
not typed
not typed
ANI
.
.
.
.
.
.
.
ANICoverage
.
.
.
.
.
.
.
MLST loci ST
.
.
.
.
.
.
.
SequencerRun_id
.
.
.
commentsExposureLabID
.
.
.
.
.
.
.
ListMemberNARMS-EBNCBISubmissionDateOtherStateIsolatePatientAgeDaysPatientAgeMonthsPatientAgeYears
.
.
.
.
PatientSex
.
.
.
.
PFGE-ApaI-file
.
.
PFGE-ApaI-rundatePFGE-AscI-file
.
.
PFGE-AscI-rundatePFGE-SmaI-filePFGE-SmaI-patternPFGE-SmaI-rundatePFGE-SmaI-statusSourceCity
.
.
.
.
SourceCountry
.
.
.
.
.
.
.
SourceCounty
.
.
.
.
SourceState
NC
VA
NC
VA
NC
VA
NC
3 [1,7]
Timeline of Listeriosis Investigation, Virginia
7/7/17: P1
Onset
4/28/18: P2 to ALF
6/14:
P2 Illness Onset
6/18: P2 Dies
6/19:
P3 Illness Onset
6/22:
Interview at ALF for
P2
6/29-7/3:
Interviews with
family of P2
7/2:
DCLS informs of
cluster
7/3:
Pork products match
Timeline of Listeriosis Investigation, Virginia
7/7/1: P1
Onset
4/28/18: P2 to ALF
6/14:
P2 Illness Onset
6/18: P2
Dies
6/19:
P3 Illness Onset
6/22: Interview at ALF for
P2
6/29-7/3: Interviews
with family of
P2
7/2:
DCLS informs
of cluster
7/3:
Pork products match
7/6:
Pork product
list received
List of Ham Products, USDA (July 6)
• Country Ham
• Whole Ham – Bone-In
• Whole Boneless Ham
• Honey Cured Spiral Sliced Ham
• Dry Cured Bacon, in slices or
slabs
• Mangalista Bacon
• Thick Cut Hickory Smoked Dry
Cured Bacon
• Fatback, cubed, sliced, or slab
• Ham Chips (Small pieces for mini
biscuits)
• Large or Split Ham Hocks
• Centers and Ends (Country Ham)
• Trimmings (Country Ham)
• End Slices (from butt of ham)
• Chunk Side Meat
• Country Ham Aitch Bones
• Iberico Ham
Timeline of Listeriosis Investigation, Virginia
7/7/17: P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
6/18: P2
Dies
6/19:
P3 Illness Onset
6/22: Interview at ALF for
P2
6/29-7/3: Interviews
with family of
P2
7/2:
DCLS informs
of cluster
7/3:
Pork products match
7/6:
Pork product
list received
7/23: ALF
Menus and
supplier list
7/26: P1
dies
Timeline of Listeriosis Investigation, Virginia
7/7/17: P1 Onset
4/28/18:
P2 to ALF
6/14:
P2 Illness Onset
6/18: P2
Dies
6/19:
P3 Illness Onset
6/22: Interview
at ALF for P2
6/29-7/3: Interviews with family
of P2
7/2:
DCLS informs
of cluster
7/3:
Pork products match
7/6:
Pork product
list received
7/23: ALF
Menus and
supplier list
7/26: P1
dies
8/24: P3 dies
List of Product Samples From FSIS
With Name Brands
Isolate KeyCollection
DateSample Product Establishment Name
Establishment
Number
Establishment
LocationBrands
USDA_853313749 3/8/2018
Product-RTE-
Other Fully
Cooked, Not
Sliced-Pork
Whole Deli
Ham
Goodnight
Brothers
Produce Co.,
Inc.
M7431 Boone, NC
Johnston County Hams Inc., Padow’s
Hams & Deli, Inc., Good Night
Brothers Country Ham, Valley
Country Hams, LLC, WayCo Ham
Company, Old Dominion Brand
Hams, Wholesome Foods, Inc.
USDA_590324576 5/12/2016
Product-RTE-
Other Fully
Cooked, Not
Sliced-Pork
Deli HamJohnston County
HamsM2646
Smithfield,
NC
Johnston County Hams Inc., Padow’s
Hams & Deli, Inc., Good Night
Brothers Country Ham, Valley
Country Hams, LLC, WayCo Ham
Company, Old Dominion Brand
Hams, Wholesome Foods, Inc.
USDA_210373329 3/28/2018
Product-RTE-
Other Fully
Cooked, Not
Sliced-Pork
Country Style
Fully Cooked
Boneless Deli
Ham
Johnston County
HamsM2646
Smithfield,
NC
Johnston County Hams Inc., Padow’s
Hams & Deli, Inc., Good Night
Brothers Country Ham, Valley
Country Hams, LLC, WayCo Ham
Company, Old Dominion Brand
Hams, Wholesome Foods, Inc.
Recalled Products
Acknowledgments
DCLS
• DCLS Microbial Reference Lab
• Epidemiologic Support and
Molecular Detection and
Characterization Group
• DCLS Molecular Subtyping Lab
VDACS
• Christy Brennan
VDH
• Kelsey Holloman, MPH
• Lisa Sollot, MPH
• Okey Utah, MPH
• Angie Myrick-West, MPH, CIC
• Lori Dixon, RN, BSN
• Seth Levine, MPH
• Christy Brennan, VDACS