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pdfFoodNet Variable List, (Site-transmitted variables)
Variable Name
Format
Length
Description
Answers (Legal Values)
Stx1;
Stx2;
Stx1&2;
Stx Undiff;
Negative;
Not Tested
Positive;
For other pathogens: What was the result of specimen testing using an
Negative;
antigen-based test (e.g. EIA or lateral flow) at a clinical laboratory?
Indeterminate;
Not Tested
Abbott Shiga Toxin Quik Chek;
Denka Seiken VTEC Screen;
Lab-developed test;
Merck Duopath STEC Rapid Test;
Meridian Curian Shiga Toxin;
For possible E.coli cases: Name of antigen-based test used at clinical labora
Meridian Premier EHEC;
Meridian ImmunoCard STAT! E. coli O157 Plus;
Meridian ImmunoCard STAT! EHEC;
Remel ProSpecT STEC;
Techlab Shiga Toxin Quik Chek
Abbott Campylobacter Quik Chek;
Meridian Curian Campy;
Meridian ImmunoCard STAT! CAMPY;
For possible Campylobacter cases: Name of antigen-based test used at
Meridian Premier CAMPY;
clinical laboratory
Remel ProSpecT Campylobacter;
Remel Xpect Campylobacter;
Techlab Campylobacter Quik Chek
Other;
For other pathogens: Name of antigen-based test used at clinical laboratory
Unknown
Age of case-patient in months if patient is <1yr
1-11
Age of case-patient in years
1-105
Stx1;
Stx2;
For possible E. coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using an antigen-based test (e.g.EIA or lateral flow) at a state
Stx Undiff;
public health laboratory?
Negative;
Not Tested
Positive
For other pathogens: What was the result of specimen testing using an
Negative
antigen-based test (e.g. EIA or lateral flow) at a state public health
Indeterminate
laboratory?
Not tested
Abbott Shiga Toxin Quik Chek;
Denka Seiken VTEC Screen;
Meridian Curian Shiga Toxin;
For possible E.coli cases: Name of antigen-based test used at state public Merck Duopath STEC Rapid Test;
health laboratory
Meridian ImmunoCard STAT! EHEC;
Meridian Premier EHEC;
Remel ProSpecT STEC;
Techlab Shiga Toxin Quik Chek
Abbott Campylobacter Quik Chek;
Meridian Curian Campy;
Meridian ImmunoCard STAT! CAMPY;
For possible Campylobacter cases: Name of antigen-based test used at
Meridian Premier CAMPY;
state public health laboratory
Remel ProSpecT Campylobacter;
Remel Xpect Campylobacter;
Techlab Campylobacter Quik Chek
For other pathogens: Name of antigen-based test used at state public health Other;
laboratory
Unknown
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Collect for all pathogens for which
culture-independent results are
available. Prior to 2011, called
'EiaClinic'.
2009-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
Site
Site
Collect for all cases
Collect for all cases
1996-current
1996-current
Demographics
Demographics
YES
YES
Site
Collect for all pathogens for which
culture-independent results are
available. Prior to 2011, called
'EiaSphl'.
2009-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
For possible E. coli cases: What was the result of specimen testing for
Shiga toxin using an antigen-based test (e.g.EIA or lateral flow) at a
clinical laboratory?
1
AgClinic
Character
30
2
AgClinicTestType
Character
100
3
4
AgeMnth
AgeYr
Numeric
Numeric
2
3
5
AgSphl
Character
30
6
AgSphlTestType
Character
100
7
AR_antibiotic_use
Character
10
FINAL 10/12/2018
Did (you/your child) take antibiotics for this illness?
Yes; No; Unknown
FoodNet Variable List (Site-transmitted variables)
Variable Name
Format
Length
8
AR_antibiotic_use_1
Character
30
What antibiotics did (you/your child) take for this illness?
9
AR_antibiotic_use_2
Character
30
What antibiotics did (you/your child) take for this illness?
10
AR_antibiotic_use_3
Character
30
What antibiotics did (you/your child) take for this illness?
11
AR_antibiotic_use_4
Character
30
What antibiotics did (you/your child) take for this illness?
12
AR_antibiotic_use_5
Character
30
What antibiotics did (you/your child) take for this illness?
13
AR_antibiotic_use_6
Character
30
What antibiotics did (you/your child) take for this illness?
14
AR_antibiotic_use_7
Character
30
What antibiotics did (you/your child) take for this illness?
15
AR_antibiotic_use_8
Character
30
What antibiotics did (you/your child) take for this illness?
16
AR_antibiotic_use30
Character
10
In the 30 days before (your/your child’s) illness began, did (you/your child)
Yes; No; Unknown
take any antibiotics?
17
AR_antibiotic_use30_1
Character
30
18
AR_antibiotic_use30_2
Character
30
19
AR_antibiotic_use30_3
Character
30
FINAL 10/12/2018
Description
Answers (Legal Values)
Amoxicillin
Amoxicillin / Clavulanate
Ampicillin
Augmentin
Azithromycin
Bactrim
Biaxin
Ceclor
Cefaclor
Ceftin
Cefixime
Ceftriaxone
Cefuorixime
Cefzil
Cefprozil
Cephalexin
Cephradine
Chloramphenicol
Ciprofloxacin / Cipro
Clarithromycin
Dapsone
Doxycycline
Duricef
Erythromycin
Erythromycin / sulfisoxazole
Flagyl
Floxin
Keflex
Keftab
Levofloxacin
Levoquin
Metronidazole
Norfloxacin / Norflox
Ofloxacin / Oflox
Pediazole
Penicillin / Pen VK
Septra
Suprax
Tetracycline
Trimox
Trimethoprim / Sulfa
Zithromax / Z-Pak
Other
Unknown
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
Amoxicillin
Amoxicillin / Clavulanate
Ampicillin
Augmentin
Azithromycin
What antibiotics did (you/your child) take in the 30 days before {your/your Bactrim
Biaxin
child's) illness began?
Ceclor
Cefaclor
Ceftin
Cefixime
Ceftriaxone
What antibiotics did (you/your child) take in the 30 days before {your/your Cefuorixime
child's) illness began?
Cefzil
Cefprozil
Cephalexin
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
FoodNet Variable List (Site-transmitted variables)
Variable Name
Format
Length
Description
Answers (Legal Values)
p
Cephradine
Chloramphenicol
Ciprofloxacin / Cipro
Clarithromycin
Dapsone
Doxycycline
Duricef
Erythromycin
Erythromycin / sulfisoxazole
Flagyl
Floxin
Keflex
Keftab
Levofloxacin
Levoquin
Metronidazole
Norfloxacin / Norflox
Ofloxacin / Oflox
Pediazole
Penicillin / Pen VK
Septra
Suprax
Tetracycline
Trimox
Trimethoprim / Sulfa
Zithromax / Z-Pak
Other
Unknown
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
20
AR_antibiotic_use30_4
Character
30
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
21
AR_antibiotic_use30_5
Character
30
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
22
AR_antibiotic_use30_6
Character
30
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
23
AR_antibiotic_use30_7
Character
30
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
24
AR_antibiotic_use30_8
Character
30
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
25
AR_comorb_abdominal
Character
10
In the 6 months before (your/your child's) illness began, did (you/your
child) have abdominal surgery (e.g., removal of appendix or gallbladder, or Yes; No; Unknown
any surgery of the stomach or large intestine)?
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
26
AR_comorb_cancer
Character
10
In the 6 months before (your/your child's) illness began, were (you/your
child) diagnosed or treated for cancer (including leukemia/lymphoma)?
Yes; No; Unknown
Site
Varies by site for Salmonella,
Campylobacter, and Shigella
2018-current
Exposure
NO
27
AR_comorb_diabetes
Character
10
In the 6 months before (your/your child's) illness began, were (you/your
child) diagnosed or treated for diabetes?
Yes; No; Unknown
Site
2018-current
Exposure
NO
28
AR_durationillness
Numeric
10
How many days were (you/your child) sick?
any number
Site
2018-current
Exposure
NO
Yes; No; Unknown
Site
2018-current
Exposure
NO
Text
Site
2018-current
Exposure
NO
Yes; No; Unknown
Site
2018-current
Exposure
NO
Yes; No; Unknown
Site
2018-current
Exposure
NO
Text
Site
Yes; No
Site
29
AR_HHtrav6mo
Character
10
30
AR_HHtrav6mo_country
Text Field
70
31
AR_hosp_icu
Character
10
32
AR_travel6mo
Character
10
33
AR_travel6mo_country
Text Field
70
34
Audit
Character
7
In the 6 months before (your/your child's) illness began, did any
member(s) of your household travel outside of the United States?
In the 6 months before (your/your child's) illness began, what countries did
the member(s) of your household visit?
During any part of the hospitalization, did you (your child) stay in an
Intensive Care Unit (ICU) or a Critical Care Unit (CCU)?
In the 6 months before (your/your child's) illness began, did (you/your
child) travel outside of the United States?
In the 6 months before (your/your child's) illness began, what countries did
(you/your child) visit?
Was case found during an audit?
35
BioId
Character
10
Was the pathogen identified by culture?
Yes; No; Unknown; Not Tested
Site
36
BloodyDiarr
Character
10
Did the case-patient have bloody diarrhea (self reported) during this
illness?
Yes; No; Unknown
37
38
County
CTNO2020
Character
Character
50
11
Case-patient's county of residence
2020 Census Tract Number
39
CultCdc
Character
30
What was the culture result at CDC? (Does not include confirmation of
isolates received.)
FINAL 10/12/2018
00000000000-99999999999
Positive;
Negative;
Unknown;
No bacterial growth;
Not tested
Positive;
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Collect for all cases
2018-current
Exposure
NO
1996-current
Other
NO
Collect for all bacterial pathogens.
Prior to 2011, called 'StecBioId'.
1996-current
Culture-Independent
Testing
YES
Site
Collect actively for Campylobacter ;
passively for other pathogens.
2011-current
Clinical Information
YES
Site
Site
Collect for all cases
Collect for all cases, optional
1996-current
2022-current
Demographics
Demographics
YES
NO
Site
Collect for all cases
2011-current (Campy) ; 2018current (others)
Lab Information
YES
FoodNet Variable List (Site-transmitted variables)
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Collect for all cases
2011-current (Campy) ; 2018current (others)
Lab Information
YES
Site
Collect for all cases
2011-current (Campy) ; 2018current (others)
Lab Information
YES
Site
Collect actively for Campylobacter
cases; passively for other pathogens.
2011-current
Clinical Information
YES
Site
Site
Site
Site
Site
Site
Site
Collect for all cases
Collect for hospitalized cases
Collect for hospitalized cases
Collect for hospitalized cases
Collect for hospitalized cases
Collect for all cases
Collect for all cases
1996-current
1996-current
2008-current
1996-current
2008-current
1996-current
2009-current
Demographics
Hospitalization
Hospitalization
Hospitalization
Hospitalization
Other
Clinical Information
NO
YES
YES
YES
YES
NO
YES
mmddyy10. Date case-pateint's specimen was received in laboratory for initial testing
Site
Collect for all cases
1996-current
Lab Information
NO
mmddyy10. Date case report form was completed
mmddyy10. Case-patient's specimen collection date
Site
Site
Collect for all cases
Collect for all cases
Collect for cases that reported
international travel during incubation
period; if recently immigrated, leave
blank
1996-current
1996-current
Other
Lab Information
NO
YES
2004-current
Travel
YES
Variable Name
Format
Length
40
CultClinic
Character
30
41
CultSphl
Character
30
42
Diarrhea
Character
10
Did the case-patient have diarrhea (self-reported) during this illness?
43
44
45
46
47
48
49
DOB
DtAdmit
DtAdmit2
DtDisch
DtDisch2
DtEntered
DtOnset
Date
Date
Date
Date
Date
Date
Date
mmddyy10.
mmddyy10.
mmddyy10.
mmddyy10.
mmddyy10.
mmddyy10.
mmddyy10.
Case patient's date of birth
Date of first hospital admission for this illness
Date of hospital admission for second hospitalization for this illness
Date of first hospital discharge for this illness
Date of hospital discharge for second hospitalization for this illness
Date case was entered into site's database
Date that the case-patient’s symptoms first began for this illness
50
DtRcvd
Date
51
52
DtRptComp
DtSpec
Date
Date
53
DtUSDepart
Date
mmddyy10.
54
DtUSReturn
Date
mmddyy10. If case-patient traveled internationally, date of return to the U.S.
55
DxO157
Character
30
For possible E.coli cases: What was the result of specimen testing for
O157 by EIA or PCR at a clinical laboratory?
56
DxO157TestType
Character
100
Name of EIA or PCR test used
57
EforsNum
Character
6
CDC NORS outbreak ID number
58
Ethnicity
Character
1
Case-patient's ethnicity
59
Fever
Character
Description
Answers (Legal Values)
Negative;
Unknown;
No bacterial growth;
Not tested
Positive;
Negative;
What was the culture result at a state public health lab? (Does not include
Unknown;
confirmation of isolates received.)
No bacterial growth;
Not tested
What was the culture result at a clinical lab?
Yes; No; Unknown
If case-patient patient traveled internationally, date of departure from the
U.S.
Site
Positive;
Negative;
Not tested
Abbott Shiga Toxin Quik Chek;
Biofire Filmarray Gastrointestinal (GI);
Diatherix Gastrointestinal;
HealthTrackRX Gastrointestinal;
Luminex xTag Gastrointestinal Pathogens;
Meridian ImmunoCard STAT! E. coli O157 Plus;
Meridian ImmunoCard STAT! EHEC;
Meridian Premier EHEC;
Metametrix;
Lab-developed test;
Principle DX Gastro-AS;
Other
1-999999;
888888='multi-state outbreak with exposure in multiple states'
999999='multi-state outbreak with a single exposure outside of the FoodNet catchment area'
H (Hispanic), N (Non-Hispanic), U (Unknown)
Site
Collect for cases that reported
international travel during incubation
period; if recently immigrated, enter
as date arrived to US
2004-current
Travel
YES
Site
Collect for E.coli cases
2014-current
Pathogen-specific
(E.coli)
YES
Site
Collect for E.coli cases
2014-current
Pathogen-specific
(E.coli)
YES
Site
Collect for cases that are part of a
recognized outbreak
2004-current
Outbreak
YES
Site
Collect for all cases
1996-current
Demographics
YES
2011-current
Clinical Information
YES
10
Did the case-patient have fever (self-reported) during this illness?
Yes; No; Unknown
Site
Collect actively for Campylobacter ;
passively for other pathogens.
Site
Collect for Shigella cases,
optional for other pathogens
2019-current
Demographics
NO
Site
Collect for all cases
1996-current
Hospitalization
YES
60
Homeless
Character
7
In the 7 days before illness, did the case-patient experience homelessness?
This includes staying in a shelter or car, building, or other structure not
intended for housing. (This does not include staying with friends or family, Yes; No; Unknown
correctional facilities, care or nursing facilities, single room occupancy, or
other transitional housing.)
61
Hospital
Character
7
Was case-patient hospitalized within (+/-) 7 days of specimen collection?
62
HospTrans
Character
7
If case-patient was hospitalized, was s/he transferred to another hospital?
Yes; No; Unknown
Site
Collect for hospitalized cases
1996-current
Hospitalization
YES
63
HUS
Character
7
Did case patient have a diagnosis of HUS?
Yes; No; Unknown
Site
Collect for E.coli cases
2009-current
Clinical Information
YES
FINAL 10/12/2018
Yes; No; Unknown
FoodNet Variable List, (Site-transmitted variables)
Variable Name
Format
Length
Immigrate
Character
7
64
Description
Did case-patient immigrate to the U.S.? (within 30 days of onset for
Salmonella Typhi, Paratyphi & Listeria, 14 days for Cyclospora, and 7
days for all other pathogens)
Answers (Legal Values)
Yes; No; Unknown
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Collect for all cases
2008-current
Travel
YES
Site
Collect for all cases
2008-current
Other
YES
Site
Site
Site
Collect for all cases
Collect for all cases
Collect for all cases
1996-current
1996-current
1996-current
Lab Information
Lab Information
ID Field
NO
NO
NO
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2011-current
Culture-Independent
Testing
YES
2004-current
Outbreak
YES
2008-current
Outbreak
NO
2008-current
Outbreak
YES
74
Outbreak
Character
7
Was the case-patient interviewed by public health (i.e. state or local health
Yes; No; Unknown
department or FoodNet staff)?
Name of submitting laboratory
Local aliquot identification number
Varies by state
Case-patient's medical record number
Varies by state
Stx1;
Stx2;
For possible E.coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using another test at the CDC?
Stx Undiff;
Negative;
Not Tested
Positive
For other pathogens: What was the result of specimen testing using
Negative
another test at CDC?
Indeterminate
Not tested
Stx1;
Stx2;
For possible E.coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using another test at a clinical laboratory?
Stx Undiff;
Negative;
Not Tested
Positive
For other pathogens: What was the result of specimen testing using another Negative
test at a clinical laboratory?
Indeterminate
Not tested
Autoflourescence
Beckman Walkaway System
Stained Wet Mount;
Microscopy Unspecified
Modified Acid-Fast
Name of other test used at a clinical laboratory
Modified Safranin Stain
Wet Mount
Vero Cell Asay;
Other;
Unknown
Stx1;
Stx2;
For possible E.coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using another test at a state public health laboratory?
Stx Undiff;
Negative;
Not Tested
Positive
For other pathogens: What was the result of specimen testing using another Negative
test at a state public health laboratory?
Indeterminate
Not tested
Autoflourescence
Beckman Walkaway System
Stained Wet Mount;
Microscopy Unspecified
For other pathogens: Name of other test used at a state public health
Modified Acid-Fast
laboratory
Modified Safranin Stain
Wet Mount;
Vero Cell Asay;
Other;
Unknown
Was the case-patient part of a recognized outbreak?
Yes; No
75
OutbrkStID
Character
30
State outbreak identification number
Varies by state
Site
76
OutbrkType
Character
50
Type of outbreak that the case-patient was part of
Foodborne; Waterborne; Animal contact; Person-to-person; Environmental contamination other than
food/water; Indeterminate; Other; Unknown
Site
65
Interview
Character
7
66
67
68
LabName
LabNum
LocalID
Character
Character
Character
25
30
16
69
OtherCdcTest
Character
30
70
OtherClinicTest
Character
30
71
OtherClinicTestType
Character
100
72
OtherSphlTest
Character
30
73
OtherSphlTestType
Character
100
FINAL 10/12/2018
Site
Collect for all cases
Collect if case is part of a recognized
outbreak
Collect if case is part of a recognized
outbreak
FoodNet Variable List (Site-transmitted variables)
Variable Name
Format
Length
77
Outcome
Character
7
78
OutFetal
Character
40
79
Pathogen
Character
40
80
PatID
Character
30
81
PcrCdc
Character
30
82
PcrClinic
Character
30
83
PcrClinicTestType
Character
100
FINAL 10/12/2018
Description
Answers (Legal Values)
Case-patient's outcome (assessed for non-hospitalized cases within 7 days
Alive; Dead; Unknown
of specimen collection date and hospitalized cases at hospital discharge)
Still pregnant;
If Listeria case was pregnancy-associated, what was the outcome of the
Fetal death;
pregnancy? Note: fetal death includes miscarriage or stillbirth; delivery is a
Delivery
live birth.
Unknown;
Campylobacter;
Cyclospora;
STEC;
Listeria;
Name of bacterial pathogen identified from the case-patient’s specimen
Salmonella;
Shigella;
Vibrio;
Yersinia;
Unique ID for case-patient's infection
Varies by state
Stx1;
Stx2;
For possible E. coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using PCR at CDC?
Stx Undiff;
Negative;
Not Tested
Vibrios
V cholerae
For Vibrio , what was the result of specimen testing using PCR at CDC?
V parahaemolyticus
(where goal of testing is primary detection not subtyping or speciation)
Vibrios&V cholerae
Negative
Not Tested
For other pathogens: What was the result of specimen testing for diagnosis Positive;
using PCR at CDC? (Do not enter PCR results if PCR was performed for Negative;
speciation or subtyping).
Not tested
Stx1;
Stx2;
For possible E. coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using PCR at a clincal laboratory?
Stx Undiff;
Negative;
Not Tested
For Campylobacter, Cyclospora, Salmonella, Shigella, Yersinia : What Positive;
was the result of specimen testing using PCR at a clinical laboratory?
Negative;
(where goal of testing is primary detection not subtyping or speciation)
Not tested
Vibrios
V cholerae
For Vibrio , what was the result of specimen testing using PCR at a clinical
V parahaemolyticus
laboratory? (where goal of testing is primary detection not subtyping or
Vibrios&V cholerae
speciation)
Negative
Not Tested
For specimens that were culture-confirmed Shigella and Shiga toxinShigella /Stx undiff
positive by PCR: What was the result of specimen testing using PCR at a
Shigella /Stx1
clinical laboratory? (For specimens that were not culture-confirmed or
Shigella /Stx2
were only positive for Shigella , indicate "positive" under Shigella section
Shigella /Stx1&2
above)
BioCode Gastrointestinal Pathogen Panel (GPP);
Biofire Filmarray Gastrointestinal (GI);
Biofire Filmarray Meningitis/Encephalitis (ME);
Biofire Filmarray Blood Culture Identification (BCID);
Biofire Filmarray Blood Culture Identification 2 (BCID2);
BD Max Enteric Bacterial;
BD Max Extended Enteric Bacterial;
Diatherix Gastrointestinal;
Genmark E Plex BCID;
Great Basin Scientific Stool;
Name of PCR assay used at a clinical lab
HealthTrackRX Gastrointestinal;
Hologic Prodesse ProGastro SSCS;
Karius Test;
Luminex Gram-Positive Blood Culture;
Luminex Verigene Enteric Pathogens;
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Collect for all cases
1996-current
Clinical Information
YES
Site
Collect for Listeria cases
1996-current
Pathogen-specific
(Listeria)
YES
Site
Collect for all cases. Prior to 2011,
called 'Isolate'.
1996-current
Lab Information
YES
Site
Collect for all cases
1996-current
ID field
NO
Site
Collect for all pathogens for which
culture-independent results are
available.
2009-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens for which
culture-independent results are
available.
2010-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens detected by
PCR in a clinical lab
2011-current
Culture-Independent
Testing
YES
FoodNet Variable List (Site-transmitted variables)
Variable Name
Format
Length
Description
Answers (Legal Values)
84
PcrSphl
Character
30
85
PcrSphlTestType
Character
100
86
PersonID
Character
30
Luminex xTag Gastrointestinal Pathogens;
Medical Diagnostics;
Principle DX Gastro-AS;
Vikor Scientific Gastro-ID;
Lab-developed test;
Unknown
Stx1;
Stx2;
For possible E. coli cases: What was the result of specimen testing for
Stx1&2;
Shiga toxin using PCR at a state public health laboratory?
Stx Undiff;
Negative;
Not Tested
For other pathogens: What was the result of specimen testing for diagnosis Positive
using PCR at the state public health laboratory? (Do not enter PCR results Negative
if PCR was performed for speciation or subtyping).
Not tested
Vibrios
V cholerae
For Vibrio , what was the result of specimen testing using PCR at a state
V parahaemolyticus
public health laboratory? (where goal of testing is primary detection not
Vibrios&V cholerae
subtyping or speciation)
Negative
Not Tested
For specimens that were culture-confirmed Shigella and Shiga toxinShigella /Stx undiff
positive by PCR: What was the result of specimen testing using PCR at a
Shigella /Stx1
clinical laboratory? (For specimens that were not culture-confirmed or
Shigella /Stx2
were only positive for Shigella , indicate "positive" under Shigella section
Shigella /Stx1&2
above)
BioCode Gastrointestinal Pathogen Panel (GPP);
Biofire Filmarray Gastrointestinal (GI);
Biofire Filmarray Meningitis/Encephalitis (ME);
Biofire Filmarray Blood Culture Identification (BCID);
Biofire Filmarray Blood Culture Identification 2 (BCID2);
BD Max Enteric Bacterial;
BD Max Extended Enteric Bacterial;
Diatherix Gastrointestinal;
Genmark E Plex BCID;
Great Basin Scientific Stool;
Name of PCR assay used at a state public health lab
HealthTrackRX Gastrointestinal;
Hologic Prodesse ProGastro SSCS;
Karius Test;
Luminex Gram-Positive Blood Culture;
Luminex Verigene Enteric Pathogens;
Luminex xTag Gastrointestinal Pathogens;
Medical Diagnostics;
Principle DX Gastro-AS;
Vikor Scientific Gastro-ID;
Lab-developed test;
Unknown
Identification number for person or patient
Varies by state
87
Pregnant
Character
7
Is this Listeria case pregnancy-associated?
Yes; No; Unknown
A (Asian);
B (Black);
I (American Indian or Alaskan Native);
M (Multi-Racial);
O (Other);
P (Pacific Islander or Native Hawaiian);
W (White);
U (Unknown)
Varies by state
Yes; No; Unknown
88
Race
Character
1
Case-patient's race
89
90
ResultID
RptComp
Character
Character
30
7
Unique identifier for laboratory result
Is all of the information for this case complete?
91
SentCDC
Character
7
Was specimen or isolate forwarded to CDC or testing or confirmation OR
Yes; No; Unknown
was there a request for analysis of sequence data to CDC?
For Campylobacter: n/a.
For Listeria : 1; 1/2a; 1/2b; 1/2c; 3a; 3b; 3c; 4; 4b; Untypeable; Unknown
For Salmonella : See Kaufmann-White scheme
FINAL 10/12/2018
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Collect for all pathogens for which
culture-independent results are
available.
2009-current
Culture-Independent
Testing
YES
Site
Collect for all pathogens detected by
PCR in a state public health lab
2015-current
Culture-Independent
Testing
YES
Site
Collect for all cases
2008-current
Site
Collect for Listeria cases
1996-current
Site
Collect for all cases
1996-current
Demographics
YES
Site
Site
Collect for all cases
Collect for all cases
2008-current
1996-current
ID field
Other
NO
YES
Site
Collect for all cases
2009-current
Lab Information
YES
ID field
Pathogen-specific
(Listeria)
NO
YES
FoodNet Variable List (Site-transmitted variables)
Variable Name
Format
Length
92
SeroSite
Character
100
93
Sex
Character
1
Description
Serotype/species of pathogen identified by culture, submitted by site
Case-patient's sex
Answers (Legal Values)
For Shigella : boydii; dysenteria;, flexneri; sonnei
For Vibrio : alginolyticus; cholerae; cincinnatiensis; damsela; fluvialis; furnissii; harveyi; hollisae;
metschnikovi; mimicus; parahaemolyticus; vulnificus; Unknown
For Yersinia : ldovae; bercovieri;enterocolitica; frederiksenii; intermedia; kristensenii; mollaretii;
pseudotuberculosis; rohdei; ruckeri; Unknown.
M (Male); F (Female); U (Unknown)
Sent by Site or
Created at CDC
Comment
Year(s) for which variable is
available
Category
Included in standard
data requests?
Site
Collect for Salmonella, Listeria,
Shigella, Vibrio, Yersinia
1996-current
Subtyping Information
NO
Site
Collect for all cases
1996-current
Demographics
YES
Site
Collect for all cases
1996-current
ID field
NO
Site
Collect for all cases for which the
isolate was sent to a state public
health lab
1996-current
Lab Information
NO
Site
Collect for all cases. If specimen
source is something other than listed
in legal values, please specify. Do not
code as 'other'.
1996-current
Lab Information
NO
Site
Collect for all cases
1996-current
Collect for E.coli cases
1996-current
Demographics
Pathogen-specific
(E.coli)
YES
Site
Site
Collect for E.coli cases
1996-current
Pathogen-specific
(E.coli)
NO
California – CDA2, CDA201, CDA20101, CDA20102, CDA20103, CDA202, CDA203, CDA6;
94
SiteID
Character
10
Site identification number
95
SLabsID
Character
30
State lab identification number
96
Colorado – CDCO;
Connecticut – CDA5,
GA GOA – CDGE;
GA MSA – CDA1, CDA101;
Maryland – CDE1;
Minnesota – CDMN;
New Mexico – CDNM;
New York – CDNF;
Oregon – CDOR;
Tennessee – CDTN
Varies by state
Abscess;
Amniotic fluid;
Blood;
Bone;
CSF;
Ear;
Gall bladder;
Genitals;
Joint;
Lung;
Peritoneal fluid;
Placenta;
Rectal swab;
Sputum;
Stool;
Urine;
Wound;
Unknown
CA; CO; CT; GA; MD; MN; NM; NY; OR; TN
1-99
999
1-999
‘555'=not O157, O antigen pending or at CDC
‘666'=not O157, O antigen unknown
’777'=not O157, O antigen unknown
‘888'=O antigen not tested
'999'=O antigen rough
60
Case patient's specimen collection source
Character
2
Case patient's state of residence
Character
30
If E. coli , what was the H-antigen number for the isolate?
StecOAg
Character
30
If E. coli, what was the O-antigen number for the isolate?
StecStx
Character
40
Was E. coli isolate Shiga toxin-producing?
Yes; No; Unknown
Site
Collect for E.coli cases
1996-current
Pathogen-specific
(E.coli)
NO
Yes; No; Unknown
Site
Collect for all cases
1996-current
Lab Information
YES
List country, or countries, visited
Site
Collect for cases that reported
international travel during incubation
period
2004-current
Travel
YES
2004-current
Travel
YES
SpecSite
Character
97
State
98
StecHAg
99
100
NO
101
StLabRcvd
Character
7
Was the isolate sent to a state public health laboratory? (Answer 'Yes' if it
was sent to any state lab, even if it was sent to a lab outside of the case's
state of residence)
102
TravelDest
Text Field
70
If case-patient traveled internationally, to where did they travel?
103
TravelInt
Character
7
Did the case patient travel internationally? (within 30 days of onset for
Salmonella Typhi, Paratyphi & Listeria , 14 days for Cyclospora , and 7 Yes; No; Unknown
days for all other pathogens)
Site
Collect for all cases
104
WGS_ID
Character
100
WGS ID Number
Varies by state: from pulsenet or NCBI
Site
Collect for all cases that were WGS
2018-current
Lab Information
NO
105
Zipcode
Character
10
Case-patient's zipcode
5 digit zipcode; 5 digit plus 4, if available.
Site
Collect for all cases
1996-current
Demographics
NO
FINAL 10/12/2018
| File Type | application/pdf |
| Author | Huang, Jennifer (CDC/OID/NCEZID) (CTR) |
| File Modified | 2024-10-08 |
| File Created | 2024-09-23 |