FoodNet Campylobacter

FoodNet Variable List, 2020
(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
Merck Duopath STEC Rapid Test;
For possible E.coli cases: Name of antigen-based test used at clinical laboratory
Meridian Premier EHEC;
Meridian ImmunoCard STAT! E. coli O157 Plus;
Meridian ImmunoCard STAT! EHEC;
Remel ProSpecT STEC;
Abbott Campylobacter Quik Chek
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
1-11
Age of case-patient in months if patient is <1yr
1-105
Age of case-patient in years
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
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;
Abbott Campylobacter Quik Chek
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
Other;
health 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

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

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_antacid_any

Character

10

In the 30 days before (your/your child’s) illness began, did (you/your
child) have any form of antacid?
What medications to block acids did (you/your child) take in the 30 days
before {your/your child's) illness began?
What medications to block acids did (you/your child) take in the 30 days
before {your/your child's) illness began?
What medications to block acids did (you/your child) take in the 30 days
before {your/your child's) illness began?

8

AR_antacid_any_1

Character

30

9

AR_antacid_any_2

Character

30

10

AR_antacid_any_3

Character

30

11

AR_antibiotic_use

Character

10

Did (you/your child) take antibiotics for this illness?

12

AR_antibiotic_use_1

Character

30

What antibiotics did (you/your child) take for this illness?

13

AR_antibiotic_use_2

Character

30

What antibiotics did (you/your child) take for this illness?

14

AR_antibiotic_use_3

Character

30

What antibiotics did (you/your child) take for this illness?

15

AR_antibiotic_use_4

Character

30

What antibiotics did (you/your child) take for this illness?

FINAL 10/12/2018

Yes; No; Unknown;
Aluminium hydroxide
Ami-Lac
Amphojel
Axid
Calcium carbonate
Cal Gest
Yes; No; Unknown
Amoxicillin
Amoxicillin / Clavulanate
Ampicillin
Augmentin
Azithromycin
Bactrim
Biaxin
Ceclor
Cefaclor
Ceftin
Cefixime
Ceftriaxone
Cefuorixime
Cefzil

Site
Site
Site
Site
Site
Site
Site
Site

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
Varies by site for Salmonella,
Campylobacter, and Shigella

Variable Name

Format

Length

16

AR_antibiotic_use_5

Character

30

17

AR_antibiotic_use_6

Character

30

1
18

AgClinic
AR_antibiotic_use_7

Character
Character

30

What antibiotics did (you/your child) take for this illness?
For possible E. coli cases: What was the result of specimen testing for
Shiga
toxin usingdid
an antigen-based
testtake
(e.g.EIA
lateral flow) at a
What antibiotics
(you/your child)
for thisorillness?
clinical laboratory?
What antibiotics did (you/your child) take for this illness?

19

AR_antibiotic_use_8

Character

30

What antibiotics did (you/your child) take for this illness?

20

AR_antibiotic_use30

Character

10

21

AR_antibiotic_use30_1

Character

30

22

AR_antibiotic_use30_2

Character

30

23

AR_antibiotic_use30_3

Character

30

24

AR_antibiotic_use30_4

Character

30

25

AR_antibiotic_use30_5

Character

30

26

AR_antibiotic_use30_6

Character

30

27

AR_antibiotic_use30_7

Character

30

28

AR_antibiotic_use30_8

Character

30

29

30

AR_comorb_abdominal

AR_comorb_cancer

Character

Character

10

10

Description

In the 30 days before (your/your child’s) illness began, did (you/your
child) take any antibiotics?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
What antibiotics did (you/your child) take in the 30 days before {your/your
child's) illness began?
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
any surgery of the stomach or large intestine)?
In the 6 months before (your/your child's) illness began, were (you/your
child) diagnosed or treated for cancer (including leukemia/lymphoma)?

31

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?

32

Ar_Diet_veal

Character

10

In the past 7 days, did (you/your child) eat any veal?

33

AR_durationillness

Numeric

10

How many days were (you/your child) sick?

34

AR_HHtrav6mo

Character

10

35

AR_HHtrav6mo_country

Text Field

70

36

AR_hosp_icu

Character

10

Amoxicillin
Amoxicillin / Clavulanate
Ampicillin
Augmentin
Azithromycin
Bactrim
Biaxin
Answers (Legal Values)
Ceclor
Cefaclor
Ceftin
Cefixime
Ceftriaxone
Cefuorixime
Cefzil
Cefprozil
Cephalexin
Yes; No; Unknown
Amoxicillin
Amoxicillin / Clavulanate
Ampicillin
Augmentin
Azithromycin
Bactrim
Biaxin
Ceclor
Cefaclor
Ceftin
Cefixime
Ceftriaxone
Cefuorixime
Cefzil
Cefprozil
Cephalexin

FoodNet Variable List, 2020
(Site-transmitted variables)
Sent by Site or
Created at CDC
Site
Site
Site
Site
Site
Site
Site
Site
Site
Site
Site
Site
Site
Site

Yes; No; Unknown
Yes; No; Unknown

any number
In the 6 months before (your/your child's) illness began, did any
Yes; No; Unknown
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
Text
the member(s) of your household visit?
During any part of the hospitalization, did you (your child) stay in an
Yes; No; Unknown
Intensive Care Unit (ICU) or a Critical Care Unit (CCU)?
In the 30 days before (you/your child's) illness began, did (you/your child)
take a probiotic?
Probiotics are live microorganims (such as certain types of bacteria) that
may benefit your health. These can take the form of pills, powders,
yogurts, and other fermented dairy products, as well as anything labeled as
containing "live and active cultures" or "probiotics."

Character

10

38

AR_travel6mo

Character

10

39

AR_travel6mo_country

Text Field

70

40

Audit

Character

7

Yes; No; Unknown
In the 6 months before (your/your child's) illness began, did (you/your
Yes; No; Unknown
child) travel outside of the United States?
In the 6 months before (your/your child's) illness began, what countries did
Text
(you/your child) visit?
Yes; No
Was case found during an audit?

41

BioId

Character

10

Was the pathogen identified by culture?

10

Did the case-patient have bloody diarrhea (self reported) during this
illness?

43

CEA_Beef

Character

10

44

CEA_Chicken

Character

10

45

CEA_Dairy

Character

10

46

FINAL 10/12/2018

CEA_Dog

Character

10

In the 7 days before illness, did you/your child eat beef or any foods
containing beef?
In the 7 days before illness, did you/your child eat chicken or any foods
containing chicken?
In the 7 days before illness, did you/your child eat or drink any dairy
products (e.g., milk, yogurt, cheese, ice cream, etc.)?
In the 7 days before illness, did you/your child have any contact with a
dog?

Included in standard
data requests?

2018-current

Exposure

NO

2018-current

Exposure

NO

2009-current
2018-current

Culture-Independent
Exposure
Testing

YES
NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

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

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

2018-current

Exposure

NO

1996-current

Other

NO

1996-current

Culture-Independent
Testing

YES

2011-current

Clinical Information

YES

Exposure

YES

Site
Site
Site
Site
Site
Site

Site

Site
Site
Site

Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown

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
Collect for all bacterial pathogens.
Prior to 2011, called 'StecBioId'.

Site

Collect actively for Campylobacter ;
passively for other pathogens.

Yes; No; Unknown
Yes; No; Unknown

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

Site
Yes; No; Unknown; Not Tested

Character

Category

Site

Yes; No; Unknown

AR_probiotic_use30

BloodyDiarr

Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Collect
for all pathogens
for which
Campylobacter,
and Shigella
culture-independent
results are
Varies by site for Salmonella,
available. Prior toand
2011,
called
Campylobacter,
Shigella
Varies by 'EiaClinic'.
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
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella
Varies by site for Salmonella,
Campylobacter, and Shigella

Year(s) for which variable is
available

Yes; No; Unknown

37

42

Comment

Site
Site
Site
Site

Collect for Salmonella
Campylobacter
Collect for Salmonella
Campylobacter
Collect for Salmonella
Campylobacter
Collect for Salmonella
Campylobacter

and
and
and
and

2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)

Exposure

YES

Exposure

YES

Exposure

YES

FoodNet Variable List, 2020
(Site-transmitted variables)
Variable Name

Format

Length

CEA_Eggs

Character

10

48

CEA_Fish

Character

10

1
49

AgClinic
CEA_Lettuce

Character

30
10

47

50

CEA_Live_poultry

Character

10

51

CEA_Milk_raw

Character

10

52

CEA_Pig

Character

10

53

CEA_Pork

Character

10

54

CEA_Reptile_amphib

Character

10

55

CEA_Ruminants

Character

10

56

CEA_Seafd

Character

10

57

CEA_Turkey

Character

10

58

County

Character

20

59

CultCdc

Character

20

60

CultClinic

Character

20

61

CultSphl

Character

20

62

Diarrhea

Character

10

Description
In the 7 days before illness, did you/your child eat any eggs?
For possible E. coli cases: What was the result of specimen testing for
In
the toxin
7 daysusing
before
did you/your
child eatorany
fishflow)
or fishat a
Shiga
an illness,
antigen-based
test (e.g.EIA
lateral
products?
clinical laboratory?
In the 7 days before illness, did you/your child eat any fresh, raw lettuce?
In the 7 days before illness, did you/your child have any contact with any
live poultry (e.g., chickens, turkeys, hens, etc.)?
In the 7 days before illness, did you/your child drink any unpasteurized
milk?
In the 7 days before illness, did you/your child have any contact with any
pigs?
In the 7 days before illness, did you/your child eat pork or any foods
containing pork?
In the 7 days before illness, did you/your child have any contact with a
reptile or amphibian (e.g., frog, snake, turtle, etc.)?
In the 7 days before illness, did you/your child have any contact with any
cattle, goats, or sheep?
In the 7 days before illness, did you/your child eat any seafood (e.g., crab,
shrimp, oysters, clams, etc.)?
In the 7 days before illness, did you/your child eat any turkey or any foods
containing turkey?
Case-patient's county of residence

Answers (Legal Values)

Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown

Positive;
Negative;
What was the culture result at CDC? (Does not include confirmation of
Unknown;
isolates received.)
No bacterial growth;
Not tested
Positive;
Negative;
What was the culture result at a clinical lab?
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
Did the case-patient have diarrhea (self-reported) during this illness?

Sent by Site or
Created at CDC

Comment

Year(s) for which variable is
available

Site

Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Collect for
all pathogens for which
Campylobacter
culture-independent
results
are
Collect for Salmonella
and
available.
Prior to 2011, called
Campylobacter
'EiaClinic'.
Collect for
Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for Salmonella and
Campylobacter
Collect for all cases

2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current
(Salm );
2009-current
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2016-current (Campy)
2014-current (Salm );
2015-current (Campy)
2014-current (Salm );
2015-current (Campy)
1996-current

Site

Collect for all cases

Site

Site
Site
Site
Site
Site
Site
Site
Site
Site
Site
Site

Category

Included in standard
data requests?

Exposure

YES

Exposure

YES

Culture-Independent
Exposure
Testing

YES

Exposure

YES

Exposure

YES

Exposure

YES

Exposure

YES

Exposure

YES

Exposure

YES

Exposure

YES

Exposure

YES

Demographics

YES

2011-current (Campy) ; 2018current (others)

Lab Information

YES

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

63
64

DOB
DtAdmit

Date
Date

mmddyy10. Case patient's date of birth
mmddyy10. Date of first hospital admission for this illness

Site
Site

Collect for all cases
Collect for hospitalized cases

1996-current
1996-current

Demographics
Hospitalization

NO
YES

65

DtAdmit2

Date

mmddyy10. Date of hospital admission for second hospitalization for this illness

Site

Collect for hospitalized cases

2008-current

Hospitalization

YES

66

DtDisch

Date

mmddyy10. Date of first hospital discharge for this illness

Site

Collect for hospitalized cases

1996-current

Hospitalization

YES

67

DtDisch2

Date

mmddyy10. Date of hospital discharge for second hospitalization for this illness

Site

Collect for hospitalized cases

2008-current

Hospitalization

YES

68
69

DtEntered
DtOnset

Date
Date

mmddyy10. Date case was entered into site's database
mmddyy10. Date that the case-patient’s symptoms first began for this illness

Site
Site

Collect for all cases
Collect for all cases

1996-current
2009-current

Other
Clinical Information

NO
YES

70

DtRcvd

Date

mmddyy10. Date case-pateint's specimen was received in laboratory for initial testing

Site

Collect for all cases

1996-current

Lab Information

NO

71
72

DtRptComp
DtSpec

Date
Date

mmddyy10. Date case report form was completed
mmddyy10. Case-patient's specimen collection date

Site
Site

1996-current
1996-current

Other
Lab Information

NO
YES

73

DtUSDepart

Date

mmddyy10.

Collect for all cases
Collect for all cases
Collect for cases that reported
international travel during incubation
period; if recently immigrated, leave
blank

2004-current

Travel

YES

74

DtUSReturn

Date

mmddyy10. If case-patient traveled internationally, date of return to the U.S.

75

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?

76

DxO157TestType

Character

100

Name of EIA or PCR test used

Yes; No; Unknown

FINAL 10/12/2018

If case-patient patient traveled internationally, date of departure from the
U.S.

Site

Positive;
Negative;
Not tested
Meridian ImmunoCard STAT! E. coli O157 Plus;
Biofire Filmarray Gastrointestinal (GI);
Diatherix Gastrointestinal;
Luminex xTag Gastrointestinal Pathogens;
Metametrix;

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

FoodNet Variable List, 2020
(Site-transmitted variables)
76

Variable Name
DxO157TestType

Character
Format

Length
100

Name of EIA or PCR test usedDescription

Answers (Legal Values)

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
CDC
FDOSS
outbreak ID number
clinical
laboratory?

Lab-developed test;
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)

77

EforsNum

Character

6

1
78

AgClinic
Ethnicity

Character
Character

30
1

Case-patient's ethnicity

79

Fever

Character

10

Did the case-patient have fever (self-reported) during this illness?

Sent by Site or
Site
Created at CDC

Year(s) for which variable is
2014-current
available

Pathogen-specific
Category
(E.coli)

Included in standard
YES
data requests?

2004-current

Outbreak
Culture-Independent
Testing
Demographics

YES

2009-current
1996-current
2011-current

Clinical Information

YES

Collect for Shigella cases

2019-current

Demographics

NO

Site

Collect for all cases

1996-current

Hospitalization

YES

Site

Collect for hospitalized cases

1996-current

Hospitalization

YES

Site

Collect for E.coli cases

2009-current

Clinical Information

YES

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

Site
Site
Site
Site

Yes; No; Unknown

80

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,
correctional facilities, care or nusing facilities, single room occupancy, or
other transitional housing.)

81

Hospital

Character

7

Was case-patient hospitalized within (+/-) 7 days of specimen collection?

82

HospTrans

Character

7

If case-patient was hospitalized, was s/he transferred to another hospital?

83

HUS

Character

7

84

Immigrate

Character

7

Did case patient have a diagnosis of HUS?
Did case-patient immigrate to the U.S.? (within 30 days of onset for
Salmonella Typhi & Listeria, 14 days for Cyclospora, and 7 days for all
other pathogens)
Was the case-patient interviewed by public health (i.e. state or local health
department or FoodNet staff)?
Name of submitting laboratory
Local aliquot identification number
Case-patient's medical record number

85

Interview

Character

7

86
87
88

LabName
LabNum
LocalID

Character
Character
Character

25
12
16

For possible E.coli cases: What was the result of specimen testing for
Shiga toxin using another test at the CDC?
89

OtherCdcTest

Character

30
For other pathogens: What was the result of specimen testing using
another test at CDC?

For possible E.coli cases: What was the result of specimen testing for
Shiga toxin using another test at a clinical laboratory?
90

OtherClinicTest

Character

30
For other pathogens: What was the result of specimen testing using
another test at a clinical laboratory?

91

OtherClinicTestType

Character

100

Name of other test used at a clinical laboratory

For possible E.coli cases: What was the result of specimen testing for
Shiga toxin using another test at a state public health laboratory?
92

OtherSphlTest

Character

30
For other pathogens: What was the result of specimen testing using
another test at a state public health laboratory?

FINAL 10/12/2018
93
OtherSphlTestType

Character

100

For other pathogens: Name of other test used at a state public health
laboratory

Site

CollectComment
for E.coli cases

Collectfor
forall
cases
that arefor
partwhich
of a
Collect
pathogens
recognized outbreak
culture-independent
results are
available.
Prior
Collect
fortoall2011,
casescalled
'EiaClinic'.
Collect actively for Campylobacter ;
passively for other pathogens.

YES
YES

Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown
Yes; No; Unknown

Yes; No; Unknown
Yes; No; Unknown
Varies by state
Varies by state
Stx1;
Stx2;
Stx1&2;
Stx Undiff;
Negative;
Not Tested
Positive
Negative
Indeterminate
Not tested
Stx1;
Stx2;
Stx1&2;
Stx Undiff;
Negative;
Not Tested
Positive
Negative
Indeterminate
Not tested
Autoflourescence
Beckman Walkaway System
Stained Wet Mount;
Microscopy Unspecified
Modified Acid-Fast
Modified Safranin Stain
Wet Mount
Vero Cell Asay;
Other;
Unknown
Stx1;
Stx2;
Stx1&2;
Stx Undiff;
Negative;
Not Tested
Positive
Negative
Indeterminate
Not tested
Autoflourescence
Beckman Walkaway System
Stained Wet Mount;

FoodNet Variable List, 2020
(Site-transmitted variables)

93

Variable Name

Format

Length

OtherSphlTestType

Character

100

Description

For
pathogens:
Name What
of other
at of
a state
publictesting
healthfor
For other
possible
E. coli cases:
wastest
theused
result
specimen
laboratory
Shiga
toxin using an antigen-based test (e.g.EIA or lateral flow) at a
clinical laboratory?

1

30

AgClinic

Character

94

Outbreak

Character

7

Was the case-patient part of a recognized outbreak?

95

OutbrkStID

Character

30

State outbreak identification number

96

OutbrkType

Character

50

Type of outbreak that the case-patient was part of

97

Outcome

Character

7

Case-patient's outcome (assessed for non-hospitalized cases within 7 days
of specimen collection date and hospitalized cases at hospital discharge)

98

OutFetal

Character

35

If Listeria case was pregnancy-associated, what was the outcome of the
pregnancy? Note: fetal death includes miscarriage or stillbirth; delivery is
a live birth.

99

Pathogen

Character

25

Name of bacterial pathogen identified from the case-patient’s specimen

100

PatID

Character

9

Unique ID for case-patient's infection

101

PcrCdc

Character

30

For possible E. coli cases: What was the result of specimen testing for
Shiga toxin using PCR at CDC?

For other pathogens: What was the result of specimen testing for diagnosis
using PCR at CDC? (Do not enter PCR results if PCR was performed for
speciation or subtyping).

For possible E. coli cases: What was the result of specimen testing for
Shiga toxin using PCR at a clincal laboratory?

102

PcrClinic

Character

30

For Campylobacter, Cyclospora, Salmonella, Shigella, Yersinia : What
was the result of specimen testing using PCR at a clinical laboratory?
(where goal of testing is primary detection not subtyping or speciation)
For Vibrio , what was the result of specimen testing using PCR at a clinical
laboratory? (where goal of testing is primary detection not subtyping or
speciation)
For specimens that were culture-confirmed Shigella and Shiga toxinpositive by PCR: What was the result of specimen testing using PCR at a
clinical laboratory? (For specimens that were not culture-confirmed or
were only positive for Shigella , indicate "positive" under Shigella section

103

PcrClinicTestType

FINAL 10/12/2018

Character

100

Name of PCR assay used at a clinical lab

Answers (Legal Values)
Microscopy Unspecified
Modified Acid-Fast
Modified Safranin Stain
Wet Mount;
Vero Cell Asay;
Other;
Unknown
Yes; No
Varies by state
Foodborne; Waterborne; Animal contact; Person-to-person; Environmental contamination other than
food/water; Indeterminate; Other; Unknown

Alive; Dead; Unknown
Still pregnant;
Fetal death;
Delivery
Unknown;
Campylobacter;
Cyclospora;
STEC;
ETEC;
Listeria;
Salmonella;
Shigella;
Vibrio;
Yersinia;
Varies by state
Stx1;
Stx2;
Stx1&2;
Stx Undiff;
Negative;
Not Tested
Positive;
Negative;
Not tested
Stx1;
Stx2;
Stx1&2;
Stx Undiff;
Negative;
Not Tested
Positive;
Negative;
Not tested
Vibrios
V cholerae
Vibrios&V cholerae
Negative
Not Tested
Shigella /Stx undiff
Shigella /Stx1
Shigella /Stx2
Shigella /Stx1&2
BioCode Gastrointestinal Pathogen Panel (GPP);
Biofire Filmarray Gastrointestinal (GI);
Biofire Filmarray Meningitis/Encephalitis (ME);
Biofire Filmarray Blood Culture Identification (BCID);
BD Max Enteric Bacterial;
BD Max Extended Enteric Bacterial;
Diatherix Gastrointestinal;
Genmark E Plex BCID
Great Basin Scientific Stool
Hologic Prodesse ProGastro SSCS;
Luminex Gram-Positive Blood Culture;
Luminex Verigene Enteric Pathogens;
Luminex xTag Gastrointestinal Pathogens;
Medical Diagnostics;
Lab-developed test

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.
Collect for all
pathogens for which

2011-current

Culture-Independent
Testing

YES

2009-current

Culture-Independent
Testing

YES

Collect for all cases
Collect if case is part of a recognized
outbreak
Collect if case is part of a recognized
outbreak

2004-current

Outbreak

YES

2008-current

Outbreak

NO

2008-current

Outbreak

YES

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

Site
Site
Site
Site

culture-independent results are
available. Prior to 2011, called
'EiaClinic'.

103

PcrClinicTestType

Character

100

Name of PCR assay used at a clinical lab

Site

Collect for all pathogens detected by
PCR in a clinical lab

2011-current

Culture-Independent
Testing

YES

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.

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

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

FoodNet Variable List, 2020
(Site-transmitted variables)
Variable Name

Format

Length

Description

Answers (Legal Values)

1

AgClinic

Character

30

104

PcrSphl

Character

30

105

PcrSphlTestType

Character

100

106

PersonID

Character

30

Unknown
Stx1;
Stx2;
Stx1&2;
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
For Vibrio , what was the result of specimen testing using PCR at a state V cholerae
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
BioCode Gastrointestinal Pathogen Panel (GPP);
Biofire Filmarray Gastrointestinal (GI);
Biofire Filmarray Meningitis/Encephalitis (ME);
Biofire Filmarray Blood Culture Identification (BCID);
BD Max Enteric Bacterial;
BD Max Extended Enteric Bacterial;
Diatherix Gastrointestinal;
Genmark E Plex BCID
Name of PCR assay used at a state public health lab
Great Basin Scientific Stool
Hologic Prodesse ProGastro SSCS;
Luminex Gram-Positive Blood Culture;
Luminex Verigene Enteric Pathogens;
Luminex xTag Gastrointestinal Pathogens;
Medical Diagnostics;
Lab-developed test
Unknown
Varies by state
Identification number for person or patient

107

Pregnant

Character

7

Is this Listeria case pregnancy-associated?

108

Race

Character

1

Case-patient's race

109
110

ResultID
RptComp

Character
Character

30
7

Unique identifier for laboratory result
Is all of the information for this case complete?

111

SentCDC

Character

7

112

SeroSite

Character

60

113

Sex

Character

1

114

SiteID

Character

10

Was specimen or isolate forwarded to CDC or testing or confirmation OR
was there a request for analysis of sequence data to CDC?
Yes; No; Unknown
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
For Shigella : boydii; dysenteria;, flexneri; sonnei
Serotype/species of pathogen identified by culture, submitted by site
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)
Case-patient's sex
California – CDA2, CDA201, CDA20101, CDA20102, CDA20103, CDA202, CDA203, CDA6;
Colorado – CDCO;
Connecticut – CDA5,
GA GOA – CDGE;
GA MSA – CDA1, CDA101;
Site identification number
Maryland - CDE1;
Minnesota –CDMN;
New Mexico – CDNM;
New York – CDNF;
Oregon – CDOR;
Tennessee – CDTN

FINAL 10/12/2018

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
For
possible
E. coli cases: What was the result of specimen testing for
clinical
laboratory?
Shiga toxin using PCR at a state public health laboratory?

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

ID field
Pathogen-specific
(Listeria)

NO
YES

FoodNet Variable List, 2020
(Site-transmitted variables)
Variable Name

Format

Length

SLabsID

Character

30

115

Description

2009-current
2010-current

Culture-Independent
Testing
Subtyping Information

YES
NO

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

Site

Collect for E.coli cases

1996-current

Pathogen-specific
(E.coli)

NO

Site

Collect for all cases

1996-current

Lab Information

YES

Site

Collect for cases that reported
international travel during incubation
period

2004-current

Travel

YES

Did the case patient travel internationally? (within 30 days of onset for
Salmonella Typhi & Listeria , 14 days for Cyclospora , and 7 days for all
Yes; No; Unknown
other pathogens)

Site

Collect for all cases

2004-current

Travel

YES

Site

Collect for all cases that were WGS

2018-current

Lab Information

NO

Site

Collect for all cases

1996-current

Demographics

NO

60

For Campylobacter , what was the species result at SPHL?

118

SpecSite

Character

30

Case patient's specimen collection source

119

State

Character

2

Case patient's state of residence

120

StecHAg

Character

3

If E. coli , what was the H-antigen number?

121

StecOAg

Character

30

If E. coli, what was the O-antigen number?

122

StecStx

Character

40

Was E. coli Shiga toxin-producing?

123

StLabRcvd

Character

7

Site
Varies by state
For Campylobacter : jejuni; jejuni subsp jejuni; jejuni subsp. doylei; coli; ,lari; lari subsp. concheus;
lari subsp. lari; upsaliensis;,helveticus; fetus; fetus subsp fetus; fetus subsp venerealis;hyointestinalis;
hyointestinalis subsp. hyointestinalis; hyointestinalis subsp. lawsonii; sputorum; sputorum bv
sputorum; sputorum bv paraureolyticus; lanienae; mucosalis;insulaenigrae; concisus; curvus; rectus;
showae;gracilis; canadenesis; peloridis;avium; cuniculorum; hominis; Unknown; Not tested.
For Campylobacter: jejuni; jejuni subsp jejuni; jejuni subsp. doylei; coli; ,lari; lari subsp. concheus;
lari subsp. lari; upsaliensis;,helveticus; fetus; fetus subsp fetus; fetus subsp venerealis;hyointestinalis;
hyointestinalis subsp. hyointestinalis; hyointestinalis subsp. lawsonii; sputorum; sputorum bv
sputorum; sputorum bv paraureolyticus; lanienae; mucosalis;insulaenigrae;concisus; curvus; rectus;
showae;gracilis; canadenesis; peloridis;avium; cuniculorum; hominis ; Unknown; Not tested.
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 = NM
1-999
‘555'=not O157, O antigen pending or at CDC
’666'=not O157, O antigen unknown
‘777'=O antigen undetermined
‘888'=O antigen not tested
'999'=O antigen rough

Yes; No; Unknown; Not Tested
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
Yes; No; Unknown
state of residence)
If case-patient traveled internationally, to where did they travel?
List country, or countries, visited

FINAL 10/12/2018

NO

Site

Character

127

Lab Information

NO

SpeciesSphl

126

1996-current

Subtyping Information

117

TravelInt

Included in standard
data requests?

2010-current

For Campylobacter, what was the species result at clinical lab?

125

Category

Collect for Campylobacter

30
60

70

Year(s) for which variable is
available

Site

Character
Character

Text Field

Comment

Site
Site

AgClinic
SpeciesClinic

TravelDest

Sent by Site or
Created at CDC

Collect for all cases for which the
isolate was sent to a state public
health lab
Collect for all pathogens for which
culture-independent results are
available. Prior to 2011, called
Collect for
Campylobacter
'EiaClinic'.

State
lab identification
number
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
116

124

Answers (Legal Values)

Character

7

WGS_ID

Character

100

WGS ID Number

Zipcode

Character

10

Case-patient's zipcode

Varies by state: from pulsenet or NCBI
5 digit zipcode; 5 digit plus 4, if available.

NO