Att 9_FNDataRequest_ActiveSurv_Variable_Definitions_

FoodNet Variable Definitions
Below is a list and description of variables included in FoodNet active surveillance data. Variable names used in the
dataset are indicated by parentheses.
Pathogen................................................................................ Page 1
Site .................................................................................................1
Age .................................................................................................1
Sex .................................................................................................1
Race ...............................................................................................1
Ethnicity .........................................................................................1
County............................................................................................1
Hospitalization ...............................................................................1
Hospitalization Dates .....................................................................1
Length of Hospital Stay..................................................................2
Hospital Transfer ............................................................................2
Death ..............................................................................................2
Bloody Diarrhea .............................................................................2
Diarrhea..........................................................................................2
Fever ..............................................................................................2
HUS ...............................................................................................2
Date of Illness Onset ......................................................................2
Outbreak-related .............................................................................2
CDC Outbreak ID ..........................................................................2
Outbreak Type................................................................................2
International Travel ........................................................................2
Travel Destination ..........................................................................2

Dates of International Travel ......................................................... 2
Immigrate ...................................................................................... 3
Specimen source ............................................................................ 3
Specimen Collection Date.............................................................. 3
Specimen Collection Month .......................................................... 3
State Lab Received ........................................................................ 3
State Lab ID ................................................................................... 3
Sent to CDC................................................................................... 3
Culture-Independent Variables ...................................................... 3
Serogroup ...................................................................................... 5
Pregnant ......................................................................................... 5
Fetal Outcome................................................................................ 5
Underlying Conditions................................................................... 5
Mom-Baby Pair ............................................................................. 5
Sterile Site ..................................................................................... 6
Where Pathogen Cultured .............................................................. 6
Where Pathogen Speciated ............................................................ 6
CSTE Case Definition ................................................................... 6
Interview ........................................................................................ 6
Serotype/Species ............................................................................ 6
Year ............................................................................................... 6

Pathogen [Pathogen]: Format (Character); Length (25). Name of bacterial or parasitic pathogen identified from the
case-patient’s specimen (prior to 2011 called ‘Isolate’). Responses include: ‘Campylobacter’, ‘Cryptosporidium’,
‘Cyclospora’, ‘E. coli’, ‘Listeria’, ‘Salmonella’, ‘Shigella’, ‘Vibrio’, and ‘Yersinia’.
Site [State]: Format (Character); Length (2). Case-patient’s state of residence (two character state abbreviations).
Age [Age]: Format (Numeric); Length (7). Age of case-patient in years (includes two decimal places). If you
would like age defined in months (for persons less than 1 year), please specify this in the comments field of the
data request form.
Sex [Sex]: Format (Character); Length (1). Case-patient’s gender. Responses are ‘M’ (Male), ‘F’ (Female), or ‘U’
(Unknown).
Race [Race]: Format (Character); Length (1). Case-patient’s race. Responses are ‘A’ (Asian), ‘B’ (Black), ‘I’
(American Indian or Alaskan Native), ‘M’ (Multiracial), ‘O’ (Other), ‘P’ (Pacific Islander or Native Hawaiian), ’W’
(White), ‘U’ (Unknown).
Ethnicity [Ethnicity]: Format (Character); Length (1). Case-patient’s ethnicity. Responses are ‘H’ (Hispanic), ‘N’
(Non-Hispanic), and ‘U’ (Unknown).
County [County]: Format (Character); Length (20). Case-patient’s county of residence.
Hospitalization [Hospital]: Format (Character): Length (7). Was the case-patient hospitalized within (+/-) 7 days of
specimen collection? Responses are ‘Yes’, ‘No’, ‘Unknown’. Visits to the emergency room are not included unless
the patient was subsequently admitted.
Hospitalization Dates
[DtAdmit]: Format (Date); Length (mmddyyyy10). Date of hospital admission.
[DtDisch]: Format (Date); Length (mmddyyyy10). Date of hospital discharge.
[DtAdmit2]: Format (Date); Length (mmddyyyy10). Date of admission for second hospitalization,
defined as > 24 hours after first hospital discharge date.
[DtDisch2]: Format (Date); Length (mmddyyyy10). Date of hospital discharge for second
hospitalization, defined as > 24 hours after first hospital discharge date.
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FoodNet Variable Definitions
If a patient is transferred from one hospital to another, [DtAdmit] will reflect date of admission to
first hospital and [DtDisch] will be date discharged from last hospital. [DtAdmit2] and [DtDisch2]
are only used if the patient is discharged for at least 24hrs and then re-admitted.
Length of Hospital Stay [HospStay]: Format (Numeric); Length (7). Total length (in days) of hospitalization.
Hospital Transfer [HospTrans]: Format (Character); Length (7). If case patient was hospitalized, was s/he
transferred to another hospital? Responses are ‘Yes’, ‘No’, ’Unknown’.
Death [Outcome]: Format (Character); Length (7). Case-patient’s outcome. Assessed for non-hospitalized cases
within 7 days of specimen collection date and hospitalized cases at hospital discharge. Responses are ‘Alive’,
‘Dead’, ‘Unknown’. Does not indicate whether the death resulted from the FoodNet infection, only that the patient
died within the specified time period.
Bloody Diarrhea [BloodyDiarr]: Format (Character); Length (10). Did the case-patient have bloody diarrhea (selfreported) during this illness? Responses are ‘Yes’, ‘No’ ‘Unknown’. Only available for selected cases from 2012 to
current.
Diarrhea [Diarrhea]: Format (Character); Length (10). Did the case-patient have diarrhea (self-reported) during this
illness? Responses are ‘Yes’, ‘No’ ‘Unknown’. Only available for selected cases from 2012 to current.
Fever [Fever]: Format (Character); Length (10). Did the case-patient have fever (self-reported) during this illness?
Responses are ‘Yes’, ‘No’ ‘Unknown’. Only available for selected cases from 2012 to current.
HUS [HUS]: Format (Character); Length (7). Did case-patient have a diagnosis of hemolytic uremic syndrome
(HUS)? Responses are ‘Yes’, ’No’, ’Unknown’. Only available for E.coli cases from 2010 to current.
Date of Illness Onset [DtOnset]: Format (Date); Length (mmddyyyy10). Date that the case-patient’s symptoms first
began. Only available from 2009 to current.
Outbreak-related [Outbreak]: Format (Character); Length (7). Was the case-patient part of a recognized outbreak?
Responses are ‘Yes’, ‘No’. Only available from 2004 to current.
CDC Outbreak ID [EforsNum]: Format (Character); Length (6). CDC FDOSS outbreak identification number.
Only available from 2004 to current.
Outbreak Type [OutbrkType]: Format (Character): Length (50). Type of transmission mode for the outbreak in
which that the case-patient was involved. Responses are ‘Foodborne’, ’Waterborne’, ‘Animal contact’, ‘Person-toPerson’, ’Environmental contamination other than food/water’, ’Indeterminate’, ‘Other’, ‘Unknown’. Only available
from 2004 to current.
International Travel [TravelInt]: Format (Character); Length (7). Did the case-patient travel internationally?
Responses are ‘Yes’, ‘No’, ‘Unknown’. Travel is assessed within 30 days of illness onset for Salmonella Typhi,
Salmonella Paratyphi, and Listeria, within 15 days of illness onset for Cryptosporidium and Cyclospora, and within
seven days of illness onset for other FoodNet pathogens. Only available from 2004 to current.
Travel Destination [TravelDest]: Format (Text); Length (70). To which country did the case-patient travel? Does
not include domestic travel destinations. Only available from 2004 to current.
Dates of International Travel
[DtUSDepart]: Format (Date); Length (mmddyyyy10). Date of departure from the U.S.
[DtUSReturn]: Format (Date); Length (mmddyyyy10). Date of return to the U.S.

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FoodNet Variable Definitions
Immigrate [Immigrate]: Format (Character); Length (7). Did the case-patient immigrate to the U.S. (within specific
time period)? Responses are ‘Yes’, ‘No’, ‘Unknown’. Immigration is assessed within 30 days of illness onset for
Salmonella Typhi, Salmonella Paratyphi, and Listeria, within 15 days of illness onset for Cryptosporidium and
Cyclospora, and within seven days of illness onset for other FoodNet pathogens. Only available from 2004 to
current.
Specimen source [SpecSrce]: Format (Character): Length (30). Categories include: ‘Abscess’, ‘Blood’, ‘CSF’,
‘Ortho’, ‘Placenta/fetal tissue’, ‘‘Stool’, ‘Urine’, ‘Other sterile site’, ’Other’, ‘Unknown’.
Specimen Collection Date [DtSpec]: Format (Date); Length (mmddyyyy10). Date of case-patient’s specimen
collection.
Specimen Collection Month [Month]: Format (Numeric); Length (2). Month of case-patient’s specimen collection.
Legal values are 1-12.
State Lab Received [StLabRcvd]: Format (Character); Length (7). Was the isolate sent to a state public health
laboratory? Responses are ‘Yes’, ‘No’, ‘Unknown’. This question indicates receipt at any state public health
laboratory, including those outside of the FoodNet catchment area.
State Lab ID [SLabsID]: Format (Character); Length (30). State laboratory isolate identification number.
Sent to CDC [SentCDC]: Format (Character); Length (7). Was specimen or isolate forwarded to CDC for testing or
confirmation? Reponses are ‘Yes’, ‘No’, ‘Unknown’.
Culture-Independent Variables
[BioID]: Format (Character); Length (10). Was the pathogen identified by culture? Responses are
‘Yes’, ’No’, ’Unknown’, ’Not Tested’.
[AgClinic]: Format (Character); Length (30). 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?
For E.coli, Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive undifferentiated’, ‘Negative’,
‘Not tested’.
For other pathogens: What was the result of specimen testing using an antigen-based test (e.g. EIA or
lateral flow) at a clinical laboratory? Responses are ‘Positive’, ‘Negative’, ‘Indeterminate’, ‘Not
tested’. For possible Cryptosporidium cases, results from rapid card testing or EIA would be entered.
[AgClinicTestType]: Format (Character); Length (100). Name of antigen-based test used at clinical
laboratory. This encompasses both EIA and lateral flow tests. Responses include the following test
types, but others can be added as new tests are identified.
E.coli test types: ‘Immunocard STAT! EHEC (Meridian) ’, ‘Duopath Verotoxins (Merck) ’,
‘Premier EHEC (Meridian)’, ‘ProSpecT STEC (Remel)’, ‘VTEC Screen (Denka Seiken)’.
Cryptosporidium test types: ‘ImmunoCard STAT! Crypto/Giardia (Meridian) ’, ‘Xpect Crypto
(Remel) ’, Xpect Crypto/Giardia (Remel) ’ ‘ColorPAC Crypto/Giardia (Becton Dickinson)’,
‘ProSpecT Crypto (Remel) ’, ProSpecT Crypto/Giardia (Remel) ‘, ‘Wampole EIA
Cryptosporidium’, ‘TechLab EIA Cryptosporidium’, ‘Crypto CELISA (Cellabs)’, ‘Para-TECHT
Crypto Antigen 96 (Medical Chemical Corporation)’, ‘Triage parasite panel (BioSite)’.
Campylobacter test types: ‘ProSpecT Campylobacter assay (Remel)’, ‘PREMIER™ CAMPY
assay (Meridian)’, ‘ImmunoCard STAT! CAMPY (Meridian)’, ‘Xpect Campylobacter assay
(Remel)’.
All pathogens: ‘Other’, ‘Unknown’.
[AgSphl]: Format (Character); Length (30).
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 state public health laboratory? Responses are
‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive undifferentiated’, ‘Negative’, ‘Not tested’.
For other pathogens: What was the result of specimen testing using an antigen-based test (e.g.
EIA or lateral flow) at a state public health laboratory? Responses are ‘Positive’, ‘Negative’,
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FoodNet Variable Definitions
‘Indeterminate’, ‘Not tested. For possible Cryptosporidium cases, results from rapid card testing
or EIA would be entered here.
[AgSphlTestType]: Format (Character); Length (100). Name of antigen-based test used at a state public
health laboratory. This encompasses both EIA and lateral flow tests. Responses include the following
test types, but others can be added as new tests are identified.
E.coli test types: ‘Immunocard STAT! EHEC (Meridian) ’, ‘Duopath Verotoxins (Merck) ’,
‘Premier EHEC (Meridian)’, ‘ProSpecT STEC (Remel)’, ‘VTEC Screen (Denka Seiken)’.
Cryptosporidium test types: ‘ImmunoCard STAT! Crypto/Giardia (Meridian) ’, ‘Xpect Crypto
(Remel) ’, Xpect Crypto/Giardia (Remel) ’ ‘ColorPAC Crypto/Giardia (Becton Dickinson)’,
‘ProSpecT Crypto (Remel) ’, ProSpecT Crypto/Giardia (Remel) ‘, ‘Wampole EIA
Cryptosporidium’, ‘TechLab EIA Cryptosporidium’, ‘Crypto CELISA (Cellabs)’, ‘Para-TECHT
Crypto Antigen 96 (Medical Chemical Corporation)’, ‘Triage parasite panel (BioSite)’.
Campylobacter test types: ‘ProSpecT Campylobacter assay (Remel)’, ‘PREMIER™ CAMPY
assay (Meridian)’, ‘ImmunoCard STAT! CAMPY (Meridian)’, ‘Xpect Campylobacter assay
(Remel)’
All pathogens: ‘Other’, ‘Unknown’.
[PcrClinic]: Format (Character); Length (30)
For possible E.coli cases: what was the result of specimen testing for Shiga toxin using PCR at a
clinical laboratory? Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive
undifferentiated’, ‘Negative’, ‘Not tested’.
For other pathogens: What was the result of specimen testing using PCR at a clinical laboratory?
Responses are ‘Positive’, ‘Negative’, ‘Not tested’. The goal of this PCR testing should be
primary detection. If PCR is being performed for subtyping or speciation, then the response
should be ‘Not tested’.
[PCRClinicTestType]: Format (Character); Length (100). Name of PCR assay used at a clinical
laboratory. Responses include (but are not limited to): ‘Diatherix’, ‘Metametrix’, ‘Seegene’, ‘Statens
Serum Institut PCR assay’, ‘Home brew assay’, ‘Unknown’.
[PcrSphl]: Format (Character); Length (30).
For possible E.coli cases: what was the result of specimen testing for Shiga toxin using PCR at a state
public health laboratory? Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive
undifferentiated’, ‘Negative’, ‘Not tested’.
For other pathogens: What was the result of specimen testing for diagnosis using PCR at a state
public health laboratory? Do not enter PCR results if PCR was performed for speciation or
subtyping. Responses are ‘Positive’, ‘Negative’, ‘Not Tested’.
[PcrCdc]: Format (Character); Length (30)
For possible E.coli cases: what was the result of specimen testing for Shiga toxin using PCR at
CDC? Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive undifferentiated’,
‘Negative’, ‘Not tested’.
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. Responses include ‘Positive’,
‘Negative’, ‘Not tested’.
[OtherClinicTest]: Format (Character); Length (30)
For possible E.coli cases: What was the result of specimen testing for Shiga toxin using another
test at a clinical laboratory? Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive
undifferentiated’, ‘Negative’, ‘Not tested’.
For other pathogens: What was the result of specimen testing using another test at a clinical
laboratory? Responses are ‘Positive’, ‘Negative’, ‘Indeterminate’, ‘Not tested’.
[OtherClinicTestType]: Format (Character); Length (100). Name of other test used at a clinical
laboratory. Responses include (but are not limited to) 'DFA-PARA-TECHTTM Cryptosporidium/Giardia
DFA 75', 'DFA-Merifluor (Meridian)', 'Cellabs Crypto Cel', 'Wet mount', ‘Trichrome stain’, ‘Modified
acid-fast’, 'Other', 'Unknown test type'. If ‘other’, please list actual name or description of test.
[OtherSphlTest]: Format (Character); Length (30)
For possible E.coli cases: What was the result of specimen testing for Shiga toxin using another
test at the state public health laboratory? Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’,
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FoodNet Variable Definitions
‘Positive undifferentiated’, ‘Negative’, ‘Not tested’.
For other pathogens: What was the result of specimen testing using another test at a state public
health laboratory? Responses are ‘Positive’, ‘Negative’, ‘Indeterminate’, ‘Not tested’.
[OtherSphlTestType]: Format (Character); Length (100). Name of other test used at the state public
health laboratory. Responses include (but are not limited to) 'DFA-PARA-TECHTTM
Cryptosporidium/Giardia DFA 75', 'DFA-Merifluor (Meridian)', 'Cellabs Crypto Cel', ‘Wet mount’,
‘Trichrome stain’, ’Modified acid-fast’, 'Other', 'Unknown test type'. If ‘other’, please list actual name or
description of test.
[OtherCdcTest]: Format (Character); Length (30)
For possible E.coli cases: What was the result of specimen testing for Shiga toxin using another
test at CDC? Responses are ‘Stx1+’,’Stx2+’, ‘Stx1+ and Stx2+’, ‘Positive undifferentiated’,
‘Negative’, ‘Not tested’.
For other pathogens: What was the result of specimen testing using another test at the CDC?
Responses are ‘Positive’, ‘Negative’, ‘Indeterminate’, ‘Not tested’.
[OtherCdcTestType]: Format (Character); Length (100). Name of other test used at CDC. Responses
include (but are not limited to): 'DFA-PARA-TECHTTM Cryptosporidium/Giardia DFA 75', 'DFAMerifluor (Meridian)', 'Cellabs Crypto Cel', ‘Wet mount’, ‘Trichrome stain’, ‘Modified acid-fast’, ‘Other',
'Unknown test type'.
Serogroup [SalGroup]: Format (Character); Length (2). Salmonella serogroup. Only available for Salmonella cases.
Pregnant [Pregnant]: Format (Character); Length (7). Is this case pregnancy-associated? Responses are ‘Yes’, ‘No’,
’Unknown’. Only available for Listeria cases.
Responses will be ‘Yes’ if case occurred in a pregnant woman, or an infant born to a mother with
a Listeria infection (Listeria isolated at birth or within 30 days of delivery; may also include
infants who developed symptoms within 30 days of delivery but are cultured >30 days after
delivery). If Listeria is isolated from both mother and an infant, both will be included in
surveillance.
This variable refers to a pregnancy-associated infection; it does not ask if the case is pregnant.
Therefore, this field can be answered ‘Yes’ for a male infant.
Fetal Outcome [OutFetal]: Format (Character); Length (35). If the case is pregnancy-associated, what was the
outcome of the fetus? Responses are ‘Survived, no apparent illness’, ‘Survived, clinical infection’, ‘Live
birth/neonatal death’, ‘Abortion/still birth’, ‘Induced abortion’, ‘Unknown’, ‘Abortion, otherwise undetermined’,
’Live birth, otherwise undetermined’, ‘Survived, otherwise undetermined’. Only available for Listeria cases.
Underlying Conditions [Comorb1], [Comorb2], [Comorb3], [Comorb4], [Comorb5]: Format (Text); Length (70).
What are the underlying causes or associated illness? Responses may include but are not limited to the following:
‘AIDS’, ‘Alcohol Abuse’, ‘Artherosclerotic Cardiovascular Disease (ASCVD/CAD)’, Asthma’, ’Blunt Trauma’,
‘Burns’, ‘Cirrhosis’, ‘CSF Leak (2 trauma/surgery)’, ‘Diabetes Mellitus’, ‘Emphysema/COPD’, ‘Heart
Failure/CHF’, ‘HIV Infection’, ‘Hodgkin's Disease’, ‘Immunoglobulin Deficiency’, ‘Immunosuppressive Therapy
(steroids, chemotherapy, radiation)’, ‘IVDU’, ‘Leukemia’, ‘Multiple Myeloma’, ‘Nephrotic Syndrome’, ‘Organ
Transplant’ , ‘Other Illness’, ‘Other Malignancy’, ‘Penetrating Trauma’, ‘Renal Failure/Dialysis’, ‘Sickle Cell
Anemia’, ‘Splenectomy/asplenia’, ‘Surgical Wound (post-operative)’, ‘Systemic Lupus Erythematosus (SLE)’,
‘Unknown’, ‘Varicella’. Only available for Listeria cases.
Mom-Baby Pair
[MomBaby]: Format (Character); Length (7). Is the case part of a mom-baby pair? Responses are
‘Yes’, ‘No’. Only available for Listeria cases.
[MomBabyID]: Format (Character); Length (20). If [MomBaby] =’Yes’, designates which other
case is part of the pair. Response will be the ‘PatID’ field of associated case. Only available for
Listeria cases.

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FoodNet Variable Definitions
Sterile Site [Sterile]: Format (Character); Length (30). Was the specimen source from a sterile body site? Responses
are ‘Yes’, ‘No’. Only available for Listeria cases.
Where Pathogen Cultured
[CultClinic]: Format (Character); Length (20). What was the culture result at the clinical lab?
Responses are ‘Positive’, ‘Negative’, ‘Unknown’, ‘No bacterial growth’, ‘Not Tested’. Only
available for Campylobacter cases from 2009 to current.
[CultSphl]: Format (Character); Length (20). What was the culture result at a state public health lab?
(Refers to primary detection; it does not include isolate confirmation). Responses are ‘Positive’,
‘Negative’, ‘Unknown’, ‘No bacterial growth’, ‘Not Tested’. Only available for Campylobacter
cases from 2009 to current.
[CultCdc]: Format (Character); Length (20). What was the culture result at CDC? Responses are
‘Positive’, ‘Negative’, ‘Unknown’, ‘No bacterial growth’, ‘Not Tested’. Only available for
Campylobacter cases from 2009 to current.
Where Pathogen Speciated [SpeciesCdc]: Format (Character); Length (60). What was the species result at CDC?
Only available for Campylobacter for 2009 to current. Responses are: ‘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 by paraureolyticus’, ‘lanienae’, ’mucosalis’, ’insulaenigrae’,
’concisus’, ’curvus’, ’rectus’, ’showae’, ’gracilis’, ’canadenesis’, ’peloridis’, ’avium’,’cuniculorum’,’hominis’,’
Unknown’, ’Not tested’.
CSTE Case Definition [CSTE]: Format (Character); Length (20). Classifies Listeria and Cryptosporidium cases
according to CSTE case definition (where it differs from FoodNet definition); for analysis. Responses are ‘Yes,
confirmed’, ‘Yes, probable’, ‘No’. Only available for Listeria and Cryptosporidium cases.
Interview [Interview]: Format (Character): Length (7). Was the case interviewed by public health (i.e. state or local
health department or FoodNet staff)? Responses are ‘Yes’, ‘No’, ‘Unknown’. Only available from 2009 to current.
Serotype/Species [SerotypeSummary]: Format (Character); Length (60). Serotype/species of pathogen.
Year [Year]: Format (Numeric); Length (4). Year of case-patient’s specimen collection.

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