FoodNET Lab Practices Volume

FoodNet Clinical Laboratory Practices and Testing Volume Surveillance (last updated 8/6/2021)

Variable Name
RecordID
Site
Month
Year
HospName
LabID
ChngTestMeth
Tonsite
Labforward
Entericscrn

Format
numeric
character
numeric
numeric
character
character
character
character
character
character

FoodNet Clincal Laboratory Survey Data Elements
Description
Legal Values
unique system generated record ID
FoodNet site providing data
CA, CO, CT, GA, MD, MN, NY, OR, TN
Month for when the survey was completed or verified
1 to 12
Year for when the survey was complete for verified
2015-present
Laboratory name
unique identifier for laboratory
During the past 6 months, has you laboratory changed testing methods used for detecting each pathogen? Yes, No
Yes, No
Does your laboratory test stool specimens (blood/CSF for Listeria) on site for each pathogen?
free text
To which laboratory do you send specimens for testing?
Yes, No (only upon request)
Is each pathogen part of your laboratory's routine (approx >80%) enteric screen?

IDCx
IDPCR
IDAG
IDOther
IDOtherSpec

character
character
character
character
character

How often does your laboratory use culture to initially detect each pathogen?
How often does your laboratory use PCR test to initially detect each pathogen?
How often does your laboratory use Antigen test (ELISA, lateral flow) to initially detect each pathogen?
How often does your laboratory use an other CIDT test to initially detect each pathogen?
If other CIDT method used, please specify?

ReflexCX

character If each pathogen is detected using CIDT, is culture of the organism attempted on site?

PCRbrand

character What is the brand name of the PCR test for each pathogen?

PCRothspec

character If other PCR test brand used, please specify?

AGbrand

character What is the brand name of the AG test for each pathogen?

Agothspec
IsolateSubmit
StoolSubmit
BrothSubmit
BloodSubmit

character
character
character
character
character

If other AG test brand used, please specify?
How often are isolates submitted to the public health laboratory?
How often are stools submitted to the public health laboratory?
How often are broth submitted to the public health laboratory?
How often are blood samples submitted to the public health laboratory?

routinely, sometimes, rarely, never
routinely, sometimes, rarely, never
routinely, sometimes, rarely, never
routinely, sometimes, rarely, never
free text
Yes, always for EIP purposes
Yes, always for antimicrobial susceptibility testing
Yes, always for public health purposes
Sometimes, when requested by a provider
Sometimes, for special projects or outbreaks
Sometimes, for special populations
No, always send to a reference laboratory
No, sometime send to a reference laboratory
No and don’t send to a reference laboratory
Becton Dickinson (BD): BD MAXTM Enteric Bacterial Panel
BioFire: FilmArray Gastrointestinal (GI) Panel
Great Basin Stool Bacterial Pathogens Panel
Hologic: Prodesse ProGastro SSCS assay
Laboratory-developed test (LDT)
Luminex: xTAG® Gastrointestinal Pathogen Panel (GPP)
Verigene® Enteric Pathogens Test (EP, formerly Nanosphere)
FilmArray (BioFire) Blood Culture Identification Panel
FilmArray (BioFire) Meningitis/Encephalitis (ME) Panel
Verigene (Nanosphere) Gram-positive Blood Culture Test
Other commercially available PCR test (specify below)
free text
ImmunoCard STAT! CAMPY assay (Meridian)
PREMIERTM CAMPY assay (Meridian)
ProSpecT Campylobacter assay (Remel)
Xpect Campylobacter assay (Remel)
Alere Shiga Toxin Quik Chek
Duopath Verotoxins (Merck)
ImmunoCard STAT! EHEC (Meridian)
PREMIERTM EHEC (Meridian)
ProSpecT Shiga Toxin E. coli (Remel)
VTEC Screen (Denka Seiken)
Other antigen test (specify below)
free text
routinely, sometimes, rarely, never
routinely, sometimes, rarely, never
routinely, sometimes, rarely, never
routinely, sometimes, rarely, never

Comments

repeats for all pathogens*
repeats for all pathogens*
repeats for all pathogens* except Listeria
repeats for all pathogens* except Listeria
repeats for all pathogens* except Listeria;
culture includes selective media for Vibrio
and Yersinia

repeats for all pathogens*, except Listeria,
Norovirus, and Cylcospora

repeats for all pathogens*

repeats for all pathogens*

repeats for Campylobacter and STEC

repeats for all pathogens*
repeats for all pathogens* except Listeria
repeats for all pathogens* except Listeria
Listeria only

FoodNet Clinical Laboratory Practices and Testing Volume Surveillance (last updated 8/6/2021)

Variable Name
Format
CSFSubmit
character
E.coliCXspecsent character
E.coliCXlab
character
STECCIDTspecsent character
STECCIDTlab
character
ListProtocolBLD

character

ListProtocolCSF

character

Norotest

character

Norotestspec
NoroGene
NoroOthMeth
Comments

character
character
character
character

Survey_method character

FoodNet Clincal Laboratory Survey Data Elements
Description
Legal Values
Comments
How often are CSF samples submitted to the public health laboratory?
routinely, sometimes, rarely, never
Listeria only
If only culture for E. coli, are specimens sent to a different laboratory for Shiga toxin testing?
Yes, No
STEC only
To which laboratory?
free text
STEC only
If ONLY non-culture based test(s), are specimens sent to a different laboratory for culture testing?
Yes, No
STEC only
free text
To which laboratory?
STEC only
PCR concurrently used with culture
PCR performed first, if positive reflex culture performed
Listeria only
Which of the following protocols are followed to detect Listeria from blood culture?
Only PCR panels, no sub-culture is performed
Only culture, no PCR test is performed
PCR concurrently used with culture
PCR performed first, if positive reflex culture performed (routin
PCR performed first, if positive reflex culture performed (provid
Which of the following protocols are followed to detect Listeria in CSF?
Listeria only
PCR or culture or some combination thereof based on
provider order
Only PCR panels, no culture is performed
Only culture, no PCR test is performed
Stool submitted to your laboratory for any enteric pathogen
Only when norovirus testing is specifically requested by a
When is norovirus test performed?
Norovirus only
clinician
Other reason (specify below)
Please specify other reason?
free text
Norovirus only
Please specify gene targets for PCR assay devloped in house or by published PCR method
free text
Norovirus only
If other antigen test, PCR, or method used, please specify
free text
Norovirus only
free text
Laboratory verified via phone/in-person visit
Laboratory verified via email/electronic survey
For this survey cycle, how were the data for this laboratory collected?
Laboratory did not respond, data from previous survey were
verified via ELR
Laboratory did not respond, data not verified

*Pathogens include Campylobacter, STEC (E.coli O157 and/or Shiga toxin), Salmonella, Shigella, Vibrio, Yersinia, Listeria, Cyclospora, and Norovirus