FoodNET Lab Practices Volume

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Overview

LabSurvey
LabVolume

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Sheet 1: LabSurvey

FoodNet Clincal Laboratory Survey Data Elements
Variable Name	Format	Description	Legal Values	Comments
RecordID	numeric	unique system generated record ID
Site	character	FoodNet site providing data	CA, CO, CT, GA, MD, MN, NY, OR, TN
Month	numeric	Month for when the survey was completed or verified	1 to 12
Year	numeric	Year for when the survey was complete for verified	2015-present
HospName	character	Laboratory name
LabID	character	unique identifier for laboratory
ChngTestMeth	character	During the past 6 months, has you laboratory changed testing methods used for detecting each pathogen?	Yes, No	repeats for all pathogens*
Tonsite	character	Does your laboratory test stool specimens (blood/CSF for Listeria) on site for each pathogen?	Yes, No	repeats for all pathogens*
Labforward	character	To which laboratory do you send specimens for testing?	free text	repeats for all pathogens* except Listeria
Entericscrn	character	Is each pathogen part of your laboratory's routine (approx >80%) enteric screen?	Yes, No (only upon request)	repeats for all pathogens* except Listeria
IDCx	character	How often does your laboratory use culture to initially detect each pathogen?	routinely, sometimes, rarely, never	repeats for all pathogens* except Listeria; culture includes selective media for Vibrio and Yersinia
IDPCR	character	How often does your laboratory use PCR test to initially detect each pathogen?	routinely, sometimes, rarely, never
IDAG	character	How often does your laboratory use Antigen test (ELISA, lateral flow) to initially detect each pathogen?	routinely, sometimes, rarely, never
IDOther	character	How often does your laboratory use an other CIDT test to initially detect each pathogen?	routinely, sometimes, rarely, never
IDOtherSpec	character	If other CIDT method used, please specify?	free text
ReflexCX	character	If each pathogen is detected using CIDT, is culture of the organism attempted on site?	Yes, always for EIP purposes	repeats for all pathogens*, except Listeria, Norovirus, and Cylcospora
			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
PCRbrand	character	What is the brand name of the PCR test for each pathogen?	Becton Dickinson (BD): BD MAXTM Enteric Bacterial Panel	repeats for all pathogens*
			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)
PCRothspec	character	If other PCR test brand used, please specify?	free text	repeats for all pathogens*
AGbrand	character	What is the brand name of the AG test for each pathogen?	ImmunoCard STAT! CAMPY assay (Meridian)	repeats for Campylobacter and STEC
			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)
Agothspec	character	If other AG test brand used, please specify?	free text
IsolateSubmit	character	How often are isolates submitted to the public health laboratory?	routinely, sometimes, rarely, never	repeats for all pathogens*
StoolSubmit	character	How often are stools submitted to the public health laboratory?	routinely, sometimes, rarely, never	repeats for all pathogens* except Listeria
BrothSubmit	character	How often are broth submitted to the public health laboratory?	routinely, sometimes, rarely, never	repeats for all pathogens* except Listeria
BloodSubmit	character	How often are blood samples submitted to the public health laboratory?	routinely, sometimes, rarely, never	Listeria only
CSFSubmit	character	How often are CSF samples submitted to the public health laboratory?	routinely, sometimes, rarely, never	Listeria only
E.coliCXspecsent	character	If only culture for E. coli, are specimens sent to a different laboratory for Shiga toxin testing?	Yes, No	STEC only
E.coliCXlab	character	To which laboratory?	free text	STEC only
STECCIDTspecsent	character	If ONLY non-culture based test(s), are specimens sent to a different laboratory for culture testing?	Yes, No	STEC only
STECCIDTlab	character	To which laboratory?	free text	STEC only
ListProtocolBLD	character	Which of the following protocols are followed to detect Listeria from blood culture?	PCR concurrently used with culture	Listeria only
			PCR performed first, if positive reflex culture performed
			Only PCR panels, no sub-culture is performed
			Only culture, no PCR test is performed
ListProtocolCSF	character	Which of the following protocols are followed to detect Listeria in CSF?	PCR concurrently used with culture	Listeria only
			PCR performed first, if positive reflex culture performed (routine)
			PCR performed first, if positive reflex culture performed (provider order)
			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
Norotest	character	When is norovirus test performed?	Stool submitted to your laboratory for any enteric pathogen	Norovirus only
			Only when norovirus testing is specifically requested by a clinician
			Other reason (specify below)
Norotestspec	character	Please specify other reason?	free text	Norovirus only
NoroGene	character	Please specify gene targets for PCR assay devloped in house or by published PCR method	free text	Norovirus only
NoroOthMeth	character	If other antigen test, PCR, or method used, please specify	free text	Norovirus only
Comments	character		free text
*Pathogens include Campylobacter, STEC (E.coli O157 and/or Shiga toxin), Salmonella, Shigella, Vibrio, Yersinia, Listeria, Cyclospora, and Norovirus

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Sheet 2: LabVolume

FoodNet Laboratory Testing Volume Data Elements
Variable Name	Format	Description	Legal Values	Comments
Record ID	numeric	unique system generated record ID
VolYear	numeric	Year volume data provided for	2018, 2019
State	character	State providing data	CA, CO, CT, GA, MD, MN, NM, NY, OR, TN
LabID	character	Local unique laboratory identificaiton number, standardize across surveillance and lab survey
Method	numeric	How volume data was obtained for values provided	1. Direct extraction from LIMS or equivalent system of total tests and positive tests for catchment area
			2. Direct extraction from LIMS or equivalent system of total tests and positive tests not limited to catchment area
			3. Direct extraction from LIMS or equivalent system of total tests for catchment area, positives extracted from state surveillance data
			4. Direct extraction from LIMS or equivalent system of total tests not limited to catchment area, positives extracted from surveillance data associated region covered
			5. Estimate of total tests for catchment area provided by microbiologist or other party that can make an estimate based on workload or ordering of supplies; positives extracted from state surveillance data
			6. Estimate of total tests not limited to catchment area provided by microbiologist or other party that can make an estimate based on workload or ordering of supplies; positives extracted from surveillance data associated region covered
Comment	character	Any comment on data method or data provided	varies by state
Pathogen	character	Name of pathogen	Salmonella, Campylobacter, Listeria, Shigella, STEC, STX, O157, Vibrio, Yersinia
TotalGenCx	numeric	No. of general stool culture tests performed	1-999999
CxGenPos	numeric	No. of these tests with a positive result	1-999999	repeating data by pathogen
TotalSynPCR	numeric	No. of multi-analytic (syndromic panel) PCR tests performed	1-999999
SynPos	numeric	No. of multi-analytic (syndrome panel) tests with a positive result	1-999999	repeating data by pathogen
TCx	numeric	No. of stool culture performed for a specific pathogen	1-999999	repeating data by pathogen
TCxPos	numeric	No. of stool culture positive for a specific pathogen	1-999999	repeating data by pathogen
TPCR	numeric	No. of single analyte PCR tests performed	1-999999	repeating data by pathogen
TPCRPos	numeric	No. of single analyte PCR tests positive	1-999999	repeating data by pathogen
TAG	numeric	No. of immuno-assay (EIA) tests performed	1-999999	repeating data by pathogen
TAGPos	numeric	No. of immuno-assay (EIA) tests positive	1-999999	repeating data by pathogen
TBldCx	numeric	No. blood culture tests performed	1-999999	Listeria only
TBldCxPos	numeric	No. blood culture tests positive	1-999999	Listeria only
TCSFCx	numeric	No. cerebrospinal fluid culture tests performed	1-999999	Listeria only
TCSFCxPos	numeric	No. cerebrospinal fluid culture tests positive	1-999999	Listeria only