aphl survey of food safety surveillance and testing practices...food safety testing 12. for calendar...

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APHL Survey of Food Safety

Surveillance and Testing Practices

The purpose of this survey is to gather information from local and state public health and

agriculture laboratories on their current practices of food safety testing. Obtaining this

information offers APHL’s Food Safety Committee the ability to assess practices, processes,

available support and future plans for food safety testing in member laboratories.

We estimate that it should take members approximately 30 minutes to complete the survey. We

thank you for your time and effort in responding to this data request and your enthusiasm in

improving foodborne disease surveillance.

Please note: For the purpose of this survey, we define a primary specimen as a raw stool,

rectal swab, CSF, blood or any other specimen that came directly from a patient.

Demographics

Please classify your laboratory.

Check all that apply.

▢ State Public Health Laboratory (5)

▢ Local Public Health Laboratory (9)

▢ State Agriculture Laboratory (10)

▢ State Chemist Laboratory (11)

PulseNet / FoodNet

1. PulseNet has recommended performing mixed pathogen WGS runs to improve turnaround

times.

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With a mixed run option, what is your anticipated turnaround time in days for WGS analysis for

enterics?

o (1)

o > 7 days (2)

o We are not a PulseNet laboratory (4)

Display This Question:

If 1. PulseNet has recommended performing mixed pathogen WGS runs to improve turnaround times. Wit... = > 7 days

1a. What factors are responsible for this estimate?

Please check all that apply.

▢ Low specimen volume (1)

▢ Staffing (2)

▢ Funding (3)

▢ IT constraints (4)

▢ Limited number of instruments (5)

▢ Other - please specify (6) ________________________________________________


If 1. PulseNet has recommended performing mixed pathogen WGS runs to improve turnaround times. Wit... = > 7 days

1b. How do you plan to address these factors to bring down your TAT?

________________________________________________________________

________________________________________________________________

________________________________________________________________

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2. What percentage of isolates sequenced in your laboratory have to be re-sequenced?

o < 0.5% (1)

o >= 0.5% to < 1.5% (2)

o >= 1.5% to < 2.5% (3)

o >= 2.5% to < 5% (4)

o >= 5% (5)

o We do not sequence enterics (6)

Skip To: Q16 If 2. What percentage of isolates sequenced in your laboratory have to be re-sequenced? = We do not sequence enterics


If 2. What percentage of isolates sequenced in your laboratory have to be re-sequenced? = < 0.5%

Or 2. What percentage of isolates sequenced in your laboratory have to be re-sequenced? = >= 0.5% to < 1.5%

Or 2. What percentage of isolates sequenced in your laboratory have to be re-sequenced? = >= 1.5% to < 2.5%

Or 2. What percentage of isolates sequenced in your laboratory have to be re-sequenced? = >= 2.5% to < 5%

Or 2. What percentage of isolates sequenced in your laboratory have to be re-sequenced? = >= 5%

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2a. In your laboratory’s experience, what are the key reason(s) why your isolates fail and need

to be re-sequenced?


▢ Contamination (1)

▢ Insufficient coverage (2)

▢ Insufficient quality (3)

▢ Insert size too small (4)

▢ Failed instrument run (5)

▢ Isolate mix up (6)


3. How has your laboratory responded to the workforce needs of implementing WGS?


Changes made in 2018 or before (1)

Anticipated action in 2019 (2)

No changes needed (3)

Retrain existing staff for positions in WGS

(1) ▢ ▢ ▢ Cross train existing

staff to assist in WGS (2) ▢ ▢ ▢

Hire new staff for WGS (3) ▢ ▢ ▢

Other - please specify (4) ▢ ▢ ▢

Page Break

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Bioinformatics

4. Outside of BioNumerics, do you have the ability to perform analysis of your WGS data

internally?

o Yes (1)

o No (2)


If 4. Outside of BioNumerics, do you have the ability to perform analysis of your WGS data internally? = Yes

4a. What resources do you have with regards to staff, equipment, and software to perform WGS

data analysis internally?


▢ Staff skills (1)

▢ Operating systems (2)

▢ Available software (3)



If 4. Outside of BioNumerics, do you have the ability to perform analysis of your WGS data internally? = No

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4b. Where are you receiving bioinformatics support to analyze your WGS data?


▢ We exclusively use BioNumerics (1)

▢ We receive peer support from other states (2)

▢ We receive support from a federal agency (3)

▢ We receive support from academic partners (4)


5. What WGS-based applications have you or do you plan to validate for reporting? (e.g.,

identification, subtyping, virulence gene characterization)?

Currently validated

(1)

Planning for validation in the future

(2)

We do not plan to validate (3)

ANI (1) o o o Seq Sero (2) o o o

Serotype finder (3) o o o ResFinder (4) o o o

Other - please specify (5) o o o

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CIFOR

6. Has your laboratory used any CIFOR tools or resources specifically for the purpose of

improving processes or procedures in place in your laboratory?

o Yes (1)

o No (2)


If 6. Has your laboratory used any CIFOR tools or resources specifically for the purpose of improvin... = Yes

6a. Which CIFOR tools or resources have you used in your laboratory?

Please check all that apply

▢ CIFOR Guidelines (1)

▢ CIFOR Toolkit (either on your own, with a group, or as part of a Toolkit Implementation

Workshop (2)

▢ Law Project (Analysis of State Legal Authorities, Menu of Legal Options, Practitioners'

Handbook on Legal Authorities) (3)

▢ Outbreaks of Undetermined Etiology (OUE) Guidelines (4)

▢ OUE Agent List (5)

▢ A tool accessed via the CIFOR Food Safety Clearinghouse (6)

▢ Performance Measures and/or Target Ranges described in the CIFOR Metrics Project

(7)

https://www.aphl.org/programs/food_safety/Pages/CIFOR-Resources-for-Response-to-Foodborne-Outbreaks.aspx

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If 6. Has your laboratory used any CIFOR tools or resources specifically for the purpose of improvin... = No

6b. Why not?

Please check all that apply

▢ Not familiar with CIFOR (1)

▢ Not sure where to find CIFOR tools and resources (2)

▢ Not applicable to us (3)

▢ No resources to implement needed changes (4)

▢ We're already in line with CIFOR recommendations (5)


7. When specimens are collected as part of a foodborne investigation, how often are the

epidemiology and/or environmental health investigators in your jurisdiction able to properly

collect, store and transport specimens/samples for a foodborne investigation?

Epi and EH staff do not

collect/store/transport (1)

< 50% of the

time (2)

50-90% of the

time (3)

> 90% of the

time (4)

We do not test this

specimen type (5)

N/A (6)

Clinical specimens (1) o o o o o o Food samples

(2) o o o o o o Environmental

samples (3) o o o o o o

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8. How likely would you be to store outbreak specimens that test negative for routine

foodborne pathogens if another laboratory offered testing for additional pathogens?

o Very likely to store (1)

o Somewhat likely to store (2)

o May/may not store (3)

o Somewhat unlikely to store (4)

o Very unlikely to store (5)

o N/A (6)

9. Has your laboratory established routine procedures for communicating with outbreak

response team members before an outbreak occurs?

o Yes (1)

o No (2)

o N/A (4)


If 9. Has your laboratory established routine procedures for communicating with outbreak response te... = Yes

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9a. How often are these routine communication procedures implemented?

o At least weekly (1)

o Monthly (2)

o Quarterly (3)

o Yearly (6)

o Less than yearly (4)

10. Has your laboratory ever participated in joint outbreak response team exercises to

ensure that each team member understands and can perform his/her role?

o Yes (1)

o No (2)

o N/A (4)


If 10. Has your laboratory ever participated in joint outbreak response team exercises to ensure tha... = Yes

10a. What year was your most recent joint exercise?

________________________________________________________________

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11. After a foodborne investigation has concluded, does your laboratory participate in

debriefings with members of your jurisdiction’s outbreak response team to identify lessons

learned and compare notes on ultimate findings?

o Often (1)

o Sometimes (2)

o Rarely (4)

o Never (3)

o N.A (5)


If 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Often

Or 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Sometimes

Or 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Rarely

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11a. What changes has your laboratory/jurisdiction made based on those debrief meetings?

Please select all that apply.

▢ Identified operational factors that compromised the investigation (1)

▢ Identified communications gaps (2)

▢ Clarified changes to procedures (3)

▢ Identified needed resouces (4)

▢ Identified training needs (5)

▢ Offered needed training (6)

▢ Adjusted agency or response team structure to optimize future investigations (7)



If 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Often

Or 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Sometimes

Or 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Rarely

Or 11. After a foodborne investigation has concluded, does your laboratory participate in debriefing... = Never

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11b. What are the barriers, if any, to debriefing your jurisdiction’s outbreak response?

Please select all that apply.

▢ Time (1)

▢ Staffing (2)

▢ Workload (3)

▢ Training on how to debrief (4)

▢ No barriers (5)


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Food Safety Testing

12. For calendar year 2018, please estimate the percentage of specimen types (Isolate, broth

or primary specimen) received from the clinical laboratories for each of the following pathogens:

Isolate %

(1) Broth %

(2) Primary

specimen % (3) Put N/A in the box if you do not

receive the clinical specimen. (4)

Campylobacter (1)

Salmonella (2)

Shigella (3)

STEC O157 (4)

STEC non-O157 (5)

Vibrio (6)

Yersinia (7)

Listeria (blood or CSF) (8)

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13. State Public Health Laboratories recently responded to the following question in the CLSS

survey. Please provide this information again so we can drill down further on testing

methodology.

For which of the following organisms or their toxins, does your laboratory provide or assure

testing for clinical specimens to assist with foodborne disease outbreak investigations?

Provide Testing (1) Assure Testing (2) Neither Provide nor Assure Testing (3)

Bacillus cereus (4) o o o Brucella sp. (5) o o o

Campylobacter sp. (6) o o o

Clostridium botulinum (7) o o o

Clostridium perfringens (8) o o o

Cryptosporidium sp. (9) o o o

Cyclospora cayetanensis (10) o o o

Listeria monocytogenes (11) o o o

Norovirus (12) o o o Salmonella sp. (Non-

Typhi) (13) o o o Salmonella Typhi (20) o o o

Shigella sp. (14) o o o Staphylococcus

aureus (from stool) (15) o o o

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O157 STEC (16) o o o Non O157 STEC (17) o o o

Vibrio cholera (21) o o o Vibrio sp. (18) o o o

Yersinia enterocolitica (19) o o o

Carry Forward Selected Choices from "13. State Public Health Laboratories recently responded to the following question in the CLSS survey. Please provide this information again so we can drill down further on testing methodology. For which of the following organisms or their toxins, does your laboratory provide or assure testing for clinical specimens to assist with foodborne disease outbreak investigations?"

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13a. Which organisms does your laboratory further characterize by traditional methods (such as

molecular subtype or perform AST) and/or further characterize by sequencing for routine clinical

testing?


Further characterize by

traditional methods Now

(1)

Plan to further characterize by

traditional methods in 2020

(2)

Further Characterize by

sequencing (Sanger or

WGS) Now (6)

Further Characterize by

sequencing (Sanger or

WGS) in 2020 (7)

Bacillus cereus (x4) o o o o

Brucella sp. (x5) o o o o Campylobacter

sp. (x6) o o o o Clostridium

botulinum (x7) o o o o Clostridium

perfringens (x8) o o o o Cryptosporidium

sp. (x9) o o o o Cyclospora

cayetanensis (x10) o o o o

Listeria monocytogenes

(x11) o o o o

Norovirus (x12) o o o o Salmonella sp.

(Non-Typhi) (x13) o o o o

Salmonella Typhi (x20) o o o o

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Shigella sp. (x14) o o o o

Staphylococcus aureus (from stool) (x15) o o o o O157 STEC

(x16) o o o o Non O157 STEC

(x17) o o o o Vibrio cholera

(x21) o o o o Vibrio sp. (x18) o o o o

Yersinia enterocolitica

(x19) o o o o

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14. State Public Health Laboratories recently responded to the following question in the CLSS


methodology.

For which of the following organisms or their toxins does your

laboratory provide or assure testing for food and or water samples to assist with foodborne

disease outbreak investigations?


Bacillus cereus (4) o o o Brucella sp. (5) o o o

Campylobacter sp. (6) o o o

Clostridium botulinum (7) o o o

Clostridium perfringens (8) o o o

Cryptosporidium sp. (9) o o o

Cyclospora cayetanensis (10) o o o

Listeria monocytogenes (11) o o o

Norovirus (12) o o o Salmonella sp. (Non-

Typhi) (13) o o o Salmonella Typhi (20) o o o

Shigella sp. (14) o o o Staphylococcus

aureus (15) o o o

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O157 STEC (16) o o o Non O157 STEC (17) o o o

Vibrio cholera (21) o o o Vibrio sp. (Non-

Cholera) (18) o o o Yersinia enterocolitica

(19) o o o

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15.State Public Health Laboratories recently responded to the following question in the CLSS


methodology.

Does your laboratory provide or assure for the following tests in food samples?


Allergens (1) o o o Arsenic (4) o o o

Biotoxins (5) o o o Cyanide (6) o o o

Filth (7) o o o Heavy Metals (8) o o o

Histamines (9) o o o Marine toxins (10) o o o

Crude oil dispersants (11) o o o

Pesticides/Residues (12) o o o

Polyaromatic Hydrocarbons (13) o o o

Sulfites/sulfates/nitrites (14) o o o

Volatile and semi-volatile organic compounds (15) o o o

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Accreditation

16. Is your lab accredited to ISO/IEC 17025?

o Yes (1)

o No (2)


If 16. Is your lab accredited to ISO/IEC 17025? = Yes

16a. For what type of samples?

Check all that apply.

▢ Food - # of methods on your scope (1)

________________________________________________

▢ Feed - # of methods on your scope (2)

________________________________________________

▢ Environmental - # of methods on your scope (3)

________________________________________________


If 16. Is your lab accredited to ISO/IEC 17025? = No

16b. Are you seeking accreditation?

o Yes (1)

o No (2)

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If 16. Is your lab accredited to ISO/IEC 17025? = No

16c. What are the reasons your laboratory has not yet become accredited to the ISO 17025

standard?

Select all that apply

▢ Cost (1)

▢ Personnel (2)

▢ Buy-in from Senior management (4)

▢ Not felt to be necessary for our laboratory at this time (5)




17. What challenges are you facing (if any) with maintaining accreditation?

Select all that apply

▢ Continued cost (1)

▢ Maintaining trained personnel (2)

▢ Don't receive enough samples to maintain competency (3)

▢ Lack of available PT for methods on scope (4)


▢ No challenges at this time with maintaining accreditation (6)

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18. What funding is your laboratory using for ISO accreditation? Select all that apply

▢ FDA ISO Bridge (1)

▢ USDA AMS (2)

▢ FERN (3)

▢ General (state) funds (4)


This is the end of the survey.

aphl survey of food safety surveillance and testing practices...food safety testing 12. for calendar...

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