1. CIFOR Guidelines for Foodborne Disease Outbreak Response and the CIFOR Toolkit: Focus Area 9: Laboratory Investigation
New York Integrated Center of Food Safety Center of Excellence – March 22, 2017
Nellie Dumas & Lisa Mingle
Wadsworth Center
New York State Department of Health
Welcome Everyone to the New York Integrated Center of Food Safety Center of Excellence CIFOR Webinar. The topic today is Focus Area 9: The Laboratory Investigation section of the CIFOR Guidelines for Foodborne Disease Outbreak Response and the CIFOR Toolkit. I would like to introduce Dr. Lisa Mingle, the Supervisor of the Enteric section of the Bacteriology Laboratory and myself, Nellie Dumas, the Associate Director of the Bacteriology Laboratory of the Wadsworth Center. Lisa and I will be co-presenting Focus Area 9: the Laboratory Investigation CIFOR section for you today.

2. Background
This is the tenth webinar in a series of monthly webinars from the New York Integrated Food Safety Center of Excellence (CoE)
Session covers CIFOR Toolkit Focus Area 9: Laboratory Investigation
Supplementary sessions will be devoted to assist states that wish to complete internal evaluations using the metrics and target ranges developed for the 16 CIFOR performance measures.
Additional topics will focus on emerging issues in food safety including culture‐independent diagnostic testing, antimicrobial resistance, and advanced molecular detection/whole genome sequencing.
All webinars will be recorded and available through the CoE website at
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3. How to Use the CIFOR Toolkit
For each Focus area, consider the “Keys to Success” listed
Describe your agency’s/jurisdiction’s current activities and procedures in relation to the Focus Area
Work as a team: epidemiology, laboratory and environmental health
Refer to written protocols/procedures and other performance measures (e.g., CIFOR target ranges for selected performance measures)
Considering the keys to success and the extreme importance to work as a team with epidemiology, environmental health and the laboratory, describe your agency’s/jurisdiction’s current activities and procedures in this Focus Area of Laboratory Investigation. Refer to written protocols, if available, and materials related to ongoing efforts in capacity development or quality improvement (e.g., CIFOR target ranges for selected performance measures). As you list current activities and procedures related to this Focus Area, indicate those which could be changed to improve your agency’s/jurisdiction’s response to foodborne disease outbreaks.

4. The Toolkit includes a worksheet so you can list your current activities or procedures and prioritize some areas for improvement.

5. How to Use the CIFOR Toolkit
Indicate those activities or procedures which could be changed to improve your agency’s/jurisdiction’s response to foodborne disease outbreaks
Review the CIFOR recommendations related to the Focus Area of interest
Rate the priority for implementing each CIFOR recommendation based on its likely impact on outbreak response at your agency/jurisdiction and available resources
PRIORITIZE CIFOR RECOMMENDATIONS TO ADDRESS NEEDED IMPROVEMENTS. Having identified activities and procedures in need of improvement, review the CIFOR recommendations related to this Focus Area (listed below).
Rate the priority for implementing each recommendation based on its likely impact on foodborne outbreak response at your agency/jurisdiction and available resources. Use a scale of 1 to 5 to rate each recommendation (1=Low priority for implementation and 5=High priority for implementation). If a recommendation is already in place in your agency/jurisdiction, check the appropriate box. If a recommendation is not relevant to your agency/jurisdiction, select N/A.
Refer to the blue underlined section number following each recommendation to view the recommendation as it appears in the CIFOR Guidelines.

6. What is Focus Area 9? Title: Laboratory Investigation
Goals for the Laboratory Investigation: Agency/jurisdiction staff provide guidance on collection, storage, and shipment of patient specimens and food/environmental samples. Agency/jurisdiction staff test patient specimens and suspect vehicles to identify the etiologic agent, mode of transmission, and vehicle in an outbreak and explore the ability of the agent to survive and grow in the implicated vehicle and how the vehicle might have become contaminated.

7. Keys to Success Staff skills and expertise
Activities, relationships, and resources that are critical to achieving success in a Focus Area
Applying metrics and measures can help you identify the success of your program or investigation process
Focus Area 9: Keys to Success
Staff skills and expertise
Specimen collection and testing
Communication
Making changes
Determining whether an agency/jurisdiction has a particular key to success in place is somewhat subjective.
Metrics, such as measures of time (e.g., rapidly, timely, and quickly), have not been defined. Your workgroup should provide its own definitions for these terms, as is appropriate for your agency/jurisdiction, and use its best judgment in deciding whether a particular key to success is fully or partially in place.

8. This 20 year classic slide is still appropriate today
This 20 year classic slide is still appropriate today. It describes the Burden of illness pyramid reflecting the proportion of foodborne illnesses that make it through each step of the diagnosis and reporting process.

9. Keys to Success: Staff Skills and Expertise
Staff have expertise in appropriate laboratory testing methodologies and access to necessary equipment, reagents, and supplies to perform testing.

10. Staff Skills and Expertise
Here we get to prioritizing the CIFOR recommendations to suggest/address improvements needed to ensure the staff have (and maintain) the skills and expertise to be competent and successful laboratory investigators.
Use a scale of 1 to 5 to rate each recommendation (1=Low priority for implementation and 5=High priority for implementation). If a recommendation is already in place in your agency/jurisdiction, check the appropriate box. If a recommendation is not relevant to your agency/jurisdiction, select N/A.
Laboratory investigator Analyzes clinical specimens, food and environmental samples (depending on the state, the food and environmental samples may be tested in di erent laboratories than the clinical specimens); interprets test results and suggests follow-up testing; coordinates testing among laboratories; advises other team members about laboratory testing, including collection, handling, storage, and transport of specimens; communicates laboratory testing methods and results and the maintenance of chain of custody to USDA- FSIS and FDA investigators or other food- regulatory agency gathering evidence of food-product adulteration. USDA-FSIS and FDA recommend food-testing laboratories work to obtain accreditation under ISO standard
Isolate/specimen submission and characterization Confer with the laboratory to determine subtyping methods available for the pathogen under study.
Training for the team
Ongoing training is critical for all members of the outbreak investigation and control team to ensure they are proficient at performing the duties assigned to them. The training should include continuing education to maintain and improve skills within their specialty and specific training in the agency’s outbreak response protocols and the member’s team role.
Agency-specific response protocol and other resources At a minimum, the outbreak investigation and control team should have been trained in specific pre-identified protocols. The team also needs access to additional resources that can help answer questions and provide information for decision-making during an outbreak. These protocols and resources should be assembled before an outbreak. Assemble a reference library (including online resources) with information about foodborne diseases, enteric illnesses, and control measures. Regularly review and update the contents of this reference library.

11. Staff Skills and Expertise
Assemble a list of resource persons who have expertise in specific disease agents and investigation methods and contact information for these persons.
Exercise teams together to ensure each team member understands and can perform his or her role according to agency-specific protocols and legal authorities and understands the roles and responsibilities of other team members. These exercises also can identify likely problem areas and gaps in resources.
Outbreaks themselves provide training opportunities. If an agency does not frequently have outbreaks, team members might be able to assist in responses to outbreaks in other jurisdictions. This can help promote learning and provide valuable insights an agency can use to refine its own protocols.

12. Keys to Success: Specimen Collection and Testing
In collaboration with laboratory staff, epidemiology and environmental health staff collect appropriate clinical specimens and food and environmental samples and store and transport them properly.
Staff link patient and clinical specimen information
Staff isolate etiologic agent (if necessary) and characterize isolates (e.g., subtyping) in a timely fashion.
Staff use standardized (currently approved) methods to analyze specimens/samples and subtype isolates.

13. Specimen Collection and Testing
Laboratory investigator
• Responsibilities
advises other team members about laboratory testing, including collection, handling, storage, and transport of specimens;
Supplies Establish, maintain, and review or verify inventory regularly (at least twice a year and preferably quarterly), particularly during and after an incident. Replace missing and expired materials and resterilize existing equipment.
Table 5.1 Investigation activities for outbreaks associated with events or establishments reported through foodborne illness complaint systems
Table 5.2 Investigation activities for outbreaks identified by pathogen specific surveillance

14. Specimen Collection and Testing
Table 5.1 Investigation activities for outbreaks associated with events or establishments reported through foodborne illness complaint systems
Table 5.2 Investigation activities for outbreaks identified by pathogen specific surveillance
Clinical specimens and food samples related to group illness Obtain clinical specimens from members of the ill group. If the presumed exposure involves food, collect and store—but do not test—food from the implicated event. Store the food appropriately, but generally test the food only after epidemiologic implication or identification of specific food-safety problems through an environmental health assessment. Food samples that are frozen when collected should remain frozen until examined. Samples should be analyzed within 48 hours after receipt. If sample analysis is not possible within 48 hours, then perishable foods should be frozen (–40oC to –80oC). Storage under refrigeration can be longer than 48 hours, if necessary, but the length of the storage period is food dependent.
Detection of microbes or toxins in food is most important for outbreaks involving preformed toxins such as enterotoxins of Staphylococcus aureus or Bacillus cereus, where detection of toxin or toxin-producing organisms in human specimens frequently is problematic. In addition, organisms such as S. aureus and Clostridium perfringens, which are commonly found in the human intestinal tract, can confound interpretation of culture results.

15. Specimen Collection and Testing
Table 5.2 Investigation activities for outbreaks identified by pathogen specific surveillance
Clinical specimens and food samples related to group illness: o cial reference testing methods must be used at a minimum for regulated products (e.g., pasteurized eggs or commercially distributed beef).
Timeline for Case Reporting and Cluster Recognition for pathogen specific surveillance The total time from onset of illness to con rmation of the case as part of an outbreak is typically 2–3 weeks.
Isolate/specimen submission and characterization Undertake subtyping as the isolates are submitted—do not wait for a specific number of specimens to accumulate before testing them. Tests such as PFGE and serotyping ideally are performed concurrently to reduce turnaround time.
Laboratory Process
Communication
Establish and use routine procedures for communicating among epidemiology, laboratory, and environmental health branches within an agency and between local and state agencies. Rapidly post subtyping results to PulseNet, and note the detection of clusters to PulseNet and foodborne outbreak electronic mailing lists to improve communication and cooperation within and among local, state, and federal public health agencies. Poor coordination within and among agencies limits the e ectiveness of pathogen-speci c surveillance.

17. Specimen Collection and Testing
Table 5.2 Investigation activities for outbreaks identified by pathogen specific surveillance
Clinical specimens and food samples related to group illness: o cial reference testing methods must be used at a minimum for regulated products (e.g., pasteurized eggs or commercially distributed beef).
Timeline for Case Reporting and Cluster Recognition for pathogen specific surveillance The total time from onset of illness to con rmation of the case as part of an outbreak is typically 2–3 weeks.
Isolate/specimen submission and characterization Undertake subtyping as the isolates are submitted—do not wait for a specific number of specimens to accumulate before testing them. Tests such as PFGE and serotyping ideally are performed concurrently to reduce turnaround time.
Laboratory Process
Communication
Establish and use routine procedures for communicating among epidemiology, laboratory, and environmental health branches within an agency and between local and state agencies. Rapidly post subtyping results to PulseNet, and note the detection of clusters to PulseNet and foodborne outbreak electronic mailing lists to improve communication and cooperation within and among local, state, and federal public health agencies. Poor coordination within and among agencies limits the e ectiveness of pathogen-speci c surveillance.

18. Specimen Collection and Testing
Table 5.1 Investigation activities for outbreaks associated with events or establishments reported through foodborne illness complaint systems
Table 5.2 Investigation activities for outbreaks identified by pathogen specific surveillance

19. Keys to Success: Communication
Staff communicate in a timely fashion and coordinate activities with epidemiology and environmental health staff.
Staff report results of laboratory tests to epidemiologic and environmental health investigators, regulatory personnel (if applicable), and appropriate national databases in a timely fashion.
This also includes other individuals in your chain of command including your press office/public information officer

20. Communication
Coordinate activities and set up good lines of communication between individuals and agencies involved in the investigation. To avoid mixed messages and incomplete information or misinformation, each investigation should have a consistent point of contact. Guidelines for coordinating multijurisdictional investigations are summarized in Chapter 7. Investigations are rarely linear. Although most procedures for investigating outbreaks follow a logical process—from determining whether an outbreak is occurring to identifying and controlling the source—most actual investigations feature multiple concurrent steps. In addition, the focus of the investigation may need to shift as the situation warrants. Maintaining close communication and coordination among members of the outbreak investigation team is the best way to ensure concurrent activities do not interfere with each other and important investigation steps are not forgotten.
Communication among the agencies and units of the outbreak investigation and control team (e.g., among epidemiology, environmental health, and laboratory)
Ensure everyone who may be involved in outbreak response knows the other team members.
Identify the persons who will be responsible for communication on behalf of their organizational unit (epidemiology, environmental health, laboratory) and for the outbreak investigation and control team. Developing a consistent approach to internal communications during an outbreak helps everyone on the team know what to expect.
Coordinate Investigation Activities
Whether the outbreak is restricted to one jurisdiction or involves multiple jurisdictions, notification and updates should be provided to other interested agencies following the Guidelines for Multijurisdictional Investigations During investigation of outbreaks detected by pathogen-speci c surveillance, the public health laboratory needs to immediately forward case information to epidemiologists for every new potentially outbreak- associated case they receive.
6.5. Communication
With Other Members of the Investigation and Control Teams Communicate actions taken and outbreak status information to all persons involved in an outbreak investigation, including those in di erent agencies or di erent departments within the agency.
Laboratory investigator
• Responsibilities
Interprets test results and suggests follow-up testing; reports results; coordinates testing among laboratories; advises other team members about laboratory testing, including collection, handling, storage, and transport of specimens; communicates laboratory testing methods and results

21. Keys to Success: Making Changes
Agency/jurisdiction conducts a debriefing among investigators following each outbreak response and refines outbreak response protocols based on lessons learned.
Agency/jurisdiction has performance indicators related to the laboratory investigation and routinely evaluates its performance in this Focus Area. .

22. Making Changes
This, too, is a critical opportunity for the team to learn from each other. It should involve the whole team.
6.7. A formal after-action meeting should:
• Identify the contributing factors and environmental antecedents of the outbreak and measures (preventive controls) to prevent additional outbreaks at this and other food establishments;
• Identify the long-term and structural control measures, and develop a plan for their implementation;
• Assess the effectiveness of outbreak control measures and difficulties in implementing them;
• Assess whether further scientific studies should be conducted;
• Clarify resource needs, structural changes, or training needs to optimize future outbreak response;
• Identify factors that compromised the investigations, and seek solutions;
• Identify necessary changes to current investigation and control guidelines and development of new guidelines or protocols as required; and
• Discuss any legal issues that might have arisen and the need for new laws to strengthen response (see Chapter 9).
Conduct a debriefing after each outbreak to identify lessons learned and refine the agency’s response protocols.
Encourage a post-outbreak meeting among investigators to assess lessons learned and compare notes on ultimate findings. Debriefing should include a review of coordination and communication during the investigations, where breakdowns may have occurred, and how prior experience and training facilitated or hindered investigation efforts.
Recommended Practices for Recovery and Follow-Up
Establish a process for creating after-action reports following investigations, with lessons learned and action items for follow-up and quality improvement.
At a minimum, document every outbreak investigation by using a standardized form to facilitate inclusion in state and national outbreak databases (e.g., CDC’s form or its equivalent).
6.8. Prepare reports for all outbreaks.
Summary data should be reported nationally to CDC’s National Outbreak Reporting System (NORS) database. The usefulness of the reports depends on the quality and quantity of information submitted. Make every effort to complete both Part 1: Basic Information, and Part 2: Additional Information, and submit the information as soon as possible.

23. Make Plans to Implement Selected CIFOR Recommendations
For selected recommendations identified in the prioritization process, identify
Lead person responsible for implementation of the recommendation
Time frame for implementation
Consider necessary antecedents to implementation or other factors that might impact success or time frame

24. Helpful Tips for Using the Toolkit
Don’t get distracted by the volume
Be clear on the process
Keep moving – don’t get caught up in too much detail
Focus on a few realistic changes
End with specific action plans with time frames and responsible persons
Appoint a facilitator and a recorder for each discussion

25. Where to Find the CIFOR Products
Online at:
Paper copies are also available from CSTE
Contact Thuy Kim at
Examples of CIFOR product use by other states:

26. Upcoming NYS CoE CIFOR Webinars
Next webinar: Focus Area 10: Control of Source and Secondary Spread
April 18, pm
Course announcement and link to register is posted on the DOH Learning Management System (LMS):

27. Resources Comments or questions for NY CoE can be directed to:
Paula Huth or Andie Newman, NYSDOH
Integrated Food Safety CoE Websites:
NY CoE:
CDC: