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Specimen Collection, Shipment and Retention Guidelines for Foodborne Outbreaks of Undetermined Etiology (OUE)

Investigators generally collect and handle foodborne outbreak specimens with a specific agent in mind. But by the time investigators establish/ conclude the etiology is undetermined, the initial specimens may no longer be available or usable. Attaining an additional specimen may prove unproductive or impossible, if the patient has recovered or died.

Current specimen collection guidelines are either agent specific or categorized by agent class (e.g. all bacteria or all viruses). These existing guidelines, while helpful when the agent is known or strongly suspected, do not offer clear guidance on outbreaks of undetermined etiology.


  • Suggest optimal, universal specimens for all outbreaks
  • Provide adequate specimens for second-tier testing and pathogen discovery
  • Use CIFOR-developed universal recommendations on collection, shipment, rule-out testing, and long-term storage of outbreak specimens

About the OUE Guidelines

  • Influenced by documents developed by the Minnesota and Wisconsin Departments of Health
  • Based on specific outbreak profiles
  • Broken down by key symptomology, including:
    • Diarrhea
    • Vomiting
    • Abdominal Cramping
    • Hemolytic Uremic Syndrome (HUS)
    • Neurological Manifestations (e.g. paresthesias, respiratory depression)
    • Hepatic Symptoms
    • Systemic Illnesses (e.g. fever, weakness, arthritis)
    • Other
  • Cover infectious and non-infectious agents
  • Includes an OUE Agent List with detailed information, including:
    • Incubation period
    • Primary signs and symptoms
    • Primary specimen(s)
    • Key epidemiological information

Target Audience

  • Primarily intended for state health departments making recommendations on specimen collection and conducting testing for foodborne outbreaks
  • Also appropriate for local health departments that conduct their own outbreak investigations (including testing) independent of the state health department.

Accessing the CIFOR OUE Guidelines for iOS app, PC, or Mac

Download OUE
In collaboration with the Oregon Integrated Food Safety Center of Excellence, the CIFOR OUE Guidelines can be accessed as a FileMaker Go iOS application or a runtime Windows version for PC.

iPad users
This file is designed for an iPad running the FileMaker Go app. Download the free app.

With FileMaker Go installed, if you're viewing this site on your iPad, this link will open the file directly in FileMaker Go: CIFOR OUE Specimen Collection

Windows PC users
View the CIFOR OUE Guidelines tool on your Windows PC (requires at least Windows 7). Download and unzip the file. You should see a "CIFOR OUE folder" -- inside that folder, double-click the "CIFOR OUE Startup" shortcut.

Questions can be emailed to:

CIFOR thanks the Oregon Integrated Food Safety Center of Excellence that created the FileMaker Go 14 app and Windows runtime version, and the CIFOR APHL OUE Guidelines Working Group for producing content and promotional material.