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​Hypothesis Generation during a Foodborne Illness Outbreak 

Hypothesis generation is a crucial step in identifying potential food vehicles during a foodborne illness outbreak. Here we summarize tools and resources on hypothesis generation from the CoEs and other organizations. 


CO CoE Hypothesis Generation ECHO Training

This Extension for Community Health Outcomes (ECHO) training series is designed to encourage foodborne epidemiologist to take advantage of a variety of data and tools available to them when they generate a hypothesis for an outbreak. ​This series is offered in partnership with the Colorado CoE, Rocky Mountain Public Health Training Center, and ECHO Colorado.

CO CoE Hypothesis Generation Toolkit

The Hypothesis Generation Toolkit is a two-page handout that provides public health professionals with tips, tools, and resources for successfully generating a hypothesis during a foodborne illness outbreak. Guidelines to consider when developing an effective hypothesis are highlighted. Links are provided to a variety of hypothesis generating resources, including questionnaires and food-pathogen pairs.​
  • Click here to view the toolkit​

Food-Pathogen Pairs 

National Outbreak Reporting System Dashboard

The NORS Dashboard is a web-based tool that includes data on outbreak since 1998 of foodborne, waterborne, and enteric diseases. Fields include year, state, etiology, setting, hospitalizations, and food/ingredient. 

CO CoE Salmonella Serotype Tables

These tables summarize food and animal sources associated with past Salmonella outbreaks by serotype. 

CDC's Atlas of Salmonella ​in the Un​ited States, 1968-2011

The Salmonella Atlas summarizes surveillance data on Salmonella isolates from humans, including analyses by age, sex, geoography, and season. It also references non-human isolates from animals and environments.  

​​FDA Bad Bug Book

The Bad Bug Book is an encyclopedia of information on foodborne pathogenic microorganisms and natural toxins, including microbiological characteristics, clinical information, epidemiology, and example outbreaks. 

​International Association for Food Protection Keys

The IAFP Keys identify the principal and potential contributing factors to consider by pathogen at each stage of the farm to fork continuum for food categories. 

Descriptive Data 

CO CoE Outbreak Source Prediction Tool

This tool is a resource to help with hypothesis generation during an enteric disease outbreak investigation. The tool uses demographic and outbreak characteristics to predict potential sources during an ongoing STEC or Salmonella investigation. 

Case Exposure Assessment

Oregon Binomial Probability Worksheet

Binomial probabilities are a tool for identifying and refining hypotheses using initial exposure information to identify if the commonalities you are seeing between cases is truly above what you would expect. 

​FoodNet Population Survey Atlas of Exposures

The FoodNet Population Survey summarizes demographic characteristics, food consumption, and animal exposure information in FoodNet sites as an average exposure in the seven days prior to interview. 

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