Outbreak Toolkit

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Outbreak investigation

WHO Foodborne disease outbreaks: Guidelines for investigation and control

This WHO document provides guidance for anyone who may be involved in the investigation and control of foodborne disease outbreaks.

ECDC Toolkit for investigation and response to Food and Waterborne Disease Outbreaks with an EU dimension

This Toolkit provides investigators with a series of tools that can be useful during investigations of food and waterborne disease outbreaks.

PHAC Food Safety Videos

This series of four videos provides an overview of how PHAC responds to large outbreaks of foodborne illness. The first video provides an overview, the second and third explain how investigation into the source of the illnesses unfolds, and the fourth provides advice on how to reduce the risk of foodborne illness.

CIFOR Guidelines for Foodborne Disease Outbreak Response (Second Edition)

The CIFOR Guidelines for Foodborne Disease Outbreak Response describe the overall approach to foodborne disease outbreaks, including preparation, detection, investigation, control, and follow-up.

Oregon Health Authority Outbreak Investigation Tools

This webpage provides a series of templates and tools for use in acute gastroenteritis outbreaks. Most of the templates can be modified by users in order to meet the needs of specific outbreaks.

ECDC Field Epidemiology Manual (FEM Wiki)

FEM Wiki is an open information sharing platform for public health experts, hosted and funded by ECDC. FEM Wiki works by sharing knowledge and experience in field epidemiology. If you work in public health and have experience in field epidemiology, then you can make relevant contributions to the texts and discussions.

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Public health partners

Toolkit acronym list

This resource contains a list of acronyms referenced within the Toolkit and/or of interest to public health professionals working in enteric outbreak response.

Canada’s Foodborne Illness Outbreak Response Protocol (FIORP)

This is the primary guidance document for multi-jurisdictional investigations of foodborne illness outbreaks in Canada; it is followed when cases are reported in more than one province or territory, or in Canada as well as another country, and when multiple agencies are involved.

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Communication & coordination

Toolkit acronym list

This resource contains a list of acronyms referenced within the Toolkit and/or of interest to public health professionals working in enteric outbreak response.

Canada’s Foodborne Illness Outbreak Response Protocol (FIORP)

This is the primary guidance document for multi-jurisdictional investigations of foodborne illness outbreaks in Canada; it is followed when cases are reported in more than one province or territory, or in Canada as well as another country, and when multiple agencies are involved.

Toolkit assessment call template

This Microsoft Word document provides an example of a typical agenda of an Assessment Call, as well as a template for taking meeting minutes.

Toolkit teleconference call template

This Microsoft Word document provides an example of a typical agenda of an Teleconference Call, as well as a template for taking meeting minutes.

Toolkit Public Health Alert (PHA) template

This Microsoft Word document provides a suggested template for the content and layout of a Public health alert (PHA).

Toolkit chronology template

This Microsoft Word document provides instructions and suggested formatting for creating chronologies for outbreak investigations.

Toolkit chronology (visual timeline of events) template

This Microsoft Powerpoint document provides formatting instructions for creating a visual timeline of events in an outbreak investigation, which documents cases over time, as well as key events and public health actions.

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Outbreak identification

Toolkit sources of public health intelligence

This tool provides a list of online resources that may be used for outbreak identification and notification purposes, as well as journals that publish enteric outbreak investigation findings.

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Laboratory methods and surveillance

National Enteric Surveillance Program (NESP)

This PDF document prepared by PHAC is a summary of data submitted to NESP by provincial/territorial public health laboratories in 2022. The report includes reference tables with a complete list of species and serotype data reported to NESP.

FoodNet Canada Reports and Publications

FoodNet Canada reports and publications provide information on the areas of greatest risk to human health to help direct food safety actions and programming as well as public health interventions, and to evaluate their effectiveness.

CIPARS Reports and Publications

The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) monitors trends in antimicrobial use and antimicrobial resistance in selected bacterial organisms from human, animal, and food sources across Canada.

PHAC Notifiable Diseases Online Database

The CNDSS on-line database provides data on national notifiable diseases including the number and rates of reported cases, data limitations, and disease descriptions.

National Collaborating Centre for Infectious Disease’s Notifiable Diseases Database

This searchable database contains the case definitions for all notifiable diseases in each of the provinces and territories.

Interpretation criteria for WGS

This reference document provides details on the strength of the evidence for interpreting WGS results. These criteria are used to assess matches among human cases, and to assess matches between food or animal isolates and human cases.

CFIA: Canada’s 10 Least Wanted Foodborne Pathogens

This infographic prepared by the CFIA includes information on symptoms, onset time, transmission, potential sources, and preventative measures for ten foodborne pathogens.

FDA Bad Bug Book: Handbook of Foodborne Pathogenic Microorganisms and Natural Toxins

The second edition of the Bad Bug Book, published by the Center for Food Safety and Applied Nutrition, of the Food and Drug Administration (FDA), U.S. Department of Health and Human Services, provides current information about the major known agents that cause foodborne illness. The information provided in this handbook is not intended to be a comprehensive scientific or clinical reference, rather, it is abbreviated and general in nature, and is intended for practical use.

WHO Collaborating Centre for Reference and Research on Salmonella: Antigenic Formulae of the Salmonella Serovars (2007, 9th Edition)

This reference document prepared for the WHO Collaborating Centre for Reference and Research on Salmonella outlines the taxonomy and nomenclature of Salmonella and includes an alphabetic list of names given to serovars with their antigenic formulae.

FDA Foodborne Illness-Causing Organisms Cheat Sheet

This PDF document provides a quick summary chart on foodborne illnesses, organisms involved, symptom onset times, signs and symptoms to expect, and food sources.

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Case finding and defining

Toolkit case definitions example table

This table in Microsoft Word summarizes case definitions used in a variety of enteric outbreaks.

Toolkit Public Health Alert (PHA) template

This Microsoft Word document provides a suggested template for the content and layout of a Public health alert (PHA).

ECDC case definitions example table

This PDF document includes a table summarizing examples of case definitions from published food- and waterborne outbreaks.

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Questionnaire design

Toolkit enteric questionnaire repository

This repository contains questionnaires for various pathogens, to be used at various stages of an outbreak investigation, including hypothesis generation, refinement, and testing.

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Case interviewing

Toolkit enteric questionnaire repository

This repository contains questionnaires for various pathogens, to be used at various stages of an outbreak investigation, including hypothesis generation, refinement, and testing.

Interview Script Examples

This Microsoft Word document provides interview script examples for initiating and concluding case interviews.

CDC Effective TB Interviewing for Contact Investigation

This TB interviewing module is a self-study tool for contact investigation. This resource offers guidance on communicating clearly with patients under different circumstances and is intended for both new and experienced TB interviewers.

Oregon Public Health Division Interviewing Cardinal Rules

This video explains the 10 cardinal rules of effective interviewing. The longer version contains more background and is very helpful for understanding outbreak investigation interviewing. The shorter 9-minute version is useful as a quick introduction to interviewers, for times when it is important to get on the phones as quickly as possible.

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Data management

Toolkit line list and data dictionary

This Microsoft Excel-based tool is designed to be used as a template for foodborne outbreak investigation line lists. Once data has been entered, common descriptive statistics are automatically calculated. A data dictionary describing each data field in the line list is available in the final tab.

Toolkit outbreak response database

This Microsoft Access Database will follow the layout and structure of the PHAC enteric hypothesis generating questionnaires. Users will be able to enter data, export select fields to a Microsoft Excel line list, generate automatic food and risk exposure summary tables, and run custom queries.
*Due to the Government of Canada’s Standard on Web Accessibility, this tool cannot be posted, but it is available upon request. Please contact us at info@outbreaktools.ca to request a copy. Please let us know if you need support or an accessible format.

EpiData Software

Epidata software is a free and open source software created for epidemiologists with two components, EpiData Entry and EpiData Analysis. EpiData Entry is primarily used for simple data entry and data documentation. EpiData Analysis performs basic statistical analysis, graphs and comprehensive data management.

Epi Info

  • Note: as of 2025, support for Epi Info is being phased out.
  • Epi Info™ is a public domain suite of software tools designed for public health practitioners and researchers. It provides for data entry form and database construction and data analyses with epidemiologic statistics, maps, and graphs for public health professionals who may lack an information technology background.

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Descriptive epidemiology

Toolkit line list and data dictionary

This Microsoft Excel-based tool is designed to be used as a template for foodborne outbreak investigation line lists. Once data has been entered, common descriptive statistics are automatically calculated. A data dictionary describing each data field in the line list is available in the final tab.

Toolkit epi curve exercise

This exercise shows how to make an epidemic curve in Microsoft Excel, where each case is represented by a single box using this data set.

Toolkit pivot tables exercise

This exercise uses an outbreak line list to create PivotTables in Microsoft Excel and use them to extract information for descriptive epidemiological summaries and create epidemic curves.

Toolkit epidemiological summary template

This Microsoft Word document provides a suggested template for the content and layout of an epidemiological summary.

Toolkit outbreak investigation report template

This Microsoft Word document provides a suggested template for the content and layout of an outbreak investigation report or final epidemiological summary.

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Hypothesis generation

Toolkit binomial probability calculation tool for food exposures

This Microsoft Excel document allows users to enter outbreak case food exposure numbers for 300 food items and automatically calculates binomial probabilities using two reference populations and flags exposures of interest for follow-up

Toolkit Outbreak Summaries overview

This PDF document provides an overview of the Outbreak Summaries application, its key features and benefits, and an example of how it can be used during an outbreak investigation.

CDC BEAM Dashboard

The BEAM (Bacteria, Enterics, Ameba, and Mycotics) Dashboard allows users to search and download data on foodborne and waterborne disease outbreaks reported to CDC starting from 1998. The database is updated periodically as new data are available. Search fields include year, state, location of consumption, and etiology (genus only). The downloaded database includes additional fields–total illnesses, hospitalizations, and deaths; and food vehicle and contaminated ingredient.

Outbreak Source Prediction Tool

The Outbreak Source Prediction Tool, developed by the Colorado Integrated Food Safety Center of Excellence, is a resource for public health professionals to help with hypothesis generation during an enteric disease outbreak investigation. The tool was developed using statistical prediction methods and historical Salmonella and shiga toxin-producing E.coli (STEC) outbreak data from the CDC’s National Outbreak Reporting System.

Food Consumption Patterns in the Waterloo Region

This food frequency study by Nesbitt et. al. was conducted in Waterloo, Ontario in 2005-2006. The study collected 7-day food consumption data from 2,332 Canadians.

CDC FoodNet Fast (Population survey 2018-2019)

This study by CDC was conducted in 10 U.S. states in 2018-2019. The study asked 38,743 respondents about their exposure to a comprehensive list of foods as well as animal exposure.

FoodNet Canada Reports and Publications

FoodNet Canada reports and publications provide information on the areas of greatest risk to human health to help direct food safety actions and programming as well as public health interventions, and to evaluate their effectiveness.

CDC FoodNet Reports

The Foodborne Diseases Active Surveillance Network (FoodNet) Annual Reports are summaries of information collected through active surveillance of nine pathogens.

Marler Clark Foodborne Illness Outbreak Database

This database provides summaries of food and water related outbreaks caused by various enteric pathogens dating back to 1984.

FDA Foodborne Illness-Causing Organisms Cheat Sheet

A quick summary chart on foodborne illnesses, organisms involved, symptom onset times, signs and symptoms to expect, and food sources.

CFIA: Canada’s 10 Least Wanted Foodborne Pathogens

This infographic prepared by the CFIA includes information on symptoms, onset time, transmission, potential sources, and preventative measures for ten foodborne pathogens.

Zanran

This search tool searches for numerical data on the web presented as graphs, tables and charts. It is a useful tool for searching for outbreak and other scientific data.

Foodbook: Canadian Food Exposure Study to Strengthen Outbreak Response

Foodbook is a population-based telephone survey that was conducted in all Canadian provinces and territories. It provides essential data on food, animal and water exposure which is used by the Agency, as well as other federal, provincial, and territorial (F/P/T) partners to understand, respond to, control and prevent enteric illness in Canada.

Toolkit outbreak response database

Note: this tool is no longer being updated as of 2024.

This Microsoft Access Database will follow the layout and structure of the PHAC enteric hypothesis generating questionnaires. Users will be able to enter data, export select fields to a Microsoft Excel line list, generate automatic food and risk exposure summary tables and run custom queries.

*Due to the Government of Canada’s Standard on Web Accessibility, this tool cannot be posted, but it is available upon request. Please contact us at info@outbreaktools.ca to request a copy. Please let us know if you need support or an accessible format.

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Analytic studies

Toolkit enteric questionnaire repository

Questionnaires for various pathogens, to be used at various stages of an outbreak investigation, including hypothesis generation, refinement, and testing.

OpenEpi

OpenEpi is a free and open source software for epidemiologic statistics. It provides statistics for counts and measurements such as stratified analysis with exact confidence limits, matched pair and person-time analysis, sample size and power calculations, random numbers, sensitivity, specificity and other evaluation statistics, R x C tables, chi-square for dose-response, and links to other useful sites.

EpiSheet

EpiSheet is a free and open source software written and developed by Dr. Kenneth Rothman. It is a downloadable Microsoft Excel spreadsheet used for analyzing epidemiologic data and is meant to support epidemiologists, analysts, and statisticians in their analytical work.

EpiData Software

Epidata software is a free and open source software created for epidemiologists with two components, EpiData Entry and EpiData Analysis. EpiData Entry is primarily used for simple data entry and data documentation. EpiData Analysis performs basic statistical analysis, graphs and comprehensive data management.

Epi Info

  • Note: as of 2025, support for Epi Info is being phased out.
  • Epi Info™ is a public domain suite of software tools designed for public health practitioners and researchers. It provides for data entry form and database construction and data analyses with epidemiologic statistics, maps, and graphs for public health professionals who may lack an information technology background.

R

R is a language and environment for statistical computing and graphics. It is free and open source.

RStudio

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. RStudio is available in open source and commercial editions.

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Weight of evidence

Weight of Evidence: Factors to Consider for Appropriate and Timely Action in a Foodborne Illness Outbreak Investigation

The document describes factors to consider and provides guidance on how much weight to assign when evaluating evidence obtained from the microbiological, epidemiological and food safety investigations.

Epidemiological assessment guide

This guide introduces and describes the recommended data and questions to consider when assessing the weight of the epidemiological evidence for a specific food as the source of an outbreak.

Epidemiological assessment template

This epi assessment template was developed to assist investigators with the assessment of the epidemiological evidence.

CFIA food recalls overview

This webpage created by the CFIA gives an overview of the five step process to investigate and recall product in Canada including the triggers for investigation, the food safety investigation, the health risk assessment, the recall process and follow-up activities.

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Prevention & control

CFIA: How Canada’s Food Safety System Works

This webpage provides links to various CFIA activities and resources related to food safety such as the Hazard Analysis Critical Control Point (HACCP), meat and poultry inspection, food complaints, food safety investigations, and food recalls.

CFIA restaurant and food service inspection in Canada

This resource provides information on the restaurant and food service inspections carried out in local/regional jurisdictions by province/territory.

CFIA food recalls overview

This CFIA webpage provides an overview of the five step process to investigate and recall product in Canada including the triggers for investigation, the food safety investigation, the health risk assessment, the recall process and follow-up activities.

Food Tracebility for Dummies Book

Food Traceability For Dummies, Carlisle Technology Edition, is a free PDF book for food producers and processors to show what food traceability is, how it works, and how companies can add traceability to internal plant processes.

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Post-outbreak

Toolkit proposal for coordination committee deactivation and declaring the outbreak over template

This Microsoft Word document provides a suggested template for the content and layout for communicating proposals to deactivate the coordination committee and declare the outbreak over.

Toolkit epidemiological summary template

This Microsoft Word document provides a suggested template for the content and layout of an epidemiological summary.

Toolkit outbreak investigation report template

This Microsoft Word document provides a suggested template for the content and layout of an outbreak investigation report or final epidemiological summary.

Toolkit Outbreak Summaries overview

This PDF document provides an overview of the Outbreak Summaries application, its key features and benefits, and an example of how it can be used during an outbreak investigation.

Toolkit chronology template

This Microsoft Word document provides instructions and suggested formatting for creating chronologies for outbreak investigations.

Toolkit chronology (visual timeline of events) template

This Microsoft Powerpoint document provides formatting instructions for creating a visual timeline of events in an outbreak investigation, which documents cases over time, as well as key events, and public health actions.

Toolkit coordination committee debrief template

This Microsoft Word document can be used as a template for a typical coordination committee debrief teleconference.

Toolkit public health conferences list

This resource contains a list of Canadian and International conferences of interest to public health professionals working in enteric outbreak response.

Hospital for Sick Children Knowledge Translation Planning Template

This template developed by Dr. Melanie Barwick at the Hospital for Sick Children provides a series of steps and checklists to consider when creating a KT plan such as identifying partners and users, strategies, evaluation, and implementation. Barwick, M. (2008, 2013). Knowledge Translation Planning Template. Ontario: The Hospital for Sick Children.

NCCMT Registry of Methods and Tools

The National Collaborating Centre for Methods and Tools (NCCMT) is one of six National Collaborating Centres for Public Health in Canada. This Registry’s inventory of methods and tools supports the planning, doing and evaluating of public health policies and practices across all four types of knowledge translation activities.

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