Action on Weatherill Report Recommendations to Strengthen the Food Safety System: Final Report to Canadians
Enhancing Surveillance and Early Detection

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The Independent Investigator found a need for improvements in surveillance and detection, both of Listeria monocytogenes in food, and of subsequent cases of foodborne illness. In response, the Government is strengthening national surveillance and early detection of foodborne illness through improvements to operational, laboratory and disease-reporting networks. These measures are key to ensuring better preparedness in cases of foodborne illness outbreak in the future.

Collaboration in Science:

"Increasingly, science is enabling risk mitigation with respect to many elements along the food continuum and risk communication within diverse groups of stakeholders with varied interests. Therefore, it should come as no surprise that there is a greater emphasis on further integration among disciplines and collaboration between diverse groups to advance their science knowledge, networks, best practices, diagnostic methods and research. Increasing our coordination and co-operation with international partners in various areas—including regulation, science, performance indicators and reporting—will assist in improving food safety outcomes."

Dr. Brian Evans, Chief Food Safety Officer for Canada

Surveillance Tools

Canadian Network for Public Health Intelligence

The Investigator recommends that governments continue to use and support surveillance and monitoring systems such as the Canadian Network for Public Health Intelligence (CNPHI)—Public Health Alerts (formerly known as the Canadian Integrated Outbreak Surveillance Centre), a system used for early notification of potential outbreaks by FPT and local public health and food safety partners. The CNPHI is a secure web-based collective of applications designed to facilitate the nationwide, integrated real-time collecting and processing of laboratory and epidemiological surveillance data; the dissemination of strategic intelligence; and the coordination of the public health response. FPT governments do in fact continue to use and support CNPHI, including via the PulseNet Canada outbreak response network, as described below.

Assessment of Multi-Jurisdictional Outbreak Management Tools

PHAC continues to maintain and support the integrated Public Health Information System, a case- and-outbreak-management system that currently operates in seven provinces and territories across Canada.

At the Investigator's suggestion, PHAC has begun to assess the Canada Health Infoway-funded Panorama system—a pan-Canadian case-management tool—in order to determine its suitability for effectively managing multi-jurisdictional foodborne illness outbreaks. In addition, PHAC is developing a strategy with respect to business intelligence tools and analytical capacity in order to take full advantage of current and future surveillance and monitoring systems. This strategy will include investigating the feasibility of integration with alerting systems such as CNPHI.

National Enteric Surveillance Program

PHAC has also made improvements to the national surveillance of listeriosis by adding Listeria monocytogenes to the National Enteric Surveillance Program (NESP). The weekly data obtained on the number of listeriosis cases reported across Canada is valuable for observing changes in trends and identifying potential outbreaks.

In addition, an enhanced listeriosis surveillance pilot project has been established to collect case-based information on listeriosis cases. This pilot project provides a timely flow of information in the form of questionnaires from local and provincial public health officials to PHAC epidemiologists. PHAC has received completed questionnaires for 79 per cent of reported cases. The questionnaires provide demographic, clinical, laboratory and epidemiological information. The questionnaire database has been useful in providing risk factor information on sporadic cases, as well as providing timely information during cluster and outbreak investigations.

The NESP data and the case information from the pilot project can be integrated to aid in the detection of clusters of the Listeria pathogen and in the investigation to identify the source of the outbreak, resulting in timelier public health responses to outbreaks of listeriosis.

PulseNet Canada

PulseNet Canada is a national network of provincial and federal laboratories that "fingerprints" bacterial samples from humans and foods using DNA technology. All of the fingerprints are submitted electronically to a database maintained by PHAC, enabling the Agency to quickly identify illnesses appearing in different parts of the country that may be related. This ensures that potential outbreaks are investigated as quickly as possible and also helps identify the source of the illness. These genetic fingerprints of bacteria are compared and shared rapidly among public health officials throughout the country during both routine surveillance and outbreaks.

A major factor in the improved ability to detect foodborne illness is the increased capacity of the PulseNet Canada network across its partner laboratories. Within this network, the PulseNet laboratory DNA fingerprinting technology is used to conduct surveillance for foodborne disease, to detect outbreaks at the earliest possible stage and to help coordinate the public health response. PulseNet is also the primary link for data sharing and communications for its partner-members—PHAC, CFIA, Health Canada and the provincial public health laboratories as represented by the Canadian Public Health Laboratory Network.

Participating clinical and food laboratories collect and share evidence (DNA fingerprints) of clusters of human disease linked to foodborne pathogens. DNA fingerprinting techniques and concurrent access to epidemiological evidence have greatly improved Canada's ability to detect contaminated food products and to identify in the laboratory a link between the consumption of such food products and cases of human disease. Laboratory information is shared and analyzed between all partners daily, including information provided by CFIA on contaminated food products that have been distributed. This rapid exchange of evidence between public health and food safety partners allows for a timely and accurate detection of foodborne disease trends and helps protect the health of Canadians. PulseNet Canada now identifies and notifies health partners whenever two or more matching Listeria DNA fingerprints are detected within a period of 120 days.

Since the 2008 listeriosis outbreak, the number of provincial and federal laboratories and laboratory staff that are certified by PulseNet Canada for work with Listeria monocytogenes has increased from nine staff in four laboratories prior to the listeriosis outbreak to 27 staff in nine laboratories across Canada.

In addition, PHAC is developing a multi-media training curriculum to teach the standardized PulseNet Canada DNA fingerprinting methodology to federal and provincial laboratory staff. This initiative will include distributing materials, protocols and controls to PulseNet Canada member laboratories. The objectives are to increase the number of locations and the numbers of staff trained and certified to use PulseNet Canada laboratory and informatics modules and to increase information sharing with the CNPHI. The development of this formalized training tool is scheduled for completion by early 2012. Once implemented, the training curriculum will assist in ensuring that laboratory capacity exists nationally for all FPT partners, in addition to ensuring surge capacity during foodborne illness outbreaks.

Adding the Canadian Food Inspection Agency to PulseNet Canada

The Public Health Agency of Canada (PHAC) has expanded its PulseNet Canada network to include the Canadian Food Inspection Agency (CFIA). With CFIA as a full partner of PulseNet Canada, the Government of Canada's ability to detect and respond to contaminated food products is greatly improved.

PHAC also links to the PulseNet networks in the United States and around the world. The PulseNet International network, which comprises 80 countries spanning Central and South America, Europe, the Middle East, Sub-Saharan Africa and the Asia-Pacific region, facilitates the identification of emerging regional and global trends and outbreaks. PHAC has access to all genetic fingerprint data in the United States, ensuring that outbreaks and emergencies that span (or potentially span) both sides of the border can be identified and investigated without delay.

As a full partner of PulseNet, CFIA can now report in real time to provincial and federal PulseNet Canada members the DNA fingerprints of potential illness-causing bacteria isolated from samples during its routine testing of food products. Real-time communication of Pulsed Field Gel Electrophoresis patterns from foods will improve our ability to identify links between human diseases and consumption of those products.

The PulseNet Canada Outbreak Detection and Investigation System


Similar to crime scene investigators, public health officials investigating foodborne illness outbreaks use forensic science to pinpoint disease-causing culprits. While criminal investigators use DNA fingerprinting to link a perpetrator to a crime, disease detectives use DNA fingerprints to link bacteria to the food source of an outbreak. Using this knowledge, public health officials are able to coordinate their efforts to identify the specific cause of disease, trace these cases to a specific food source and then remove that product from the Canadian marketplace.

Individuals infected with bacteria sharing the same DNA fingerprint will have been infected from a common source. It is important for public health officials to pinpoint the source of contaminated food and link these cases together so that contaminated items can be removed from the market.

A critical test used to accurately identify contaminated food sources and to properly track foodborne illness is the Pulsed Field Gel Electrophoresis method used for DNA fingerprinting. When they find similar patterns through PulseNet, scientists can determine whether an outbreak is occurring, even when the cases of illness are geographically dispersed. Through PulseNet, outbreaks and their causes can be identified in hours rather than days, which leads to timelier interventions that reduce the impact on public health.

Work is also being done by Health Canada, CFIA and PHAC to create an inventory of the capabilities of federal laboratories (for example, staffing levels, scientific expertise and available equipment/technologies) and to identify what partnerships have been established to increase the capacity for rapid detection of, and response to, potential foodborne illness outbreaks. PulseNet Canada is seen as a model of integrated food safety and public health systems, available to guide the development of the larger network of networks initiative (aimed to link human disease, food and animal labs), as recommended by the Independent Investigator.

A Network of Networks

The Investigator found that surveillance and testing of pathogens such as Listeria monocytogenes in food could be improved by better integrating the work of food safety and public health laboratories. In particular, the Weatherill Report suggests that governments should proceed to establish a national integrated laboratory network—a network of networks.

The goal of this initiative is to be better prepared for future foodborne illness outbreaks through the creation of a nationwide operational system of laboratory networks. This national system will be capable of coordinated action and the timely provision of high-quality data for early detection and effective management of foodborne illness or other events requiring an integrated laboratory response.

To achieve this goal, representatives from CFIA, Health Canada, PHAC, Environment Canada, Fisheries and Oceans Canada and AAFC are working together to prepare a project plan that lays out the requirements for establishing a network of networks.

An inaugural workshop was held in March 2011, where prospective network members (representatives from various sectors of the federal, provincial, industry and academic laboratory communities across Canada) met with CFIA, PHAC and international experts to identify common interests, explore current laboratory capacity, and discuss how the networking of food, animal health and public health laboratories can build capability for the future.

The establishment of a fully integrated Canadian laboratory network is a complex enterprise that will require time and resources to complete. The March 2011 workshop marked the beginning of a process that will result in enhanced laboratory testing capacity, investigative support and surge capacity for faster outbreak response in the future.

Novel Detection Technologies


During the 2008 listeriosis outbreak, PHAC implemented novel laboratory technologies, notably whole-genome sequencing, to obtain definitive characterizations of the outbreak-associated Listeria strains. Genomics began as a research tool, but technological advances have made it feasible and suitable for use during public health investigations of bacterial diseases. Evidence provided by whole-genome sequencing combined with epidemiological evidence to determine the cause and scope of human illness is all but indisputable. These new genomic methods promise to revolutionize the ability of the laboratory to provide information and evidence with respect to disease-causing pathogens. PHAC is now able to perform whole-genome sequencing for outbreak-associated Listeria strains that are causing disease in Canada.

As part of the work, PHAC and Health Canada are conducting joint studies that use the latest generation of genomics technologies and a diverse set of Listeria isolates. The purpose of these studies is to investigate and understand the distribution and characteristics of Listeria populations that have previously been associated with outbreaks and contaminated food products, and thereby develop a foundation of genetic evidence that can be used for future investigations.

genome testing

PHAC's National Microbiology Laboratory is now working with public health and food safety partners to regularly implement these modern genomics technologies in their laboratories. Recently, PHAC engaged these new skill sets, both within Canada and in collaboration with other countries, to assist in the response to the Haitian cholera outbreak of 2010-11, and to the 2011 German E. coli outbreak. PHAC collaborated in genomic efforts with Haiti and the United States to determine the origin of the Haitian outbreak strain, and with Ontario to confirm and determine the genetic features of the single Canadian case identified in the German E. coli outbreak.

By addressing the Investigator's recommendations concerning laboratories and the use of technology, PHAC is now better able to detect foodborne illness and to respond more quickly when there is an outbreak, and it has been recognized as an international innovator for public health genomics, which is becoming an essential and innovative part of outbreak response.

Faster Lab Tests

A critical part of any food safety investigation is the lab test that confirms whether the food is contaminated. Faster testing times directly affect how quickly contaminated food can be pulled from shelves, and in some cases could prevent it from getting to consumers in the first place.

During the 2008 listeriosis outbreak, the standard waiting time to get reliable test results for Listeria was seven to ten days. All of the tests were completed within that time frame.

However, following the outbreak, the Government of Canada invested heavily to improve the technology to detect Listeria more quickly. Health Canada has developed a new lab test that will reliably detect Listeria in three to five days. The method is currently being validated and will be made available by the end of 2011.

Through a partnership with the National Research Council, Health Canada is now investigating the development of new testing technologies that could generate definitive lab results in hours instead of days. A prototype microchip-based method has been developed by government scientists, and it is now being tested in departmental laboratories.

Health Canada, in collaboration with PHAC, continues to operate the Listeriosis Reference Service for Canada, with objectives that include examining suspect foods and clinical specimens submitted for analysis, and maintaining reference cultures of Listeria monocytogenes. The Listeriosis Reference Service holds all strains and characterization data indefinitely, which facilitates the comparison of various strains. The Foodborne Illness Outbreak Response Protocol (FIORP [2010]) includes an appendix on the Listeriosis Reference Service that describes the purpose of the Service and the procedures to follow when foodborne listeriosis is suspected.

The surveillance and detection efforts described in this section all serve to help make more rapid decisions. As a result, industry and government partners have at their disposal an evolving suite of validated detection tools that allow action to be taken at the earliest opportunity in a foodborne illness outbreak or emergency situation. Regulatory authorities are able to make decisions more rapidly, act quickly to determine which food products may be causing illness and establish the source of the contaminated food products.

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