Surveillance for foodborne pathogens is critical to the planning and management of food safety programs as it aims to detect and prevent foodborne infections, while providing evidence that the food moving through the food chain is safe for consumers. Surveillance systems typically collect information from multiple sources to provide a picture of a particular disease in the community, potential sources and to identify areas where control points can be introduced. As a result, a foodborne surveillance system aims to:
- Determine the magnitude and monitor trends of foodborne infections;
- Identify outbreaks of foodborne infections at an early stage to implement control measures, including product recalls;
- Identify the role of food products on human illness, risky behaviours and vulnerable populations;
- Contribute information for the comparison of interventions, direct actions and advance public health policy related to foodborne infections;
- Assess the effectiveness of food safety activities and public health interventions and measure performance.
In order to be captured by a surveillance system, a person must seek medical care, be requested to submit a clinical sample, must provide a clinical sample for testing, a test has to be successfully performed by private/hospital laboratories and a report submitted to the provincial/territorial/national levels. This complex chain of activities sets significant limitations on the ability of any surveillance system to identify case, which contributes to the under-reporting of foodborne illness. In addition, the collection of surveillance data can be performed through different mechanisms, depending on the resources available, ranging from no formal surveillance systems to a fully integrated food safety continuum surveillance system. In circumstances where no formal system is in place, the identification of cases may be based on absences from schools, illnesses after an event or within a closed environment (e.g., long term care centre), or other community measures. Although this might identify outbreaks or clusters of disease, it will not provide information on trends or illnesses occurring outside of these groups, nor will it identify the causative organism. Similarly, a syndromic surveillance system based on standard case definitions or pharmaceutical sales does not collect information on the organism that is causing disease or any demographic or exposure information related to the case but can provide limited trend information.
National monitoring of VTEC in Canada is conducted through different surveillance systems coordinated by the PHAC. It is recognized that most cases of acute diarrhoea are self-limiting, but there are certain circumstances that require the testing of samples, particularly for public health reporting purposes. In 2011, guidelines on when to test and treat cases of infectious diarrhoea were published in the Canadian Medical Association Journal (Hatchette and Farina, 2011), including guidelines for testing potential VTEC cases. The published guidelines recommend that patients presenting with non-bloody diarrhoea should be tested to detect E. coli O157 only if the patient resides in a closed facility (e.g., long-term care facility), is a daycare worker, food handler or health care worker. In addition, the presence of dehydration, fever or underlying comorbidities among cases with non-bloody diarrhoea would also lead to testing for VTEC O157. All patients presenting with bloody diarrhoea are to be tested for E. coli O157.
Unfortunately, diagnosis and monitoring of non-O157 VTEC was hampered by the absence of standardized guidelines for when or how to test for these pathogens. However, in 2018, National guidelines to address this lack of standardization were published by the Canadian Public Health Laboratory Network (Chui et al., 2018). Recommendations include the use of either a chromogenic agar culture or a culture-independent diagnostic test (CIDT) for screening stool samples. If a CIDT method is positive for VTEC, laboratories should be able to culture and isolate VTEC in order to support surveillance and outbreak response. The overall objective of these recommendations is to improve detection of VTEC in patients presenting with diarrhoea, particularly when caused by non-O157 serotypes.
National Enteric Surveillance Program
The National Enteric Surveillance Program (NESP) is a national surveillance system jointly administered by the PHAC’s National Microbiology Laboratory (NML) and the Centre for Foodborne, Environmental and Zoonotic Infectious Diseases (CFEZID) since 1997 (NESP). It currently collects information on 14 different bacterial, viral and parasitic enteric pathogens. NESP’s main objectives are to detect and respond to multi-jurisdictional outbreaks through weekly analysis and reporting of laboratory confirmed enteric disease cases in Canada; and to integrate with national and international efforts to monitor and limit the spread of enteric diseases. The collection of weekly enteric disease data allows for timely reporting and provides PHAC and provincial/territorial partners with the first signals that a significant disease trend is emerging. The collection of baseline data on enteric disease in Canada also facilitates understanding of trends in organism subtypes over time and supports research, inter-provincial and international comparisons, and planning and decision making for laboratorians, epidemiologists and other public health stakeholders.
NESP is a passive surveillance system relying on provincial public health laboratories to provide weekly reports for organisms isolated from Canadians that sought medical attention. All data is provided to NESP in an aggregate and anonymous manner and includes only the number of isolates from new cases identified at the provincial laboratory that week, or provides updates to previously reported numbers. Data analysis is conducted on the weekly data by PHAC to determine if case counts are significantly “higher than expected” based on a 5-year moving average. NESP weekly reports are produced and are only available to health professionals involved with monitoring enteric disease, working at the federal, provincial/territorial and regional/local levels with a public health mandate. NESP also produces Annual Summary reports, which are published on-line (NESP Reports).
The NESP determined rate of VTEC illness for Canada in 2016 was 1.7 per 100,000, of which 1.1 per 100,000 can be attributed to VTEC O157 and 0.6 per 100,000 to other VTEC serotypes (Government of Canada. 2018). From 1997 to 2007, the national rate of VTEC O157 illness in Canada was in the range of 3 to 5 per 100,000 (Figure 4). Following 2007, the rate of VTEC O157 has declined and remained stable around 1.2 per 100,000. In contrast the rate of non-O157 VTEC has steadily increased since 2011. There is also considerable regional variation in reported incident rates of VTEC, with Nunavut, Prince Edward Island and the Yukon reporting significantly greater incidence rates than the national rate in 2016.
Due to limitations in laboratory testing and reporting, there are inherent limitations to the data provided and presented by NESP. Therefore, the numbers reported in the provincial reports and the NESP data are an under-representation of the true incidence of disease in Canada. While VTEC O157 is routinely forwarded to provincial or central reference laboratories for further subtyping, non-O157 cases are poorly captured by NESP and are under-represented. With the introduction of whole genome sequencing and the development of new testing guidelines for the identification of non-O157 cases, it is expected that this limitation will be reduced and that cases reported to NESP will be closer to the true incidence of this disease in Canada.
Led by the PHAC’s National Microbiology Laboratory (NML), PulseNet Canada is the national real-time molecular subtyping network for foodborne disease surveillance (PulseNet). The laboratory network has been in operation at PHAC since approximately 2000, with comprehensive real-time data being collected and analyzed on a daily and weekly basis since 2004.
The objectives of PulseNet Canada are to:
- Collect molecular and genomic subtyping data from cases of bacterial foodborne disease from all provincial public health laboratories, and from bacterial pathogens isolated by the CFIA, in real-time;
- Analyze these molecular data on a daily basis for the purpose of detecting potential outbreaks, particularly multijurisdictional outbreaks as early as possible; and to;
- Provide the laboratory investigation during multijurisdictional outbreak response and support for single jurisdiction response to enable timely public health action to protect the health of Canadians.
PulseNet Canada has links to other PHAC surveillance activities, specifically, NESP and FoodNet Canada surveillance systems. Each of these surveillance systems collects data on foodborne pathogens, with PulseNet Canada focusing on the detection of potential outbreaks by identifying clusters of isolates with shared subtyping profiles. By capturing strain-level data, PulseNet compliments the species or serotype level data captured by NESP. PulseNet Canada data is analyzed jointly with NESP on a weekly basis. Currently, PulseNet Canada is carrying out whole genome sequencing for all VTEC isolates and performing cluster analyses on a weekly basis. If available, food, animal and environmental samples are included in these weekly analyses.
FoodNet Canada (FNC) is a national food safety “sentinel site” surveillance system facilitated by PHAC (FoodNet Canada). FNC activities are intended to integrate human, food, and environmental monitoring. The Region of Waterloo, Ontario was selected as FNC’s first sentinel pilot site with surveillance activities beginning in 2005. In 2010, a second sentinel site was established within the Fraser Health Authority region, in British Columbia. In 2014, a third sentinel site was launched in the Calgary and Central zones of Alberta. Also in 2014, the Ontario site moved from Waterloo Region to the Middlesex-London Public Health unit area. Each sentinel site is a geographically defined area where samples from the local public health unit, retail food outlets, farms and local water sources are linked to generate information that is representative of the broader population.
FoodNet Canada’s primary objectives are to:
- Determine what food and other sources are making Canadians ill;
- Determine significant risk factors for enteric illness;
- Accurately track disease rates and risks over time;
- Provide practical prevention information to prioritize risk mitigation/risk management efforts; compare interventions, direct actions and advance policy; and assess effectiveness of food safety activities and public health interventions and measure performance.
FoodNet Canada conducts a combination of active (farm, retail and water components) and passive (human) surveillance. Using a standardized questionnaire, epidemiological information is collected on every illness case and linked to laboratory results from work performed by provincial laboratories or NML. On a weekly basis, grocery stores are visited in the sentinel sites to purchase samples of raw meat and seafood available to the consumer. Samples are tested for the presence of several targeted enteric pathogens that are similar to those tested in food animals and water, including VTEC. Untreated surface water samples are collected bi-weekly and are tested for the presence of several targeted enteric pathogens and water quality indicators are recorded. The active surveillance of food animals is accomplished through the analysis of manure sampled on farms within each site, including fresh fecal matter, stocked manure or slurry. Sampling is conducted in four commodity groups with each farm visited once a year: swine, dairy, beef, and broiler chicken operations. Laboratory results are linked with data provided through a sample collection form.
All data is integrated to compare pathogens found in retail food, water and on farms with human infections to help identify what food and other sources are making Canadians ill. Data is further analysed to produce an annual report (FoodNet Canada Publications). Results from the food animal surveillance component are disseminated to each producer through an individualized report of their results on a yearly basis. Additional analyses are performed upon request by the sentinel sites, CFEZID-Outbreak Management Division, or federal partners. A summary of FoodNet VTEC test results for the period 2014 to 2017 is provided in Tables 6 and 11.
All human VTEC isolates recovered under FNC activities are characterised in the PulseNet Canada system, currently this includes WGS, which provides further subtyping information to differentiate among the non-O157 subtypes. VTEC isolates recovered from retail, farm or environmental samples are also sequenced and shared with PulseNet Canada. The inclusion of these non-human isolates allows for the detection of possible sources of infection, transmission routes of the pathogen along the food chain, and informs the generation of hypothesis for outbreak investigations.
National monitoring of VTEC illness in Canada is conducted through three programs, the National Enteric Surveillance Program, PulseNet Canada and FoodNet Canada. The primary features of these programs are:
- Information on the rate of VTEC illness in Canada is captured by the NESP, based on data provided by provincial public health laboratories. This data allows reporting of incident rates and identification on changes in incident trends.
- Due to limitations in laboratory testing and case reporting, NESP incident rates of VTEC are understood to be an underestimate.
- The incident rate of VTEC illness for Canada in 2016 was 1.7 per 100,000. Incident rates have been relatively stable since 2008, declining from 3 to 5 per 100,000 in the previous decade.
- Incident rates of VTEC vary regionally. For example, Nunavut, Prince Edward Island and Yukon reported significantly greater incidence rates than the national rate in 2016.
- PulseNet Canada conducts whole genome sequencing for all VTEC isolates available, including isolates from clinical, food, animal and environmental samples. To support the identification of potential outbreaks and exposure sources cluster analyses is conducted to identify related isolates.
- FoodNet Canada conducts active surveillance at three sentinel sites: the Fraser Health Authority region, in British Columbia, the Calgary and Central zones of Alberta, and the Middlesex-London Public Health unit area in Ontario. To identify causes and sources of foodborne illness FoodNet collects and tests samples from the local public health unit, retail food outlets, farms and local water sources for enteric pathogens, including VTEC.