A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing.

Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.

The impact of publicly funded rotavirus immunization programs on Canadian children.

BACKGROUND: In 2008, the National Advisory Committee on Immunization recommended routine rotavirus immunizations in healthy Canadian infants. Over the following seven years, eight provinces and two territories introduced the rotavirus vaccine into their publicly funded immunization programs. OBJECTIVE: Assess the burden of rotavirus infections before and after implementation of publicly funded immunization programs. METHODS: We analyzed laboratory-confirmed community cases of rotavirus reported to the National Enteric Surveillance Program and hospitalizations of children younger than three years old from 2007 to 2017 with rotavirus diagnosis-specific ICD-10 codes. Rates of illness were calculated for each province for the two years prior to and after implementation of public funding of the vaccine. The year of implementation was not included to accommodate the uptake period of the vaccine. Age-specific rates were assessed in jurisdictions where five years of data were available the year after the vaccine was publicly funded. The pre-post and difference-in-difference (DID) methodologies were applied to hospital discharge data to evaluate changes between the funding and non-funding jurisdictions. RESULTS: Community cases of laboratory-confirmed rotavirus infection reported to the National Enteric Surveillance Program declined by 54% between 2010 and 2017. Rates of hospital discharges decreased significantly among children in six provinces after the adoption of the rotavirus vaccine. Hospital discharge rates in Alberta, Manitoba, Ontario and Prince Edward Island dropped between 53% and 71%, and by 75% for British Columbia and Saskatchewan. CONCLUSION: Public funding of the rotavirus vaccine appeared to lead to significant reductions in laboratory-confirmed rotavirus cases reported to the National Enteric Surveillance Program and in the rates of rotavirus gastroenteritis-related hospital discharges.

The use of an online survey for collecting food exposure information, Foodbook sub-study, February to April 2015.

BACKGROUND: During foodborne illness outbreak investigations, comparing food exposure frequencies of cases to those of a control population can help identify suspect food sources. The Public Health Agency of Canada (PHAC) conducted an online survey between February and April 2015 to collect seven-day food exposures from a convenience sample. The study period overlapped with a national, population-based exposure survey being conducted via telephone using random digit dialling. A subset of the food exposure questions from the telephone-based survey was included in the online survey. OBJECTIVE: The online survey study objectives were to: 1) describe the survey methodology, survey respondents and response behaviour; and 2) determine if the online methodology is an appropriate alternative to telephone surveys by comparing food exposures. METHODS: The online survey link was distributed via email to employees and public health partners, and was promoted on the PHAC website and social media channels. RESULTS: In total 2,100 surveys were completed. The majority of respondents were female, with high income and education, aged 30 to 39 years. The proportion reporting consuming the food items in the online survey was generally higher than those reported in the telephone survey, with a mean difference of 6.0% (95% CI: 4.2, 7.8). CONCLUSION: In an outbreak investigation, the 6.0% bias could make it more difficult to detect a difference between the case and control food exposures. Nevertheless, given the speed of response and lower resource expenditure of online surveys as well as the willing, able and convenient sample, a bias of 6.0% is considered small enough to be acceptable for future surveys.

Country food consumption in Yukon, Northwest Territories and Nunavut, Foodbook study 2014-2015.

BACKGROUND: This article presents a descriptive summary of the consumption of various country food (i.e. locally harvested plant and animal foods) products by residents of Yukon (YT), Northwest Territories (NT) and Nunavut (NU). Data were collected as part of the Foodbook study in 2014-2015. METHODS: The Foodbook study was conducted by telephone over a one-year period. Respondents were asked about consumption of a wide range of food products over the previous seven days. Residents of the territories were also asked about consumption of regionally-specific country food. Data were weighted to develop territorial estimates of consumption. Data on age, gender, location, income and education were also collected. RESULTS: The national response rate for the Foodbook survey was 19.9%. In total, 1,235 residents of the territories participated in the study (YT, n=402; NT, n=458; NU, n=375). Consumption of any country food during the previous seven days was reported by 77.5%, 60.7%, and 66.4% of participants in NU, NT and YT, respectively. CONCLUSION: Responses to country food questions asked alongside the main Foodbook questionnaire provide insight on country food consumption in YT, NT and NU.

Canadian Consumer Food Safety Practices and Knowledge: Foodbook Study.

Understanding consumers' food safety practices and knowledge supports food safety education for the prevention of foodborne illness. The objective of this study was to describe Canadian consumer food safety practices and knowledge. This study identifies demographic groups for targeted food safety education messaging and establishes a baseline measurement to assess the effectiveness of food safety interventions over time. Questions regarding consumer food safety practices and knowledge were included in a population-based telephone survey, Foodbook, conducted from November 2014 to March 2015. The results were analyzed nationally by age group and by gender. The results showed that approximately 90% of Canadians reported taking the recommended cleaning and separating precautions when handling raw meat to prevent foodborne illness. Only 29% of respondents reported using a food thermometer when cooking any meat, and even fewer (12%) reported using a food thermometer for small cuts of meat such as chicken pieces. The majority (>80%) of Canadians were aware of the foodborne illness risks related to chicken and hamburger, but fewer (<40%) were aware of the risks related to frozen chicken nuggets, alfalfa sprouts, soft unpasteurized cheese, and unpasteurized juices. Generally, men were less likely to follow cooking instructions on packaging and took fewer steps to prevent cross-contamination than women. The youngest (18 to 29 years) age group was less likely to take steps to avoid cross-contamination and was less aware of the risks associated with eating an undercooked hamburger. The oldest (60+ years) respondents were less likely to be aware of the risks associated with raw eggs, alfalfa sprouts, and unpasteurized juice than the middle (30 to 59 years) age group. As a priority, food safety education in Canada should focus on increasing people's awareness of high-risk foods, specifically foods for which the awareness of risk found in this study was low; targeting messaging to demographic groups as appropriate; and promoting the use of food thermometers when cooking meat and poultry.

Source attribution of human campylobacteriosis at the point of exposure by combining comparative exposure assessment and subtype comparison based on comparative genomic fingerprinting.

Human campylobacteriosis is a common zoonosis with a significant burden in many countries. Its prevention is difficult because humans can be exposed to Campylobacter through various exposures: foodborne, waterborne or by contact with animals. This study aimed at attributing campylobacteriosis to sources at the point of exposure. It combined comparative exposure assessment and microbial subtype comparison with subtypes defined by comparative genomic fingerprinting (CGF). It used isolates from clinical cases and from eight potential exposure sources (chicken, cattle and pig manure, retail chicken, beef, pork and turkey meat, and surface water) collected within a single sentinel site of an integrated surveillance system for enteric pathogens in Canada. Overall, 1518 non-human isolates and 250 isolates from domestically-acquired human cases were subtyped and their subtype profiles analyzed for source attribution using two attribution models modified to include exposure. Exposure values were obtained from a concurrent comparative exposure assessment study undertaken in the same area. Based on CGF profiles, attribution was possible for 198 (79%) human cases. Both models provide comparable figures: chicken meat was the most important source (65-69% of attributable cases) whereas exposure to cattle (manure) ranked second (14-19% of attributable cases), the other sources being minor (including beef meat). In comparison with other attributions conducted at the point of production, the study highlights the fact that Campylobacter transmission from cattle to humans is rarely meat borne, calling for a closer look at local transmission from cattle to prevent campylobacteriosis, in addition to increasing safety along the chicken supply chain.

A Comparative Exposure Assessment of Campylobacter in Ontario, Canada.

To inform source attribution efforts, a comparative exposure assessment was developed to estimate the relative exposure to Campylobacter, the leading bacterial gastrointestinal disease in Canada, for 13 different transmission routes within Ontario, Canada, during the summer. Exposure was quantified with stochastic models at the population level, which incorporated measures of frequency, quantity ingested, prevalence, and concentration, using data from FoodNet Canada surveillance, the peer-reviewed and gray literature, other Ontario data, and data that were specifically collected for this study. Models were run with @Risk software using Monte Carlo simulations. The mean number of cells of Campylobacter ingested per Ontarian per day during the summer, ranked from highest to lowest is as follows: household pets, chicken, living on a farm, raw milk, visiting a farm, recreational water, beef, drinking water, pork, vegetables, seafood, petting zoos, and fruits. The study results identify knowledge gaps for some transmission routes, and indicate that some transmission routes for Campylobacter are underestimated in the current literature, such as household pets and raw milk. Many data gaps were identified for future data collection consideration, especially for the concentration of Campylobacter in all transmission routes.

Using environmental health officers' opinions to inform the source attribution of enteric disease: further analysis of the "most likely source of infection".

BACKGROUND: Policies and programs are needed to mitigate the burden of enteric disease in Canada. Source attribution, a goal of FoodNet Canada, can inform such strategies and can be accomplished with the information provided by expert opinion. This includes environmental health officers' (EHOs) opinions on the "most likely source of infection" (MLSI) of confirmed cases of enteric disease that are investigated by the Fraser Health Authority in British Columbia, FoodNet Canada's second sentinel site. METHODS: Exposure data from the MLSI were categorized into ten groups and summarized for five enteric disease groups using endemic cases in the first analysis, and a combination of endemic and international travel cases for the second analysis. An exploratory analysis was also conducted on risk setting information in the MLSI. The final analysis involved using a logistic regression model (Wald test) to describe the inherent biases in the data. RESULTS: Exposure proportions, by disease group, were similar to those of an analysis of MLSI data from FoodNet Canada's Ontario sentinel site. Food exposure represented the greatest proportion of overall enteric disease (32.0%), as well as for salmonellosis (45.0%), verotoxigenic E. coli (VTEC) infection (38.1%), and campylobacteriosis (30.0%) cases. The majority of parasitic diseases (41.2%) were attributed to water exposure. Food safety practices and consuming unpasteurized products were more frequently reported for campylobacteriosis (19.7% and 5.4%, respectively) compared to other enteric diseases. More VTEC infection was attributed to domestic travel (4.8%) than the other enteric diseases. Among endemic and international travel-related cases combined, VTEC infection was attributed more to endemic food exposure (35.5%) than international travel (16.1%), but similar proportions of campylobacteriosis were attributed to endemic food exposure (25.1%) and international travel (25.1%). Variations existed in the exposure and risk setting information that EHOs included in the MLSI, and in their propensity to enter food sources over other types of exposures. CONCLUSIONS: Results from the MLSI analysis for exposure, risk setting, and EHO bias, are valid contributions for informing source attribution. Important considerations from this work, including strategies to standardize and improve the quality of MLSI data, will enhance source attribution hypotheses.