Population structure, case clusters, and genetic lesions associated with Canadian Salmonella 4,[5],12:i:- isolates.

Monophasic Salmonella 4,[5]:12:i:- are a major public health problem because they are one of the top five Salmonella serotypes isolated from clinical cases globally and because they can carry resistance to multiple antibiotics. A total of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium whole genome sequences (WGS) were generated. The various genetic lesions causing the Salmonella 4,[5]:12:i:- genotype were identified and assessed with regards to their distribution in the population of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium isolates, their geographical and temporal distribution, and their association with non-human sources. Several clades were identified in the population structure, and the largest two were associated almost exclusively with a short prophage insertion and insertion of a mobile element carrying loci encoding antibiotic and mercury resistance. IS26-mediated deletions and fljB point mutants appeared to spread clonally. 'Inconsistent' Salmonella 4,[5]:12:i:- isolates associated with specific, single amino acid changes in fljA and hin were found in a single clade composed of water, shellfish, and avian isolates. Inclusion of isolates from different case clusters identified previously by PFGE validated some of the clusters and invalidated others. Some wgMLST clusters of clinical isolates composed of very closely related isolates contained an isolate(s) with a different genetic lesion, suggesting continuing mobility of the implicated element responsible. Such cases may need to be left out of epidemiological investigations until sufficient numbers of isolates are included that statistical significance of association with sources is not impaired. Non-human sources were frequently found in or near clinical case clusters. Prospective surveillance and WGS of non-human sources and retrospective analysis by WGS of isolates from existing culture collections provides data critical for epidemiological investigations of food- and waterborne outbreaks.

Antimicrobial resistance and recovery of Salmonella, Campylobacter, and Escherichia coli from chicken egg layer flocks in Canadian sentinel surveillance sites using 2 types of sample matrices.

Eggs are important to the diet of Canadians. This product is one of the supply-managed commodities in Canada, but unlike other commodities, where food safety risks are extensively explored and reported, information on the prevalence of enteric organisms (e.g., Salmonella, Campylobacter) and antimicrobial resistance (AMR) in layers in Canada are limited. This study was conducted to determine the prevalence of select bacteria and the associated AMR patterns in layer flocks using 2 sample matrices. Farms were located within FoodNet Canada and the Canadian Integrated Program for Antimicrobial Resistance Surveillance sentinel sites (SS). Fecal samples (Ontario: ONSS1a, ONSS1b) and environmental sponge swabs (British Columbia: BCSS2a) were collected. Salmonella prevalence was 29% and 8% in ONSS1a and ONSS1b, respectively, and 7% in BCSS2a. S. Kentucky and S. Livingstone were the most frequently isolated serovars and no S. Enteritidis was detected. Campylobacter was not detected in the BC sponge swabs but was isolated from 89% and 53% of Ontario fecal samples (ONSS1a and ONSS1b, respectively). Seven C. jejuni from Ontario were ciprofloxacin-resistant. Escherichia coli prevalence was high in both sample types (98%). Overall, tetracycline resistance among E. coli ranged from 26% to 69%. Resistance to ceftiofur (n = 2 isolates) and gentamicin (n = 2) was relatively low. There were diverse resistance patterns (excludes susceptible isolates) observed among E. coli in Ontario (10 patterns) and British Columbia (14 patterns). This study revealed that fecal samples are more informative for farm-level monitoring of pathogen and AMR prevalence. Without further validation, sponge swabs are limited in their utility for Campylobacter detection and thus, for public health surveillance.

Les oeufs sont importants pour l'alimentation des Canadiens. Ce produit est l'un des produits soumis à la gestion de l'offre au Canada, mais contrairement à d'autres produits, où les risques pour la salubrité des aliments sont largement étudiés et signalés, des informations sur la prévalence des organismes entériques (p. ex. Salmonella, Campylobacter) et la résistance aux antimicrobiens (RAM) chez les pondeuses au Canada sont limitées. Cette étude a été menée pour déterminer la prévalence de certaines bactéries et les patrons de résistance aux antimicrobiens associés dans les troupeaux de pondeuses en utilisant deux matrices d'échantillons. Les fermes étaient situées au sein de FoodNet Canada et des sites sentinelles (SS) du Programme intégré canadien de surveillance de la résistance aux antimicrobiens. Des échantillons de matières fécales (Ontario : ONSS1a, ONSS1b) et des éponges environnementales (Colombie-Britannique : BCSS2a) ont été prélevés. La prévalence de Salmonella était de 29 % et 8 % pour ONSS1a et ONSS1b, respectivement, et de 7 % pour BCSS2a. Salmonella Kentucky et S. Livingstone étaient les sérotypes les plus fréquemment isolés et aucun S. Enteritidis n'a été détecté. Campylobacter n'a pas été détecté dans les éponges de la Colombie-Britannique, mais a été isolé de 89 % et 53 % des échantillons de matières fécales de l'Ontario (ONSS1a et ONSS1b, respectivement). Sept C. jejuni de l'Ontario étaient résistants à la ciprofloxacine. La prévalence d'Escherichia coli était élevée dans les deux types d'échantillons (98 %). Dans l'ensemble, la résistance à la tétracycline chez E. coli variait de 26 % à 69 %. La résistance au ceftiofur (n = 2 isolats) et à la gentamicine (n = 2) était relativement faible. Divers profils de résistance (à l'exclusion des isolats sensibles) ont été observés chez E. coli en Ontario (10 profils) et en Colombie-Britannique (14 profils). Cette étude a révélé que les échantillons fécaux sont plus informatifs pour la surveillance au niveau de la ferme de la prévalence des agents pathogènes et de la résistance aux antimicrobiens. Sans validation supplémentaire, les éponge sont limitées dans leur utilité pour la détection de Campylobacter et donc pour la surveillance en santé publique.(Traduit par Docteur Serge Messier).

Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype.

Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide. Multiple genetic events associated with different genetic elements can result in the monophasic phenotype. Several jurisdictions have reported the emergence of a Salmonella 4,[5],12:i:- clone with SGI-4 and a genetic element (MREL) encoding a mercury resistance operon and antibiotic resistance loci that disrupts the second phase antigen region near the iroB locus in the Salmonella genome. We have sequenced 810 human and animal Canadian Salmonella 4,[5],12:i:- isolates and determined that isolates with SGI-4 and the mercury resistance element (MREL; also known as RR1&RR2) constitute several global clades containing various proportions of Canadian, US, and European isolates. Detailed analysis of the data provides a clearer picture of how these heavy metal elements interact with bacteria within the Salmonella population to produce the monophasic phenotype. Insertion of the MREL near iroB is associated with several deletions and rearrangements of the adjacent flaAB hin region, which may be useful for defining human case clusters that could represent outbreaks. Plasmids carrying genes encoding silver, copper, mercury, and antimicrobial resistance appear to be derived from IS26 mediated acquisition of these genes from genomes carrying SGI-4 and the MREL. Animal isolates with the mercury and As/Cu/Ag resistance elements are strongly associated with porcine sources in Canada as has been shown previously for other jurisdictions. The data acquired in these investigations, as well as from the extensive literature on the subject, may aid source attribution in outbreaks of the organism and interventions to decrease the prevalence of this clone and reduce its impact on human disease.

Targeting discriminatory SNPs in Salmonella enterica serovar Heidelberg genomes using RNase H2-dependent PCR.

We report a novel RNase H2-dependent PCR (rhPCR) genotyping assay for a small number of discriminatory single-nucleotide polymorphisms (SNPs) that identify lineages and sub-lineages of the highly clonal pathogen Salmonella Heidelberg (SH). Standard PCR primers targeting numerous SNP locations were initially designed in silico, modified to be RNase H2-compatible, and then optimized by laboratory testing. Optimization often required repeated cycling through variations in primer design, assay conditions, reagent concentrations and selection of alternative SNP targets. The final rhPCR assay uses 28 independent rhPCR reactions to target 14 DNA bases that can distinguish 15 possible lineages and sub-lineages of SH. On evaluation, the assay correctly identified the 12 lineages and sub-lineages represented in a panel of 75 diverse SH strains. Non-specific amplicons were observed in 160 (15.2%) of the 1050 reactions, but due to their low intensity did not compromise assay performance. Furthermore, in silico analysis of 500 closed genomes from 103 Salmonella serovars and laboratory rhPCR testing of five prevalent Salmonella serovars including SH indicated the assay can identify Salmonella isolates as SH, since only SH isolates generated amplicons from all 14 target SNPs. The genotyping results can be fully correlated with whole genome sequencing (WGS) data in silico. This fast and economical assay, which can identify SH isolates and classify them into related or unrelated lineages and sub-lineages, has potential applications in outbreak identification, source attribution and microbial source tracking.

Diagnostic Interpretation Guidance for Pediatric Enteric Pathogens: A Modified Delphi Consensus Process.

BACKGROUND: We sought to develop diagnostic test guidance definitions for pediatric enteric infections to facilitate the interpretation of positive test results in the era of multianalyte molecular diagnostic test platforms. METHODS: We employed a systematic, two-phase, modified Delphi consensus process consisting of three web-based surveys and an expert panel face-to-face meeting. In phase 1, we surveyed an advisory panel of North American experts to select pathogens requiring diagnostic test guidance definition development. In phase 2, we convened a 14-member expert panel to develop, refine, and select the final definitions through two web-based questionnaires interspersed with a face-to-face meeting. Both questionnaires asked panelists to rate the degree to which they agreed that if the definition is met the pathogen is likely to be causative of clinical illness. RESULTS: The advisory panel survey identified 19 pathogens requiring definitions. In the expert panel premeeting survey, 13 of the 19 definitions evaluated were rated as being highly likely ("agree" or "strongly agree") to be responsible for acute gastroenteritis symptoms by ≥67% of respondent panel members. The definitions for the remaining six pathogens (Aeromonas, Clostridium difficile, Edwardsiella, nonenteric adenovirus, astrovirus, and Entamoeba histolytica) were indeterminate. After the expert panel meeting, only two of the modified definitions, C. difficile and E. histolytica/dispar, failed to achieve the a priori specified threshold of ≥67% agreement. CONCLUSIONS: We developed diagnostic test guidance definitions to assist healthcare providers for 17 enteric pathogens. We identified two pathogens that require further research and definition development.

Prevalence and molecular characterization of Toxoplasma gondii DNA in retail fresh meats in Canada.

Toxoplasma gondii is a protozoan parasite which infects a wide variety of mammals and birds worldwide, including humans. Human toxoplasmosis is primarily transmitted through the ingestion of tissue cysts in raw or poorly cooked meat and organs of infected animals, or through the ingestion of oocysts in food, water or soil contaminated with cat faeces. There is a distinct paucity of information on the prevalence and molecular characteristics of T. gondii in retail meats in Canada. This study reports the presence of T. gondii DNA in 4.3% (12 of 281) of packages of fresh ground beef, chicken breasts and ground pork purchased at retail in three Canadian provinces. T. gondii prevalence was very similar among all three meat types tested, and among the provinces sampled. Genotyping of positive samples by means of PCR-RFLP and DNA sequencing demonstrated the presence of both T. gondii type II (66.7%) and type III (33.3%). These findings provide baseline data on the prevalence of T. gondii DNA in fresh meats purchased at retail in Canada and will allow for more accurate and meaningful health risk assessments for the purposes of developing food safety guidelines and policies.

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.

The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data.

A fundamental assumption in the use and interpretation of microbial subtyping results for public health investigations is that isolates that appear to be related based on molecular subtyping data are expected to share commonalities with respect to their origin, history, and distribution. Critically, there is currently no approach for systematically assessing the underlying epidemiology of subtyping results. Our aim was to develop a method for directly quantifying the similarity between bacterial isolates using basic sampling metadata and to develop a framework for computing the epidemiological concordance of microbial typing results. We have developed an analytical model that summarizes the similarity of bacterial isolates using basic parameters typically provided in sampling records, using a novel framework (EpiQuant) developed in the R environment for statistical computing. We have applied the EpiQuant framework to a data set comprising 654 isolates of the enteric pathogen Campylobacter jejuni from Canadian surveillance data in order to examine the epidemiological concordance of clusters obtained by using two leading C. jejuni subtyping methods. The EpiQuant framework can be used to directly quantify the similarity of bacterial isolates based on basic sample metadata. These results can then be used to assess the concordance between microbial epidemiological and molecular data, facilitating the objective assessment of subtyping method performance and paving the way for the improved application of molecular subtyping data in investigations of infectious disease.

Evidence for the benefits of food chain interventions on E. coli O157:H7/NM prevalence in retail ground beef and human disease incidence: A success story.

OBJECTIVES: Human infection with Escherichia coli O157:H7/NM has historically been associated with consumption of undercooked ground beef. The purpose of this paper is to investigate the correlation of the decline in E. coli O157:H7/NM infections in Canada with the introduction of control efforts in ground beef by industry. METHODS: The human incidence of E. coli O157:H7/NM, prevalence in ground beef and interventions from 1996 to 2014 were analyzed. Pathogen prevalence data were obtained from federal government and industry surveillance and inspection/compliance programs. A survey of the largest ground beef producers in Canada was conducted to identify when interventions were implemented. RESULTS: The incidence of E. coli O157:H7/NM infections in Canada declined from ≈4 cases/100 000 to ≈1 case/100000 from 2000 to 2010. Verotoxigenic Escherichia coli (VTEC) prevalence in ground beef sold at retail declined from about 30% around the year 2000 to <2% since 2012. Other measures of the prevalence of E. coli, VTEC, and E. coli O157:H7/NM in beef and ground beef also declined. The number and types of interventions implemented in the major beef processing establishments in Canada increased from 1996 to 2016. CONCLUSION: The observed decline in human illnesses and pathogen levels in relation to retail meats was associated with the introduction of control efforts by industry, federal and provincial/territorial governments, and the general population. Industry-led changes in beef processing along with the introduction of food safety policies, regulations, and public education have led to improved food safety in Canada.

The Incidence of Acute Gastrointestinal Illness in Canada, Foodbook Survey 2014-2015.

Acute gastrointestinal illness (AGI) is an important public health issue, with many pathogen sources and modes of transmission. A one-year telephone survey was conducted in Canada (2014-2015) to estimate the incidence of self-reported AGI in the previous 28 days and to describe health care seeking behaviour, using a symptom-based case definition. Excluding cases with respiratory symptoms, it is estimated that there are 0.57 self-reported AGI episodes per person-year, almost 19.5 million episodes in Canada each year. The proportion of cases seeking medical care was nearly 9%, of which 17% reported being requested to submit a sample for laboratory testing, and 49% of those requested complied and provided a sample. Results can be used to inform burden of illness and source attribution studies and indicate that AGI continues to be an important public health issue in Canada.

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.

Non food-related risk factors of campylobacteriosis in Canada: a matched case-control study.

BACKGROUND: Campylobacteriosis is a prominent bacterial gastrointestinal infection worldwide with several transmission pathways. Its non-foodborne routes have been less documented and quantified. The study aimed to quantitatively explore the role of potential risk factors not directly associated with food for sporadic cases of C. jejuni infection in Canada. METHODS: This retrospective matched case-control study was built on an enhanced campylobacteriosis surveillance system and on a survey of healthy people and their behaviour with regards to potential risk factors for gastrointestinal infections that occurred in the same area in Canada. Eighty-five cases were individually matched by age and season to 170 controls. RESULTS: Through conditional logistic regression, risk factors were found only among water-related factors (drinking untreated water, using tap filter, drinking water from well and swimming in natural water), whereas drinking bottled water was protective. Among the 32 non-water related factors explored, 12 were surprisingly 'protective' factors without relevant explanation for that effect (for example gardening, attending a barbecue, eating food from a fast-food restaurant), suggesting that human infection by Campylobacter may be more frequently acquired at home than outside the home. CONCLUSIONS: This study confirms and quantifies the importance of the waterborne transmission of campylobacteriosis. People are encouraged to drink only treated water and to avoid the ingestion of natural water as much as possible while swimming or playing in water. Globally, general hygiene and proper food handling and cooking practices at home should continue to be encouraged.

Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human, Animal, and Food Sources.

Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian S Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes.

Spatial-temporal epidemiology of human Salmonella Enteritidis infections with major phage types (PTs 1, 4, 5b, 8, 13, and 13a) in Ontario, Canada, 2008-2009.

BACKGROUND: In Ontario and Canada, the incidence of human Salmonella enterica serotype Enteritidis (S. Enteritidis) infections have increased steadily during the last decade. Our study evaluated the spatial and temporal epidemiology of the major phage types (PTs) of S. Enteritidis infections to aid public health practitioners design effective prevention and control programs. METHODS: Data on S. Enteritidis infections between January 1, 2008 and December 31, 2009 were obtained from Ontario's disease surveillance system. Salmonella Enteritidis infections with major phage types were classified by their annual health region-level incidence rates (IRs), monthly IRs, clinical symptoms, and exposure settings. A scan statistic was employed to detect retrospective phage type-specific spatial, temporal, and space-time clusters of S. Enteritidis infections. Space-time cluster cases' exposure settings were evaluated to identify common exposures. RESULTS: 1,336 cases were available for analysis. The six most frequently reported S. Enteritidis PTs were 8 (n = 398), 13a (n = 218), 13 (n = 198), 1 (n = 132), 5b (n = 83), and 4 (n = 76). Reported rates of S. Enteritidis infections with major phage types varied by health region and month. International travel and unknown exposure settings were the most frequently reported settings for PT 5b, 4, and 1 cases, whereas unknown exposure setting, private home, food premise, and international travel were the most frequently reported settings for PT 8, 13, and 13a cases. Diarrhea, abdominal pain, and fever were the most commonly reported clinical symptoms. A number of phage type-specific spatial, temporal, and space-time clusters were identified. Space-time clusters of PTs 1, 4, and 5b occurred mainly during the winter and spring months in the North West, North East, Eastern, Central East, and Central West regions. Space-time clusters of PTs 13 and 13a occurred at different times of the year in the Toronto region. Space-time clusters of PT 8 occurred at different times of the year in the North West and South West regions. CONCLUSIONS: Phage type-specific differences in exposure settings, and spatial-temporal clustering of S. Enteritidis infections were demonstrated that might guide public health surveillance of disease outbreaks. Our study methodology could be applied to other foodborne disease surveillance data to detect retrospective high disease rate clusters, which could aid public health authorities in developing effective prevention and control programs.

A Systematic Review and Meta-Analysis of the Campylobacter spp. Prevalence and Concentration in Household Pets and Petting Zoo Animals for Use in Exposure Assessments.

Animal contact is a potential transmission route for campylobacteriosis, and both domestic household pet and petting zoo exposures have been identified as potential sources of exposure. Research has typically focussed on the prevalence, concentration, and transmission of zoonoses from farm animals to humans, yet there are gaps in our understanding of these factors among animals in contact with the public who don't live on or visit farms. This study aims to quantify, through a systematic review and meta-analysis, the prevalence and concentration of Campylobacter carriage in household pets and petting zoo animals. Four databases were accessed for the systematic review (PubMed, CAB direct, ProQuest, and Web of Science) for papers published in English from 1992-2012, and studies were included if they examined the animal population of interest, assessed prevalence or concentration with fecal, hair coat, oral, or urine exposure routes (although only articles that examined fecal routes were found), and if the research was based in Canada, USA, Europe, Australia, and New Zealand. Studies were reviewed for qualitative synthesis and meta-analysis by two reviewers, compiled into a database, and relevant studies were used to create a weighted mean prevalence value. There were insufficient data to run a meta-analysis of concentration values, a noted study limitation. The mean prevalence of Campylobacter in petting zoo animals is 6.5% based on 7 studies, and in household pets the mean is 24.7% based on 34 studies. Our estimated concentration values were: 7.65x103cfu/g for petting zoo animals, and 2.9x105cfu/g for household pets. These results indicate that Campylobacter prevalence and concentration are lower in petting zoo animals compared with household pets and that both of these animal sources have a lower prevalence compared with farm animals that do not come into contact with the public. There is a lack of studies on Campylobacter in petting zoos and/or fair animals in Canada and abroad. Within this literature, knowledge gaps were identified, and include: a lack of concentration data reported in the literature for Campylobacter spp. in animal feces, a distinction between ill and diarrheic pets in the reported studies, noted differences in shedding and concentrations for various subtypes of Campylobacter, and consistent reporting between studies.

Area-level global and local clustering of human Salmonella Enteritidis infection rates in the city of Toronto, Canada, 2007-2009.

BACKGROUND: Salmonella enterica serotype Enteritidis (S. Enteritidis) remains a major foodborne pathogen in North America yet studies examining the spatial epidemiology of salmonellosis in urban environments are lacking. Our ecological study combined a number of spatial statistical methods with a geographic information system to assess area-level heterogeneity of S. Enteritidis infection rates in the city of Toronto. METHODS: Data on S. Enteritidis infections between January 1, 2007 and December 31, 2009 were obtained from Ontario's surveillance system, and were grouped and analyzed at the forward sortation area (FSA)-level (an area signified by the first three characters of the postal code). Incidence rates were directly standardized using the FSA-level age- and sex-based standard population. A spatial empirical Bayes method was used to smooth the standardized incidence rates (SIRs). Global clustering of FSAs with high or low non-smoothed SIRs was evaluated using the Getis-Ord G method. Local clustering of FSAs with high, low, or dissimilar non-smoothed SIRs was assessed using the Getis-Ord Gi* and the Local Moran's I methods. RESULTS: Spatial heterogeneity of S. Enteritidis infection rates was detected across the city of Toronto. The non-smoothed FSA-level SIRs ranged from 0 to 16.9 infections per 100,000 person-years (mean = 6.6), whereas the smoothed SIRs ranged from 2.9 to 11.1 (mean = 6.3). The global Getis-Ord G method showed significant (p ≤ 0.05) maximum spatial clustering of FSAs with high SIRs at 3.3 km. The local Getis-Ord Gi* method identified eight FSAs with significantly high SIRs and one FSA with a significantly low SIR. The Local Moran's I method detected five FSAs with significantly high-high SIRs, one FSA with a significantly low-low SIR, and four significant outlier FSAs (one high-low, and three low-high). CONCLUSIONS: Salmonella Enteritidis infection rates clustered globally at a small distance band, suggesting clustering of high SIRs in small distinct areas. This finding was supported by the local cluster analyses, where distinct FSAs with high SIRs, mainly in downtown Toronto, were detected. These areas should be evaluated by future studies to identify risk factors of disease in order to implement targeted prevention and control programs. We demonstrated the usefulness of combining several spatial statistical techniques with a geographic information system to detect geographical areas of interest for further study, and to evaluate spatial processes that influenced S. Enteritidis infection rates. Our study methodology could be applied to other foodborne disease surveillance data.

Estimates of foodborne illness-related hospitalizations and deaths in Canada for 30 specified pathogens and unspecified agents.

Foodborne illness estimates help to set food safety priorities and create public health policies. The Public Health Agency of Canada estimates that 4 million episodes of foodborne illness occur each year in Canada due to 30 known pathogens and unspecified agents. The main objective of this study was to estimate the number of domestically acquired foodborne illness-related hospitalizations and deaths. Using the estimates of foodborne illness for Canada along with data from the Canadian Hospitalization Morbidity Database (for years 2000-2010) and relevant international literature, the number of hospitalizations and deaths for 30 pathogens and unspecified agents were calculated. Analysis accounted for under-reporting and underdiagnosis. Estimates of the proportion foodborne and the proportion travel-related were incorporated for each pathogen. Monte Carlo simulations were performed to account for uncertainty generating mean estimates and 90% probability intervals. It is estimated that each year there are 4000 hospitalizations (range 3200-4800) and 105 (range 75-139) deaths associated with domestically acquired foodborne illness related to 30 known pathogens and 7600 (range 5900-9650) hospitalizations and 133 (range 77-192) deaths associated with unspecified agents, for a total estimate of 11,600 (range 9250-14,150) hospitalizations and 238 (range 155-323) deaths associated with domestically acquired foodborne illness in Canada. Key pathogens associated with these hospitalizations or deaths include norovirus, nontyphoidal Salmonella spp., Campylobacter spp., VTEC O157 and Listeria monocytogenes. This is the first time Canada has established pathogen-specific estimates of domestically acquired foodborne illness-related hospitalizations and deaths. This information illustrates the substantial burden of foodborne illness in Canada.

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.

Evaluating area-level spatial clustering of Salmonella Enteritidis infections and their socioeconomic determinants in the greater Toronto area, Ontario, Canada (2007 - 2009): a retrospective population-based ecological study.

BACKGROUND: There have been only a few region-level ecological studies conducted in Canada investigating enteric infections in humans. Our study objectives were to 1) assess the spatial clustering of Salmonella enterica serotype Enteritidis (S. Enteritidis) human infections in the Greater Toronto Area, and 2) identify underlying area-level associations between S. Enteritidis infection rates and socioeconomic status (SES) indicators that might explain the clustering of infections. METHODS: Retrospective data on S. Enteritidis infections from 2007 to 2009 were obtained from Ontario's reportable disease surveillance database and were grouped at the forward sortation area (FSA) - level. A spatial scan statistic was employed to identify FSA-level spatial clusters of high infection rates. Negative binomial regression was used to identify FSA-level associations between S. Enteritidis infection rates and SES indicators obtained from the 2006 Census of Canada. Global Moran's I statistic was used to evaluate the final model for residual spatial clustering. RESULTS: A spatial cluster that included nine neighbouring FSAs was identified in downtown Toronto. A significant positive curvilinear relationship was observed between S. Enteritidis infection rates and FSA-level average number of children at home per census family. Areas with high and areas with low average median family income had higher infection rates than FSAs with medium average median family income. Areas with a high proportion of visible minority population had lower infection rates than FSAs with a medium proportion of visible minority population. The Moran's I statistic was not significant, indicating that no residual spatial autocorrelation was present after accounting for the SES variables in the final model. CONCLUSIONS: Our study demonstrated that FSAs with high and low average median family income, medium proportion of visible minority population, and high average number of children at home per census family had the highest S. Enteritidis infection rates. These areas should be targeted when designing disease control and prevention programs. Future studies are needed in areas with high S. Enteritidis infection rates to identify sources of environmental contamination of the local food supply, to assess food safety practices at local food markets, retail stores, and restaurants, and to identify novel individual-level risk factors.

A Canadian application of one health: integration of Salmonella data from various Canadian surveillance programs (2005-2010).

Most bacterial pathogens associated with human enteric illness have zoonotic origins and can be transmitted directly from animals to people or indirectly through food and water. This multitude of potential exposure routes and sources makes the epidemiology of these infectious agents complex. To better understand these illnesses and identify solutions to reduce human disease, an integrative approach like One Health is needed. This article considers the issue of Salmonella in Canada and interprets data collected by several Canadian surveillance and research programs. We describe recovery of Salmonella from various samples collected along the exposure pathway and compare the serovars detected in the different components under surveillance (animal, food, environment, and human). We then present three examples to illustrate how an approach that interprets multiple sources of surveillance data together is able to address issues that transcend multiple departments and jurisdictions. First, differences observed in recovery of Salmonella from different cuts of fresh chicken collected by different programs emphasize the importance of considering the surveillance objectives and how they may influence the information that is generated. Second, the high number of Salmonella Enteritidis cases in Canada is used to illustrate the importance of ongoing, concurrent surveillance of human cases and exposure sources to information domestic control and prevention strategies. Finally, changing patterns in the occurrence of ceftiofur-resistant Salmonella Heidelberg in retail meats and humans demonstrates how integrated surveillance can identify an issue in an exposure source and link it to a trend in human disease. Taken together, surveillance models that encompass different scales can leverage infrastructure, costs, and benefits and generate a multidimensional picture that can better inform disease prevention and control programs.