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.

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.

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.

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.

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.

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.

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.

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.

Incidence, distribution, seasonality, and demographic risk factors of Salmonella Enteritidis human infections in Ontario, Canada, 2007-2009.

BACKGROUND: In Canada, surveillance systems have highlighted the increasing trend of Salmonella enterica serovar Enteritidis (S. Enteritidis) human infections. Our study objectives were to evaluate the epidemiology of S. Enteritidis infections in Ontario using surveillance data from January 1, 2007 through December 31, 2009. METHODS: Annual age-and-sex-adjusted incidence rates (IRs), annual and mean age-adjusted sex-specific IRs, and mean age-and-sex-adjusted IRs by public health unit (PHU), were calculated for laboratory-confirmed S. Enteritidis cases across Ontario using direct standardization. Multivariable Poisson regression with PHU as a random effect was used to estimate incidence rate ratios (IRRs) of S. Enteritidis infections among years, seasons, age groups, and sexes. RESULTS: The annual age-and-sex-adjusted IR per 100,000 person-years was 4.4 [95% CI 4.0-4.7] in 2007, and 5.2 [95% CI 4.8-5.6] in both 2008 and 2009. The annual age-adjusted sex-specific IRs per 100,000 person-years ranged from 4.5 to 5.5 for females and 4.2 to 5.2 for males. The mean age-adjusted sex-specific IR was 5.1 [95% CI 4.8-5.4] for females and 4.8 [95% CI 4.5-5.1] for males. High mean age-and-sex-adjusted IRs (6.001-8.10) were identified in three western PHUs, one northern PHU, and in the City of Toronto. Regression results showed a higher IRR of S. Enteritidis infections in 2009 [IRR = 1.18, 95% CI 1.06-1.32; P = 0.003] and 2008 [IRR = 1.17, 95% CI 1.05-1.31; P = 0.005] compared to 2007. Compared to the fall season, a higher IRR of S. Enteritidis infections was observed in the spring [IRR = 1.14, 95% CI 1.01-1.29; P = 0.040]. Children 0-4 years of age (reference category), followed by children 5-9 years of age [IRR = 0.64, 95% CI 0.52-0.78; P < 0.001] had the highest IRRs. Adults ≥ 60 years of age and 40-49 years of age [IRR = 0.31, 95% CI 0.26-0.37; P < 0.001] had the lowest IRRs. CONCLUSIONS: The study findings suggest that there was an increase in the incidence of S. Enteritidis infections in Ontario from 2007 to 2008-2009, and indicate seasonal, demographic, and regional differences, which warrant further public health attention.

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.

Estimates of the burden of foodborne illness in Canada for 30 specified pathogens and unspecified agents, circa 2006.

Estimates of foodborne illness are important for setting food safety priorities and making public health policies. The objective of this analysis is to estimate domestically acquired, foodborne illness in Canada, while identifying data gaps and areas for further research. Estimates of illness due to 30 pathogens and unspecified agents were based on data from the 2000-2010 time period from Canadian surveillance systems, relevant international literature, and the Canadian census population for 2006. The modeling approach required accounting for under-reporting and underdiagnosis and to estimate the proportion of illness domestically acquired and through foodborne transmission. To account for uncertainty, Monte Carlo simulations were performed to generate a mean estimate and 90% credible interval. It is estimated that each year there are 1.6 million (1.2-2.0 million) and 2.4 million (1.8-3.0 million) episodes of domestically acquired foodborne illness related to 30 known pathogens and unspecified agents, respectively, for a total estimate of 4.0 million (3.1-5.0 million) episodes of domestically acquired foodborne illness in Canada. Norovirus, Clostridium perfringens, Campylobacter spp., and nontyphoidal Salmonella spp. are the leading pathogens and account for approximately 90% of the pathogen-specific total. Approximately one in eight Canadians experience an episode of domestically acquired foodborne illness each year in Canada. These estimates cannot be compared with prior crude estimates in Canada to assess illness trends as different methodologies were used.

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.

Comparison of molecular typing methods useful for detecting clusters of Campylobacter jejuni and C. coli isolates through routine surveillance.

Campylobacter spp. may be responsible for unreported outbreaks of food-borne disease. The detection of these outbreaks is made more difficult by the fact that appropriate methods for detecting clusters of Campylobacter have not been well defined. We have compared the characteristics of five molecular typing methods on Campylobacter jejuni and C. coli isolates obtained from human and nonhuman sources during sentinel site surveillance during a 3-year period. Comparative genomic fingerprinting (CGF) appears to be one of the optimal methods for the detection of clusters of cases, and it could be supplemented by the sequencing of the flaA gene short variable region (flaA SVR sequence typing), with or without subsequent multilocus sequence typing (MLST). Different methods may be optimal for uncovering different aspects of source attribution. Finally, the use of several different molecular typing or analysis methods for comparing individuals within a population reveals much more about that population than a single method. Similarly, comparing several different typing methods reveals a great deal about differences in how the methods group individuals within the population.

Development and validation of a comparative genomic fingerprinting method for high-resolution genotyping of Campylobacter jejuni.

Campylobacter spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance- and outbreak-based epidemiologic investigations of Campylobacter spp. is critical to our understanding of sources and routes of transmission and the development of mitigation strategies to reduce the incidence of campylobacteriosis. We describe the development and validation of a rapid and high-resolution comparative genomic fingerprinting (CGF) method for C. jejuni. A total of 412 isolates from agricultural, environmental, retail, and human clinical sources obtained from the Canadian national integrated enteric pathogen surveillance program (C-EnterNet) were analyzed using a 40-gene assay (CGF40) and multilocus sequence typing (MLST). The significantly higher Simpson's index of diversity (ID) obtained with CGF40 (ID = 0.994) suggests that it has a higher discriminatory power than MLST at both the level of clonal complex (ID = 0.873) and sequence type (ID = 0.935). High Wallace coefficients obtained when CGF40 was used as the primary typing method suggest that CGF and MLST are highly concordant, and we show that isolates with identical MLST profiles are comprised of isolates with distinct but highly similar CGF profiles. The high concordance with MLST coupled with the ability to discriminate between closely related isolates suggests that CFG40 is useful in differentiating highly prevalent sequence types, such as ST21 and ST45. CGF40 is a high-resolution comparative genomics-based method for C. jejuni subtyping with high discriminatory power that is also rapid, low cost, and easily deployable for routine epidemiologic surveillance and outbreak investigations.

Effects of the Campylobacter jejuni CJIE1 prophage homologs on adherence and invasion in culture, patient symptoms, and source of infection.

BACKGROUND: Prophages of enteric bacteria are frequently of key importance for the biology, virulence, or host adaptation of their host. Some C. jejuni isolates carry homologs of the CJIE1 (CMLP 1) prophage that carry cargo genes potentially involved in virulence. Possible role(s) of CJIE1 homologs in the biology and virulence of C. jejuni were therefore investigated by using in vitro cell culture assays and by assessing the association of C. jejuni isolates with and without these prophages with patients' symptoms, with source, and with clonal lineages within the C. jejuni population. RESULTS: Four C. jejuni isolates, three carrying the CJIE1-like prophage and one without, were tested in cell culture assays for adherence and invasion. Both adherence and invasion of C. jejuni to cells in culture were increased by the presence of the CJIE1-family prophage. Differences in motility and growth rate did not appear to be responsible. The CJIE1 prophage was present in 23% of isolates from human and non-human sources combined that were obtained through sentinel-site surveillance, and the distribution of CJIE1 in this population showed modest clonal associations. There was no correlation between the presence of the CJIE1 prophage in C. jejuni and patient symptoms, although there was some statistical support for lower rates of abdominal pain and fever when the prophage was present. Little evidence was found for a role of the prophage in host adaptation or host specificity. CONCLUSION: These biological effects suggest that the presence of the prophage may be a marker for differential virulence of some C. jejuni isolates. Ongoing research into the effects of the prophage on protein expression may provide additional insights into the roles the prophage may play in the biology of its host bacterium.

Detection and characterization of Giardia duodenalis and Cryptosporidium spp. on swine farms in Ontario, Canada.

As part of the C-EnterNet surveillance program of the Public Health Agency of Canada, 122 pooled swine manure samples from 10 farms in Ontario, Canada were collected and tested for Giardia and Cryptosporidium. Giardia duodenalis cysts and Cryptosporidium spp. oocysts were detected using immunofluorescence microscopy. Nested-polymerase chain reaction protocols were performed to amplify the small subunit rRNA gene and the ß-giardin gene for G. duodenalis, and the small subunit rRNA gene and the heat shock protein-70 gene for Cryptosporidium spp. The DNA amplicons were sequenced to determine genotypes and species. A mixed multivariable method was used to compare the presence of Giardia and Cryptosporidium in different stages of production. Both Giardia cysts and Cryptosporidium oocysts were present on all tested farms, with 50.8% of the samples positive for G. duodenalis and 44.3% positive for Cryptosporidium spp. by microscopy, and 66.4% and 55.7%, respectively, positive by polymerase chain reaction (PCR). No significant agreement was observed between microscopy and PCR method to detect Giardia and Cryptosporidium (p<0.05). The prevalence of Giardia in manure pits and finisher pigs did not differ (p>0.05), however, it was less frequent (odds ratio, OR=0.21 [0.07, 0.63]) among sows. Cryptosporidium was more likely (OR=3.6 [1.3, 9.9]) to be detected in manure pits and weaners (OR=3.3 [1.1, 10.0]) compared to finisher pigs, and it was less frequent (OR=0.06 [0.007, 0.55]) in sows than in finishers (p<0.05). DNA sequencing demonstrated that 92.1% of the Giardia isolates were Assemblage B and 7.9% were Assemblage E. The most prevalent Cryptosporidium were Cryptosporidium parvum (55.4%), and Cryptosporidium sp. pig genotype II (37.5%). These findings indicate that the occurrence of zoonotic isolates of G. duodenalis and Cryptosporidium is very high on swine farms in southern Ontario, and that there is a potential for transmission between swine and humans by means of cyst and oocyst contaminated water or foods.

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).

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.

Rotaviruses from Canadian farm samples.

Animal rotavirus (RoV) strains detected in Canadian swine and dairy cattle farms were characterized by sequence analysis of viral protein 4 (VP4), VP6, VP7 and non-structural protein 4 segments from 15 RoV strains. Some porcine strains were found to contain a mixture of segments typical of human and animal viruses. One strain represented a novel VP6 genotype "I14", G2-P[27]-I14. Other strains detected in porcine samples represented multiple different segment types. These results illustrate the active evolution of animal RoV strains and underline the need for surveillance of both animal and human strains in public health-monitoring programs.