Bureau of Food Surveillance and Science Integration

Ottawa, Canada

Bureau of Food Surveillance and Science Integration

Ottawa, Canada
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Bertinato J.,Nutrition Research Division | Bertinato J.,University of Ottawa | Wang K.C.,Bureau of Food Surveillance and Science Integration | Hayward S.,Bureau of Food Surveillance and Science Integration
Nutrients | Year: 2017

Total serum magnesium (Mg) concentration (SMC) is commonly used to assess Mg status. This study reports current SMCs of Canadians and their associations with demographic factors, diabetes, and measures of glycemic control and insulin resistance using results from the Canadian Health Measures Survey cycle 3 (2012–2013). Associations were examined in adults aged 20–79 years using linear mixed models. Mean SMCs and percentile distributions for 11 sex-age groups between 3 and 79 years (n = 5561) are reported. SMCs were normally distributed and differences (p < 0.05) among sex and age groups were small. Between 9.5% and 16.6% of adult sex-age groups had a SMC below the lower cut-off of a population-based reference interval (0.75–0.955 mmol·L-1) established in the United States population as part of the NHANES I conducted in 1971–1974. Having diabetes was associated with 0.04 to 0.07 mmol·L-1 lower SMC compared to not having diabetes in the various models. Body mass index, glycated hemoglobin, serum glucose and insulin concentrations, and homeostatic model assessment of insulin resistance were negatively associated with SMC. This is the first study to report SMCs in a nationally representative sample of the Canadian population. A substantial proportion of Canadians are hypomagnesaemic in relation to a population-based reference interval, and SMC was negatively associated with diabetes and indices of glycemic control and insulin resistance. © 2017 by the authors. Licensee MDPI, Basel, Switzerland.


Nasheri N.,National Food Virology Reference Center | Petronella N.,Bureau of Food Surveillance and Science Integration | Ronholm J.,McGill University | Bidawid S.,National Food Virology Reference Center | Corneau N.,National Food Virology Reference Center
Frontiers in Microbiology | Year: 2017

Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use a de novo assembly of near-complete genome sequences. The resultant consensus sequences were then used to identify inter-host nucleotide variations that occur after direct transmission, analyze amino acid variations in the major capsid protein, and provide evidence of recombination events. The analysis of intra-host quasispecies diversity was possible due to high coverage-depth. We also observed a linear relationship between NoV viral load in the clinical sample and the number of sequence reads that could be attributed to NoV. The method demonstrated here has the potential for future use in whole genome sequence analyses of other RNA viruses isolated from clinical, environmental, and food specimens. © 2017 Nasheri, Petronella, Ronholm, Bidawid and Corneau.


Ronholm J.,Microbiology Research Division | Petronella N.,Bureau of Food Surveillance and Science Integration | Tamber S.,Microbiology Research Division
Genome Announcements | Year: 2016

A 2014 foodborne salmonellosis outbreak in Canada and the United States implicated, for the first time, sprouted chia seed powder as the vehicle of transmission. Here, we report the draft whole genome sequences of two Salmonella enterica strains isolated from sprouted powders related to the aforementioned outbreak. © Crown copyright 2016.


Ronholm J.,Microbiology Research Division | Petronella N.,Bureau of Food Surveillance and Science Integration | Tamber S.,Microbiology Research Division
Genome Announcements | Year: 2016

The diversity of the genus Salmonella is reflected in the physiological adaptations used by its members in response to stressors such as high pressure. Here we report the draft whole genome sequences of 11 Salmonella enterica strains, five sensitive strains and six demonstrating high levels of pressure resistance. © Crown copyright 2016.


Pightling A.W.,U.S. Food and Drug Administration | Petronella N.,Bureau of Food Surveillance and Science Integration | Pagotto F.,U.S. Food and Drug Administration
BMC Microbiology | Year: 2015

Background: Next-generation sequencing provides a powerful means of molecular characterization. However, methods such as single-nucleotide polymorphism detection or whole-chromosome sequence analysis are computationally expensive, prone to errors, and are still less accessible than traditional typing methods. Here, we present the Listeria monocytogenes core-genome sequence typing method for molecular characterization. This method uses a high-confidence core (HCC) genome, calculated to ensure accurate identification of orthologs. We also developed an evolutionarily relevant nomenclature based upon phylogenetic analysis of HCC genomes. Finally, we created a pipeline (LmCGST; https://sourceforge.net/projects/lmcgst/files/) that takes in raw next-generation sequencing reads, calculates a subject HCC profile, compares it to an expandable database, assigns a sequence type, and performs a phylogenetic analysis. Results: We analyzed 29 high-quality, closed Listeria monocytogenes chromosome sequences and identified loci that are reliable targets for automated molecular characterization methods. We identified 1013 open-reading frames that comprise our high-confidence core (HCC) genome. We then populated a database with HCC profiles from 114 taxa. We sequenced 84 randomly selected isolates from the Listeriosis Reference Service for Canada's collection and analysed them with the LmCGST pipeline. In addition, we generated pulsed-field gel electrophoresis, ribotyping, and in silico multi-locus sequence typing (MLST) data for the 84 isolates and compared the results to those obtained using the CGST method. We found that all of the methods yielded results that are generally congruent. However, due to the increased numbers of categories, the CGST method provides much greater discriminatory power than the other methods tested here. Conclusions: We show that the CGST method provides increased discriminatory power relative to typing methods such as pulsed-field gel electrophoresis, ribotyping, and multi-locus sequence typing while it addresses several shortcomings of other methods of molecular characterization with next-generation sequence data. It uses discrete, well-defined groupings (types) of organisms that are phylogenetically relevant and easily interpreted. In addition, the CGST scheme can be expanded to include additional loci and HCC profiles in the future. In total, the CGST method provides an approach to the molecular characterization of Listeria monocytogenes with next-generation sequence data that is highly reproducible, easily standardized, portable, and accessible. © 2015 Pightling et al.


Becalski A.,Food Research Division | Halldorson T.,University of Manitoba | Hayward S.,Bureau of Food Surveillance and Science Integration | Roscoe V.,Regions and Programs Bureau
Journal of Food Composition and Analysis | Year: 2016

Forty samples of commercially brewed coffee samples from 3 national chains and 48 samples of non-brewed coffee samples were collected from retail outlets located in a single Canadian city and analyzed for furan, 2-methylfuran and 3-methylfuran by headspace gas chromatography-mass spectrometry. Non-brewed samples were analyzed "as is" and some were also analyzed after brewing in the laboratory using several preparation techniques. The three analytes were detected in all samples. The rank order of concentrations for all samples was 2-methylfuran >furan > 3-methylfuran. Ground coffee types sampled included regular ground, decaffeinated and cartridge type coffee; mean furan concentrations for these coffee types were 2200, 2450 and 2360 ng/g; 9470, 10400 and 10700 ng/g for 2-methylfuran; and 447, 463 and 508 ng/g for 3-methylfuran respectively. Mean levels for both regular and decaffeinated instant coffee powders were lower with mean furan concentrations of 233 and 327 ng/g; 1600 and 1800 ng/g for 2-methylfuran and 72.9 and 75.2 ng/g for 3-methylfuran respectively. Commercially brewed coffee types sampled included regular ground, decaffeinated and espresso coffee; mean furan concentrations for these coffee types were 38.7, 53.1 and 157 ng/g; 172, 184 and 583 ng/g for 2-methylfuran; and 6.4, 6.7 and 19 ng/g for 3-methylfuran respectively. Brewing coffee samples in laboratory as per manufacturers' instructions resulted in 27-85% loss of furans-as compared to not brewed samples, loss of methyl furans exceeded that of furan by 10-15%. Brewed coffee stored/standing for up to 30 min resulted in further losses of furans, from 3 to 47%. Degree of loss was not analyte dependent but was highly influenced by storage conditions. © 2016 Published by Elsevier Inc.


Kalmokoff M.,Agriculture and Agri Food Canada | Franklin J.,Agriculture and Agri Food Canada | Petronella N.,Bureau of Food Surveillance and Science Integration | Green J.,Bureau of Nutrition | Brooks S.P.J.,Bureau of Nutrition
Nutrients | Year: 2015

Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA) comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut. Differentially abundant genes in each environment supported this shift away from the Firmicutes in the cecum (e.g., motility) towards the Bacteroidetes in feces (e.g., Bacteroidales transposons). We suggest that this phylum level change reflects a shift to ammonia as the primary source of nitrogen used to support continued microbial growth in the distal gut. © 2015 by the authors; licensee MDPI, Basel, Switzerland.


Rawn D.F.K.,Food Research Division | Sadler A.R.,Food Research Division | Quade S.C.,Food Research Division | Sun W.-F.,Food Research Division | And 4 more authors.
Chemosphere | Year: 2012

Chicken eggs from five different production types (conventional, omega-3 enriched, free range, organic and free run) were collected, when available, from three regions (west, central and east) of Canada to determine persistent organic pollutant (POP) concentrations. Total polychlorinated biphenyl (PCB) concentrations (∑37 congeners) in yolks from the eggs ranged from 0.162ngg-1 lipid to 24.8ngg-1 lipid (median 1.25ngg-1 lipid) while the concentration of the sum of the 6 indicator PCBs ranged from 0.100ngg-1 lipid to 9.33ngg-1 lipid (median 0.495ngg-1 lipid). Total polychlorinated dibenzo-p-dioxin/dibenzofuran (PCDD/F) concentrations ranged from 2.37pgg-1 lipid to 382pgg-1 lipid (median 9.53pgg-1 lipid). The 2005 WHO toxic equivalency (TEQ) ranged from 0.089pg TEQPCDD/F+dioxin-like[DL]-PCBg-1 lipid to 12.8pg TEQPCDD/F+DL-PCBg-1 lipid (median 0.342pg TEQPCDD/F+DL-PCBg-1 lipid). PCB and PCDD/F concentrations were significantly different (p<0.001) in egg yolks from different regions of collection. In contrast to observations in Europe, PCB and PCDD/F concentrations in Canadian egg yolks were not impacted solely by the production type (e.g., conventional, free range, organic, etc.) used to maintain the laying chickens. Additionally, only one Canadian free range yolk from western Canada (12.8pg TEQPCDD/F+DL-PCBg-1 lipid) exceeded the European toxic equivalent concentration limits for eggs (5pg TEQPCDD/F+DL-PCBg-1 lipid). This differs from observations in Europe where free range/home produced eggs frequently have higher POP concentrations than eggs from other production types. Median PCB dietary intake estimates based on consumption of eggs were less than 10ngd-1 while median PCDD/F intakes were less than 45pgd-1. © 2012.


Ronholm J.,Bureau of Microbial Hazards | Nasheri N.,Bureau of Microbial Hazards | Petronella N.,Bureau of Food Surveillance and Science Integration | Pagotto F.,Bureau of Microbial Hazards | Pagotto F.,Listeriosis Reference Center
Clinical Microbiology Reviews | Year: 2016

The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. WithWGS,unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated withWGSin comparison to traditional molecular subtyping techniques. © Crown copyright 2016.


PubMed | Bureau of Food Surveillance and Science Integration and Microbiology Research Division
Type: Comparative Study | Journal: Applied and environmental microbiology | Year: 2016

Vibrio parahaemolyticus is a bacterial pathogen that can cause illness after the consumption or handling of contaminated seafood. The primary virulence factors associated with V. parahaemolyticus illness are thermostable direct hemolysin (TDH) and Tdh-related hemolysin (TRH). However, clinical strains lacking tdh and trh have recently been isolated, and these clinical isolates are poorly understood. To help understand the emergence of clinical tdh- and trh-negative isolates, a genomic approach was used to comprehensively compare 4 clinical tdh- and trh-negative isolates with 16 environmental tdh- and trh-negative isolates and 34 clinical isolates positive for tdh or trh, or both, with the objective of identifying genomic features that are unique to clinical tdh- and trh-negative isolates. The prevalence of pathogenicity islands (PAIs) common to clinical isolates was thoroughly examined in each of the clinical tdh- and trh-negative isolates. The tdh PAI was not present in any clinical or environmental tdh- and trh-negative isolates. The trh PAI was not present in any environmental isolates; however, in clinical tdh- and trh-negative isolate 10-4238, the majority of the trh PAI including a partial trh1 gene was present, which resulted in reclassification of this isolate as a tdh-negative and trh-positive isolate. In the other clinical tdh- and trh-negative isolates, neither the trh gene nor the trh PAI was present. We identified 862 genes in clinical tdh- and trh-negative isolates but not in environmental tdh- and trh-negative isolates. Many of these genes are highly homologous to genes found in common enteric bacteria and included genes encoding a number of chemotaxis proteins and a novel putative type VI secretion system (T6SS) effector and immunity protein (T6SS1). The availability of genome sequences from clinical V. parahaemolyticus tdh- and trh-negative isolates and the comparative analysis may help provide an understanding of how this pathotype is able to survive in vivo during clinical illness.

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