Variation in plasmid conjugation among nontyphoidal serovars.

Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors.

Comparative genomic analysis of Fischer F344 rat livers exposed for 90 days to 3-methylfuran or its parental compound furan.

Furan is a naturally forming compound found in heat-processed foods such as coffee, canned meats, and jarred baby food. It is concurrently found with analogues including 2-methylfuran (2-MF) and 3-methylfuran (3-MF), and toxicity studies demonstrate all are potent liver toxins. Toxicity studies found 3-MF is more toxic than either furan, or 2-MF.

Automated centrifugal microfluidic system for the preparation of adaptor-ligated sequencing libraries.

The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup.

A Bayesian method for identifying associations between response variables and bacterial community composition.

Determining associations between intestinal bacteria and continuously measured physiological outcomes is important for understanding the bacteria-host relationship but is not straightforward since abundance data (compositional data) are not normally distributed. To address this issue, we developed a fully Bayesian linear regression model (BRACoD; Bayesian Regression Analysis of Compositional Data) with physiological measurements (continuous data) as a function of a matrix of relative bacterial abundances. Bacteria can be classified as operational taxonomic units or by taxonomy (genus, family, etc.

Characterization of Atypical Shiga Toxin Gene Sequences and Description of Stx2j, a New Subtype.

Shiga toxin (Stx) is the definitive virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx variants are currently organized into a taxonomic system of three Stx1 (a, c, and d) and seven Stx2 (a, b, c, d, e, f, and g) subtypes. In this study, seven STEC isolates from food and clinical samples possessing sequences that do not fit current Shiga toxin taxonomy were identified.

Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries.

Background: Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes.

Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood.

Geographic food fraud - misrepresenting the geographic origin of a food item, is very difficult to detect, and therefore this type of fraud tends to go undetected. This potentially negatively impacts the health of Canadians and economic success of our seafood industry. Surveillance studies have shown that up to a significant portion of commercially sold seafood items in Canada are mislabeled or otherwise misrepresented in some way.

Shiga toxin-producing Escherichia coli survives storage in wheat flour for two years.

Wheat flour has recently been recognised as an exposure vehicle for the foodborne pathogen Shiga toxin-producing Escherichia coli (STEC). Wheat flour milled on two sequential production days in October 2016, and implicated in a Canada wide outbreak of STEC O121:H19, was analysed for the presence of STEC in November 2018. Stored in sealed containers at ambient temperature, the water activity of individual flour samples was below 0.

Foodborne viral outbreaks associated with frozen produce.

Over the past decade, frozen fruits have been a major vehicle of foodborne illnesses mainly attributed to norovirus (NoV) and hepatitis A virus (HAV) infections. Fresh produce may acquire viral contamination by direct contact with contaminated surface, water or hands, and is then frozen without undergoing proper decontamination. Due to their structural integrity, foodborne viruses are able to withstand hostile conditions such as desiccation and freezing, and endure for a long period of time without losing their infectivity.

Changes detected in the genome sequences of , , , and after serial subculturing.

Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures.

Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique.

Background: Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide.

The mechanisms that regulate Vibrio parahaemolyticus virulence gene expression differ between pathotypes.

Most Vibrio parahaemolyticus isolates found in marine environments are non-pathogenic; however, certain lineages have acquired genomic pathogenicity islands (PAIs) that enable these isolates to cause human illness. The V. parahaemolyticus PAI contains one or both of two toxins: thermostable direct haemolysin (TDH) or TDH-related haemolysin (TRH) and type III secretion system 2 (T3SS2).

Impact of β2-1 fructan on faecal community change: results from a placebo-controlled, randomised, double-blinded, cross-over study in healthy adults.

Healthy adults (n 30) participated in a placebo-controlled, randomised, double-blinded, cross-over study consisting of two 28 d treatments (β2-1 fructan or maltodextrin; 3×5 g/d) separated by a 14-d washout. Subjects provided 1 d faecal collections at days 0 and 28 of each treatment. The ability of faecal bacteria to metabolise β2-1 fructan was common; eighty-seven species (thirty genera, and four phyla) were isolated using anaerobic medium containing β2-1 fructan as the sole carbohydrate source.

An Analysis of Factors Associated with 25-Hydroxyvitamin D Levels in White and Non-White Canadians.

Vitamin D status was assessed in 19-79 year old whites (8351 participants of European ancestry) and non-whites (1840 participants encompassing all other ancestries) from cycles 1 to 3 (years 2007-2013) of the Canadian Health Measures Survey. Status was assessed using the U.S.

Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach.

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.

Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted Chia and Flax Seed Powders.

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.

Draft Genome Sequences of 11 Salmonella enterica Strains with Variable Levels of Barotolerance.

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.

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing.

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. With WGS, 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.

Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error.

Background: The influences that different programs and conditions have on error rates of single-nucleotide polymorphism (SNP) analyses are poorly understood. Using Illumina short-read sequence data generated from Listeria monocytogenes strain HPB5622, we assessed the performance of four SNP callers (BCFtools, FreeBayes, UnifiedGenotyper, VarScan) under a variety of conditions, including: (1) a range of sequencing coverages; (2) use of four popular reference-guided assemblers (Burrows-Wheeler Aligner, Novoalign, MOSAIK, SMALT); (3) with and without read quality trimming and filtering; and (4) use of different reference sequences.

Results: At 8-fold coverage the proportions of true positive calls ranged from 0.

Genomic Features of Environmental and Clinical Vibrio parahaemolyticus Isolates Lacking Recognized Virulence Factors Are Dissimilar.

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).

The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data.

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.

Phylum level change in the cecal and fecal gut communities of rats fed diets containing different fermentable substrates supports a role for nitrogen as a factor contributing to community structure.

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.

Draft Whole-Genome Sequences of 14 Vibrio parahaemolyticus Clinical Isolates with an Ambiguous K Serogroup.

Vibrio parahaemolyticus is a bacterial pathogen responsible for mild to severe gastroenteritis, wound infections, and septicemia resulting from the ingestion or handling of raw or undercooked contaminated seafood. Here, we report the draft whole-genome sequences and annotations of 14 Canadian V. parahaemolyticus clinical isolates that were serologically identified as K group II using polyvalent antisera but were not specifically K serogrouped using monovalent antisera.

Draft Genome Sequences of Four Vibrio parahaemolyticus Isolates from Clinical Cases in Canada.

Vibrio parahaemolyticus is a leading cause of bacterial gastroenteritis following ingestion of contaminated seafood. This report presents the draft genome sequences of four clinical strains of V. parahaemolyticus isolated in Canada.

Draft Genome Sequence of Bacillus megaterium Type Strain ATCC 14581.

Bacillus megaterium is a Gram-positive, rod-shaped, spore-forming bacterium of biotechnological importance. Here, we report a 5.7-Mbp draft genome sequence of B.