A5030694979- Salmonella and Campylobacter epidemiology
- Genomics and Phylogenetic Studies
- Viral gastroenteritis research and epidemiology
- Bacteriophages and microbial interactions
- Escherichia coli research studies
- Vibrio bacteria research studies
- Gut microbiota and health
- Listeria monocytogenes in Food Safety
- Microbial Community Ecology and Physiology
- Aquaculture disease management and microbiota
- Probiotics and Fermented Foods
- Animal Virus Infections Studies
- Microbial Metabolites in Food Biotechnology
- Enterobacteriaceae and Cronobacter Research
- Biosensors and Analytical Detection
- Pediatric health and respiratory diseases
- Plant Pathogenic Bacteria Studies
- Drug Transport and Resistance Mechanisms
- Identification and Quantification in Food
- Virus-based gene therapy research
- Metabolomics and Mass Spectrometry Studies
- Health, Environment, Cognitive Aging
- Molecular Biology Techniques and Applications
- Yersinia bacterium, plague, ectoparasites research
- Advanced biosensing and bioanalysis techniques
Health Canada
2014-2024
University of Ottawa
2011-2013
The wide availability of whole-genome sequencing (WGS) and an abundance open-source software have made detection single-nucleotide polymorphisms (SNPs) in bacterial genomes increasingly accessible effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between (i.e., true SNPs) are detected at high rates the influences errors (such as false positive SNPs, ambiguously called sites, gaps) mitigated is utmost importance. choices researchers make regarding...
Shiga toxin (Stx) is the definitive virulence factor of toxin-producing Escherichia coli (STEC). Stx variants are currently organized into a taxonomic system three Stx1 (a, c, and d) seven Stx2 b, d, e, f, g) subtypes. In this study, STEC isolates from food clinical samples possessing stx2 sequences that do not fit current taxonomy were identified. Genome assemblies strains created Oxford Nanopore Illumina sequence data. The presence atypical was confirmed by Sanger sequencing, as expression...
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 still less accessible than traditional typing methods. Here, we present the Listeria monocytogenes core-genome method for This uses high-confidence core (HCC) genome, calculated ensure accurate identification orthologs. We also developed an evolutionarily...
Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization outbreak 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 genomes directly from clinical samples obtained 8 linked patients. Enough depth was each sample use de novo assembly...
ABSTRACT 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. are thermostable direct hemolysin (TDH) and Tdh-related (TRH). However, clinical strains lacking tdh trh have recently been isolated, these isolates poorly understood. To help understand emergence - -negative isolates, genomic approach was used to comprehensively compare 4 16 environmental 34 positive for ,...
Geographic food fraud - misrepresenting the geographic origin of a item, is very difficult to detect, and therefore this type tends go undetected. This potentially negatively impacts health Canadians economic success our seafood industry. Surveillance studies have shown that up significant portion commercially sold items in Canada are mislabeled or otherwise misrepresented some way. The current study aimed determine if microbiome fresh shellfish could be used as an accurate marker harvest...
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 four SNP callers (BCFtools, FreeBayes, UnifiedGenotyper, VarScan) under a variety conditions, including: (1) range sequencing coverages; (2) use popular reference-guided assemblers (Burrows-Wheeler Aligner, Novoalign, MOSAIK,...
Human norovirus is the leading cause of viral gastroenteritis globally, and GII.4 has been most predominant genotype for decades. This numerous variants that have caused repeated epidemics worldwide. However, molecular evolutionary signatures among not elucidated throughout genome. A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine sequences from clinical samples. Herein, obtained deep-sequencing data employed analyze full-genomic prevailing...
Abstract Background Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence this pathogen food often hampered by background microflora that may present as (false positives). False positive isolates belonging to genus Citrobacter can be difficult distinguish from due similarities their genetics, cell surface antigens, other phenotypes. In order understand genetic basis these similarities,...
Vitamin D status was assessed in 19-79 year old whites (8351 participants of European ancestry) and non-whites (1840 encompassing all other ancestries) from cycles 1 to 3 (years 2007-2013) the Canadian Health Measures Survey. Status using U.S. Institute Medicine (IOM) 25-hydroxyvitamin [25(OH)D] cut point values 30 40 nmol/L. Overall, median 25(OH)D concentrations were significantly higher [58.9 (28.6, 100.1) nmol/L; 5th 95th percentile] compared with [43.5 (19.0, 83.2); P < 0.001]. Values...
Fermentation differs between the proximal and distal gut but little is known regarding how bacterial communities differ or they are influenced by diet. In order to investigate this, we compared community diversity in cecum feces of rats 16S rRNA gene content DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut composition was dependent on source substrate included Cecal were dominated Firmicutes, contained a higher abundance Lachnospiraceae...
Abstract Healthy adults ( n 30) participated in a placebo-controlled, randomised, double-blinded, cross-over study consisting of two 28 d treatments β 2-1 fructan or maltodextrin; 3×5 g/d) separated by 14-d washout. Subjects provided 1 faecal collections at days 0 and each treatment. The ability bacteria to metabolise was common; eighty-seven species (thirty genera, four phyla) were isolated using anaerobic medium containing as the sole carbohydrate source. altered community determined...
Vibrio parahaemolyticus is a leading cause of bacterial gastroenteritis following ingestion contaminated seafood. This report presents the draft genome sequences four clinical strains V. isolated in Canada. All lack traditional pathogenic markers and possess uniquely individual characteristics identified using other typing criteria.
Using an advanced pneumatic centrifugal microfluidic technology and simple injected devices, we demonstrate a complete ligation-based library preparation procedure apply it to the characterization of foodborne pathogens.
Most Vibrio parahaemolyticus isolates found in marine environments are non-pathogenic; however, certain lineages have acquired genomic pathogenicity islands (PAIs) that enable these to cause human illness. The V. PAI contains one or both of two toxins: thermostable direct haemolysin (TDH) TDH-related (TRH) and type III secretion system 2 (T3SS2). Recently, a few do not this were obtained from clinical samples, there has been interest determining whether possess novel virulence factors. In...
Vibrio parahaemolyticus is a bacterial pathogen responsible for mild to severe gastroenteritis, wound infections, and septicemia resulting from the ingestion or handling of raw undercooked contaminated seafood. Here, we report draft whole-genome sequences annotations 14 Canadian V. clinical isolates that were serologically identified as K group II using polyvalent antisera but not specifically serogrouped monovalent antisera.
Bacillus megaterium is a Gram-positive, rod-shaped, spore-forming bacterium of biotechnological importance. Here, we report 5.7-Mbp draft genome sequence B. ATCC 14581, which the type strain species.
Clostridium botulinum is important for food safety and studies of neurotoxins associated with human botulism. We present the draft genome sequences two strains belonging to group II type B: one collected from Pacific Ocean sediments (DB-2) another obtained during a botulism outbreak (KAPB-3).
Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS significantly higher than that techniques, readily allows infrequent differences occur between 2 closely related strains to be found. In this investigation, was used identify the changes occurred in genomes of 13 foodborne pathogens after 100 serial subcultures. Pure cultures Shiga-toxin-producing Escherichia coli,...