A5078853574- Antimicrobial Resistance in Staphylococcus
- Streptococcal Infections and Treatments
- Botulinum Toxin and Related Neurological Disorders
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Viral gastroenteritis research and epidemiology
- Vibrio bacteria research studies
- Plant Pathogenic Bacteria Studies
- Bacterial biofilms and quorum sensing
- Aquaculture disease management and microbiota
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Infective Endocarditis Diagnosis and Management
- Diphtheria, Corynebacterium, and Tetanus
- Identification and Quantification in Food
- Antibiotic Resistance in Bacteria
- Listeria monocytogenes in Food Safety
- Animal Virus Infections Studies
- Escherichia coli research studies
- Acne and Rosacea Treatments and Effects
- Salmonella and Campylobacter epidemiology
- Oral Health Pathology and Treatment
- Pediatric health and respiratory diseases
- Insect Resistance and Genetics
- Hereditary Neurological Disorders
Health Canada
2016-2025
Medscape
2023
University of California, Irvine
2023
BC Centre for Disease Control
2023
McGill University
2023
Nunavik Regional Board of Health and Social Services
2023
Public Health Agency of Canada
2011-2017
Western University
2006
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development new bioinformatics tools, including a notable proliferation phylogenomics pipelines designed infectious surveillance and outbreak investigation. Transitioning use WGS data out research laboratory into front lines response requires user-friendly, reproducible scalable that have been well validated. Single Nucleotide Variant Phylogenomics (SNVPhyl) is pipeline...
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...
Abstract Two methods were compared for their ability to accurately identify Vibrio species of interest: whole genome sequencing as the reference method and MALDI-TOF MS (matrix-assisted laser desorption/ionization-time flight mass spectrometry) proteome fingerprinting. The accuracy spectrometry–based identification was evaluated its isolates cholerae parahaemolyticus . Identification result each isolate obtained by spectrometry (WGS). system had excellent performance V. grown on a...
ABSTRACT Human noroviruses are the leading cause of non-bacterial shellfish-associated gastroenteritis. In 2022, a multi-jurisdictional norovirus outbreak associated with contaminated oysters occurred that involved hundreds illnesses. Here, we conducted genetic analysis on 30 clinical samples this oyster outbreak. We first determined capsid genotypes by Sanger sequencing and viral titers droplet-digital reverse transcription PCR. Multiple were identified in outbreak, which could indicate...
Cutibacterium acnes is a bacterial skin commensal that often isolated during routine testing of blood products like platelet concentrates (PCs). Due to the slow growing nature this bacterium in culture media, C. contaminated PCs are transfused into vulnerable patients before retrieval these units can be initiated. This study aimed at obtaining whole genome sequence six isolates derived from and phylotype, compare, assess their genetic backgrounds. Furthermore, genomes PC were compared...
Cutibacterium acnes is a bacterial skin commensal that often isolated during routine testing of blood products like platelet concentrates (PCs). Due to the slow-growing nature this bacterium in culture media, C. contaminated PCs are transfused into vulnerable patients before retrieval these units can be initiated. This study aimed at obtaining whole-genome sequence six isolates derived from PCs, comparing and assessing their genetic backgrounds. Furthermore, whole genomes PC were compared...
Abstract Motivation The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development new bioinformatics tools, including a notable proliferation phylogenomics pipelines designed infectious surveillance and outbreak investigation. Transitioning use WGS data out research lab into front lines response requires user-friendly, reproducible, scalable that have been well validated. Results SNVPhyl (Single Nucleotide Variant...
We sequenced 175 Clostridium botulinum type E strains isolated from food, clinical, and environmental sources northern Canada analyzed their neurotoxin (bont) coding sequences (CDSs). In addition to bont/E1 bont/E3 variant types, sequence analysis identified two novel BoNT variants termed E10 E11. Strains producing were found along the eastern coastlines of Hudson Bay shores Ungava Bay, while E11 only in Koksoak River region Nunavik. BoNT/E3 widespread throughout Canada, with exception coast Bay.
Clostridium botulinum group II isolates (n = 163) from different geographic regions, outbreaks, and neurotoxin types subtypes were characterized in silico using whole-genome sequence data. Two clusters representing a variety of (BoNT) identified by multilocus typing (MLST) core single nucleotide polymorphism (SNP) analysis. While one cluster included BoNT/B4/F6/E9 nontoxigenic members, the other comprised wide BoNT/E subtype strain. In MLST SNP methods consistent terms clade-level isolate...
Pulsed-field gel electrophoresis and DNA sequence analysis of 26 strains Group II (nonproteolytic) Clostridium botulinum type B4 showed that 23 carried their neurotoxin gene cluster on a 47–63 kb plasmid (three lacked any hybridization signal for the gene, presumably having lost plasmid). Unexpectedly, no genes were found chromosome. This apparent constraint transfer to chromosome stands in marked contrast I C. botulinum, which clusters are routinely both locations. The three main classes...
The ready availability of vast amounts genomic sequence data has created the need to rethink comparative genomics algorithms using ‘big data’ approaches. Neptune is an efficient system for rapidly locating differentially abundant content in bacterial populations exact k-mer matching strategy, while accommodating mismatches. Neptune’s loci discovery process identifies sequences that are sufficiently common a group target and absent from non-targets probabilistic models. uses parallel...
Analysis of more than 150 Clostridium botulinum Group II type E genomes identified a small fraction (6%) where neurotoxin-encoding genes were located on plasmids. Seven closely related (134–144 kb) neurotoxigenic plasmids subtypes E1, E3, and E10 characterized; all carried associated with plasmid mobility via conjugation. Each contained the same 24-kb neurotoxin cluster cassette (six six flanking genes) that had split helicase gene, rather common chromosomal rarA. The cassettes evolved as...
We present the genome sequence of Staphylococcus aureus strain PS/BAC/317/16/W, which was isolated from contaminated platelet concentrates by National Health Service Blood and Transplant in England (2017). Genome analysis revealed presence one chromosome (2,665,983 bp) two plasmids (4,265 bp 2,921 this strain.
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies inform public health and food safety decision-making. This study 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 2011, including nine outbreaks, was undertaken (1) characterize their phylogenetic relationship at finished genome-level resolution, (2) elucidate the underlying genetic diversity within an endemic subtype, CC8, (3)...
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.
Whole-genome sequence analysis of noroviruses is routinely performed by employing a metagenomic approach. While this methodology has several advantages, such as allowing for the examination co-infection, it some limitations, requirement high viral load to achieve full-length or near genomic sequences. In study, we used pre-amplification step obtain amplicons from 39 Canadian GII isolates, followed deep sequencing on Illumina and Oxford Nanopore platforms. This approach significantly reduced...
SUMMARY An outbreak of Legionnaires' disease occurred in an inner city district Calgary, Canada. This spanned a 3-week period November–December 2012, and total eight cases were identified. Four these critically ill requiring intensive care admission but there was no associated mortality. All tested positive for Legionella pneumophila serogroup 1 (LP1) by urinary antigen testing. Five the patients culture LP1 from respiratory specimens. These isolates further identified as Knoxville...
Here, we report the high-quality complete genome sequences and plasmid arrays of Priestia megaterium ATCC 14581 T two clinical strains (2008724129 2008724142) isolated from human samples in United States.
Metagenomics analysis of foods has the potential to provide comprehensive data on presence and prevalence antimicrobial resistance (AMR) genes in microbiome foods. However, AMR are generally present low abundance compared other bacterial food consequently require multiple rounds in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting plasmid genes, is used characterize resistome plasmidome retail beef, chicken, oyster, shrimp, veal enrichment...
Foodborne botulism is a neuroparalytic disease caused by ingestion of foods contaminated with botulinum neurotoxin (BoNT), produced Clostridium . In 1995 husband and wife from Québec, Canada, were hospitalized for several months prolonged muscle paralysis after ingesting commercial pâté de campagne Examination faecal samples both patients the viable Group I (proteolytic) C. type B each three samples. Whole genome sequencing revealed that all isolates contain identical bont/B5 bont/F2 genes...
The spore-forming, anaerobic bacterium, Clostridium botulinum, can cause intestinal toxemia (colonization) botulism in adults and infants by colonizing the gut producing botulinum neurotoxin situ. In 2006, peanut butter was identified as a lab-confirmed source of C. spores for an adult colonization case Canada. It is recommended to be exposed at early age help prevent development allergy, yet prevalence retail butters currently unknown. This report details survey that conducted 2007 presence...
Staphylococcus aureus has been involved in transfusion-transmitted fatalities associated with platelet concentrates (PCs) due to its heightened pathogenicity enhanced by genome-encoded virulence and antibiotic resistance genes. This may be facilitated mobile genetic elements (MGEs) that can cause rearrangements. Several factors contribute S. virulence, including the type VII secretion system (T7SS), composed of six core genes conserved across strains. In this study, we conducted comparative...
The ready availability of vast amounts genomic sequence data has created the need to rethink comparative genomics algorithms using “big data” approaches. Neptune is an efficient system for rapidly locating differentially abundant content in bacterial populations exact k -mer matching strategy, while accommodating mismatches. Neptune’s loci discovery process identifies sequences that are sufficiently common a group target and absent from non-targets probabilistic models. uses parallel...
We found that heterozygous mutant alleles of E(Pc) and esc increased homologous recombination from an allelic template in somatic cells a P-element-induced double-strand break repair assay. Flies for these genes showed genome stability decreased levels apoptosis imaginal discs concomitant increase survival following ionizing radiation. propose this was caused by genomewide cells. A double had no additive effect, showing act the same pathway. Finally, we deficiency histone deacetylase, Rpd3,...