A5019488638- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Antibiotic Resistance in Bacteria
- Biomedical Text Mining and Ontologies
- Vibrio bacteria research studies
- Gut microbiota and health
- Semantic Web and Ontologies
- Influenza Virus Research Studies
- RNA and protein synthesis mechanisms
- Respiratory viral infections research
- Salmonella and Campylobacter epidemiology
- Mycobacterium research and diagnosis
- Bioinformatics and Genomic Networks
- Ethics in Clinical Research
- Data-Driven Disease Surveillance
- Microbial Community Ecology and Physiology
- Plant Virus Research Studies
- Microbial infections and disease research
- Animal Disease Management and Epidemiology
- Oral microbiology and periodontitis research
- Traditional Chinese Medicine Studies
- Genomics and Rare Diseases
- Linguistics and Cultural Studies
- Molecular Biology Techniques and Applications
- Clostridium difficile and Clostridium perfringens research
Simon Fraser University
2009-2025
BC Centre for Disease Control
2012-2024
University of British Columbia
2013-2023
Genome British Columbia
2023
Bridge University
2022
Faculty of Public Health
2022
Public Health Agency of Canada
2021-2022
Provincial Health Services Authority
2015-2020
Public Health Laboratory
2019
Kainan University
2013
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses high-quality data sequences within controlled vocabulary, Ontology (ARO), designed by biocuration team to integrate with software development efforts for resistome analysis prediction, such as CARD's Gene Identifier (RGI)...
Abstract The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation interpretation of resistomes. As version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, 5057 detection models that can be used by accompanying Gene Identifier (RGI) software annotate genomic or...
Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes wide range of compounds and represents genus considerable industrial interest. has one the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in linear chromosome three plasmids. A targeted insertion methodology was developed determine telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich oxygenases (203)...
Despite widespread use of antibiotics for the treatment life-threatening infections and research on role commensal microbiota, our understanding their effects host is still very limited.Using a popular mouse model microbiota depletion by cocktail antibiotics, we analysed combining intestinal transcriptome together with metagenomic analysis gut microbiota. In order to identify specific microbes microbial genes that influence phenotype in antibiotic-treated mice, developed applied transkingdom...
The construction of high capacity data sharing networks to support increasing government and commercial exchange has highlighted a key roadblock: the content existing Internet-connected information remains siloed due multiplicity local languages dictionaries. This lack digital lingua franca is obvious in domain human food as materials travel from their wild or farm origin, through processing distribution chains, consumers. Well defined, hierarchical vocabulary, connected with logical...
Abstract Summary: Genomic islands (clusters of genes potential horizontal origin in a prokaryotic genome) are frequently associated with particular adaptation microbe that is medical, agricultural or environmental importance, such as antibiotic resistance, pathogen virulence, metal resistance. While many sequence features have been adopted separately applications for analysis genomic islands, including pathogenicity there no single application integrates multiple island detection. IslandPath...
Abstract Background Genomic islands (GIs) are clusters of genes in prokaryotic genomes probable horizontal origin. GIs disproportionately associated with microbial adaptations medical or environmental interest. Recently, multiple programs for automated detection have been developed that utilize sequence composition characteristics, such as G+C ratio and dinucleotide bias. To robustly evaluate the accuracy methods, we propose a dataset be constructed using criteria independent...
Microbial genes that are "novel" (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests there many more such novel yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification putative (clusters probable horizontal origin a prokaryotic genome) 63 genomes, then characterized the distribution features. All but few genomes examined contained...
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...
Abstract Background Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, may lead to severe life-threatening infections. These polymicrobial with high bacterial diversity. Understanding the spatial transition microbiota from normal oral cavities through infected root canal acute periapical abscess can improve our knowledge pathogenesis endodontic more effective treatment. We obtained samples cavity, 8 patients (5 localized 3 systemic infections)....
Background It has been noted that many bacterial virulence factor genes are located within genomic islands (GIs; clusters of in a prokaryotic genome probable horizontal origin). However, such studies have limited to single genera or isolated observations. We performed the first large-scale analysis multiple diverse pathogens examine this association. additionally identified found predominantly pathogens, but not non-pathogens, across using 631 complete genomes, and we common trends for GIs....
Bacterial diversity in endodontic infections has not been sufficiently studied. The use of modern pyrosequencing technology should allow for more comprehensive analysis than traditional Sanger sequencing. This study investigated bacterial through taxonomic classification based on 16S rRNA gene sequences generated by 454 GS-FLX and conventional capillary sequencing technologies. Sequencings were performed 7 specimens from infections. On average, 47 vs. 28,590 obtained per sample...
Select bacteria, such as Escherichia coli or coliforms, have been widely used sentinels of low water quality; however, there are concerns regarding their predictive accuracy for the protection human and environmental health. To develop improved monitoring systems, a greater understanding bacterial community structure, function, variability across time is required in context different pollution types, agricultural urban contamination. Here, we present year-long survey free-living DNA...
Giardia causes the diarrheal disease known as giardiasis; transmission through contaminated surface water is common. The protozoan parasite's genetic diversity has major implications for human health and epidemiology. To determine extent of from wildlife water, we performed whole-genome sequencing (WGS) to characterize 89 duodenalis isolates both outbreak sporadic infections: 29 raw 38 humans, 22 veterinary sources. Using single nucleotide variants (SNVs), combined with epidemiological data,...
Abstract Background The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools resources, advocate greater openness, interoperability, accessibility, reproducibility in public health microbial bioinformatics. In face current pandemic, PHA4GE has identified need fit-for-purpose, open-source SARS-CoV-2...
Abstract Background Acinetobacter baumannii has recently emerged as a significant global pathogen, with surprisingly rapid acquisition of antibiotic resistance and spread within hospitals health care institutions. This study examines the genomic content three A. strains isolated from distinct body sites. Isolates blood, peri-anal, wound sources were examined in an attempt to identify genetic features that could be correlated each isolation source. Results Pulsed-field gel electrophoresis,...
MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied pathogen outbreak surveillance. Traditionally, based on identifying types from small number of housekeeping genes. With the increasing availability whole-genome sequencing data, methods have evolved towards larger typing schemes, few hundred genes [core genome (cgMLST)] to thousand [whole (wgMLST)]. Such large-scale schemes been shown provide finer resolution and are increasingly used in various...
Abstract Whole genome sequencing (WGS) is a powerful tool for public health infectious disease investigations owing to its higher resolution, greater efficiency, and cost-effectiveness over traditional genotyping methods. Implementation of WGS in routine microbiology laboratories impeded by lack user-friendly automated semi-automated pipelines, restrictive jurisdictional data sharing policies, the proliferation non-interoperable analytical reporting systems. To address these issues, we...
Globalization of food networks increases opportunities for the spread foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping promises to vastly improve our ability track control disease, but do so it must be combined with epidemiological, clinical, laboratory other health care data (called "contextual data") meaningfully interpreted regulatory interventions, outbreak investigation, risk assessment. However, current multi-jurisdictional...
(MABS) is a pathogenic bacterium that can cause severe lung infections, particularly in individuals with cystic fibrosis. MABS colonies exhibit either smooth (S) or rough (R) morphotype, influenced by the presence absence of glycopeptidolipids (GPLs) on their surface, respectively. Despite clinical significance these morphotypes, relationship between GPL levels, morphotype and pathogenesis infections remains poorly understood.