A5109974922- Microbial Natural Products and Biosynthesis
- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Yersinia bacterium, plague, ectoparasites research
- Bacillus and Francisella bacterial research
- Tuberculosis Research and Epidemiology
- Pharmaceutical and Antibiotic Environmental Impacts
- Bacterial Identification and Susceptibility Testing
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
- Mycobacterium research and diagnosis
- RNA and protein synthesis mechanisms
- Vector-borne infectious diseases
- Microbial Metabolism and Applications
- Biochemical and Structural Characterization
- Carbohydrate Chemistry and Synthesis
- Antimicrobial Resistance in Staphylococcus
- Evolution and Genetic Dynamics
- Zoonotic diseases and public health
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Environmental DNA in Biodiversity Studies
- Escherichia coli research studies
- Plant-based Medicinal Research
- Enzyme function and inhibition
Sinai Health System
2024
McMaster University
2013-2023
University of Toronto
2022
Mount Sinai Hospital
2022
The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis genes, proteins and mutations involved in AMR. CARD ontologically structured, model centric, spans breadth AMR drug classes mechanisms, including intrinsic, mutation-driven acquired resistance. It built upon Ontology (ARO), custom built, interconnected hierarchical...
ABSTRACT The field of antibiotic drug discovery and the monitoring new resistance elements have yet to fully exploit power genome revolution. Despite fact that first genomes sequenced free living organisms were those bacteria, there been few specialized bioinformatic tools developed mine growing amount genomic data associated with pathogens. In particular, are study genetics genomics how it impacts bacterial populations, ecology, clinic. We initiated development such in form Comprehensive...
The latest DNA recovery and sequencing technologies have been used to reconstruct the genome of Yersinia pestis bacterium responsible for Black Death pandemic bubonic plague that spread across Europe in fourteenth century. was pieced together from total extracted skeletal remains four individuals excavated a large cemetery on site Royal Mint East Smithfield London, where more than 2,000 victims were buried 1348 1349. draft sequence does not differ substantially modern Y. strains, providing...
Antibiotic resistance is a global challenge that impacts all pharmaceutically used antibiotics. The origin of the genes associated with this significant importance to our understanding evolution and dissemination antibiotic in pathogens. A growing body evidence implicates environmental organisms as reservoirs these genes; however, role anthropogenic use antibiotics emergence controversial. We report screen sample culturable microbiome Lechuguilla Cave, New Mexico, region cave has been...
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial archaeal genomes. GIs are clusters genes probable horizontal origin, high interest since they disproportionately encode involved medically environmentally important adaptations, including antimicrobial resistance virulence. We now report major new release IslandViewer, last 2013. 3 incorporates completely genome visualization tool,...
The 14th–18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. reasons plague’s persistence and abrupt disappearance are poorly understood, but could have been due to either the presence now-extinct plague foci itself, or successive introductions from other locations. Here we present five Y. genomes one last European plague, 1722 Marseille, France. lineage identified has not found any extant sampled date, its ancestry strains obtained...
In the 19th century, there were several major cholera pandemics in Indian subcontinent, Europe, and North America. The causes of these outbreaks genomic strain identities remain a mystery. We used targeted high-throughput sequencing to reconstruct Vibrio cholerae genome from preserved intestine victim 1849 outbreak Philadelphia, part second pandemic. This O1 biotype has 95 97% similarity with classical O395 genome, differing by 203 single-nucleotide polymorphisms (SNPs), lacking three...
The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of genome evolution, antibiotic resistance virulence genes. Metadata, including genomic phenotypic data each isolate collection, are available through Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy results that emerged from first 389 genomes. With as yet unmatched resolution, confirm P. strains can be divided into three major groups...
Significance Environmental microorganisms are a source of diverse antibiotic resistance determinants. With the appropriate selection pressure, these genes can be mobilized to clinically relevant pathogens. Identifying and characterizing elements environmental resistome provides an early warning what we may expect encounter in clinic. We uncover conserved genetic element associated with various rifamycin antibiotic-inactivating mechanisms. This led identification new gene enzyme responsible...
The lipopeptide daptomycin is a member of the newest FDA-approved antimicrobial class, exhibiting potency against broad range Gram-positive pathogens with only rare incidences clinical resistance. Environmental bacteria harbor an abundance resistance determinants orthologous to those in and thus may serve as early-warning system for future emergence. A collection morphologically diverse environmental actinomycetes demonstrating unprecedented frequencies high levels by antibiotic inactivation...
ABSTRACT Vancomycin-resistant enterococci (VRE) are notorious clinical pathogens restricting the use of glycopeptide antibiotics in clinic setting. Routine surveillance to detect VRE isolated from patients relies on PCR bioassays and chromogenic agar-based test methods. In recent years, we others have reported emergence enterococcal strains harboring a “silent” copy vancomycin resistance genes that confer vancomycin-susceptible phenotype (vancomycin-susceptible [VSE]) thus escape detection...
Abstract Background Identification of transmission networks carbapenemase-producing organisms (CPO) is critical to identifying their reservoirs and limiting spread. This study aimed use whole-genome sequencing identify genomic relationships between CP Enterobacter (CP-Ent) in Ontario, Canada over a 15-year period. Methods All CP-Ent cases identified by prospective population-based surveillance the Toronto/Peel Region from first isolate 2007 2021, hospital sinks (2016-2019), wastewater...
ABSTRACT Invasive Group A streptococcal (iGAS) infections are rising in Canada and wordwide. The 2022–2023 Ontario iGAS season was among the highest recorded, a trend continuing 2023–2024. We sequenced 38 invasive (blood) 117 non-invasive (pharyngeal) Streptococcus pyogenes clinical isolates from Toronto (January–May 2023) to compare between two cohorts against published sequences determine if any genomic changes accounted for trend. Results demonstrated limited clustering with one small...
ABSTRACT Identifying and understanding the collection of all antibiotic resistance determinants presented in global microbiota, resistome, provides insight into evolution critical information for development future antimicrobials. The rifamycins are broad-spectrum antibiotics that target bacterial transcription by inhibition RNA polymerase. Although mutational alteration drug is predominant mechanism to this family clinic, a number diverse inactivation mechanisms have also been reported. In...
Abstract Rifampin (RIF) phosphotransferase (RPH) confers antibiotic resistance by conversion of RIF and ATP, to inactive phospho-RIF, AMP P i . Here we present the crystal structure RPH from Listeria monocytogenes (RPH- Lm ), which reveals that enzyme is comprised three domains: two substrate-binding domains (ATP-grasp RIF-binding domains); a smaller phosphate-carrying His swivel domain. Using solution small-angle X-ray scattering mutagenesis, reveal mechanism where domain transits between...