ABSTRACTTyping of group AStreptococcus (GAS) is crucial for infection control and epidemiology. While whole-genome sequencing (WGS) is revolutionizing the way that bacterial organisms are typed, it is necessary to provide backward... more
ABSTRACTTyping of group AStreptococcus (GAS) is crucial for infection control and epidemiology. While whole-genome sequencing (WGS) is revolutionizing the way that bacterial organisms are typed, it is necessary to provide backward compatibility with currently used typing schemas to facilitate comparisons and understanding of epidemiological trends. Here, we sequenced the genomes of 191 GAS isolates representing 42 differentemmtypes and used bioinformatics tools to derive commonly used GAS typing information directly from the short-read WGS data. We show thatemmtyping and multilocus sequence typing can be achieved rapidly and efficiently using this approach, which also permits the determination of the presence or absence of genes associated with GAS tissue tropism. We also report on how the WGS data analysis was instrumental in identifying ambiguities present in the commonly usedemmtype database hosted by the U.S. Centers for Disease Control and Prevention.
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Research Interests: Genetics, Microbiology, Medical Microbiology, Biology, Virology, and 14 moreMedicine, India, Phylogeny, Humans, Sequence alignment, Infant, Genotype, Genotyping, Genetic variation, Amino Acid Sequence, Base Sequence, Respiratory Syncytial Virus Infections Industry, Molecular Sequence Data, and Child preschool
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The button mushroom, Agaricus bisporus , is a commercially important cultivated filamentous fungus. During the last decade, the button mushroom industry has depended mainly on two strains (or derivatives of these two strains). Using one... more
The button mushroom, Agaricus bisporus , is a commercially important cultivated filamentous fungus. During the last decade, the button mushroom industry has depended mainly on two strains (or derivatives of these two strains). Using one of these highly successful strains (strain U1) we examined the phenomenon of strain instability, specifically, the production of irreversible sectors. Three “stromatal” and three “fluffy” sectors were compared with a healthy type U1 strain and with a wild-collected isolate. Compost colonization and fruit body morphology were examined. The main objective of this study, however, was to examine the meiotic stability of the sectored phenotype. Single basidiospores were isolated and subjected to a grain bioassay in which the ability to produce sectors was measured. Our results were as follows: (i) basidiospore cultures obtained from a wild-collected isolate showed no tendency to produce sectors; (ii) approximately 5% of the basidiospore cultures obtained ...
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outbreak investigations require the development of reliable typing methods to better understand the genetic relationships of the isolates involved. Here, we report the draft genome sequences of four clinical isolates obtained between 2000... more
outbreak investigations require the development of reliable typing methods to better understand the genetic relationships of the isolates involved. Here, we report the draft genome sequences of four clinical isolates obtained between 2000 and 2012 in Ontario, Canada.
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Despite its first appearance in 1962, human enterovirus D68 (EV-D68) has been recognized as an emerging respiratory pathogen in the last decade when it caused outbreaks and clusters in several countries including Japan, the Philippines,... more
Despite its first appearance in 1962, human enterovirus D68 (EV-D68) has been recognized as an emerging respiratory pathogen in the last decade when it caused outbreaks and clusters in several countries including Japan, the Philippines, and the Netherlands. The most recent and largest outbreak of EV-D68 associated with severe respiratory illness took place in North America between August 2014 and January 2015. Between September 1 and October 31 2014, EV-D68 infection was laboratory confirmed among 153/907 (16.9%) persons tested for the virus in Ontario, Canada, using real time RT-PCR and subsequent genotyping by sequencing of partial VP1 gene. In order to understand the evolutionary history of the 2014 North American EV-D68 outbreak, we conducted phylogenetic and phylodynamic analyses using available partial VP1 genes (n = 469) and NCBI available whole genome sequences (WGS) (n = 38). The global EV-D68 phylogenetic tree (n = 469) reconfirms the divergence of three distinct clades A,...
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Adult invasive disease caused by Group B Streptococcus (GBS) is increasing worldwide. Whole-genome sequencing (WGS) now permits rapid identification of recombination events, a phenomenon that occurs frequently in GBS. Using WGS, we... more
Adult invasive disease caused by Group B Streptococcus (GBS) is increasing worldwide. Whole-genome sequencing (WGS) now permits rapid identification of recombination events, a phenomenon that occurs frequently in GBS. Using WGS, we described that strain NGBS375, a capsular serotype V GBS isolate of sequence type (ST)297, has an ST1 genomic background but has acquired approximately 300 kbp of genetic material likely from an ST17 strain. Here, we examined the virulence of this strain in an in vivo model of GBS adult invasive infection. The mosaic ST297 strain showed intermediate virulence, causing significantly less systemic infection and reduced mortality than a more virulent, serotype V ST1 isolate. Bacteremia induced by the ST297 strain was similar to that induced by a serotype III ST17 strain, which was the least virulent under the conditions tested. Yet, under normalized bacteremia levels, the in vivo intrinsic capacity to induce the production of pro-inflammatory cytokines was s...
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Serotype IV group B Streptococcus (GBS) is emerging in Canada and the United States, with rates as high as 5% of the total burden of adult invasive GBS disease. To understand this emergence, we studied the population structure and... more
Serotype IV group B Streptococcus (GBS) is emerging in Canada and the United States, with rates as high as 5% of the total burden of adult invasive GBS disease. To understand this emergence, we studied the population structure and assessed the antimicrobial susceptibility of serotype IV isolates causing adult invasive infection in Manitoba and Saskatchewan, Canada, between 2010 and 2014. Whole-genome sequencing was used to determine multilocus sequence typing information and identify antimicrobial resistance-encoding genes in 85 invasive serotype IV GBS strains. Antimicrobial susceptibility testing was performed by standard methods. Strain divergence was assessed using genome-wide single-nucleotide polymorphism analysis. Serotype IV strains were responsible for 16.9% of adult invasive GBS infections in Manitoba and Saskatchewan during the period. The majority of serotype IV isolates (89%) were clonally related, tetracycline- erythromycin- and clindamycin-resistant sequence type (ST)...
Research Interests: Biology, Adolescent, Medicine, Clinical Microbiology, Biological Sciences, and 15 morePhylogeny, Humans, Female, Manitoba, Male, Cluster Analysis, Aged, Middle Aged, Genotype, Adult, Bacteremia, Microbial Sensitivity Tests, Multilocus sequence typing, Molecular Sequence Data, and Medical and Health Sciences
We report on an influenza B outbreak in an Ontario long-term care facility in which 2 immunized residents receiving oseltamivir prophylaxis for at least 5 days developed laboratory-confirmed influenza B infection. All isolates were tested... more
We report on an influenza B outbreak in an Ontario long-term care facility in which 2 immunized residents receiving oseltamivir prophylaxis for at least 5 days developed laboratory-confirmed influenza B infection. All isolates were tested for the most common oseltamivir resistance, and none of them had resistance identified.
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Research Interests: Long Term Care, Medical Microbiology, Medicine, Emerging Infectious Diseases, Molecular Epidemiology, and 15 moreDisease Outbreaks, Humans, Nursing Homes, Female, Male, Streptococcus Pyogenes, Ontario, Clinical Sciences, Antibiotics, Aged, Anti-Bacterial Agents, Public health systems and services research, Outbreak, Homes for the Aged, and Streptococcal infections
Research Interests: Microbiology, Medical Microbiology, Biology, Emerging Infectious Diseases, Disease Outbreaks, and 13 moreWater Supply, Humans, Campylobacter, Animals, Ontario, Phenotype, Clinical Sciences, Cattle, Genotype, Public health systems and services research, Water Microbiology, Outbreak, and Campylobacter jejuni
The ability of vancomycin resistance determinants to be horizontally transferred within enterococci species is a concern. Identification and characterization of vancomycin resistant enterococci (VRE) in a clinical isolate has a... more
The ability of vancomycin resistance determinants to be horizontally transferred within enterococci species is a concern. Identification and characterization of vancomycin resistant enterococci (VRE) in a clinical isolate has a significant impact on infection control practices. In this study, we describe a clinical isolate of E. gallinarum exhibiting high level resistance to vancomycin and teicoplanin. Genetic characterization of this isolate showed the presence of vanA and vanB genes in addition to naturally carrying vanC gene. vanA was identified on pA6981, a 35,608-bp circular plasmid with significant homology to plasmid pS177. vanB operon was integrated into the bacterial chromosome and showed high level of homology to previously reported Tn1549 and Tn5382. To the best of our knowledge, this is the first report of E. gallinarum carrying both vanA and vanB operons, indicating the importance of identifying vancomycin resistance mechanism in non- E. faecium and -E. faecalis enteroc...
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Research Interests: Epidemiology, Adolescent, Medicine, Multidisciplinary, Multivariate Analysis, and 14 moreDisease Outbreaks, Humans, Child, United States, Female, Male, Regression Analysis, Ontario, PLoS one, Odds ratio, Respiratory Tract Infections, Case Control Studies, Child preschool, and multiplex polymerase chain reaction
Immunocompromised patients are predisposed to infections caused by influenza virus. Influenza virus may produce considerable morbidity, including protracted illness and prolonged viral shedding in these patients, thus prompting higher... more
Immunocompromised patients are predisposed to infections caused by influenza virus. Influenza virus may produce considerable morbidity, including protracted illness and prolonged viral shedding in these patients, thus prompting higher doses and prolonged courses of antiviral therapy. This approach may promote the emergence of resistant strains. Characterization of neuraminidase (NA) inhibitor (NAI)-resistant strains of influenza A virus is essential for documenting causes of resistance. In this study, using quantitative real-time PCR along with conventional Sanger sequencing, we identified an NAI-resistant strain of influenza A (H3N2) virus in an immunocompromised patient. In-depth analysis by deep gene sequencing revealed that various known markers of antiviral resistance, including transient R292K and Q136K substitutions and a sustained E119K (N2 numbering) substitution in the NA protein emerged during prolonged antiviral therapy. In addition, a combination of a 4-amino-acid delet...