Publications by authors named "Taryn B T Athey"
Here, we introduce , an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of = 0.001).
View Article and Find Full Text PDFBackground: The number of invasive group A (iGAS) infections due to hitherto extremely rare type strains has increased in several Canadian provinces since late 2015. We hypothesized that the cases recorded in the different provinces are linked and caused by strains of an clone that recently emerged and expanded explosively.
Methods: We analyzed both active and passive surveillance data for iGAS infections and used whole-genome sequencing to investigate the phylogenetic relationships of the strains responsible for these invasive infections country-wide.
Article Synopsis
- The study focused on understanding how pili, which help group B Streptococcus (GBS) infect hosts, are structured and differ across various strains in Toronto, Canada.
- Researchers analyzed 1332 GBS isolates using PCR and whole genome sequencing, discovering a new variant of a key pilin protein, named BP-1b, which showed only 63% similarity to the standard version of the protein.
- The findings highlighted that this new variant appears frequently in specific GBS serotypes but is undetectable with common testing methods, suggesting that incorporating new PCR primers could improve the accuracy of identifying strains.
The capsular polysaccharide (CPS) is the major virulence factor of the emerging zoonotic pathogen Streptococcus suis. CPS differences are also the basis for serological differentiation of the species into 29 serotypes. Serotypes 2 and 1/2, which possess identical gene content in their cps loci, express CPSs that differ only by substitution of galactose (Gal) by N-acetylgalactosamine (GalNAc) in the CPS side chain.
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- Invasive group A Streptococcus (iGAS) disease is on the rise globally, particularly due to the emergence of a new variant called clade 3, which has unclear clinical characteristics.
- A study conducted in Toronto over 14 years analyzed the genetic data of iGAS isolates, revealing a significant increase in clade 3 cases after its emergence, with overall disease incidence rising from 0.14 to 0.22 per 100,000 people.
- Clade 3 strains are associated with more cases of arthritis but fewer instances of necrotizing fasciitis, and they predominantly affect younger and middle-aged individuals.
Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by . In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65.
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- Shiga toxin-producing E. coli strains, particularly O157:H7, are linked to outbreaks and infections globally.
- This study focuses on the high-quality draft genome sequences of 19 O157:H7 strains isolated in Argentina.
- The findings contribute to a better understanding of these strains and their incidence in human health.
We report several cases of recombination events leading to capsular switching among sequence type (ST) 1 group B Streptococcus strains. These strains otherwise shared a common genome backbone with serotype V ST1 strains. However, the genomes of ST1 serotype V strains and those of serotypes VI, VII, and VIII strains differed substantially.
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- * A specific GBS strain, NGBS375, has a unique genetic makeup, combining elements from different strains, which affects its virulence during infection.
- * Although strain NGBS375 causes less severe infections compared to a more virulent strain, it has a similar ability to provoke an immune response, suggesting that its lower virulence is likely due to its limited growth and spread in the bloodstream.
Article Synopsis
- Researchers have developed a new pipeline that allows for the identification of all 29 serotypes of Streptococcus suis directly from whole-genome sequencing (WGS) data.
- This automated system uses a custom database and differential alignment techniques, successfully differentiating between previously indistinguishable serotypes through specific genetic mutations.
- The pipeline has shown high accuracy in identifying serotypes, with a 99% match to traditional methods and a 92% match using additional genomic data, thereby resolving a long-standing challenge in S. suis classification.
Article Synopsis
- Researchers studied bacterial clones of Streptococcus suis, a pig pathogen, and found both encapsulated and unencapsulated forms existed in over half of the endocarditis samples.
- Genome sequencing revealed unique mutations in the cps gene across pairs of isolates, with distinct differences in mutation rates between two sequence types (ST1 and ST28).
- The study suggests that these dual phenotypes (encapsulated and unencapsulated) emerged independently through random mutations, highlighting the genetic diversity and adaptability of bacteria in the same environment.
Article Synopsis
- Strains of serotype 2 Streptococcus suis cause infections in both pigs and humans, and this study explored genetic diversity within the common ST25 lineage using whole-genome sequencing.
- The analysis of 51 strains from Canada, the U.S., and Thailand revealed significant genomic rearrangements and indicated that lateral gene transfer and recombination contribute to the genetic diversity of ST25.
- The research identified two distinct clades corresponding to Thai and North American strains with unique antimicrobial resistance patterns and highlighted the limitations of multilocus sequence typing (MLST) for understanding S. suis evolution.
An outbreak of type emm59 invasive group A Streptococcus (iGAS) disease was declared in 2008 in Thunder Bay District, Northwestern Ontario, 2 years after a countrywide emm59 epidemic was recognized in Canada. Despite a declining number of emm59 infections since 2010, numerous cases of iGAS disease continue to be reported in the area. We collected clinical information on all iGAS cases recorded in Thunder Bay District from 2008 to 2013.
View Article and Find Full Text PDFStreptococcus suis is a major swine pathogen and a zoonotic agent. Serotype 2 strains are the most frequently associated with disease. However, not all serotype 2 lineages are considered virulent.
View Article and Find Full Text PDFSerotype 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 genes encoding antimicrobial resistance in 85 invasive serotype IV GBS strains.
View Article and Find Full Text PDFTyping of group A Streptococcus (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 different emm types and used bioinformatics tools to derive commonly used GAS typing information directly from the short-read WGS data.
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