Catherine Yoshida

Catherine Yoshida
Public Health Agency of Canada | PHAC · National Microbiology Laboratory at Guelph

M.Sc.

About

37
Publications
4,899
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
611
Citations

Publications

Publications (37)
Article
Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the...
Preprint
Full-text available
BioHansel performs high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k -mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically stru...
Article
Full-text available
Previously we developed and tested the Salmonella GenoSerotyping Array (SGSA), which utilized oligonucleotide probes for O- and H- antigen biomarkers to perform accurate molecular serotyping of 57 Salmonella serotypes. Here we describe the development and validation of the ISO 17025 accredited second version of the SGSA (SGSA v. 2) with reliable an...
Data
Reported and predicted serotypes for publicly available NCBI Illumina WGS isolates used for testing the SGSA v. 2 in silico protocol. (XLSX)
Data
Primers and probe sequences for the SGSA v. 2. (XLSX)
Data
Reported and predicted serotypes for isolates used for testing the SGSA v. 2 in vitro protocol. (XLSX)
Data
In silico performance summary of the SGSA v. 2 on Illumina based on serotype. (XLSX)
Article
Full-text available
We report here 32 completed closed genome sequences of strains representing 30 serotypes of Salmonella . These genome sequences will provide useful references for understanding the genetic variation within Salmonella enterica serotypes, particularly as references to aid in comparative genomics studies, as well as providing information for improving...
Article
Full-text available
We report here the completed closed genome sequences of strains representing 36 serotypes of Salmonella . These genome sequences will provide useful references for understanding the genetic variation between serotypes, particularly as references for mapping of raw reads or to create assemblies of higher quality, as well as to aid in studies of comp...
Article
Full-text available
Public health and food safety institutions around the world are adopting whole genome sequencing (WGS) to replace conventional methods for characterizing Salmonella for use in surveillance and outbreak response. Falling costs and increased throughput of WGS have resulted in an explosion of data, but questions remain as to the reliability and robust...
Article
Full-text available
Salmonella serotyping remains the gold-standard tool for the classification of Salmonella isolates and forms the basis of Canada’s national surveillance program for this priority foodborne pathogen. Public health officials have been increasingly looking toward whole genome sequencing (WGS) to provide a large set of data from which all the relevant...
Article
Full-text available
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS databas...
Article
Full-text available
Purpose of review Non-typhoidal Salmonella (NTS) are among the most commonly reported cause of bacterial foodborne zoonoses. In this review, we discuss the current status of non-typhoidal salmonellosis with respect to its epidemiology, pathogenesis, antimicrobial resistance, and prevention and control measures. Recent findings Among the NTS, a rel...
Article
Classification by serotyping is the essential first step in the characterization of Salmonella isolates and is important for surveillance, source tracking and outbreak detection. In order to improve detection and reduce the burden of Salmonellosis, several rapid and high throughput molecular Salmonella serotyping methods have been developed. The a...
Article
Full-text available
We report the draft genome sequences of 25 Salmonella enterica strains representing 24 different serotypes, many of which were not available in public repositories during our selection process. These draft genomes will provide useful reference for the genetic variation between serotypes and aid in the development of molecular typing tools.
Article
Full-text available
For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-...
Data
A cgMLST clustering threshold of 85% similarity balances the proportion of genomes in multi-isolate cgMLST clusters and the serovar specificity of cgMLST clusters. Analyses in this study were performed at a cgMLST clustering threshold of 85% profile similarity. This value maximized the proportion of genomes in clusters with a minimum cluster size o...
Data
Information on genomes (n = 4,291) used to test and validate the SISTR platform. Included are error codes described in Fig 1, along with in silico predictions, and genome quality metrics. (XLSX)
Article
Full-text available
We have developed a Salmonella genoserotyping array (SGSA) which rapidly generates an antigenic formula consistent with the White-Kauffmann-Le Minor scheme, currently the gold standard for Salmonella serotyping. A set of 287 strains representative of 133 Salmonella serovars was assembled to validate the array and to test the array probes for accura...
Article
A DNA-based microarray designed to detect somatic (O) and flagellar (H) antigens present in the five most commonly isolated Salmonella serovars within Canada was developed as an alternative to the traditional Kauffmann-White serotyping scheme currently used to serotype salmonellae. Short oligonucleotide probes were designed based on publicly availa...
Article
Although Haemophilus parasuis is an important bacterial pathogen of swine, little is known about its pathogenesis or why some strains seem to be more virulent than others. Therefore, we used differential display reverse transcription-polymerase chain reaction (DDRT-PCR) to search for virulence-associated genes in a pathogenic serotype 5 strain, H....