Funding period: 2023-2028
Lead: Adam Koziol and Catherine Carrillo
Total GRDI funding: $274,000
Regulatory food safety agencies work to protect the food supply using informed, risk-based approaches. Getting the most information possible from laboratory testing is crucial for an effective response. Genomics technologies, like next-generation sequencing, offer fast and more comprehensive analyses. Over the past decade, CFIA food microbiology laboratories have sequenced nearly 10,000 bacterial isolates, including a collection of over 4,000 foodborne pathogens from inspection and surveillance samples. This whole-genome sequence database is a valuable asset for the agency that can be mined to support both research and diagnostic objectives.
However, providing reliable access to this massive dataset has been a challenge. To solve this, the Ottawa Laboratory Carling team developed and actively develops FoodPort, a user-friendly cloud application. FoodPort provides direct access to genome data and is used for genome analysis within the CFIA's regulatory food testing program.
This project aims to support the continued development of the FoodPort platform on the CFIA's Microsoft Azure cloud tenant, ensuring CFIA scientists can reliably access and interpret food microbiology sequencing data. As part of this effort, the team has also implemented methods for the in silico validation of test methods using large, comprehensive panels of bacterial pathogens. These ongoing enhancements are essential for driving efficient regulatory responses and keeping the food supply safe.
Research tool / process
PrimerFinder is a software tool that was added as an enhancement to FoodPort to offer the following functionalities: 1) PrimerValidator, which evaluates binding of primer pairs against curated inclusivity/exclusivity panels; 2) PrimerVerifier, which evaluates binding of one or more primer pairs against flexible inclusivity/exclusivity panels; 3) PrimerFinder, which evaluates binding of one or more primer pairs against assemblies
AmpliSeq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment. The FoodPort implementation of AmpliSeq allows users to upload sequencing reads, select primer sequences, read trimming and filtering options, taxonomy options, genus/genera to exlude, and the database, including the version of the database to use.
FileZone is a collection of tools on FoodPort that allow users to manage containers located in Azure cloud. There are three main functionalities of the FileZone: 1) Select an Existing Container, which allows users to specify a container name, and view, upload, or download files in the container; 2) Create a New Container, which allows users to create a new container, and upload files to the container; 3) Located files, which allows users to search for files and/or containers using regular expressions.
Dataset / database
Shiga Toxin Allele Database (StxDB): A comprehensive, curated database of Shiga toxins including all known nucleotide and protein sequence variants to enable accurate determination of Shiga-toxin variants. This database has now been curated to provide accession numbers for representative genomes to enable database users to assess reliability of results.
Contact us
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca