New Competitive Research Grants Awarded to the Agriculture and Food Laboratory

Submitted by on Thu, 07/22/2021 - 11:18

The Agriculture and Food Laboratory has been awarded two competitive research grants funded by the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) under the Canadian Agricultural Partnership, a five-year federal-provincial-territorial initiative program (



OAF-2019-100450 - Comprehensive evaluation of a high throughput culture-independent diagnostic test (CIDT) against standard methods for simultaneous detection of common food-borne pathogens in foods 

Principle Researcher: Dr. Shu Chen, the Agriculture and Food Laboratory, University of Guelph  

Project Duration: December 2020 – January 2023   

Project Description: Food-borne diseases are caused by a long list of foodborne pathogens. Current methods for pathogen detection are limited to detect one or a few organisms at a time. A targeted selective testing approach is currently used in monitoring programs based on prior knowledge of pathogen prevalence in a food commodity. This approach is complicated and resource-consuming, and may not capture all pathogens present. We have developed a high throughput culture-independent sequencing method based on the combined 16S and 23S rRNA gene sequences of bacteria to simultaneously detect common foodborne bacterial pathogens and indicators in one test. This project aims to evaluate the method against standard methods using naturally contaminated foods from monitoring and surveillance programs. The project is expected to result in an improved assay and analytical data that can help to understand the value and the impacts of the CIDT on food safety testing to support future food safety programs in Ontario. 


OAF-2019-100464 - Evaluation of a High Throughput CRISPR Sequence-Based Method for Identification of Multiple Salmonella Serovars in a Sample from Poultry Production Environments  

Principle Researchers: Dr. Shu Chen and Dr. Carlos Leon-Velarde, the Agriculture and Food Laboratory, University of Guelph  

Project Duration: December 2020 – August 2022  

Project Description: Salmonella is one of the most important agents of human food-borne illness. Public Health Agency of Canada estimates Salmonella causes 80,000 cases each year in Canada. Salmonella resides with poultry as a major reservoir and consists of over 2600 serotypes which can differ in transmission route and pathogenic capacity. Poultry production environments are known to have a high risk of Salmonella contamination associated with many different serotypes. Current detection methods often identify only a single Salmonella serotype in a sample missing secondary or additional serotypes. Intervention efforts, then, are based on a partial picture of Salmonella in poultry environments, compromising the effectiveness of efforts to minimize food-borne Salmonella infections.  

 High throughput sequencing (HTS) approaches are now reported for the identification of multiple Salmonella serotypes at once. However, these methods cannot be used directly without their adaptation and validation under applied conditions. This project aims to evaluate an HTS-based method for simultaneous detection of numerous Salmonella serotypes in poultry environmental samples in a single test. The method, once validated, can be used to support improved interventions in poultry monitoring programs to enhance food safety.