Welcome to Episode 7 in the CosmosID Microbiome Webinar Series where we’ll be exploring foodborne microbial pathogens.
For this webinar, Dr. Dele Ogunremi will be talking about his collaborative work with others on how genomics and bioinformatics have been applied leading to develop a universal detection methodology for microbial organisms in food.
The majority of pathogens contaminating food and capable of causing harm in humans are either not routinely tested for or sometimes escape detection, mitigating against a rational control strategy aimed at keeping the consumer safe. Given the diversity of the various microbial hazards, the development of a universal detection methodology is predictably faced with a plethora of challenges. Yet, a reliable universal protocol will overcome endless number of technical challenges that span different scientific fields including microscopy, virology, bacteriology, parasitology, molecular biology and statistics. Often enough, analyses of food samples result in lack of detection of the contaminating pathogen or inaccurate, suspicious and ambiguous outcomes and unactionable inferences. The application of genomics and bioinformatics layered on a foundational and sound understanding of the biology of the various microbial pathogens has led to the development of a unified protocol consisting of distinct steps that include: (a) global amplification of the DNA of the metagenome derived from a food sample, (b) nanopore sequencing of amplified DNA, and (c) optimized bioinformatics detection of targets using the CosmosID proprietary technology. Our protocol has led to the sensitive and accurate detection and identification to the species level of microbial contamination of lettuce (25 g) following spiking with bacteria, viruses and/or parasites at levels that include low pathogen load, namely: 1 colony forming unit of Salmonella, 5 oocysts of Cryptosporidium parvum and 500 plaque forming units of Hepatitis A virus. We have confirmed the approach using (1) spiked food samples blindly submitted to the testing laboratory and (2) naturally contaminated food samples that were the subjects of regulatory food recall. Although potentially disruptive, a reliable universal detection method will simplify and democratize hazard identification with the promise of application in both a controlled laboratory environment and on the field.
Dele Ogunremi is a research scientist at the Canadian Food Inspection Agency (CFIA), Ottawa Laboratory Fallowfield, and is a trained veterinarian with doctoral and postdoctoral training in Molecular Biology and Immunology. He obtained DVM (1984) and MVSc (1986) from the University of Ibadan, Nigeria and PhD from the University of Saskatchewan, Canada (1993), where he also completed a postdoctoral training (1996). He has worked for the Federal Government of Canada as a scientist for 25 years where he has developed research programs and projects in Animal Health, Food Safety and Genomics. He has developed over 30 new diagnostic protocols, completed over 50 research projects and achieved over 50 innovations, developed a DNA vaccine for avian influenza in chickens and has two patents granted in the United States and New Zealand, and one patent pending in Canada. He has served on the Editorial Boards of the Canadian Journal of Microbiology and Scientific World Journal. He is an Adjunct Professor in the Department of Food Science, University of Guelph, Canada. Over the last decade, he has focussed on the application of whole genome sequencing for the identification and characterization of foodborne microbial hazards.