U.S – A research initiative led by Kerry Cooper, Ph.D., Assistant Professor of Food Safety and Epidemiology at the University of Arizona, is examining the potential of a handheld genetic sequencing device for in-field microbial characterization of irrigation water in the produce industry.

Funded by the Center for Produce Safety, this innovative project aims to enhance microbial safety practices in crop irrigation, ultimately benefiting the entire produce supply chain.

Dr. Cooper drew inspiration from the Oxford MinION handheld genome sequencer’s successful use in Africa for genetic sequencing of lowland gorillas.

Recognizing its rapid results potential, Dr. Cooper and his team embarked on a journey to validate the device’s effectiveness for the produce industry. The goal was to ensure that the portable device could deliver results comparable to the industry-standard Illumina technology.

Collaborating with colleagues Kelly Bright, Ph.D., Channah Rock, Ph.D., and Walter Betancourt, Ph.D., from the University of Arizona, Dr. Cooper employed shotgun metagenomic sequencing, a cutting-edge approach creating genetic fingerprints of all organisms in a sample. This method allows for comprehensive microbial analysis, essential for assessing irrigation water safety.

Through rigorous testing using irrigation water samples from Yuma and Maricopa production areas, the researchers encountered challenges with high turbidity levels affecting sequencing success.

Despite this, the Oxford MinION demonstrated proficiency in detecting bacterial pathogens, albeit with limitations in detecting viruses and protozoa.

Promising potential

Dr. Cooper remains optimistic about the MinION’s potential in the produce industry, especially for bacterial detection.

The ongoing research aims to refine detection limits, particularly for bacteria, and explore strategies to extract protozoan genetic information effectively. These efforts align with industry needs for advanced microbial characterization tools, highlighting the project’s significance in advancing food safety practices.

The successful integration of portable genetic sequencers like the MinION could revolutionize microbial safety protocols in the produce sector. Rapid and accurate in-field microbial characterization would enable timely interventions, enhancing overall food safety standards and consumer confidence.

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