With funding from the Center for Produce Safety, a researcher from the University of Arizona is exploring the usefulness of a handheld genetic sequencing device for in-field microbial characterization of irrigation water by the produce industry.
Inspired by the use of the Oxford MinION handheld genome sequencer in Africa for sequencing genetic information from lowland gorillas, Kerry Cooper, Ph.D., Assistant Professor of Food Safety and Epidemiology at the University of Arizona sought to determine whether the tool could be used by the produce industry to ensure the microbial safety of crop irrigation water. Although the Oxford MinION could provide results rapidly—in a few days or less, which would greatly benefit the produce industry in moving their products while they are as fresh as possible—Dr. Cooper and his team first had to make sure that the portable device could produce results comparable to the industry gold-standard sequencing method, Illumina technology.
Joining Dr. Cooper as co-investigators in the project are his University of Arizona colleagues, Kelly Bright, Ph.D., Channah Rock, Ph.D., and Walter Betancourt, Ph.D.
The new detection method is based in a relatively new technology called shotgun metagenomic sequencing. This approach involves the creation of genetic fingerprints for all the organisms in a sample, rather than testing for genetic information specific to an individual microbe, which is more labor- and cost-intensive. When given an irrigation water sample, the Oxford MinION sequences the DNA for all of the bacteria, fungi, and viruses that are present. Next, a computer program matches the DNA sequences to a genetic database of known organisms for identification.
To test the Oxford MinION against the Illumina, the researchers used irrigation water samples collected from the Yuma and Maricopa production areas and spiked with varying quantities of three bacteria, two viruses, and one protozoan pathogen. Notably, however, the spiking levels used in the study were much higher than populations typically found in irrigation water.
The handheld device worked well in detecting bacterial pathogens, but was not as effective when it came to the protozoan pathogen. The Oxford MinION was also unable to detect any DNA or RNA associated with viruses, which Dr. Cooper believes could be due to the general physiology and make up of viruses that makes them more challenging to detect than bacteria or protozoa.
Water turbidity also affected sequencing success, with issues arising at high turbidity levels. However, even the low turbidity levels used in the study would be pushing the sediment limits that the produce industry typically uses. In high-turbidity samples, the researchers first had to drop out the sediments before sequencing.
Limitations aside, Dr. Cooper believes the MinION holds promise for the produce industry, and his findings thus far show that the portable sequencer can potentially work for bacteria. The researchers plan to continue to work with the MinION to try to reduce bacterial detection limits from what they initially observed. They hope that by applying different technologies, the device’s detection limits will be brought down to real-world levels. The team is also working on ways to get extract protozoan genetic information.
