The njp Science of Food journal recently published an article about handheld DNA sequencing devices for monitoring environmental factors in food factories.
The study was completed by scientists from the Teagasc food research program and APC Microbiome Ireland's Scientific Foundation Ireland Research Centre, and it looked at using portable DNA sequencers as a routine microbial monitoring tool in food production facilities. Funding was provided by the Department of Agriculture, Food, and the Marine.
Routine checks are necessary in production sites, because microbes in food can cause spoilage and disease. Correct identification of microorganisms in the food chain allow sources of contamination to be identified, and therefore control measures can be put in place. Researchers have noted that current techniques, although proven to work, do have some limitations.
The senior author of the study, Professor Paul Cotter, has said that microbiology testing in the food chain continues to reply on older testing such as the use of agar and Petri dishes. However, this is a time-consuming approach, and only microorganisms that are being specifically test for are able to be identified.
DNA sequencing is able to rapidly analyze bacterial DNA and identify the species in a sample, versus culturing bacterial samples in Petri dishes. Unfortunately, conventional sequencing uses expensive lab-based equipment, and only highly-trained technicians can do the procedure and analyze the results. Therefore, it would not be a good fit for routing microbial surveillance in busy food production plants.
Professor Cotter and his colleagues compared Oxford Nanopore Technologies' performance and Illumina sequencing to culture-based methods, in their evaluation of environmental monitoring of a dairy plant.
Oxford Nanopores' MinION handheld device has potential as a routine monitoring device in food production, as it was similar to the larger lab-based sequencing system in terms of the number of bacterial species it can identify in samples. However, the MinION device requires a minimum amount of DNA before it can function efficiently and correctly.
The study looked at eight locations in the dairy facility, which were swabbed on three different days from October–December 2018. The swabs were taking after cleaning in place, but before the next round of dairy processing.
In the cleaned facility, there weren't enough bacteria in some of the samples, so researchers had to amplify the bacterial DNA before they were able to analyze it. Further development of the technology may help to overcome this issue in the future.
Previously, scientists were able to determine the ability of MinION-based rapid sequencing to correctly classify a four-strain, mock community of related spore-forming microorganisms. These microorganisms have relevance to the dairy processing chain, including Bacillus cereus, which can cause infection in humans.
Cotter said that the study represents a key step towards a day when non-experts can use DNA sequencing tools to carry out microbiology testing in the food chain. The use of this technology can enhance food qualify and safety, which can have an impact on everyday life.