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Scientists Evaluate Handheld DNA Sequencers for Microbial Monitoring of Food

Image created by Dr. Michael J. Miller

Researchers have evaluated a handheld DNA sequencing device for use in environmental monitoring at food factories.

The study, by researchers from the Teagasc food research program and APC Microbiome Ireland’s Science Foundation Ireland Research Centre, tested portable DNA sequencers as a routine microbial monitoring tool in food production facilities. It was funded by the Department of Agriculture, Food and the Marine (DAFM).

Small, portable, DNA sequencers provide the first steps toward real-time industry paced microbial classification and analysis, said researchers in the journal npj Science of Food.

Microbes in food can cause spoilage and disease, so routine checks in production sites are necessary. Accurate identification of microorganisms in the food chain allows sources of contamination to be identified and control measures to be put in place. However, current techniques, while tried and tested, have some limitations, researchers reported.

Advancing microbiology

“Microbiology testing in the food chain has, and continues to, rely on older, classical microbiology testing such as the use of agar and petri dishes. This is a time-consuming approach and only microorganisms that are being specifically tested for are identified,” said professor Paul Cotter, the study’s senior author.

Instead of culturing bacterial samples in petri dishes, DNA sequencing can rapidly analyze bacterial DNA and identify the species in a sample. However, conventional sequencing involves expensive lab-based equipment and only highly trained technicians can do the procedure and analyze results. This means it isn’t a good fit for routine microbial surveillance in busy food production plants.

Professor Cotter and colleagues, led by Aoife McHugh, compared the performance of Oxford Nanopore Technologies and Illumina sequencing to culture-based methods for environmental monitoring of a dairy plant.

Oxford Nanopore’s MinION handheld device was similar to the larger lab-based sequencing system in terms of the number of bacterial species it could identify in samples, suggesting it has potential as a routine monitoring device in food production. However, the small device requires a minimum amount of DNA before it can function correctly.

A step toward non-experts using DNA sequencing tools

Eight locations in the facility were swabbed on three different days in October, November, and December 2018, after cleaning in place but before the next round of dairy processing.

In the cleaned dairy facility there weren’t enough bacteria in many of the samples, so researchers had to perform an extra step to amplify the bacterial DNA before there was enough to analyze. They said further development of the technology may help to overcome this issue.

Researchers previously determined the ability of MinION-based rapid sequencing to correctly classify a four-strain, mock community of related spore-forming microorganisms of relevance to the dairy processing chain including Bacillus cereus, which can cause infections in humans.

Cotter said the use of DNA sequencing technologies to enhance food quality and safety can have an impact on everyday life.

“This study represents a key step toward a day when non-experts can use DNA sequencing tools to carry out microbiology testing in the food chain.”


McHugh, A.J., Yap, M., Crispie, F. et al. Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples. npj Sci Food 5, 4 (2021).

Source: Food Safety News

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