Monitoring microbes with handheld DNA sequencers

Researchers from the Teagasc Food Research Centre and APC Microbiome Ireland have tested handheld DNA sequencers as a routine microbial monitoring solution for food production facilities, finding that they have key advantages in ease of use and in identifying a broad variety of bacteria. Their study has been published in npj Science of Food.

Microbes can cause food spoilage and disease, so routine checks on the microbial life in food production facilities is a necessity. However, current techniques to achieve this, while tried and tested, have some limitations.

“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,” said senior study author Professor Paul Cotter, from the Teagasc Food Research Centre and APC Microbiome Ireland. “This is a time-consuming approach and only microorganisms that are being specifically tested for are identified.”

DNA sequencing offers an alternative. Instead of culturing bacterial samples in petri dishes, it can rapidly analyse bacterial DNA and identify the species in a sample. The problem is that conventional DNA sequencing involves expensive lab-based equipment and only highly trained lab technicians can perform the procedure and analyse the results, which isn’t ideal for routine microbial surveillance in busy food production facilities.

A newer technology offers rapid DNA sequencing with an easy-to-use handheld device, but no one had tested its potential in food production — until now. Prof Cotter and colleagues, led by Teagasc’s Dr Aoife McHugh, set out to investigate how such portable sequencing technology would compare with lab-based sequencing, using swab samples from a working dairy facility.

Strikingly, the handheld device proved to be similar to the larger lab-based sequencing system in terms of the number of bacterial species it could identify in the 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, and in the well-cleaned dairy facility there simply weren’t enough bacteria in many of the samples. The researchers therefore had to perform an extra step to amplify the bacterial DNA before there was enough to analyse; further developments with the technology may help to overcome this minor hurdle.

“As microbiologists, the use of DNA sequencing has revolutionised our understanding of fascinating microbial communities at the bottom of oceans, the tops of icebergs and a huge range of other environments,” said Prof Cotter. “While such studies have the potential to impact on our lives in the longer term, the use of these technologies to enhance food quality and safety can have a very rapid impact on everyday life. This 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.”

Image credit: ©stock.adobe.com/au/freshidea

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