Will hygiene monitoring be the next big application for DNA sequencing?

Genome sequencing appears destined to become a standard clinical test. But what about applications of sequencing beyond health care?

Detecting microbial contamination is vital to ensure the safety of food, drinking water, or cosmetics, in biodefence, hospitals, and many other fields. A perfect monitoring system would be sensitive enough to quickly detect contamination by potentially dangerous microbes, and specific enough to avoid false alarms. There are reasons to believe that DNA sequencing could provide such a system.

Until now sequencing has been too expensive to be practical, but this is changing rapidly. I believe that as a result, hygiene monitoring could be one of the first commercially viable applications of sequencing outside of its traditional uses in research and the clinic.

Sequencing would be a uniquely valuable technology whenever it is necessary to distinguish between harmful and harmless microbes. For example, the bacterium E. coli is mostly harmless and can commonly be found in the gut of healthy humans. However, some strains can cause serious food poisoning and lead to human suffering and economic damage: The pathogenic O104:H4 strain of E. coli caused 50 deaths and $2.8bn in damages in Europe last summer. Distinguishing between strains is vital for many applications, and can in principle be achieved by sequencing.

Tests that detect the presence of any form of microbe indiscriminately already exist. There are also technologies that are specific for single microbial strains. Sequencing, at least initially, is more likely to be useful in applications where perfect sterility cannot be enforced, and where there is more than one microbial strain that could be harmful.

In my post next week, I will ask what the markets are for which these conditions apply, and where, as a consequence, early adoption of sequencing-based technologies for microbial monitoring is likely to make sense.