Hygiene monitoring by sequencing - which applications?

The microbial testing market is large, and it is growing. It was worth a respectable $5.5bn in 2011. The part of the microbial testing market to which sequencing would be most relevant is the automated testing segment, which was worth $3.2bn, and is forecast to grow at an annualised rate of 8% in the next years.

Size of the microbial testing market, in US Dollar. Automated Microbial Testing is the market segment which is most relevant to sequencing technology

Last week, I theorised that the unique advantage of microbial testing by sequencing would be the ability to distinguish between harmful and harmless microbes. This week, I consider how this could be relevant to the three largest applications of microbial testing: the food industry, hospital hygiene, and water quality monitoring.

Market segments by application, Automated Microbial Testing, 2011

The food industry is the largest consumer of automated microbial tests. This market is likely to keep growing, driven by shifting industry food safety priorities, increasing regulation and increasing worldwide consumption of processed food.Common hazards such as aflatoxins, Salmonella and Listeria, that currently lead to thousands of product recalls per year, have microbial origins and could be detected by sequencing.

Sequencing is well suited to detect hospital-specific pathogens for two reasons. Firstly, a sequence database can easily be updated should newly arising pathogenic strains be identified. Secondly, sequencing can distinguish between closely related strains of bacteria, such as MRSAand the closely related but harmless and common strains of Staphylococcus aureus.

DNA sequencing may also be the ideal choice for monitoring water quality. Apart from safeguarding drinking water supplies, sequencing could also be used to monitor irrigation water supplies and environmental waters.

Other opportunities may be found in the aviation, marine, automotive and petroleum sectors, where bacterial contamination of equipment and fuel can cause problems, in cosmetics manufacturing, where microbial contamination is an important reason for product waste, and in biodefence. I'm sure there are other opportunities I have not thought of as well - any suggestions?