Genetic sequencing

In the first of three articles, Graham Godfrey and The Technology Partnership (TTP) explore advances in sensing and analysis technology and the impact they will have on product quality and verification challenges the food industry faces.

Work in other industries by TTP, a technology and product development company based near Cambridge, UK, has moved the technology of genetic testing into a new environment.

The business specialises in helping to bring new techniques out of the laboratory and into practical application. TTP works with either end users who need new capabilities or companies looking to expand their existing product offering. It has a strong background in technology for the life sciences, and believes there is clear opportunity right now to bring these ideas to the food industry.

Your promise to the customer

A brand is a promise to the customer – the promise of consistent quality. Customers want to know that the product they buy is exactly what they are expecting – and both sourcing and manufacturing have a part to play in delivering on that promise.

However, the rise of complex global supply chains means that certainty about the sourcing, composition and purity of ingredients is more important than ever.

A single sourcing failure such as the horsemeat scandal can be amplified by both conventional and social media into a huge problem for a global brand. Brand damage can rapidly spread between markets through the media, even if the issue was only ever in one particular country. It only takes one supplier to cut corners to bring your brand value crashing down around your ears. This applies to small and medium sized producers as much as it does to global ones. SMEs frequently use ingredient sourcing and purity as a major unique selling proposition (USP) and being able to confirm such claims is a potentially important part of this.

Now, a relatively new technology – genetic testing – offers the industry a reliable and cost-effective way to confirm that the product arriving in your loading bay is exactly what you ordered. It offers the best chance the industry has for preventing a media outcry over a sourcing failure while still maintaining the benefits of open and flexible supply chains. This technology is developing into something which is accessible and readily usable by all manufacturers, large and small.

How do I know what I’m buying?

The need for origin validation applies not just to major ingredients such as cocoa, nuts or fruit, but equally to high value components such as natural flavours and colours where demand is increasing and supply is finite and sometimes unreliable.

When you claim on a label ‘Ghanaian cocoa’ or ‘Madagascan vanilla’, how can you be certain that this what you are really selling? Your suppliers may reassure you, but what if they have been deceived? What about a fair trade ingredient? How do you know that it’s really from such a source? Are you avoiding ingredients produced using undesirable labour practices or storage conditions? Some of these issues can be resolved currently but the techniques are frequently expensive, time consuming and require access to specialist laboratories. Fortunately, advances in technology mean that techniques that once required a laboratory full of specialist staff can now be carried out quickly and easily using a machine no bigger than a desktop PC.

Genetic testing – getting cheaper faster than transistors

Genetic testing is an immensely powerful technique, but has a reputation for being expensive. In recent years, a revolution has taken place in this technology which has transformed its potential applications – making it readily accessible to food manufacturers for the first time.

Figure 1 shows that the cost of gene sequencing has fallen as fast, or faster, than the cost of computing (the so-called Moore’s Law) for each of the last 15 years. On top of this development of the core technology, a similar revolution has taken place in the automation and cost reduction of sample preparation for genetic analysis.

TTP is a developer of this technology and has platforms that can be adapted to the automated analysis of most biological products used by the food industry once the genetic markers of interest are known. Figure 2 shows the general shape and size of one of TTP’s automated genetic testing platforms.

The platform consists of two parts: a compact, benchtop instrument (see the smartphone in the illustration for scale), and a disposable cartridge about the size of a small coffee cup. The cartridge contains all the necessary reagents, and provides the mechanical and chemical sample preparation: a small piece of sample is inserted through a hole in the cartridge and then sealed. Once the cartridge is placed in the instrument, the whole preparation and analysis process then happens automatically. At the end of test, the cartridge is disposed of without the need for special precautions or procedures.

Depending on the assay required, an answer can be available in as little as 30 minutes. Because the reagents are provided within the cartridge, the instrument is very flexible, cartridges can be manufactured to test for a whole range of ingredients or contaminants and the same instrument can be used for all of them. This means that the system is very cost-effective – the instruments can be relatively inexpensive, and the user pays for only the cartridges they require.

How can genetic testing help?

Genetic testing is already widely used in plant breeding and the technique is ready for transfer to the food and ingredient quality control environment, where it can be developed for rapid and accurate analysis of a wide range of aspects of ingredients.

Areas which are difficult to validate at present and would be suitable for genetic testing include:

  • Acceptable microbiological counts and absence of toxins (bacterial and mycological) by identifying the presence, or former presence, of organisms of concern
  • Detection of ‘taint’ – non-poisonous microbial activity can still create unwanted tastes in food even when present at extremely low quantities. The genetic material, or genetic residue, from these microbes can be detected at the necessary low levels using genetic testing techniques. DNA amplification is so efficient that even taint due to microbial activity on pallets and packaging can be detected
  • Product specific performance factors such as gelling potential and fat content variation due to variation of the biological source
  • Confirmation of ‘natural’ claims – natural flavours and colours are expensive and in greater demand from consumers. This creates a strong incentive to substitute low cost artificial ingredients which usually have different genetic markers
  • GMO detection – in a similar way to the validation of a ‘natural’ source, key markers indicating genetic modification can be detected using genetic sequencing in food. This is not to criticise GMO technology, but there remains a strong element within Europe that demands GMO free products and there is commercial value in addressing that market
  • Confirmation of source and varietal. Again, each variety of food has distinct genetic markers which can be measured. If you are paying for (and claiming on a label) source ‘X’ or variety ‘Y’ then this can be quickly tested. It must be better for the manufacturer to find this quickly than an external party to find it on the retail shelf
  • Compliance with local dietary or religious requirements, for example being able to demonstrate gelatin sourcing and purity, or to confirm that something is truly vegetarian or vegan, without animal contamination
  • Water quality verification. Bacteria and other organic contaminants can be monitored in water sources, particularly where borehole or surface water is used, as well in the product manufactured and the waste discharge from the factory.

There are of course many more factors which are important to specific ingredients and products, and others which apply to packaging materials but the list above provides some sense of the opportunity.

In addition to its ability to perform diagnostic functions that are not possible using existing techniques genetic testing techniques offer wider benefits in a factory environment. These include:

  • Speed of analysis is increasingly important as it allows reduced stockholding and more rapid response to market changes. It also allows manufacturers to explore the opportunities which can arise as politics, sourcing and climate change alter the choice and availability of many food ingredients
  • The impact of ingredient variation on process operations and product quality can also be reduced and anticipated, improving efficiency and reducing waste, as well as allowing better and more rapid decision making on the value of alternative sources.Procurement groups within companies are under unrelenting pressure to globalise sourcing to find cheaper sources of ingredients and the ability to rapidly ‘define’ current and alternative sources can be invaluable in identifying opportunities and discarding potentially troublesome sources which may otherwise appear viable
  • Predictability and consistency of result. DNA amplification and genetic sequencing are much more predictable than many conventional techniques as they are specific in their detection and DNA replication is a more controlled process that biological growth. Uncertainty due to human interpretation of the resulting microbes is also removed. This is particularly significant where this is done outside a specialist laboratory
  • Improved hygiene. It is intuitively sensible not to try to grow bacteria in a food factory. DNA amplification creates more DNA but does not create more viable organisms
  • Democratisation and flexibility of testing. To date, genetic techniques have required sophisticated testing equipment and highly trained staff and have therefore been the preserve of specialist laboratories and outside the reach of all but the largest organisations.

The move to on-site, deskilled testing creates large savings from improvements in workflow and staff resourcing and training.

Moving out of the lab: a case study

An important genetic testing product from Smiths Detection was originally developed to test for H5N1 bird flu, but a huge outbreak of foot and mouth disease across the UK in 2001 resulted in the slaughter and burning of some 10 million animals together with massive cost and disruption to the entire rural economy.

The extent of the outbreak was largely attributed to the complex, interconnected supply chain that characterises modern agriculture and which quickly moved this highly infectious disease around. The huge scale of the slaughter, which resulted from 2,000 actual disease cases, was because of a policy of culling every animal in a wide area around any infection, whose scale is fixed by the expected extent to which the infection could have spread during the incubation period of the animal displaying symptoms.

The availability of a rapid diagnostic test for the disease would have massively reduced the scale of the slaughter.

In response, Smiths Detection added foot and mouth detection to its genetic testing system which can be rushed to farms across the country in the event of a new outbreak to find and contain the outbreak before it can spread.

A similar test can be rapidly carried out on the surrounding farms and a cull carried out only if the genetic markers for foot and mouth are found. The device is highly robust, including waterproof enough to be dropped into a bucket of disinfectant before moving to the next farm to prevent farm-farm contagion by the testing equipment.

The sample preparation system, developed by TTP, is a single use consumable item that contributes to the overall ease of use and reliability of the test, even when carried out by semi-skilled staff operating under strong time pressure to contain an outbreak. Similar mechanical and user interface techniques are highly applicable to rapid factory based genetic analysis of food.

Realising the opportunity

There will clearly need to be some development work to realise the opportunity which this technology could bring to the confectionery and wider food industries.

The first task will probably be to identify where the most important and potentially valuable issues arise and how these can be approached, as well as determining the size of the potential market.

Once a number of ideal ‘targets’ have been identified, the complexity, cost and value to the industry can be considered and ways of developing the technique and bringing it to market identified.

The confectionery industry is historically very conservative, but this technology has the potential to bring real benefits in a world where there is a very clear focus on the ability to corroborate claims.

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