Molecular analysis also has drawbacks. Namely, it requires a skilled molecular biologist, is more expensive, and it cannot confirm viability. As such, it is not expected to entirely replace culture. However, PCR, if properly implemented, should allow food safety officers to rapidly assess the risk of some food items, thereby allowing them to quickly decide how to handle food lots of varying risk levels.
For example, samples that are found to not have DNA from pathogenic organisms would be deemed as low-risk items that could be shipped directly to customers, whereas samples that are found to contain DNA from pathogenic organisms would be deemed higher risk and slated to be either processed differently (i.e. heated to kill the pathogens) or tested by culture to confirm whether the positive genetic test could be attributed to residual dead pathogens or if the signal was due to viable pathogens that could cause disease.
Another drawback to PCR is that major sample types cannot easily be processed for PCR because some matrices are just too challenging. For example, it is hard to envision genetic analysis being performed directly on a 25-gram beef sample, as the technology is just not designed to handle this volume or type of matrix. Likewise, it is very difficult to process viscous food items like peanut butter. For these types of matrices, upfront culture will be required to achieve the desired sensitivity, which eliminates the speed advantage of molecular analysis.
In contrast, it is easy to envision genetic analysis being performed on liquid samples that don’t have too much particulate matter and are not too viscous (i.e. the media from swabs, fruit and vegetable wash, and the water that’s used to rinse grains). So, companies that are interested in exploring the advantages of genomics must first realize that the initial scope of use for genetic analysis within the food safety sector is limited. Nonetheless, sufficient testing happens on these types of matrices to warrant serious attention.
The incredible sensitivity of PCR makes it the most attractive molecular technology for detecting pathogenic organisms in food processing plants. However, although it is sensitive, it doesn’t currently fully address the desire for a shortened time-to-result since the work must be done by trained molecular biologists who typically do not work night shifts, which is problematic for companies that operate 24/7. The better solution is to take the “skilled” human entirely out of the equation and have a fully automated instrument perform PCR analysis on the samples. This way, sample testing can happen around the clock.
Multiple companies are working hard to simplify the complexity of PCR into an automated solution. Successes have already been realized in other industries, namely human clinical diagnostics. However, these same successes have not yet filtered down to the food safety industry, where the acceptable price point for each sample that’s tested is substantially lower. Nonetheless, advances are being made on reducing the cost per sample down to a price point that potentially will spur widespread adoption in the food industry. This advancement will likely become commercially available in the next year or two.
The Ideal Solution
For many in the food safety industry, the ideal solution would be to have an instrument that is easy enough to be used by factory workers who have no training in microbiology or molecular biology and, as such, could be placed inside of the factory close to where the final products are packaged. The same factory workers who now package up samples to be sent to a food contract lab for testing, would instead load samples directly onto an instrument in their facility for automated onsite testing.