In the food industry, producers continually evaluate their processes to ensure the highest level of profitability, and a significant portion of the equation focuses on risk management. Risks like drought, flood, and pest infestation are considered acts of nature to which consumers are forgiving; however, other risks, such as releasing contaminated food items to consumers, is viewed by the public as preventable and less forgivable.
According to a study commissioned by the Grocery Manufacturers Association, 77 percent of respondents estimated the financial impact of a Class I recall to be up to $30 million dollars; 23 percent reported even higher costs. The prospect of these types of losses frighten large companies and can bankrupt small companies.
The Food Safety Modernization Act rules and regulations now require food producers to perform pathogen testing to minimize the probability of recalls. Although there is a willingness to perform pathogen testing, food producers don’t want to excessively pay for testing, as it bites into their bottom line. Hence, food safety testing programs are all about sufficiently managing risk, while preserving the bottom line.
Over the past few decades, the incidence of food recalls has not declined, which is troubling. However, there is a reason for optimism as new technologies are under development that may provide better tools for food safety officers to carry out their jobs, presuming that they are more sensitive than current methods and can detect problems in a timelier manner.
The Problems with Culture
The practice of growing pathogens (i.e. culture) has long been used in the industry since it is relatively affordable, simple to perform, and confirms viability, but it does have two major drawbacks. First, it is slow and takes several days to return a result. For perishable products, every day that’s lost waiting for results impacts the product’s value since there is less time for those products to be sold. The delay in getting test results is responsible for additional incurred expenses for transporting the food products to a storage facility and then paying for refrigerated storage, if needed. Although indirect, these costs need to be factored into the cost per sample tested.
The second drawback is that no single medium and growth condition works for all pathogens. This is problematic since splitting a sample across two or more growth strategies can double or triple the cost, which forces a decision as to whether or not to screen for certain pathogens. This is not a decision that’s taken lightly, considering that foodborne illnesses are not only caused by bacteria but can also be caused by viruses and fungi. The failure to screen for pathogens like norovirus, hepatitis A, and mycotoxin-producing fungi leaves many companies exposed to more risk than is desirable, but the added cost of screening for these pathogens is often prohibitive with the current methods.
Pros and Cons of Molecular Testing
Antibody/immunoassay methods are inexpensive, generally look for just one pathogen at a time, and are easy to perform. Although these tests take just a few minutes to perform, their overall time-to-result is relatively poor because culture is first required to overcome their poor sensitivity. In contrast, molecular DNA-based methods are so sensitive that skipping culture can be entertained in some cases. Some have even argued that polymerase chain reaction (PCR)-based testing is too sensitive and would cause a dilemma in deciding how to handle samples since many would come up as positive, where previously they were thought to be negative. This is where quantitative PCR (qPCR) may have utility since a threshold in quantity for a positive sample can be set. Another benefit of molecular testing is that it is more amendable to multiplex analysis, allowing for samples to be screened for multiple pathogens at a time.
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.
Ideally, the instrument will be able to process large volumes of fluid to minimize the chances of a false negative result. The automated instrument will need to have the capability to concentrate the particulates in liquid samples, purify the genetic material from these particulates, and then assemble, perform, and analyze the results of multiplex qPCR tests that are designed to detect the most common pathogens that cause foodborne illness.
An added benefit would be to simultaneously quantify the level of indicator species so that the cleanliness of the product and cleaning processes in the facility could be monitored. To not hold up the packaging and shipping processes, the instrument will need to be able to return results in about an hour. This will allow food safety officers to quickly make decisions as to whether or not food items should be loaded onto trucks that are destined for the consumer or onto trucks that are destined for a test-and-hold warehouse (while they await results from samples that are pulled for traditional culture analysis).
The bottom line is that the food safety industry is in need of better tools to prevent foodborne illnesses. The industry has a willingness to pay for more expensive methods if the new methods translate into operational efficiencies and lower risk. Advancements in the industry are moving quickly, and prices are coming down. Expectations are that the wait for new technologies isn’t far away.
These new technologies are expected to empower food safety officers to change business practices where most food lots can be shipped directly to the customer, reserving only those that are found to be at a higher risk to be tested via culture. The hope is that new technologies will allow food producers to deliver fresher and safer foods to consumers, while also allowing them to maintain economic efficiencies.
Dr. Regan is the CEO and founder of LexaGene, a biotechnology company that develops automated and sensitive instrumentation for rapid pathogen detection. Reach him at firstname.lastname@example.org.