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From: Food Quality & Safety magazine, June/July 2012

PCR a Simple Solution for a More Sustainable Lab

by Wendy Lauer

We see it all around us—households, schools, and businesses trying to be more “green.” Whether it is by recycling, buying a hybrid car, or eating locally grown food, people are trying to do their part. Food safety laboratories are no different. Sustainability is important and can be measured. Small changes can make a difference in the amount of waste that is generated, the time required to run tests, the space needed to house them, and most importantly, the amount of money that it all costs. Savings in all of these areas can make a huge difference when it comes to product testing.

An in-depth evaluation of sustainability and cost analysis was performed by a service laboratory that runs, on average, 25,000 Salmonella and 20,000 Listeria monocytogenes tests per year. The lab found that it was able to decrease waste by 97% per year, spend significantly less money, and test samples for pathogens as much as a full day faster by using Bio-Rad Laboratories’ iQ-Check real-time polymerase chain reaction (PCR) method instead of its current automated enzyme-linked immunosorbent assay-based test method. What follows is a portrait of how much money and time this lab saved by switching its rapid food pathogen detection system.

The Techniques

The ELISA method depends on an antibody interaction with a specific antigen expressed by the target organism. This detection can often be complicated by similar competing organisms in food producing similar antigens, resulting in a cross-reaction. Conversely, polymerase chain reaction is based on amplification of the DNA of target pathogens. In the case of real-time PCR, specificity is increased by the use of probes and primers designed to target highly conserved regions of the target genome. The iQ-Check kits use a patented probe technology for increased sensitivity and specificity.

The ELISA method depends on an antibody interaction with a specific antigen expressed by the target organism; polymerase chainreaction is based on amplification of the DNA of target pathogens.

A key difference between ELISA and PCR tests is detection limit. Typically, an ELISA-based method will have a limit of 104-106 CFU/ml, whereas a PCR method can detect in the range of 103 CFU/ml. This difference in detection limit usually means that a longer enrichment time is required for an ELISA method. In order to combat overgrowth of competing non-target bacteria in a food sample, a secondary selective enrichment is typically required in an ELISA method to give the target bacteria a chance to grow. Selective enrichment is not required for the PCR method because of the selectivity of the probes and primers used in the assay.

Quit Wasting Away

Because sustainability is often characterized in terms of waste, an in-depth look at just how much waste each of these techniques generates was considered. Over the course of a year, this service lab calculated that its ELISA use would require two tons of tubes for transfers, resulting in 166 waste containers. In addition to the tubes, 45,000 strips and tips generated around 0.6 tons, equivalent to 150 waste containers. In total, the amount of waste this lab generated in a year was equal to 311 containers.

After evaluating the real-time PCR method, which utilized the high throughput sample prep system, the lab found that it generated significantly less waste, mainly due to the fact that 94 samples can be processed at one time in a deep well microplate format. In a year, this lab calculated it would use 450 extraction plates, weighing 121 pounds in total, as well as 450 PCR plates that weigh 123 pounds. This added up to seven waste containers per year—304 fewer waste containers than ELISA. When calculating the cost of disposing of these waste containers, the lab figured savings of $10,300 per year, solely in waste management (Figure 1).

click for large version
Figure 1. Comparison of consumables used with ELISA vs. PCR.

Because PCR rids you of thousands of test tubes and strips and runs on a higher throughput instrument, the lab saved on bench space—a precious commodity in a busy lab. To keep up with its volume, the lab would need three ELISA instruments, taking up 10 feet of bench space. Comparably, the iQ-Check PCR machine takes up only a foot of space and is 350 pounds lighter than the combined weight of the ELISA machines.

Faster Results Save Days

Another important point in the sustainability discussion is time to results. As part of the cost analysis in this case study, technician handling time was also evaluated. This included subculturing to secondary enrichment broth for ELISA tests, a step that is not required for iQ-Check PCR. Overall, 775 hours of technician time was saved annually by using this PCR method, which equates to savings of almost $32,000 per year. For a processor, shortened time to results also translates into a reduction in warehouse storage cost for products in a “test and hold” situation. It can also mean prolonged shelf life of a food product in the marketplace.

The Bottom Line

PCR offers numerous advantages over ELISA as a sustainable alternative, with fewer manipulations for technicians, less waste, saved laboratory space, and reduced time to results. This case study took a detailed look at actual price per test by drilling down through all aspects associated with pathogen testing.

The study did not take into account the very important issue of false positive results. If cultural confirmations are required for presumptive positive samples, the cost of confirming samples that are positive because of a cross-reaction and not because of the presence of a target organism could be substantial. The confirmation cost is not as high as the cost of destroying product based on incorrect data, however.

The newest technologies in real-time PCR can provide food labs with accurate results, while saving time and money, with the added bonus of transforming labs into a more sustainable environment.


Wendy Lauer is senior product manager in the Food Science Division of Bio-Rad Laboratories.



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