Whether you are a professional lab testing products from brands or a manufacturer looking to test ingredients and equipment in-house, consider the following factors when choosing a qPCR microbial testing technology.
1. Menu
The first thing you will want to investigate is whether the vendor offers assays that can detect the types of organisms you are interested in finding, such as E. coli, Salmonella, Listeria, Pseudomonas argigenosa, or Total Aerobic Bacteria.
Assays fall into two main categories: presence-absence and total count. Presence-absence tests deliver a yes or no result. They inform the user when the target is present, but do not quantify the amount. Total count tests give the user an estimated number of colony-forming units (CFUs) value based on a conversion equation.
2. Validation Data
Carefully review each potential vendor’s validation documents, which demonstrate how their assays perform under specific conditions. It is a major red flag if vendors cannot share validation data or if the information is incomplete. You will want to pay particular attention to the following sections of the document.
🚩Red Flag: Vendors that can’t or won’t provide validation documents
Limit of Detection (LOD)
The LOD value is the smallest amount of a target that an assay can reliably detect.
For presence-absence tests (i.e., E. Coli, Salmonella, Listeria, and Staph), the LOD should be 1 CFU. Presence-absence tests require an enrichment step that provides time for low levels of contamination to replicate to a point where they are easily detected. The length of that enrichment can vary depending on the organism and the vendor.
🚩Red Flag: Presence-absence tests that do not require enrichment
Total count tests (i.e., Total Aerobic Count and Total Yeast and Mold) do not use enrichment, which means their limit of detection (LOD) is much greater than 1 CFU. Therefore, you want to ensure the assay’s LOD is below the threshold your client or your company has set for a certain type of organism.
Inclusivity and Exclusivity
Assays should be broad enough to include all the species and subspecies of your target, but also specific enough to exclude off-target organisms. Vendors typically report this information in a section called Inclusivity and Exclusivity. It’s not uncommon to find obscure off-target organisms in a vendor’s inclusivity table, after all, biology is never 100%. In fact, if you compare multiple assays, you may often find their tables share similar off-target organisms. Take the time to research any off-target organisms to make sure they are not native to your region or commonly found in the samples you will be testing.
Matrix Compatibility
Lastly, you want to consider the assay’s compatibility with the sample type (matrix) you are going to test (i.e., supplements, natural products, cannabis, food). Some sample types contain compounds or materials that may interfere with the qPCR reaction and alter the results. Furthermore, assays should be designed to avoid cross-reactivity with the samples they are testing. That was a problem in the cannabis industry when labs used assays designed for food products on cannabis flower.
3. Certifications
While the manufacturer’s internal validation data is great, certification from a third-party association, such as AOAC International, is a strong signal that the qPCR method performs the way the manufacturer claims.
The AOAC Performance Tested Methods (PTM) program is a widely accepted certification that means a test method’s performance meets the appropriate standard for its intended use. The certification is awarded after a thorough third-party review that evaluates accuracy, precision, reliability, and consistency.
4. Workflow
If the method is difficult to perform or takes too long to get results, it may not be worth your investment. In particular, manufacturers, who often have limited laboratory experience, should choose a method that is easy to perform. Otherwise, manufacturers may need to hire lab technicians to perform the method, which isn’t always realistic given the volume of testing.
The easiest workflows often use robotic liquid handling equipment to perform tedious pipette steps. Not only does this automation make the process simpler and save time for the operator, but it also minimizes human error and provides consistency across instrument runs.
Testing labs benefit from automated workflows as well. Even though labs have the staff expertise to perform complex methods, automated solutions enable them to process more samples and minimize bottlenecks. It also frees up their staff to use their expertise on more specialized tasks and analysis.
5. Cost per Test, Throughput, and Speed
Any business would be foolish not to consider cost when making decisions on new equipment or processes. In particular, you will want to calculate the cost of each sample you need to test. The Detection Assay cost alone will not provide the full picture. You should also consider any additional consumables and reagents needed to perform:
- Sample Preperation
- Enrichment broth
- Antibiotics (if applicable)
- Free DNA Removal (if applicable)
- 96-well plates
- DNA Extraction
- Lysis Buffer
- Ethenol (if applicable)
- 96-well plates
- qPCR Setup
- qPCR Amplification Mix
- Detection Assays
- Positive Controls
- 96-well plates or strip tubes
TIP: Multiplex Assays allow users to test multiple targets in a single run, eliminating the need for additional sample preparation, DNA extraction, and qPCR setup costs.
But don’t forget; time is money. A method that is scalable and delivers quick results may be worth the added cost if it improves your lab’s throughput and turnaround time.
Conclusion
Choosing the right qPCR microbial testing technology is ultimately about balancing scientific rigor with operational practicality. By prioritizing the menu, internal and external validation data, workflow efficiency, and throughput and cost, manufacturers and labs can ensure their testing program delivers fast, reliable, and defensible results. The right platform not only protects product safety and regulatory compliance, but also supports faster release times, reduced recalls, and stronger brand trust—making microbial testing a strategic advantage rather than just a quality-control requirement.
Contact us today to learn more about our qPCR microbial testing solutions. Our best-in-class support team is ready to help you select a package that fits your goals and your budget.
