Tag Archives: pathogen

Thomas R. Weschler, Founder and President, Strategic Consulting, Inc (SCI)

Faster, Better, Cheaper… What’s Most Important in a Pathogen Test?

By Thomas R. Weschler
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Thomas R. Weschler, Founder and President, Strategic Consulting, Inc (SCI)


For close to 20 years, Strategic Consulting Inc. (SCI) has been following the industrial microbiology market, and food safety testing applications in particular. As part of the data gathering for our most recent report, Industrial Microbiology Market Review, SCI interviewed 15 senior managers at major food companies and food contract labs (FCLs) to understand their priorities when choosing a pathogen diagnostic method. The interviews were roughly split between food companies and food contract labs.

SCI identified ten important attributes for evaluating a diagnostic method or instrument, and asked the interviewees to stack rank the top five items most important to them.

The three top-ranked choices were the same at both food companies and FCLs, with sensitivity/specificity the most important attribute. Second in importance was the ability of the method to be utilized in a broad range of food matrices. Ranking third was the cost-per-test for diagnostic reagents.

For food companies, time-to-results (TTR) was tied for third in the stack ranking, followed by ease-of-use (EOU)/automation in fifth place. Clearly food companies want quick results but only after they are assured that the pathogen diagnostic they are using provides accurate results and is able to work with a range of food types.

For food contract labs, the cost of the pathogen diagnostic instrument ranks fourth, and TTR is tied with the cost of labor per test for fifth. For FCLs, most of the key attributes in method selection are based on operational considerations, which makes perfect sense given testing is their business.

Ask the Experts – Automation Pathogen Detection

An ideal pathogen detection solution should provide increased confidence in results, high reproducibility and robustness to routine testing labs, fit seamlessly in laboratory workflow without disrupting it, and work well for medium-to high-throughput testing laboratories. This Q&A provides some insights.

Q: How can an automation system help safeguard against false negative pathogen results?

Pathogen testing can typically be broken up into three categories:

  1. Raw material testing;
  2. Finished product testing; and
  3. Environmental monitoring.

Regardless of the type of testing that is done, it is clear that pathogen detection is an important component of any hazard analysis and risk-based preventative control program. Verification of results is crucial, particularly negative results. When performing pathogen testing with a real-time PCR based assay, the presence of an internal amplification control is critical. When present for each individual sample, the internal control monitors for inhibition, which can be common with matrices such as spices and chocolate. When a negative result is obtained, it is important to know if that sample is truly negative because the pathogen of interest is not present or if the reaction was inhibited.

Another potential for false negative results can come from technician error. If a sample is not actually added to the reaction block, tube or strip for testing, the result will be negative. Therein lies the power of an automation system. The iQ-Check Prep automation system employs a liquid level sensing volume verification step at the beginning of the run. Utilizing monitored air displacement technology and conductive pipette tips, users are alerted if a sample was missed in the setup. The user then has the option to add the sample or skip it and continue the run. If the sample is not added, the result is flagged as invalid. Combining the internal control of iQ-Check real-time PCR detection kits with the verification of the iQ-Check Prep automation system, users can be confident in their results and safeguard against false negatives.

Q: How can an automation system be incorporated into a laboratory without disrupting existing workflow?

Incorporating an automation system into a laboratory can greatly increase efficiency, traceability and throughput…if it is the right solution for the lab. Many factors need to be taken into consideration, for example batch processing. Examining time intervals at which samples finish incubation can determine how batch processing fits into the lab workflow. Technician responsibilities also play a part. Does the system require monitoring and continuous feeding of samples or is it a walk away system that frees technicians up to perform other lab duties? Another important consideration is maintenance. The scheduled upkeep of the system needs to be evaluated not only for the amount of time required but for the cost associated with the maintenance.

The iQ-Check Prep system was designed with efficiency in mind. Samples are processed in batches (plates of 94 samples at a time) for a throughout of >500 samples per instrument per eight hour shift. The system is a true walk away system that does not require constant monitoring or continuous feeding. The maintenance is self-contained and completed by the instrument in 5 minutes. These are just a few questions to ask when considering an automation system for the laboratory. The chosen system should fit effortlessly into the laboratory workflow and increase throughput and efficiency without causing major disruptions.

For more information, visit Bio-rad.com

Thomas R. Weschler, Founder and President, Strategic Consulting, Inc (SCI)

High False Positive Rates for Pathogen Food Safety Testing

By Thomas R. Weschler
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Thomas R. Weschler, Founder and President, Strategic Consulting, Inc (SCI)

This article looks at proficiency testing (PT) for pathogen analysis, and the recent finding by the the American Proficiency Institute (API) of a 6.6 percent false-negative rate on food safety PT samples (14-year average for the 1999-2012 period).

While at IAFP this year, I met with Heather Jordan, who directs food PT programs at API. The proficiency testing programs are used at many food labs in conjunction with lab accreditation programs. Proficiency testing is done at food plant labs (FPLs) and corporate labs, as well as at food contract testing labs (FCLs) as a way to demonstrate quality results in their food micro and chemistry testing.

More proficiency testing but less proficiency?

In fact, the use of PTs is increasing in food labs, which is probably tied in part to the push for lab accreditation by FSMA and non-government groups like GFSI. Yet it seems to me that the current use of PTs doesn’t go far enough to enable an FPL or FCL to demonstrate overall laboratory competency, and gain or maintain accreditation (ISO 17025).

In most labs, PTs are done just a few times a year. And really, they test the competency of the lab technician and protocols used in analyzing the PT samples. They are not a holistic measure of the lab and its ability to consistently generate quality results on every test run by every operator in the lab.

In a previous life I ran a group of environmental testing labs, which also are required to run PT samples during the year. From this experience, I know that lab personnel are aware that PTs are in-house: The sample-receiving group logs them in, and then alerts management. As a result, the best operators usually are assigned to run the PTs. This kid-glove treatment is not representative of day-to-day practices and processes. If we really want to validate and accredit the proficiency of an entire lab, shouldn’t every operator be tested on all protocols in use?

Plus, if labs know when they are running PT samples, and likely have their best operators running them, shouldn’t there be few, if any, false-negative or false-positive results? Surprisingly, that’s not what the API research found…

API study: Performance accuracy for food pathogens remains problematic

In a retrospective study, “Pathogen Detection in Food Microbiology Laboratories: An Analysis of Proficiency Test Performance,” API analyzed the results from 39,500 food proficiency tests conducted between 1999 and 2012 to see how U.S. labs are doing in detecting or ruling out contamination of four common food pathogens.

Over the 14-year period, “False negative results ranged from 3.3 percent to 14.0 percent for E. coli O157:H7; 1.9 percent to 10.6 percent for Salmonella spp; 3.4 percent to 11.0 percent for L. monocytogenes; and 0 percent to 19.8 percent for Campylobacter spp.” Most concerning is that while both false positive and false negative rates were down in the last year of the study, the cumulative false negative rate for the 14-year period was 6.6 percent.

As we know, false positive results (in which a sample that does not contain pathogens is incorrectly shown as positive) are a nuisance. But false negative test results—which fail to detect true pathogenic organisms in the sample—are not unacceptable.


The cumulative average false positive rate was 3.1 percent, less than half of the false negative rate for the same period.

The objective of the study—and, I would think, of proficiency testing in general—is to demonstrate improvement in lab performance year over year. The results of the API report concluded to the contrary, however: “Performance accuracy for food pathogens remains problematic with the recent cumulative trend showing a slight decrease for false positive and false negative results.”

Clearly if false negatives happen in proficiency programs, they happen in the course of regular testing at food labs. I’m told that many FCLs and FPLs rely on other parts of their QA systems to make sure testing is being conducted properly. Even so, the documentation of ongoing and unacceptably high false negative rates in PT testing is a big concern for everyone. It also points to a number of follow-on questions:

  • Would the false negative and false positive results be even higher if every technician, rather than the best operator, performed the analysis?
  • PT samples are created in only a couple of sample matrices. Would results be even worse if performed on the myriad of sample matrices present in the food industry?
  • What are the performance results among all of the pathogen methods available? Are some methods better than others when measured in real world conditions? Do the more complex protocols of some pathogen diagnostic systems result in poorer PT performance results?
  • Would PT results and, even more important, lab proficiency improve if the frequency of PTs increased, and were required of every technician involved with real food samples?
  • How can proficiency testing be used to isolate problem areas, whether in the pathogen diagnostic method or the competency of lab operators and processes?
  • And finally, is the performance data different between food contract labs and food plant labs? And are all FCLs are equal, or are some more able to deliver quality results?