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Study: Pooling and Concentrating DNA from Nasopharyngeal Swabs Prior to RT-PCR Saves Money

NEW YORK(GenomeWeb) – A group of researchers in France and Saudi Arabia have demonstrated a new method that led to a nearly 40 percent cost savings in RT-PCR-based pathogen detection.

In a study published online in The Journal of Clinical Chemistry last week, researchers at Aix Marseille Université and the Saudi Ministry of Health used RT-PCR assays to test a total of 2,380 nasopharyngeal swabs. The group screened these samples for Streptococcus pneumonia, Klebsiella pneumoniae, and Haemophilus influenzae, both on a per-sample basis as well as in a total of 119 pools of 20 samples each.

While pooling samples for PCR is a fairly common technique, it can suffer from reduced sensitivity because it essentially dilutes the target. The pooled samples were therefore freeze-dried, or lyophilized, and then rehydrated in order to concentrate pathogen DNA.

The researchers calculated the time to run each of the three assays on all samples — a total of 7,140 individual tests — was 85 hours. The pooling method, on the other hand, took only 55 hours.

Costs included reagents, consumables, and technician time. Using pools containing 20 samples each resulted in a 37 percent reduced cost, and showed specificity and sensitivity of 86 percent and 96 percent, respectively. The researchers estimated 2,623 tests could be saved by using a pool size of 20 samples, and provided extrapolations of savings for smaller groupings.

"The pooling of clinical samples is especially profitable if the bacterial prevalence is low because each sample in a positive pool is retested individually," the authors noted.

Lyophilization could potentially concentrate PCR inhibitors as well, but the authors argued that whether or not this occurred, it did not appear to affect the detection of DNA in pools versus individual samples in their case.

Freeze drying of PCR components is becoming more common, with new low-cost ways to freeze dry reagents recently described, and reports of an increased demand for lyophilization of reagents by some companies in the diagnostics arena.

Pooled nucleic acid testing has also been recently shown to reduce costs of acute HIV screening. Initial HIV infection produces large amounts of viral nucleic acid. Detection of acute infection is thus well suited for PCR-based techniques but it can be missed by antibody testing. PCR testing is costly, but using pooled testing saves money and can potentially save lives, according to the authors of the study.

Interestingly,S. pneumonia was also recently used as a model organism in another cost-saving method: fingerprinting pathogens using high-resolution melt curve analysis. In a study described in GenomeWeb in October, a group used machine learning to classify 92 known serotypes of S. pneumoniae with 99 percent accuracy after nine learning trials. A team in Kenya, meanwhile, recently combined nested PCR with HRM as a way to potentially save money on malaria detection.