College of American Pathologists
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Contamination and causality

May 2001
William Check, PhD

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While assays based on nucleic acid amplification have contributed greatly to the diagnosis of microbial pathogens, they need to be handled and interpreted carefully, cautions Dr. Michael Wilson, director of the Department of Pathology and Laboratory Services at the Denver Health Medical Center. Two major issues are contamination and causality.

Because these tests greatly amplify any nucleic acid present in the sample, there is a high risk of contamination. Rigorous quality control is necessary. Specialized laboratories are keenly aware of the danger of carryover contamination and run multiple controls with every batch. "Someone who has never worked in a molecular biology laboratory might not be aware of the need for this degree of QC," Dr. Wilson notes. "Any well-run laboratory can probably do commercial amplification assays successfully if they follow the directions," he acknowledges, especially using kits that include safeguards against contamination. "But I do not think just any nonmolecular laboratory can set up an in-house assay adequately."

The high analytic sensitivity of amplification assays also raises the issue of etiology. "Just because you detect DNA doesn’t mean you can always make the jump to causality," Dr. Wilson says. If an assay detects herpes virus nucleic acid, is that replication or simply shedding from a latent infection?

Dr. Wilson advocates "healthy skepticism" toward molecular assays. "Think critically," he urges. "Like any other laboratory test, nucleic acid amplification just gives a result. It doesn’t replace other pertinent laboratory tests, and it doesn’t replace clinical judgment."