An important step in diagnosing infectious diseases and determining the optimum approach to treatment and management is rapid and accurate diagnostic testing. Many different testing methods are used, particularly bacterial culture (at least for bacterial diseases). Molecular testing has revolutionized the field of microbiology, and is making inroads into the field of diagnostic testing. Polymerase chain reaction (PCR) testing is a very powerful tool that can be used to detect DNA or RNA from specific microorganisms.  This technique can be very useful, but it can also be easily misused or misinterpreted.

The potential PROS of molecular diagnostic testing include:

• Rapid turnaround time: Testing can take as little as a few hours versus a few days for other tests like bacterial culture.
• Sensitivity: Organisms that are difficult or impossible to grow in a lab can be detected, and they can often be detected at lower levels than with other diagnostic methods.

The potential CONS of molecular diagnostic testing include:

• Sample contamination: This is a common concern with highly sensitive molecular tests – even a minute amount of contamination in the sample can cause a false positive result.
• Test inhibition: Samples from complex biological sites (e.g. stool) can contain substances that interfere with the many complex molecular reactions upon which the tests rely. Without good (and proven) methods to prepare the sample, this can result in a false negative result.
• Biologically irrelevant results: Some bacteria that cause disease are also commonly found as part of the normal microflora in healthy animals – simply finding it does not tell you that it is necessarily relevant to the problem. For example, Clostridium difficile can be found in the intestine of approximately 10% of healthy dogs and cats (or more, in some situations), but the diagnosis of C. difficile diarrhea requires detection of the bacterial toxins in stool samples, not just the bacterium itself.  A molecular test that simply identifies the presence of C. difficile, even if it identifies strains that possess the genes to produce toxins, tells you nothing about whether the bacterium was actually producing toxins in the animal.
• Lack of validation: This is a common problem with many (if not most) molecular tests. Some companies, especially those that just run molecular tests, offer a huge array of completely unvalidated and sometimes illogical tests.  It is also important to remember that tests must be validated for each species in which they are used – a test that works well in people will not necessarily work on a sample from a horse or a dog.

Molecular testing can be useful in some situations. If you are unsure, here are some things to ask the lab:

• Do they have a validated test that provides relevant results?  If they don’t have good data (ideally published data) that their test is useful, accurate and reproducible, I’d avoid it.
• Do they have a quality control program, which includes running positive and negative control samples with each test batch?

Finally, as with any test that we use in veterinary (or human) medicine, it’s important to evaluate all  results in the context of what is happening with the animal – treat the patient, not the test result.