PCR testing has also been developed that can detect a mutation in the organism that leads to resistance to a specific antimicrobial. It is important to recognize that while PCR can be used to detect sections of identified genomes, it is unable to determine whether there is a live or dead organism (such as a virus) in the sample. It is also unable to determine whether that organism is actually resistant to an antimicrobial, but only whether it has the genetic capability to be resistant or not. In addition, other issues can arise when the target sequences chosen for detection are later determined to overlap with other strains or species, causing previously reported positives to be possible false positives. False-negative results can occur due to improper sample collection, collecting too early in the course of infection, or viral mutations occurring in the section of the genome used to detect the organism. False positives, false negatives, sensitivity, and specificity of a specific test can vary between manufacturers and dependent on the organisms tested. When PCR testing protocols are developed, it is also important to recognize that running amplification cycles greater than 35 times can increase the likelihood of detecting viral particles that are too small to cause infection. As with any laboratory test, it is also important to remember that results should be used in conjunction with history as well as clinical signs and symptoms.
This image shows the amplification cycles in reverse transcription PCR used to evaluate the presence of the mutation in Influenza A (H7N9) that causes oseltamivir (Tamiflu) resistance.
