The page below is a sample from the LabCE course Respiratory Case Study: Possible Pertussis Infection. Access the complete course and earn ASCLS P.A.C.E.-approved continuing education credits by subscribing online.

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Nucleic Acid Amplification Testing (NAAT)

Although culture is considered the gold standard for identification of B. pertussis, it may take up to two weeks for growth to appear on culture media, limiting usefulness of the culture for clinical diagnosis and treatment.
In many clinical laboratories, nucleic acid amplification tests (NAAT) such as polymerase chain reaction (PCR) have become the routine methods for the diagnosis of pertussis.
In this respiratory case study, the laboratory also performed a NAAT method. Compared to culture, which has higher specificity, NAAT has greater sensitivity (as it is not dependent on viable organisms) and faster turnaround time.
Limitations of NAAT
The Bordetella genus includes several different species: B. ansorpii, B. avium, B. bronchiseptica, B. hinzii, B. holmesii, B. parapertussis, B. pertussis, B. petrii, and B. trematum. Each of these organisms share segments of identical genetic sequences. In fact, so much of their DNA is shared among the species that scientists have not yet identified a unique target sequence specific only to B. pertussis. One NAAT method that was recently approved by the FDA (in 2014) targets the IS481 insertional element of the Bordetella genome, which is present in B. Holmesii and some strains of B. bronchiseptica as well as B. pertussis.
At the current time, the CDC recommends that NAAT be used in conjunction with culture when feasible, rather than as an alternative test. Even when a laboratory has validated its NAAT method, culturing for B. pertussis should continue. CDC states that this is especially important to confirm the circulation of B. pertussis when an outbreak is suspected.

Reference: Manual for the surveillance of vaccine-preventable diseases-- Chapter 10: Pertussis. CDC website. Available at: http://www.cdc.gov/vaccines/pubs/surv-manual/chpt10-pertussis.html. Accessed May 31, 2016.