Nasopharyngeal Swab Type for Pertussis PCR Testing
Order a Dacron or rayon swab of the nasopharynx for Bordetella pertussis PCR testing—never use calcium-alginate swabs as they inhibit PCR amplification. 1, 2
Recommended Swab Types
Dacron swabs are the preferred choice for both PCR and culture, as explicitly recommended by the CDC and supported by laboratory validation studies showing no PCR inhibition. 3, 1, 2
Rayon swabs are an equally acceptable alternative to Dacron, performing identically for both PCR detection and culture recovery of B. pertussis. 2
Nasopharyngeal aspirates are superior to swabs when available, showing higher culture positivity (30/33 vs 26/33 positive specimens) and allowing specimen division for multiple assays, though they are less commonly used in routine practice. 3, 4
Critical Swab Types to Avoid
Never use calcium-alginate swabs for pertussis PCR testing—these swabs contain substances that directly inhibit the polymerase chain reaction, leading to false-negative results despite adequate specimen collection. 2
Avoid Amies with charcoal transport media as this system performs poorly for B. pertussis culture recovery. 2
Specimen Collection Technique
Collect the specimen from the posterior nasopharynx, not just the anterior nares, as B. pertussis colonizes the nasopharyngeal mucosa. 3, 1
Begin testing as early as possible in the illness course—PCR sensitivity remains 80-100% even after 2 weeks of symptoms, but culture sensitivity drops to only 1-3% after 3 weeks of cough. 1
Do not delay specimen collection if the patient has already started antibiotics—PCR remains 2-3 times more sensitive than culture even after antibiotic initiation, though both decline in sensitivity after 2+ days of treatment. 1
Why PCR Over Culture Alone
The CDC now endorses PCR for pertussis diagnosis when clinical criteria are met (cough >2 weeks with paroxysms, whooping, or post-tussive vomiting), representing a shift from the 2006 ACCP guidelines that stated "PCR is not recommended as there is no universally accepted, validated technique." 3, 1 This change reflects the superior sensitivity of PCR (80-100%) compared to culture (30-60% in practice), faster turnaround time (24-48 hours vs 1-2 weeks), and maintained performance in patients who are older, vaccinated, or already treated with antibiotics. 1, 5, 6
Common Pitfalls
Using the wrong swab material (calcium-alginate) will cause PCR inhibition and false-negative results despite proper collection technique. 2
Collecting only anterior nasal specimens rather than posterior nasopharyngeal specimens reduces diagnostic yield significantly. 3
Waiting for test results before starting treatment—the CDC recommends starting macrolide antibiotics immediately upon clinical suspicion without waiting for confirmation, as early treatment within 2 weeks decreases paroxysms and prevents transmission. 1, 7