Oropharyngeal swabs show higher bacterial loads than nasopharyngeal swabs for PCR detection of pertussis: a multicenter prospective study

OBJECTIVE: Pertussis remains a significant public health concern despite widespread vaccination, with a resurgence observed following the COVID-19 pandemic. The optimal sampling site for PCR-based detection of Bordetella pertussis remains uncertain. METHODS: We conducted a multicenter prospective study across five institutions in Japan between October 2024 and May 2025. A total of 475 patients presenting with cough were enrolled. Nasopharyngeal and oropharyngeal swabs were collected and analyzed using real-time polymerase chain reaction (PCR). PCR positivity was defined as a positive result in either specimen. Bacterial load, age distribution, temporal diagnostic patterns, and macrolide resistance-associated mutations were evaluated. RESULTS: Of 475 patients, 113 (23.8%) were PCR-positive. Among 96 PCR-positive patients with paired nasopharyngeal and oropharyngeal specimens, oropharyngeal swabs showed significantly higher bacterial loads than nasopharyngeal swabs (P < .001). PCR positivity peaked in adolescents, particularly those aged 13-15 years. PCR detection was highest within 2 weeks of symptom onset and declined thereafter, whereas serological responses increased after three weeks. Macrolide resistance-associated mutations were detected in 89.0% of patients and increased to 94.0% over time. CONCLUSIONS: Oropharyngeal swabs may improve PCR-based detection of pertussis in clinical practice. Adolescents represent a key target population, and diagnostic strategies should consider both specimen type and timing of testing. The high prevalence of macrolide resistance underscores the need for ongoing surveillance and reconsideration of treatment strategies.