Objective:

To compare bacterial loads in oropharyngeal and nasopharyngeal swabs used for PCR-based detection of *Bordetella pertussis* and evaluate age distribution and temporal patterns of PCR and serologic results.

Approach:

• Study Design: A multicenter prospective study of 475 patients presenting with cough at five medical institutions in Fukuoka Prefecture, Japan, from October 2024 through May 2025. Nasopharyngeal and oropharyngeal swabs were tested using real-time PCR.

Key Findings:

• Of 475 patients, 113 (23.8%) were PCR-positive for *B pertussis*.
• Among 96 PCR-positive patients with paired specimens, oropharyngeal swabs had significantly higher bacterial loads than nasopharyngeal swabs.
• The cohort’s median age was 13.0 years, with no significant age or sex differences between PCR-positive and PCR-negative patients.
• Pertussis vaccination was reported in 95.4% of participants; PCR positivity did not differ significantly by vaccination status.
• PCR positivity peaked at ages 13 to 15 years and within 2 weeks of symptom onset, whereas serologic responses increased later.

Interpretation:

Oropharyngeal swabs may improve PCR-based pertussis detection, although the difference in the number of positive cases identified by the two specimen types did not reach statistical significance.

Limitations:

• All participating institutions were in one region of Japan, potentially limiting generalizability.
• Oropharyngeal specimens were unavailable for some patients, limiting paired comparisons and potentially introducing selection bias.
• Serologic testing was performed at clinicians’ discretion and was temporarily unavailable during some periods.
• Clinical outcomes and treatment responses were not evaluated.

Conclusion:

Oropharyngeal swabs may be a practical alternative to nasopharyngeal swabs for PCR-based pertussis diagnosis. Specimen type, patient age, and time from symptom onset should be considered when selecting a diagnostic strategy.