PCR sensitivity for Mycoplasma pneumoniae detection in nasopharyngeal and oropharyngeal swabs: a comparative study

The differential impact of sample type on polymerase chain reaction (PCR) detection of Mycoplasma pneumoniae (MP) has rarely been investigated. The study aimed to evaluate the diagnostic performance of PCR for the detection of MP and to measure MP DNA load between nasopharyngeal and oropharyngeal swabs. Nasopharyngeal and oropharyngeal samples were obtained simultaneously to evaluate their diagnostic performance in children with suspected MP. Two commercially available PCR tests, multiplex PCR and Smart Gene Myco, were used to analyze the nasopharyngeal and oropharyngeal samples, respectively. Furthermore, real-time PCR (RT-PCR) tests were conducted on both sample residues to validate the results. In total, 422 participants underwent simultaneous PCR testing using nasopharyngeal and oropharyngeal swabs; 139 samples (32.9%) from nasopharyngeal swabs and 176 samples (41.7%) from oropharyngeal samples that tested positive using commercially available tests. RT-PCR tests were positive for 136 (32.2%) nasopharyngeal and 183 (43.4%) oropharyngeal residual samples. With the RT-PCR test of the residual extract from oropharyngeal swabs as a reference, the sensitivity and specificity of detecting MP were 74.9% (95% confidence interval 67.9%-81.0%) and 99.2% (97.0%-99.9%) with the multiplex PCR test on nasopharyngeal swabs, and 96.2% (92.3%-98.4%) and 100.0% (98.5%-100.0%) with the Smart Gene Myco on oropharyngeal samples. A negative correlation was observed between fluoroquinolone use and oropharyngeal DNA loads (P = 0.004). The sensitivity of MP detection was significantly better in oropharyngeal samples than in nasopharyngeal samples. This study indicates that oropharyngeal samples should be used to detect MP rather than nasopharyngeal samples.IMPORTANCEObtaining the best sample is crucial for the accurate diagnosis of Mycoplasma pneumoniae (MP) and timely and appropriate treatment. This study aimed to assess the diagnostic performance of MP detection using polymerase chain reaction (PCR) tests between nasopharyngeal and oropharyngeal samples. This study showed that the sensitivity of detecting MP was 74.9% (95% confidence interval 67.9%-81.0%) with a commercially available PCR test on nasopharyngeal swabs, and 96.2% (92.3%-98.4%) with a commercially available PCR test on oropharyngeal samples. The sensitivity of MP detection was significantly better in oropharyngeal samples than in nasopharyngeal samples. This study supports the idea that oropharyngeal samples should be used to detect MP. The results contribute to guidance in the recommendation regarding sampling methods to detect MP. Accurate identification of MP is crucial not only for timely and appropriate antimicrobial treatment but also for efficient epidemiological surveillance.