Jing Guo, Weiyuan Zhuo, Chenglan Yan, Jialing Ruan, Linlin Li
Among children with LRTIs, qPCR showed higher positivity rates of S. pneumoniae and provided co-detection profiles. Ct values from qPCR serve as a reference for relative target nucleic acid level, but should be interpreted with caution. Traditional bacterial culture has important value for antimicrobial susceptibility testing, while limited concordance was observed between the two assays. Appropriate use of both assays and proper interpretation of their results can support clinical management decisions.
OBJECTIVE: Bacterial pathogens are common causes of lower respiratory tract infections (LRTIs) in children, particularly Streptococcus pneumoniae (S. pneumoniae). Multiplex real-time quantitative PCR (qPCR) and traditional bacterial culture are two routine clinical assays for the detection of S. pneumoniae. Understanding their differing detection profiles supports appropriate interpretation and application of test results. This study aimed to analyze the positivity rates, concordance, and clinical correlates of paired qPCR and culture for S. pneumoniae in pediatric LRTIs.
METHODS: This single-center retrospective cross-sectional study enrolled 684 hospitalized children with LRTIs who underwent paired sputum qPCR and bacterial culture from June 2024 to August 2025. Positivity rates, concordance between the two assays, and correlations of cycle threshold (Ct) values with culture results for S. pneumoniae were assessed, together with co-detection patterns of bacteria. Exploratory comparative analyses of clinical characteristics were performed among children with different S. pneumoniae detection results, with Benjamini-Hochberg false discovery rate (FDR) correction for multiple testing; multivariable logistic regression adjusting for major confounders was also performed. Antimicrobial susceptibility profiles of S. pneumoniae isolates were described.
RESULTS: Among 684 specimens, 463 were positive for S. pneumoniae by at least one assay: 174 positive by both assays, 288 positive solely by qPCR, and 1 positive solely by culture. Of the 462 qPCR-positive samples, 69.05% were co-detected with other pathogens, and Haemophilus influenzae was the most prevalent. The overall agreement rate between the two methods was 57.75% (κ = 0.279, P < 0.001). For qPCR-positive specimens, the culture-positive rate was significantly higher in the Ct < 30 group than in the Ct ≥ 30 group (P = 0.002). Patients with S. pneumoniae qPCR-positive results were exploratorily stratified into culture-positive and culture-negative groups. In multivariable logistic regression adjusting for major confounders, between-group differences were observed for bronchoalveolar lavage (BAL) utilization (multivariable-adjusted P = 0.001) and post-tussive vomiting (multivariable-adjusted P = 0.018); under multiple-testing correction, only BAL utilization retained significance (FDR-adjusted P = 0.033). When exploratorily stratified into S. pneumoniae single detection and co-detection groups, the same regression model identified a between-group difference for rhinorrhea (multivariable-adjusted P = 0.002); under multiple-testing correction, no variables retained statistical significance. Antimicrobial susceptibility testing showed that all 175 S. pneumoniae isolates were susceptible to rifampin, vancomycin and linezolid, exhibited high susceptibility to penicillin and levofloxacin, and showed high resistance to tetracycline, clindamycin and erythromycin.
CONCLUSION: Among children with LRTIs, qPCR showed higher positivity rates of S. pneumoniae and provided co-detection profiles. Ct values from qPCR serve as a reference for relative target nucleic acid level, but should be interpreted with caution. Traditional bacterial culture has important value for antimicrobial susceptibility testing, while limited concordance was observed between the two assays. Appropriate use of both assays and proper interpretation of their results can support clinical management decisions.