Nasopharyngeal pneumococcal colonization in children with respiratory symptoms in a pre-pneumococcal vaccine era

Streptococcus pneumoniae commonly colonizes the human nasopharynx without causing disease but remains a leading cause of both invasive and non-invasive infections, including pneumonia, sepsis, and meningitis. Children under five years are at the highest risk of colonization, which contributes to individual morbidity and community transmission. Understanding nasopharyngeal colonization and its clinical implications is critical for guiding public health strategies. This study aimed to determine the prevalence of nasopharyngeal colonization by S. pneumoniae in children with respiratory symptoms at the Children’s Medical Center in Tehran, Iran, and to investigate associations with clinical, radiological, and laboratory findings, as well as potential risk factors, including underlying medical conditions. A cross-sectional study was conducted from April 2023 to April 2024, including children under 18 years admitted with respiratory symptoms. Nasopharyngeal swabs were analyzed using culture and polymerase chain reaction (PCR) targeting the lytA gene, with cpsB used to identify encapsulated strains. Demographic characteristics, underlying medical conditions, radiological findings, laboratory data, hospitalization history, antibiotic use, and vaccination status were extracted from medical records. Statistical analyses were performed using SPSS version 18.0. A p-value < 0.05 was considered statistically significant. A total of 195 children were included (129 males, 66 females; median age 44 months, IQR 7–78 months). None had received pneumococcal vaccination, and 24.1% ( n = 47) had underlying medical conditions. S. pneumoniae was detected in 14 patients (7.2%) by culture and in 60 patients (30.8%) by lytA PCR; all culture-positive samples were also lytA PCR-positive. Only 9 of 60 lytA PCR-positive samples (15%) carried the cpsB gene, indicating a predominance of non-encapsulated strains. Pneumococcal colonization was more frequent in children with underlying conditions (p-value = 0.045) and was associated with abnormal chest imaging findings and longer hospital stays (median 9 vs. 5 days, p-value < 0.001). Colonization was most commonly observed among patients diagnosed with pneumonia and empyema. In this study, nasopharyngeal colonization with S. pneumoniae was common among hospitalized children with respiratory symptoms and was detected substantially more frequently by lytA PCR than by culture, suggesting the higher sensitivity of molecular methods for identifying pneumococcal carriage. Most lytA PCR-positive samples lacked the cpsB gene, indicating a predominance of non-encapsulated strains. Pneumococcal colonization was more frequent among children with underlying medical conditions and was associated with radiological abnormalities and longer hospital stays; however, these associations should be interpreted cautiously, as nasopharyngeal detection reflects colonization rather than confirmed clinical infection and may be influenced by disease severity and other confounding factors.