Emergence of Non-vaccine Serotypes and Antibiotic Resistance in Pneumococcal Carriage Among Korean Children: A Cross-sectional Study

Background: Streptococcus pneumoniae colonization in children sustains transmission and often precedes invasive disease. As Korea transitions from the 13-valent pneumococcal conjugate vaccine (PCV13) to a 15-valent vaccine (PCV15) that offers broader serotype coverage, up-to-date data on circulating serotypes and antibiotic susceptibility are needed to guide immunization policy. Methods: We conducted a cross-sectional pneumococcal carriage survey from 2024 to 2025 in 37 daycare centers across Seoul and Gyeonggi-do and at a pediatric outpatient clinic, enrolling 601 children (primarily 7–59 months old). Nasopharyngeal swabs were collected and processed using World Health Organization–recommended methods; Streptococcus pneumoniae isolates were serotyped by the Quellung reaction with type-specific antisera. Potential risk factors for carriage (eg, age, sibling number) were assessed via a parental questionnaire and analyzed using logistic regression. Results: Among 601 children, pneumococcal carriage prevalence was 32.4% (195/601). Of the 195 pneumococcal isolates, only 5.1% (10 isolates) were PCV13 serotypes (all 19A or 19F), while non-vaccine serotypes predominated (86.2%, 168/195), and 8.7% (17/195) were nontypeable. The most common serotypes were 15C, 15B, 34 and 6C. Antimicrobial nonsusceptibility was frequent: 35.4% of isolates were nonsusceptible to penicillin, 37.4% to cefotaxime and 95.9% to erythromycin. In risk factor analysis, younger age (6–23 months vs. ≥60 months) was associated with higher odds of carriage (adjusted odds ratio aOR 5.75, 95% confidence interval CI 1.72–19.27). Having no siblings (aOR 0.23, 95% CI 0.08–0.61) or only 1 sibling (aOR 0.35, 95% CI 0.14–0.87) was associated with significantly lower odds of carriage compared to having 2 or more siblings. Conclusions: Nasopharyngeal pneumococcal carriage in Korean children is now dominated by non-vaccine serotype strains with near-universal macrolide resistance. These findings underscore the importance of ongoing serotype and resistance surveillance. Introduction of next-generation vaccines with expanded serotype coverage and continued prudent antibiotic use will be critical to address the evolving pneumococcal landscape.