Nasopharyngeal carriage of Streptococcus pneumoniae in children aged two to five years old in the conjugate vaccine era: A cross-sectional study in Salvador, Brazil

Background Monitoring the prevalence and serotype distribution of Streptococcus pneumoniae nasopharyngeal carriage is essential for understanding transmission dynamics and assessing the impact of pneumococcal conjugate vaccines (PCVs). In Brazil, PCV10-GSK is routinely administered at 2 and 4 months of age with a booster at 12 months. This study aimed to determine the nasopharyngeal carriage rate, serotype distribution, antimicrobial susceptibility, and factors associated with carriage among healthy children aged 2–5 years vaccinated with PCV10-GSK under the Brazilian routine immunization program. Methods A cross-sectional study was conducted from August to November 2023 among children aged two to five years from 10 randomly selected schools in Salvador, Brazil. Within each school, all eligible children whose parents or legal guardians provided written informed consent were enrolled. Nasopharyngeal swabs were collected, and demographic, vaccination, and risk factor data were recorded. S. pneumoniae isolates were serotyped using multiplex polymerase chain reaction and/or the Quellung reaction. Antimicrobial susceptibility was evaluated using disk diffusion and gradient strip minimum inhibitory concentration methods. Risk factors for carriage were assessed using univariate and multivariable logistic regression analysis. Results Among the 400 children enrolled, the overall S. pneumoniae carriage rate was 39.5%. White race was independently associated with lower odds of carriage compared with mixed race, whereas none of the evaluated factors was significantly associated with carriage of non-PCV20 serotypes among colonized children. The most frequent serotypes were 6C (17.9%), 19A (13.0%), 11A (9.3%), 15B (8.6%), 23A (8.6%), and 15A (7.4%). Estimated vaccine serotype carriage was 3.2% for PCV10-GSK, 17.3% for PCV13/PCV15/PCV10-SII, and 39.5% for PCV20. Penicillin non-susceptibility was observed in 21.8% of isolates, with the highest rates among serotypes 19A (71.4%), 23A (35.7%), and 6C (20.7%). Conclusions A high pneumococcal carriage rate, predominantly involving non-PCV10-GSK serotypes, was observed among children vaccinated under the Brazilian PCV10-GSK program. The limited serotype coverage of PCV10-GSK, together with antimicrobial resistance among circulating serotypes, underscores the need for ongoing surveillance to guide vaccine policy and antimicrobial stewardship in Brazil.