Monitoring nasopharyngeal (NP) carriage of Streptococcus pneumoniae is central to understanding transmission dynamics and evaluating the indirect effects of pneumococcal conjugate vaccines (PCVs). Brazil implemented the PCV10-GSK (Synflorix®) schedule in 2010 with doses at 2 and 4 months and a booster at 12 months. Although PCV10-GSK has substantially reduced invasive pneumococcal disease caused by vaccine serotypes, NP carriage data from regions outside Brazil’s Southeast remain limited. This study aimed to estimate NP carriage prevalence, describe serotype distribution and antimicrobial susceptibility, and identify factors associated with carriage among children aged 2–5 years vaccinated under the national PCV10-GSK program in Salvador, Brazil.
A cross-sectional survey was conducted from August 31 to November 9, 2023. The target population comprised children aged 2–5 years enrolled in municipal preschools in Salvador, a northeastern Brazilian city. To ensure geographic representation, one municipal preschool was randomly selected from each of the city’s 10 administrative regions, yielding 10 participating schools. All eligible children at each selected school whose parents or legal guardians provided written informed consent were enrolled. The final sample included 400 children.
On the day of sample collection, trained personnel interviewed parents or legal guardians using a standardized questionnaire to capture demographic and epidemiologic information, including underlying medical conditions, recent hospitalizations, and occurrence of upper respiratory tract infection (URTI) within the preceding month. Nasopharyngeal swabs were obtained from enrolled children during school visits for bacteriologic culture and subsequent testing.
Isolates identified as S. pneumoniae were serotyped using multiplex polymerase chain reaction (PCR) and/or the Quellung reaction. Antimicrobial susceptibility testing combined disk diffusion and gradient strip minimum inhibitory concentration (MIC) methods. These laboratory approaches were used to determine serotype-specific distribution and to assess susceptibility to penicillin and other antimicrobials reported in the study.
Univariate and multivariable logistic regression analyses were used to evaluate risk factors associated with overall pneumococcal carriage and, among colonized children, carriage of serotypes not covered by PCV20. Variables collected via questionnaire were included in modeling to identify independent associations. The analysis approach is consistent with standard cross-sectional carriage studies designed to account for potential confounders.
Among the 400 enrolled children aged two to five years, the overall NP carriage prevalence of S. pneumoniae was 39.5%. Demographic and clinical variables were collected and evaluated for associations with carriage. In multivariable analysis, white race was independently associated with lower odds of carriage when compared with mixed race. Other evaluated factors were not reported as independently associated with overall carriage in the manuscript extract provided.
The most frequent serotypes identified among isolates were 6C (17.9%), 19A (13.0%), 11A (9.3%), 15B (8.6%), 23A (8.6%), and 15A (7.4%). The study reported estimated carriage attributable to vaccine serotypes by product: 3.2% for PCV10-GSK, 17.3% for PCV13/PCV15/PCV10-SII combined coverage, and 39.5% for PCV20. These estimates highlight that the majority of circulating carriage in this population consisted of serotypes not included in the national PCV10-GSK formulation.
Overall, penicillin non-susceptibility was observed in 21.8% of pneumococcal isolates. Serotype-specific non-susceptibility rates were highest for 19A (71.4%), followed by 23A (35.7%) and 6C (20.7%). Antimicrobial resistance among the predominant non-PCV10 serotypes was emphasized as a concern in the reported results.
Multivariable analysis identified white race as independently associated with lower odds of overall pneumococcal carriage relative to mixed race. Among colonized children, the investigators examined factors associated with carriage of non-PCV20 serotypes but reported that none of the evaluated factors showed significant associations in this subgroup according to the provided summary.
The study documented a high NP carriage rate of S. pneumoniae in a cohort of children vaccinated under Brazil’s routine PCV10-GSK program, with carriage predominantly involving serotypes not included in PCV10-GSK. The distribution was dominated by serotypes such as 6C and 19A, which have been reported elsewhere to increase after reductions in vaccine-type carriage and are frequently associated with antimicrobial resistance. The presence of substantial penicillin non-susceptibility, particularly in serotype 19A, emphasizes the dual challenge of serotype replacement and resistance.
These findings support the need for ongoing, regionally representative surveillance of pneumococcal carriage and resistance patterns to inform evidence-based decisions about potential adoption of expanded-valency PCVs and to guide antimicrobial stewardship strategies.
In this cross-sectional sample of 400 children aged 2–5 years in Salvador, Brazil, carried S. pneumoniae at a rate of 39.5%, largely comprised of non-PCV10-GSK serotypes. Penicillin non-susceptibility affected more than one in five isolates, with particularly high rates in serotype 19A. The study concludes that limited serotype coverage of PCV10-GSK and the antimicrobial resistance profile among circulating serotypes warrant continued surveillance to inform vaccine policy and stewardship efforts. The manuscript recommends sustained monitoring to guide potential incorporation of higher-valency vaccines and to track resistance trends.
The study reported funding support from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and the Merck Investigator Studies Program (MISP). All relevant data were stated to be available within the manuscript and supporting information files. Competing interests disclosed that one author (JNR) has received grant support from MSD Inc.; all other authors declared no conflicts of interest.