---
title: "Nasopharyngeal carriage of Streptococcus pneumoniae in vaccinated Brazilian children aged 2–5 years"
id: "plos-one-9-nasopharyngeal-carriage-of-streptococcus-pneumoniae-in-children-aged-two-to"
canonical_url: "https://medichelpline.com/clinical-feed/plos-one-9-nasopharyngeal-carriage-of-streptococcus-pneumoniae-in-children-aged-two-to"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "PLOS ONE (Medicine)"
source_url: "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357903"
published_at: "2026-09-09T14:00:00.000Z"
evidence_level: "Journal Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Nasopharyngeal carriage of Streptococcus pneumoniae in vaccinated Brazilian children aged 2–5 years
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/plos-one-9-nasopharyngeal-carriage-of-streptococcus-pneumoniae-in-children-aged-two-to
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** PLOS ONE (Medicine)
- **Source URL:** [Original Journal Publication](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357903)
- **Published At:** 2026-09-09T14:00:00.000Z
- **Evidence Rating:** Journal Feed
## Executive GIST (TL;DR)
- This cross-sectional study surveyed nasopharyngeal (NP) carriage of **Streptococcus pneumoniae** in 400 healthy children aged 2–5 years in Salvador, Brazil, between August and November 2023. - Children were enrolled from 10 randomly selected municipal preschools, with written informed consent obtained from parents or guardians. - Nasopharyngeal swabs were collected and isolates were serotyped by multiplex PCR and/or Quellung reaction; antimicrobial susceptibility was tested by disk diffusion and gradient strip MIC methods. - Overall NP carriage prevalence was 39.5%. 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 carriage of vaccine serotypes was 3.2% for **PCV10-GSK**, 17.3% for PCV13/PCV15/PCV10-SII, and 39.5% for PCV20. - Penicillin non-susceptibility was found in 21.8% of isolates overall; highest non-susceptibility rates occurred in serotype 19A (71.4%), 23A (35.7%), and 6C (20.7%). - In multivariable analysis, white race was independently associated with lower odds of carriage compared with mixed race; no evaluated factors were significantly associated with carriage of non-PCV20 serotypes among colonized children. - Findings indicate high carriage dominated by non-PCV10-GSK serotypes despite routine PCV10-GSK immunization, underscoring the need for continued surveillance to inform vaccine policy and antimicrobial stewardship in Brazil.
## Clinical Analysis & Structured Key Points
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 | PLOS One Browse Subject Areas ? Click through the PLOS taxonomy to find articles in your field. For more information about PLOS Subject Areas, click here . Article Authors Metrics Comments Media Coverage Reader Comments Figures Figures Abstract 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. Citation: Sousa IO, Leite JLP, Melo AOdS, Monteiro ASS, Xavier CFC, Santos VdJ, et al. (2026) 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. PLoS One 21(9): e0357903. https://doi.org/10.1371/journal.pone.0357903 Editor: David J. Diemert, George Washington University School of Medicine and Health Sciences, UNITED STATES OF AMERICA Received: February 27, 2026; Accepted: August 24, 2026; Published: September 9, 2026 Copyright: © 2026 Sousa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: All relevant data are within the manuscript and its Supporting Information files. Funding: This work was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; grant 309564/2022 to JNR), the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES; Finance Code 001 to AOSM), and the Merck Investigator Studies Program (MISP; grant #100719 to JNR). The funders had no role in study design, data collection, analysis, decision to publish, or manuscript preparation. Competing interests: JNR has received grant support from MSD Inc. All other authors declare no conflict of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Introduction Streptococcus pneumoniae remains a leading cause of morbidity and mortality worldwide, particularly among children under five years of age, despite substantial advances in prevention and treatment strategies [ 1 ]. The human nasopharynx serves as the primary reservoir for S. pneumoniae , playing a critical role in both disease development and transmission within the community [ 2 – 4 ]. Pneumococcal carriage is influenced by several host and environmental factors, including age, daycare attendance, number of siblings, and vaccination status [ 5 , 6 ]. As a result, isolates colonizing the nasopharynx often reflect those circulating strains in the community, some of which may also cause invasive infections. Over recent decades, the development and global implementation of pneumococcal conjugate vaccines (PCVs) have significantly reduced the burden of invasive pneumococcal disease (IPD) related with the specific serotypes included in the vaccine. These vaccines are highly effective not only in preventing IPD caused by vaccine serotypes but also in reducing nasopharyngeal (NP) carriage of these serotypes [ 7 , 8 ]. Currently, five PCVs are available worldwide for the prevention of IPD in children. These include the 10-valent vaccine (PCV10, Synflorix®, GSK), which targets the serotypes: 1, 4, 5, 6B, 7F, 9V, 14, 18C, 19F, and 23F; the 13-valent vaccine (PCV13, Prevenar13®, Pfizer), which includes all PCV10-GSK serotypes plus serotypes 3, 6A, and 19A; the 10-valent Serum Institute of India vaccine (PCV10-SII PNEUMOSIL®), covering the serotypes:1, 5, 6A, 6B, 7F, 9V, 14, 19A, 19F, and 23F; the 15-valent vaccine (PCV15, Vaxneuvance®, Merck Sharp & Dohme Corp.), which adds 22F and 33F to the PCV13 formulation; and the 20-valent vaccine (PCV20, Prevenar 20, Pfizer Inc.), which expands PVC15 with serotypes 8, 10A, 11A, 12F, and 15B [ 9 , 10 ]. Brazil introduced PCV10-GSK (Synflorix®) into its national childhood immunization program in March 2010. The current schedule recommends a two-dose primary series at 2 and 4 months of age, followed by a booster dose at 12 months. As of 2023, vaccination coverage among children under one year of age reached 83.4% [ 11 ]. Several studies have documented the vaccine’s impact on reducing IPD caused by PCV10-GSK serotypes, both in the short and long term. Data from Brazil’s national laboratory-based surveillance system showed an 85.6% reduction in IPD caused by PCV10-GSK serotypes among children aged two months to five years within five years of vaccine introduction [ 12 ]. Another study, over a nine-year post-vaccine period, reported an 84.7% decline in overall IPD cases and a 98.0% reduction in IPD due to PCV10-GSK serotypes [ 13 ]. Despite this success, data on the impact of PCV10-GSK vaccine on NP carriage remain limited, especially outside Brazil’s Southeast region. Studies from that region have demonstrated a marked decline in vaccine-type carriage, alongside an increase in non-vaccine serotypes, particularly serotypes 6C and 19A, which are frequently associated with resistance to penicillin and ceftriaxone [ 14 – 16 ]. Updated data on pneumococcal carriage in the context of a mature PCV10-GSK immunization program are crucial to inform policy decisions regarding the adoption of newer or higher-valency PCVs. This study aimed to estimate the prevalence of pneumococcal NP carriage among children under five years of age in Salvador, the fifth most populous city in Brazil, located in the country’s Northeast region [ 17 ], and to identify factors associated with overall pneumococcal carriage and given the near elimination of PCV10-GSK serotypes, carriage of serotypes not covered by PCV20, which currently predominate in the study population. These findings will contribute to evidence-based policymaking regarding the potential incorporation of expanded-valency pneumococcal conjugate vaccines in Brazil. Materials and methods Study area and population The city of Salvador, located in the northeastern Brazil, has an estimated 153,587 children under five years of age and offers 19,838 school placements across 433 schools, including 120 municipal schools distributed across the city’s 10 administrative regions. To ensure geographic representation, all eligible municipal preschools within each administrative region were listed, and one school per region was randomly selected, resulting in a total of 10 participating schools. A cross-sectional survey was conducted between August 31 and November 9, 2023, among children aged 2–5 years enrolled in the selected schools. During scheduled school visits, all children who met the eligibility criteria were invited to participate. Parents or legal guardians were interviewed on the day of sample collection, and children were enrolled only after written informed consent had been obtained. No additional sampling of children was performed within the selected schools. Data and specimen collection On the day of NP specimen collection, immediately prior to specimen collection, trained study personnel administered a standardized questionnaire to the parent or legal guardian of each participating child to obtain demographic and epidemiologic information, including underlying medical conditions, history of hospitalization, occurrence of upper respiratory tract infection (URTI) during the preceding month, recent antibiotic use (within the previous four weeks), and household environmental exposures, including tobacco smoke. PCV10-GSK vaccination status was verified by reviewing the child’s immunization card, and children were classified according to their compliance with the age-appropriate PCV10-GSK schedule recommended by the Brazilian National Immunization Program. NP specimens were collected using flocked swabs (Copan, Brescia, Italy). Immediately after collection, swabs were placed into cryotubes containing 1 mL of skim milk–tryptone–glucose–glycerol (STGG) transport medium and transported in a cooler with ice packs. Within four hours of collection, the STGG medium was vigorously vortexed for 20–30 seconds, and the specimens were stored at −70°C until further analysis. Laboratory methods For pneumococcal culture, frozen vials were thawed at room temperature and then vortexed for 20–30 seconds. Aliquots of 200 μl were transferred to 5 mL of TYS broth (Todd-Hewitt broth supplemented with 0.5% yeast extract and 1 mL of rabbit serum) and incubated at 35–37°C for six hours. Subsequently, 10 µl of cultured broth was plated onto sheep blood agar and incubated at 35–37°C in 5% CO 2 . After 18–24 hours, plates were examined for alpha-hemolytic colonies consistent with Streptococcus species. Three to four presumptive S. pneumoniae colonies were confirmed by optochin susceptibility test (Oxoid, Basingstok, UK) and the bile solubility test. Confirmed isolates were stored at −70°C in 40% sterile glycerin bouillon for further analysis. Pneumococcal isolates were serotyped using a sequential conventional multiplex polymerase chain reaction (cmPCR) method [ 18 , 19 ], followed by confirmation with the Quellung reaction when required at the Brazilian reference laboratory of the Adolfo Lutz Institute. Antimicrobial susceptibility was assessed using the disk-diffusion method according to CLSI guidelines [ 20 ]. Susceptibility to oxacillin, ceftriaxone, erythromycin, clindamycin, trimethoprim-sulfamethoxazole, vancomycin, and levofloxacin was tested using commercial disks (OXOID, Basingstoke, England). Isolates with an inhibition zone diameter 2.0 μg/mL), and 28 isolates (17.5%) showed intermediate resistance (MIC 0.125 – < 2.0 μg/mL). Additionally,
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