Nasopharyngeal pneumococcal carriage and serotype landscape in children, adolescents and young adults in Türkiye

Abstract

After the widespread use of pneumococcal conjugated vaccines (PCVs), pneumococcal carriage, especially due to some vaccine serotypes, has been shown to decrease, but carriage with non-vaccine serotypes and some persistent vaccine types of lineages has been demonstrated to continue. Evaluation of pneumococcal carriage helps to understand disease epidemiology. In this multicenter study, we aimed to determine pneumococcal carriage and serotype distribution in children, adolescents, and young adults aged 0-24 years in Türkiye after the pandemic era. This multicenter study was conducted between April and August 2022 in 1585 healthy children, adolescents, and young adults (aged between 0 and 24 years) in nine centers in Türkiye. Demographics, schooling/day‑care, smoking exposure, recent upper respiratory tract infection (URTI), antibiotic use (1 and 3 months), COVID‑19 infection/vaccination, and pneumococcal vaccination history were recorded. Nasopharyngeal swab samples were taken from all participants. Streptococcus pneumoniae was detected by real‑time polymerase chain reaction (PCR); positives were serotyped by singleplex real‑time PCR assays targeting 33 serotypes/serogroups. Among 1 585 participants (797 female; age distribution 0-5 years 22.0%, 6-10 years 29.3%, 11-15 years 16.8%, 16-18 years 12.9%, 19-24 years 19.0%), overall pneumococcal carriage prevalence was 19.6% (311/1 585). Age‑specific prevalences were 20.7% (0-5 years), 21.8% (6-10 years; peak), 19.1% (11-15 years), 15.6% (16-18 years), and 18.2% (19-24 years). Two‑thirds (66.2%) had received ≥ 1 PCV dose (coverage ≥ 82% through 15 years, declining to 43.9% at 16-18 years and 13.3% at 19-24 years). Vaccination was associated with significantly lower carriage only in children ≤ 10 years: 0-5 years 17.8% vs 43.6% (OR 0.28, 95% CI 0.13-0.60, p < 0.001); 6-10 years 19.7% vs 32.4% (OR 0.51, 0.28-0.93, p = 0.021). No significant differences were seen in older strata or overall (18.8% vs 21.3%, OR 0.85, 0.65-1.12). Of 311 isolates, 225 (72.4%) were typed (27 serotypes) and 86 (27.6%) were not defined. Dominant serotypes were 19F, 6A/B, 3, 23F, and 15B/C; PCV13 serotypes comprised 77.3% of typed isolates. Theoretical vaccine coverage among 225 typed isolates increased from 61-64% (PCV7/10) to 77.3% (PCV13), 78.2% (PCV15), 88.4-90.2% (PCV20/24), plateauing at 93.3-93.8% for PCV31/25. Theoretical vaccine coverage in children aged below 5 years of age was 66.7% for PCV13, 70.0% for PCV15, and 88.3% for PCV20. The frequency of PCV13 serotypes in children vaccinated with PCV13 was significantly lower than in unvaccinated children in children below 5 years of age.

Conclusion: Post‑pandemic pneumococcal carriage in Türkiye remains 19.6% across childhood. Direct protection against nasopharyngeal carriage was evident in children ≤ 10 y. Higher‑valency PCVs and enhanced genomic serotype surveillance are needed to address residual carriage and guide future immunization strategies.

What is known: • Pneumococcal conjugate vaccines (PCVs) have substantially reduced invasive pneumococcal disease, but nasopharyngeal colonization persists due to serotype replacement. • After the COVID-19 pandemic, major shifts in respiratory pathogen epidemiology occurred, yet contemporary post-pandemic data on pneumococcal carriage and serotype distribution remain scarce.

What is new: • This is the first multicenter post-COVID pneumococcal carriage study in Türkiye covering the full 0-24-year age spectrum, showing that carriage remains stable at ~20%. • Direct vaccine protection against carriage is confined to children ≤10 years, with no measurable impact in adolescents or young adults. Some vaccine serotypes and non-vaccine serotypes still dominate carriage, and higher-valency PCVs would markedly improve theoretical coverage.

Keywords: Carriage; Conjugated pneumococcal vaccine; Pneumococci.

Fig. 1

Age‑specific prevalence of nasopharyngeal Streptococcus pneumoniae carriage in Türkiye, 2022. Vertical bars show the proportion of carriers in each 5‑year age stratum (0–5, 6–10, 11–15, 16–18, 19–24 years) and in the overall cohort (Total, n = 1585). Exact prevalence is printed above each bar

Fig. 2

Carriage prevalence by pneumococcal‑conjugate‑vaccine (PCV) status and age group. Grouped bars compare PCV‑vaccinated (blue) and unvaccinated (orange) participants within each age stratum and overall. Percentages are annotated above each bar. Statistically significant differences (χ.² test) are flagged with bold p‑values above the corresponding bar clusters (0–5 years, p < 0.001; 6–10 years, p = 0.021)

Fig. 3

Frequency distribution of pneumococcal serotypes isolated from 311 carriers. Horizontal bars rank all serotypes detected (≥ 1 isolate) plus the ND in descending order of frequency. Bar length corresponds to the absolute isolate count; counts are printed at bar termini. Data combine all age groups. ND, not-defined

Fig. 4

Heat‑map legend of serotype distribution according to age groups. Rows: 0–5 years, 6–10 years, 11–15 years, 16–18 years, 19–24 years: age strata of study participants. Columns (left to right): numeric serotypes listed in ascending order represent the percentage of that age group’s isolates belonging to the given serotype; deeper blue indicates higher prevalence. In‑cell numbers show the exact percentage to one decimal place; blank cells (white) denote 0%