Impact of Pneumococcal Conjugate Vaccine Immunization on Nasopharyngeal Carriage of <i>Streptococcus pneumoniae</i> in Vaccinated Children Under 5 Years Old in El Salvador

Abstract Background Following pneumococcal conjugate vaccine (PCV) introduction in El Salvador, data on pneumococcal nasopharyngeal (NP) carriage in children are limited. This study assessed NP carriage of Streptococcus pneumoniae in healthy Salvadoran children aged 1–4 years to evaluate the impact of different vaccine schedules (PCV10, PCV13, or PCV10 plus PCV13). Methods In this analytical cross-sectional study, 380 fully vaccinated children attending well-child visits were enrolled over 1 year. Nasopharyngeal swabs were collected to determine S. pneumoniae carriage prevalence, serotype distribution, antimicrobial susceptibility, and associated risk factors. Results Overall carriage prevalence was 14.2%. Carriage was 3 times higher in children receiving PCV10 alone compared to PCV13 alone (adjusted odds ratio [aOR] 3.0, 95% CI 1.5–6.1). No carriers were identified in the PCV10 + PCV13 group. The most frequent serotype was 22F (non-vaccine type), followed by 23B, 19F, and 19Fv. Only 22% of isolated serotypes were covered by available PCVs. Significant risk factors for carriage included younger age (1 year; aOR 2.8, 95% CI 1.4–5.6) and maternal education below high school level (aOR 2.2, 95% CI 1.1–4.3). Carriage decreased significantly with increasing age. Isolates showed high sensitivity to penicillin and other common antibiotics. Conclusions Vaccine type significantly influences NP carriage. The predominance of non-vaccine serotypes and lower carriage with PCV13 and mixed schedules highlights the need for ongoing serotype surveillance to update national immunization strategies and optimize protection against pneumococcal disease.