Pneumococcal nasopharyngeal carriage, serotype distribution, and vaccination status in hospitalized children in Latvia: A cross-sectional study during the post-PCV13, pre-PCV15/PCV20 transition period

Streptococcus pneumoniae remains a leading cause of invasive disease in children, and nasopharyngeal carriage surveillance is essential for monitoring vaccine-driven changes in serotype distribution. However, carriage data from the Baltic states are scarce. We conducted a cross-sectional study to assess pneumococcal carriage prevalence, serotype distribution, and associated factors in 321 hospitalized children aged 0–18 years at the Children’s Clinical University Hospital of Latvia between January 2021 and September 2022, a period representing the post-PCV13, pre-PCV15/PCV20 era. Pneumococcal carriage was detected by PCR targeting the lytA and sp2020 genes; serotyping was performed on PCR-positive samples. Overall carriage prevalence was 21.8% (70/321; 95% CI: 17.6–26.6%). Of the PCR-positive samples, 78.6% (55/70) were non-typeable and only 21.4% (15/70) yielded identifiable serotypes. Among these 15 typeable isolates, the most frequently detected serotypes were 20, 13, and 48, appearing in complex combinations, followed by 15A/15F, 23B1/23B, and 09N/09L—none of which are covered by PCV13; given the small number of typeable isolates, serotype findings are exploratory. PCV vaccination coverage was 63.2% (203/321), with PCV10 (Synflorix) predominating. No significant association was found between vaccination status and carriage prevalence (vaccinated: 25.6% vs. unvaccinated: 16.7%; p = 0.138). Children aged 1–5 years had the highest carriage prevalence at 30.9%. These data constitute the first comprehensive pneumococcal carriage assessment from the Baltic region during this transitional period and may serve as a reference for evaluating the impact of PCV15 and PCV20 following their introduction.