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.