Effect of pneumococcal conjugate vaccine six years post-introduction on pneumococcal carriage in Ulaanbaatar, Mongolia

Abstract

Limited data from Asia are available on long-term effects of pneumococcal conjugate vaccine introduction on pneumococcal carriage. Here we assess the impact of 13-valent pneumococcal conjugate vaccine (PCV13) introduction on nasopharyngeal pneumococcal carriage prevalence, density and antimicrobial resistance. Cross-sectional carriage surveys were conducted pre-PCV13 (2015) and post-PCV13 introduction (2017 and 2022). Pneumococci were detected and quantified by real-time PCR from nasopharyngeal swabs. DNA microarray was used for molecular serotyping and to infer genetic lineage (Global Pneumococcal Sequence Cluster). The study included 1461 infants (5-8 weeks old) and 1489 toddlers (12-23 months old) enrolled from family health clinics. We show a reduction in PCV13 serotype carriage (with non-PCV13 serotype replacement) and a reduction in the proportion of samples containing resistance genes in toddlers six years post-PCV13 introduction. We observed an increase in pneumococcal nasopharyngeal density. Serotype 15 A, the most prevalent non-vaccine-serotype in 2022, was comprised predominantly of GPSC904;9. Reductions in PCV13 serotype carriage will likely result in pneumococcal disease reduction. It is important for ongoing surveillance to monitor serotype changes to potentially inform new vaccine development.

Fig. 1. Nasopharyngeal carriage prevalence per age group and year.

A Carriage prevalence of all pneumococci, B 13-valent pneumococcal conjugate vaccine (PCV13) serotype pneumococci, and C non-PCV13 serotype pneumococci in two different age groups, in healthy children in Mongolia in 2015 (N = 950), 2017 (N = 999) and 2022 (N = 999). Error bars depict 95% confidence intervals for carriage prevalence (%). Source data are provided as a Source Data file.

Fig. 2. Nasopharyngeal carriage prevalence of individual pneumococcal serotypes in healthy Mongolian children over three carriage surveys, 2015, 2017 and 2022.

A PCV13 serotypes in children aged 5-8 weeks, B PCV13 serotypes in children aged 2-23 months, C most common non-PCV13 serotypes in children aged 5-8 weeks, and D most common non-PCV13 serotypes in children aged 2-23 months. Source data are provided as a Source Data file.

Fig. 3. Carriage prevalence of PCV13 serotypes and the most common non-PCV13 serotypes in 5-8 week old infants, pre-PCV13 (2015) and six-years post-PCV13 (2022) introduction.

Solid bars indicate carriage that was detected as a single or major (dominant) serotype, open bars indicate carriage that was detected as a minor (second or third) serotype. NT2, NT3b and NT4b refer to different lineages of non-encapsulated pneumococci. Other NVT includes all other identified non-PCV13 serotypes not listed individually. Source data are provided as a Source Data file.

Fig. 4. Carriage prevalence of PCV13 serotypes and the most common non-PCV13 serotypes in 12-23 month old children, pre-PCV13 (2015) and six-years post-PCV13 (2022) introduction.

Solid bars indicate carriage that was detected as a single or major (dominant) serotype, open bars indicate carriage that was detected as a minor (second or third) serotype. NT2, NT3b and NT4b refer to different lineages of non-encapsulated pneumococci. Other NVT includes all other identified non-PCV13 serotypes not listed individually. Source data are provided as a Source Data file.

Fig. 5. Number of samples belonging to each GPSC in the top 10 most common serotypes across all surveys.

Global Pneumococcal Sequence clusters (GPSCs) were inferred for the calls with the highest relative abundance using DNA microarray and were analysed for lineage composition. Bars are coloured by age. Other refers to GPSCs that were found in fewer than five samples for the corresponding serotype. Source data are provided as a Source Data file (5–8 weeks N = 190, 12–23 months N = 533).