Abstract

Background Streptococcus pneumoniae is an important cause of pneumonia in older adults, however, serotyping and indirect impact information from low and middle-income countries is lacking. Mongolia has a childhood 13-valent pneumococcal conjugate vaccine (PCV13) program, but no adult pneumococcal vaccination program. We describe pneumococcal carriage rates, disease and serotype distribution among adults hospitalised with pneumonia, and explore changes over the COVID-19 pandemic period. Methods Adults (≥ 18 years) hospitalised with clinical pneumonia were enrolled over 3 years (March 2019-February 2022) into a prospective pneumonia surveillance program. Nasopharyngeal swabs were tested to detect pneumococci using lytA qPCR and molecular serotyping by DNA microarray and metagenomics. Pneumococcal pneumonia was identified using serotype-specific urinary antigen detection and BinaxNOW® assays. Pneumococcal carriage and pneumonia prevalence were assessed over the COVID-19 period with log-binomial regression used to estimate prevalence and adjusted prevalence ratios (pre- versus early- and late-COVID-19 periods). Results Of 3,178 pneumonia cases, S. pneumoniae was identified in 12.1% (333/2,759) of swabs and 8.6% (253/2,925) of urine samples. PCV13 serotype carriage prevalence was 3.1% (82/2,663) and non-PCV13 serotype carriage prevalence 5.7% (152/2,663). In the late-COVID-19 period, pneumococcal carriage prevalence was reduced by 66% (aPR 0.34, 95%CI 0.25–0.46) and pneumococcal pneumonia by 82% (aPR 0.18, 95%CI 0.12–0.27) compared with the pre-COVID-19 transmission period. Conclusion Despite paediatric vaccination with high coverage, we identified some residual PCV13 serotypes with predominance of non-PCV13 serotypes carried and causing disease in adults. Direct adult vaccination which targets these serotypes will potentially reduce disease in adults in Mongolia.