Streptococcus pneumoniae nasopharyngeal carriage in Vietnamese children during the first five years of life: a post hoc analysis

Background: (the pneumococcus) is one of the main causes of childhood mortality. Understanding pneumococcal serotype and lineage distribution in children is important for vaccine decision-making. We undertook a secondary analysis of nasopharyngeal swabs collected from unvaccinated children as part of pneumococcal vaccine studies to provide a comprehensive picture of pneumococcal carriage epidemiology in Vietnamese children during the first 60 months of life. Methods: We analysed 4375 nasopharyngeal swabs from unvaccinated children to assess overall and vaccine-type pneumococcal carriage at 6, 12, 18, 24, and 60 months of age. For the latter three age groups, serotype distribution and genetic lineages (Global Pneumococcal Sequence Cluster, GPSCs) were described overall and by age. We also evaluated the prevalence of antimicrobial resistance (AMR) genes and multi-drug resistance (MDR), comparing vaccine-type and non-vaccine-type pneumococci. Findings: Overall pneumococcal carriage was 21·7% (952/4375) with a total of 27 serotypes detected. Serotype coverage was similar across products Pneumosil (68·6% [95% CI 65·5-71·7%], 595/867), Prevenar13 (70·0% [95% CI 67·0-73·1%], 607/867), and Vaxneuvance (70·0% [95% CI 67·0-73·1%], 607/867), and lower for Synflorix (41·5% [95% CI 38·2-44·8%], 360/867) p < 0·05 vs Pneumosil, Prevenar13 or Vaxneuvance. In total, 2444 swabs were tested at 18, 24, and 60 months. Thirty distinct GPSCs were identified, with their distribution remaining stable across these ages. AMR genes were highly prevalent, detected in 98·9% (360/364) of samples. Interpretation: Synflorix provided lower serotype coverage than other PCVs, largely driven by the prevalence of serotype 6A, which is not included in Synflorix formulation. Serotype, lineage distribution, and prevalence of AMR genes across the sampled age groups remained consistent, indicating that these distributions are broadly representative of young unvaccinated children, helping to guide optimal approaches for pneumococcal surveillance in low- and middle-income countries. Funding: National Health and Medical Research Council, Bill & Melinda Gates Foundation, Murdoch Children's Research Institute.