Genomic epidemiology of Streptococcus pneumoniae reveals globally disseminated lineages and capsular switching in the Arabian Gulf region

Background Streptococcus pneumoniae remains a major cause of pneumococcal disease globally despite widespread use of pneumococcal conjugate vaccines (PCVs). Genomic data from the Arabian Gulf remain limited, and ongoing changes in pneumococcal population structure may complicate serotype-based surveillance and vaccine impact assessment. Methods Whole-genome sequencing was performed on 250 S. pneumoniae isolates collected in the United Arab Emirates and Kuwait. Population structure was analysed using Global Pneumococcal Sequence Clusters (GPSCs). Serotypes and sequence types were determined, and capsule switching was assessed by discordance between lineage assignment and capsular type, supported by recombination analysis. Results Extensive serotype diversity was observed, comprising 51 capsular serotypes with predominance of Serotype 3 (n=33), followed by serotypes 11A (n=15), 8 (n=12), 23B (n=12), 35B (n=11), and 9N (n=11). The isolates were assigned to 61 Global Pneumococcal Sequence Clusters (GPSCs), with four dominant lineages (GPSC10, GPSC12, GPSC6, and GPSC3) accounting for 28.8% of isolates. GPSC10 (n=27) was the predominant lineage and was mainly associated with serogroup 15 (15B/15C), with all isolates exhibiting multidrug resistance. PCV13 serotypes accounted for 29.2% of isolates, increasing to 50.0% and 65.2% for PCV20 and PCV21, respectively. Five sequence types were associated with two distinct serotypes, consistent with putative capsule-switching events and recombination evidence was identified in one lineage. Conclusion Pneumococcal populations in the Arabian Gulf are dominated by globally distributed lineages with substantial serotype diversity. Evidence of capsular switching underscores the limitations of serotype-based surveillance, supporting integration of lineage-resolved genomic surveillance to inform PCV strategies in highly connected regions.