Association between 12 common respiratory pathogens and Streptococcus pneumoniae detection among hospitalized children in Hainan, and characterization of antimicrobial resistance and molecular epidemiology in pneumococcal isolates

Data from the COVID-19 pandemic demonstrated a strong association between reduced invasive pneumococcal disease and decreased circulation of specific respiratory viruses. However, studies investigating the association between common respiratory pathogens and Streptococcus pneumoniae ( S. pneumoniae ) detection rates remain limited, and molecular epidemiology data for pediatric S. pneumoniae infections in Hainan are lacking. From July 2021 to June 2025, we retrospectively analyzed the detection profiles of 12 common respiratory pathogens in hospitalized children. Spearman correlation was used to examine the relationship between each pathogen’s monthly detection rate and its co-detection rate with S. pneumoniae . Separately, 434 consecutive S. pneumoniae isolates collected from May 2023 to April 2024 underwent Quellung serotyping, antimicrobial susceptibility testing, and whole-genome sequencing. During the study period, S. pneumoniae detection rates among hospitalized children in Hainan ranged from 20% to 40% without a clear seasonal pattern, but were higher during strict COVID-19 lockdowns than after policy relaxation. Positive ecological correlations were observed between S. pneumoniae detection rates and 12 common respiratory pathogen circulation. Age-stratified analysis revealed distinct correlation patterns: HMPV, IAV, RSV, and CoV showed the strongest associations with S. pneumoniae co-detection in children aged 0–3 years; M. pneumoniae , HMPV, HRV, and RSV in those aged 4–6 years; and IAV, IBV, AdV, and HMPV in those aged 7–18 years. Among 434 S. pneumoniae isolates, 21 serotypes and 85 sequence types (24 novel) were identified. The six most prevalent serotypes were 19 F, 6B, 23 F, 19 A, 6 A, and 15 A, with ST271 as the dominant sequence type. All non-meningitis isolates were penicillin-susceptible at non-meningitis breakpoints, and serotype 19 F exhibited the highest antimicrobial resistance rates. PCV13 and PPV23 covered 78.3% and 76.5% of isolates, respectively. A 13.8% discordance rate was observed between Quellung serotyping and molecular serotyping, with discrepancies concentrated in serogroup 6. Additional discrepancies arose when molecular serotyping results were compared across different platforms. Our findings suggest that the circulation of RSV, M. pneumoniae , HMPV, HRV, and influenza viruses may influence S. pneumoniae detection in hospitalized children. These findings pertain to this clinical population and should not be extrapolated to colonization rates in healthy individuals. Finally, accurate pneumococcal surveillance in the post-vaccine era would benefit from integrating genomic and traditional phenotypic approaches.