Genomic Surveillance Reveals Vaccine-Associated Shifts in Pediatric Invasive Streptococcus pneumoniae in Tunisia

Background/Objectives: Streptococcus pneumoniae (S. pneumoniae) remains a leading cause of invasive bacterial disease in children worldwide. In Tunisia, the 10-valent pneumococcal conjugate vaccine (PCV10) was introduced into the national immunization program in 2019 for children under two years of age. This study aimed to assess molecular epidemiology, antimicrobial resistance, and vaccine impact on pediatric invasive pneumococcal disease (IPD) before and after PCV10 introduction. Methods: A retrospective study was conducted at Bechir Hamza Children's Hospital (Tunis, Tunisia) between 2016 and 2022. IPD isolates were characterized by multiplex PCR, antimicrobial susceptibility testing, and whole-genome sequencing. Serotyping was performed using three approaches: multiplex PCR, SeroBA, and a novel cpsB gene-based algorithm. Genomic diversity and population structure were analyzed through molecular typing approaches. Incidence trends were calculated using national population data. Results: Among 150 confirmed IPD isolates, vaccine-type (VT-PCV10) strains decreased significantly from 69.8% before to 47.2% after vaccine introduction (p = 0.013), with serotype 14 showing the largest decline. Genomic analysis identified 43 sequence types and 27 global pneumococcal sequence clusters, reflecting high genetic heterogeneity. The cpsB approach demonstrated strong concordance with PCR (κ = 0.67) and SeroBA (κ = 0.85). The mean annual incidence of VT disease in children aged 0-4 years declined from 1.28 to 0.86 cases per 100,000 population, while non-vaccine serotypes showed a modest increase. Conclusions: PCV10 introduction was associated with a marked reduction in vaccine-type IPD among young children, supporting its public health benefit. Ongoing genomic surveillance remains essential to monitor serotype replacement and antimicrobial resistance in Tunisia.