Aim: To assess the impact of COVID-19 on the incidence and molecular epidemiology of invasive infections caused by Streptococcus pneumoniae and Streptococcus pyogenes in the Czech Republic, with a focus on post-pandemic trends and genomic characteristics of emerging strains.

Methods: Epidemiological data on invasive pneumococcal disease (IPD) and invasive group A streptococcal infections (iGAS) from 2018 to 2024 were analyzed. WGS was conducted on selected isolates at the National Reference Laboratory for Streptococcal Infections (NRL/STR) to investigate GPSC, MLST in S.pneumoniae strains, and the presence of the M1_UK sublineage among S.pyogenes emm1 strains.

Results: A 47% decrease in IPD-incidence was observed between 2018–2019 and 2020–2021, followed by a 133% increase between 2020–2021 and 2023–2024. In comparison to 2018–2019, IPD cases in 2023–2024 increased by 24%. Post-pandemic data revealed an increase in certain S.pneumoniae serotypes compared to the pre-pandemic period (e.g., serotypes 3, 4, 8, 22F). The majority of these were serotypes not targeted by the 10-valent or 13-valent pneumococcal vaccines, with the exception of serotype 4, which has increased in prevalence despite being included in the 7-valent, 10-valent, and 13-valent conjugate vaccines. Comparison of WGS data from isolates collected in the pre-pandemic and post-pandemic periods revealed no changes in GPSC or MLST profiles.

Conclusion: COVID-19 significantly altered the epidemiology of invasive streptococcal infections in the Czech Republic. The post-pandemic period has seen the resurgence of IPD and the emergence of toxigenic S. pyogenes strains, particularly the M1_UK sublineage.