Population analysis of Streptococcus pneumoniae serotype 19A by whole genome sequencing in the Czech Republic and in Europe after serotype 19A inclusion in pneumococcal conjugate vaccine

Aim: To present the results of whole genome sequencing (WGS) analysis of Streptococcus pneumoniae serotype 19A and to compare them with the respective data from Europe. The vaccine serotype 19A is widely distributed in the Czech Republic. Material and methods: WGS was used in this study as the most powerful available method for detailed characterization of S. pneumoniae. Nineteen Czech isolates of S. pneumoniae 19A were analysed and compared with 415 European isolates included in the PubMLST database. Results: S. pneumoniae serotype 19A causes all types of pathogen - host interaction, from carriage to noninvasive and invasive pneumococcal disease (IPD). In 2010 - 2019, 3872 cases of IPD were reported within the surveillance programme in the Czech Republic, with 323 of these caused by serotype 19A. WGS data of the Czech serotype 19A isolates show a numerous and genetically related subpopulation of three sequencing types: ST-199, ST-416, and ST-3017. Within this subpopulation, the largest is the cluster of nine ST-199 isolates. High relatedness of ST-199 isolates is also confirmed by the fact that all but one isolate, 117/2019 (novel rST-137805), share the same ribosome sequencing profile - rST-11365. Outside the above-mentioned subpopulation, there are only four isolates that form three separate genetic lines of serotype 19A. A highly similar situation is observed across European countries, where about half of all serotype 19A isolates form a genetically closely related subpopulation (ST-199, ST-416, ST-450, ST-667, ST-3017, and ST-10360) while isolates which are not part of this subpopulation represent a large number of unrelated genetic lines. Conclusions: The study has shown a mostly homogeneous population of S. pneumoniae serotype 19A to circulate in the post-vaccination era in both the Czech Republic and Europe, with some unrelated isolates located outside this population.