Detection of Streptococcus pneumoniae serotypes causing invasive and non-invasive infections using whole-genome sequencing

Objective.

Seroyping of the Streptococcus pneumoniae strains obtained from patients with invasive and non-invasive forms of pneumococcal infection circulating in Russia using whole-genome sequencing.

Materials and Methods.

The 144 invasive and 90 non-invasive S. pneumoniae strains isolated in 2002– 2023 during the multicenter epidemiological study «PEGASus» were investigated. Real-time PCR and whole-genome sequencing were used to determine serotypes. The 16 serotyping targets were examined by PCR technique. Whole-genome sequencing was performed on the Illumina equipment. Sequencing results were processed using the PubMLST software and PneumoCaT, SeroBA and PneumoKITy programs.

Results.

The whole-genome sequences were obtained and strains serotypes were determined, while the efficiency of serotype determination by software was 97% (serotypes of 8 strains were determined ambiguously). The serotypes distribution in the invasive and non-invasive strains differed, along with it the proportion of invasive strains included as vaccine components was higher than non-invasive ones. Statistically significant differences between the groups of invasive and non-invasive strains were observed for 13-, 15- and 23-valent vaccine components.

Conclusions.

The whole-genome based analysis allows us to obtain comprehensive information about the genetic and antigenic features of S. pneumoniae pathogens. The information about serotypes distribution allows the vaccines effectiveness and provides the necessary information for routine PCR based serotypes monitoring and planning vaccination.