Genetic Characteristics of Streptococcus pneumoniae Strains Isolated From Children With Community-Acquired Pneumonia

Bacteria of the species Streptococcus pneumoniae, dominant in the etiological structure of community-acquired pneumonia in children, are represent a serious problem in the field of human infectious pathology. Detailed molecular and genetic characteristics of eleven S. pneumoniae strains isolated from sputum samples of children with community-acquired pneumonia were obtained using whole genome sequencing and bioinformatic analysis. Based on the analysis of the nucleotide sequences of seven housekeeping genes (aroE, gdh, gki, recP, spi, xpt, ddl), it was found that S. pneumoniae strains included in the study belong to six sequence types: ST1367, ST819, ST1262, ST180, ST15069, ST66. Using SeroBA algorithm S. pneumoniae strains were assigned to five serotypes:11C, 22F, 15C, 9N, 3. Genome annotation using ResFinder and CARD databases allowed us to identify determinants of resistance to macrolides (ermB, RImA), fluoroquinolones (patA, patB, pmrA), lincosamides (RImA), aminoglycosides (aph(3')-Ia) and tetracyclines (tetM and tet32). A high frequency of detection of pathogenicity genes encoding choline-binding proteins, fibronectin-binding proteins, pneumolysin, autolysin, hyaluronidase, neuraminidase, capsule proteins, zinc metalloproteinase in the genome of S. pneumoniae strains was noted.  Phylogenetic analysis of the nucleotide sequences of the genome of Nishny Novgorod strains and strains deposited in GenBank/NCBI showed a high level of genetic variability of pneumococci circulating both in Russia and abroad.