PCR-based Identification and Serotyping of Russian Streptococcus pneumoniae Strains

Abstract

The techniques for PCR-based identification and serotyping of Streptococcus pneumoniae were optimized for using in Russian epidemiologic situation. One hundred and thirteen strains isolated from children under 5 years of age in 15 Russian cities were tested; 85 of children had pneumonia. Real-time PCR assays using lytA and psaA genes gave true positive results with all S. pneumoniae strains. Five strains were negative in cpsA-based PCR assay and, possibly, did not produce a capsule. Of the remaining 108 strains, the serotype/serogroup was identified for 94 strains; 18 different serovariants of pneumococci were found (2, 3, 4, 6A, 6B, 7FA, 8, 9NL, 9VA, 11AD, 14, 15AF, 15BC, 18ABCF, 19F, 22FA, 23B, 23F). Noteworthy, all twelve strains of serogroup 19 belonged to «vaccine» serotype 19F, and 11 of twelve serogroup 23 strains had «vaccine» serotype 23F. Serotypes 6B and 6A were differentiated by pyrosequencing; 7 strains belonged to serotype 6B and 11 strains had serotype 6A. The set of 24 primers pairs is joined in four PCR assays and provides the possibility to indentify all serotypes included in 10-valent or 13-valent pneumococcal vaccine, as well as most «non-vaccine» serotypes prevalent in Russia. We expect that the technique will help to reveal the serotype of more than 85% S. pneumoniae strains causing clinical disease, and thus to estimate the potential protective efficacy of available conjugated pneumococcal vaccines.