Discrimination of vaccine preventable serotypes of Streptococcus pneumoniae by PCR and sequencing

Abstract

Streptococcus pneumoniae is a bacterium that causes significant morbidity and mortality worldwide, and vaccines have been developed against a certain number of its serotypes. Serotyping of S. pneumoniae is important to monitor disease epidemiology and assess the impact of pneumococcal vaccines. Traditionally, the Quellung reaction used serotype-specific antibodies to classify isolates based on differences in capsular antigens. More recently, serotype deduction using multiplex PCR (cmPCR) has been applied broadly for pneumococcal surveillance, and relies on differences in the capsule biosynthesis genes (cps loci). However, PCR lacks discrimination between certain serotypes, including some vaccine-preventable serotypes. For example, the vaccine-preventable serotypes 6A and 6B would need to be discriminated for the non-vaccine serotypes 6C and 6D, and similarly, 7F from 7A; 9V from 9A; 9N from 9L; 11A from 11D; 12F from 12A, 12B, 44 and 46; 15B from 15C; 18C from 18F, 18A, 18B; 22F from 22A, and 33F from 33A and 37.

This study evaluated two new molecular approaches that could resolve vaccine-preventable serotypes of S. pneumoniae: 1) next generation sequencing and comparative genomic was used to identify novel serotype-specific PCR targets outside the cps loci; and 2) PCR targeted sequencing was used for specific molecular signature inside the cps loci. In both approaches, specificity was tested using all 92 serotypes of S. pneumoniae previously characterized by Quellung reaction, as well as 32 other members of the Streptococcaceae family. Reproducibility was evaluated using multiple isolates of each S. pneumoniae serotype under evaluation, which differed temporally and geographically. Overall, this study showed that the select PCR targets outside the cps loci could not reproducibly discriminate S. pneumoniae serotypes, whereas PCR and sequencing targets inside the cps loci showed 82% accuracy compared to traditional serotyping Quellung. While discrepant analyses are required and underway, the sequence-based approach shows much promise for discrimination of vaccine-preventable serotypes of S. pneumoniae. Since serotyping is important to monitor S. pneumoniae epidemiology and determine the proportion of disease is vaccine-preventable, this study represents a significant technological advance for pneumococcal disease surveillance.