Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae.

ABSTRACT: Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequ

SUBMITTER: Henares D 

PROVIDER: S-EPMC10729682 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature