Next-generation technologies and bioinformatic pipelines for S. pneumoniae capsular typing

Study which aimed to determine the capsular types of pneumococci causing IPD at Hospital Sant Joan de Deu between 2013-2019 using both QR and in silico serotyping with NGS. In addition, we aimed to compare the performance of the in silico programs described using two different approaches: short-read sequencing of pneumococcal strains followed by serotyping with PneumoCaT, SeroBA and Pathogenwatch vs long read sequencing approach by MinION-ONT coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes.Raw fastq files from Illumina and ONT sequences have been uploaded for each sample included in the study (n=119).