Comparison of Illumina and Oxford Nanopore Technology systems for the genomic characterization of Streptococcus pneumoniae

This study provides a detailed evaluation of whole genome sequencing technologies and bioinformatics pipelines for the characterization of Streptococcus pneumoniae. It represents an in-depth investigation of Illumina and Oxford Nanopore technologies (ONT) systems for bacterial sequencing. It sheds light on the performance of each platform in various aspects of sequencing, including raw and assembly statistics, capsular typing, pbp typing, GPSC, AMR, and MLST prediction. This study offers a comprehensive overview of S. pneumoniae genomics and a guide for clinical and research laboratories seeking to adopt bacterial sequencing, by providing important considerations when choosing sequencing platforms and analysis pipelines. We report a strong case for the implementation of WGS in the clinical setting, based on its high concordance with conventional molecular and phenotypic methods. Furthermore, the flexibility and portability of the investigated pipelines facilitates their use in clinical applications.