PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data.

ABSTRACT: Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoKITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyping. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1  %) of the 93 serotypes in the SSI Diagnostica phenotypical se

SUBMITTER: Sheppard CL 

PROVIDER: S-EPMC9837567 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature