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 PneumoK-ITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyp-ing. Mash k-mer screening is more sequence specific and much faster than the mapping method used in Pneu..