Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing

Abstract

ABSTRACT Serotyping of Streptococcus pneumoniae is a critical tool in the surveillance of the pathogen and development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software requires samples to be pure (or nearly pure) and only contain a single pneumococcal serotype. We introduce a new software tool called SeroCall, which can identify and quantitate the serotypes present in samples, even when several serotypes are present. The sample preparation, library preparation..