Background. Serotype 8 has emerged as a common non-vaccine serotype causing invasive pneumococcal disease (IPD) in children and adults globally after the introduction of pneumococcal conjugate vaccine...

Please cite this pipeline if you have used it in your work: https://doi.org/10.1038/s41467-025-64018-5 What's Changed (since v1.1.0) New Features Cap assemblers max thread count to 16 if not speci...

A worldwide genomic survey of the impact of vaccination on the pathogen population - Global Pneumococcal Sequencing (GPS) Project

Background. Streptococcus pneumoniae is a major human pathogen responsible for invasive pneumococcal diseases (IPDs). We utilized whole-genome sequencing to assess the impact of pneumococcal conjugate vaccines (PCVs) on the pneumococcal population ...

The reference genomes for common Global Pneumococcal Sequence Clusters (GPSCs) - GlobalPneumoSeq/gpsc-reference-genomes

The GPS Pipeline enables accessible and scalable genomic surveillance of Streptococcus pneumoniae. It performs quality control and in silico typing of sequencing reads with high accuracy using a single simple command, without requiring the internet.

Streptococcus pneumoniae remains a leading respiratory pathogen for children and the elderly. In Taiwan, a national PCV13 catch-up vaccination programme for children began in March 2013. This study in...

Barton et al. identify Streptococcus pneumoniae promoters containing repetitive nucleotide sequences that promote DNA strand slippage and accumulation of promoter sequence mutations. This drives popul...

In 2017, 553,000 clinical cases of Streptococcus pneumoniae in children were reported in China, although the pneumococcal conjugate vaccine (PCV), which targets the pneumococcal capsule, is not includ...

Homepage of The Global Pneumococcal Sequencing Project

The unprecedented number of Streptococcus pneumoniae (the pneumococcus) genomes sequenced in recent years has accelerated the discovery of novel serotypes and highlighted the genetic diversity both be...

In the Netherlands, the 7-valent pneumococcal conjugate vaccine (PCV) was introduced to the childhood immunization programme in 2006 and replaced by the 10-valent PCV (PCV10, GSK) in 2011. To describe...

Background and aims. Despite the introduction of pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae still remains an important cause of morbidity and mortality, especially among children...