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Global Pneumococcal Sequencing Project

@globalpneumoseq.bsky.social

GPS, the Global Pneumococcal Sequencing project funded by The Bill and Melinda Gates Foundation is sequencing ~50,000 pneumococci to monitor global vaccine implementation and impact. https://www.pneumogen.net/gps/

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Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 3mo ago

New paper! NICD team traces the global expansion of GPSC3 within serotype 8 following the introduction of the PCV13 in South Africa 🇿🇦. An increase in invasive disease incidence of non-vaccine type serotype 8 is observed after PCV introduction. www.microbiologyresearch.org/content/jour...

Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent pneumococcal conjugate vaccine introduction, South Africa

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...

microbiologyresearch.org

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 5mo ago

GPS Pipeline v1.2.0 is here! We have just released a major update to the GPS Pipeline, focusing on stability and accuracy improvements. Upgrade today for a more robust Streptococcus pneumoniae genomes analysis experience: github.com/GlobalPneumo...

Release v1.2.0: Images & Databases Updates · GlobalPneumoSeq/gps-pipeline

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...

github.com

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 5mo ago

The latest version of PopPUNK GPS Database v11 for assigning GPSC of S. pneumoniae is now available. It can assign more lineages with a greatly reduced database size (12 → 4.5GB). (PopPUNK v2.7.7 or above required) Download: github.com/GlobalPneumo...

Global Pneumococcal Sequencing (GPS) Project

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

github.com

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 6mo ago

GPS funded placement awardee Dr Fatima Dakroub has published her finding in Microbial Genomics, highlighting the replacement of PCV13 with PCV10 (Pneumosil) will reduce the coverage of circulating serotypes in Lebanon. pmc.ncbi.nlm.nih.gov/articles/PMC...

Genomic characterization of invasive disease-causing Streptococcus pneumoniae in Lebanon, 2003–2025

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 ...

pmc.ncbi.nlm.nih.gov

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 10mo ago

Performing GPSC/lineage-specific analysis? We have made assemblies and annotations for 73 common GPSCs more accessible than ever: github.com/GlobalPneumo... Annotations were generated using Bakta v1.11.4 with the v6.0 full database.

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

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

github.com

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 12mo ago

🦠🧪🧬 Excited to share that our GPS Pipeline, the portable and scalable genomic pipeline for Streptococcus pneumoniae surveillance, is now published in @natcomms.nature.com 🔗 nature.com/articles/s41... #GPS_project

GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project - Nature Communications

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.

nature.com

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · 12mo ago

[🚨 New paper] The first nationwide, longitudinal WGS analysis of Streptococcus pneumoniae in Taiwan (2006–2022). 1,343 isolates from 27 hospitals, we track serotype, AMR, and genomic lineage before and after PCV13. #GPS_project #PCV13_impact #Taiwan www.microbiologyresearch.org/content/jour...

Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022

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...

microbiologyresearch.org

Stephanie Lo@stephlo.bsky.social · last yr.

[New paper alert 🚨 ] What happens when pneumococci 'slip' and 'add' just one extra A in a promoter spacer of a sugar scavenging gene? 🧬 www.cell.com/cell-host-mi...

Naturally acquired promoter variation influences Streptococcus pneumoniae infection outcomes

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...

cell.com

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · last yr.

Each year, over half a million of pneumococcal disease in children were reported in China Our paper showed 1) 94.3% serotypes covered by PCV13 2) 99.8% isolates resistant to ≥1 antibiotics Routine PCV in children will ↘️ pneumococcal disease and AMR! www.microbiologyresearch.org/content/jour...

Genomic analysis of invasive and non-invasive disease-causing Streptococcus pneumoniae isolated from children between 2014 and 2023 in Suzhou, China

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...

microbiologyresearch.org

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · last yr.

Do you need a #bioinformatic tool to detect almost all serotypes in #pneumococci? The new SeroBA v2.0 can detect 102 of 107 known pneumococcal serotypes www.biorxiv.org/content/10.1...

SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae

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...

biorxiv.org

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · last yr.

What does a two-decade surveillance on pneumococcal bacteraemia in Gelderland Netherlands tell us? www.microbiologyresearch.org/content/jour...

Investigating two decades of Streptococcus pneumoniae bacteraemia in the Gelderland area, the Netherlands, using whole-genome sequencing

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...

microbiologyresearch.org

Global Pneumococcal Sequencing Project @globalpneumoseq.bsky.social · last yr.

As part of the #GPS_project, @Abel_AberaN led us to understand the circulating #pneumococcal lineages (carriage and disease)!in Ethiopia after #PCV10 www.microbiologyresearch.org/content/jour...

Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia

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...

microbiologyresearch.org