Global Pneumococcal Sequencing Project

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

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.

This is the combined effort of @harryhung.bsky.social
Narender Kumar
Victoria Dyster @stephlo.bsky.social
Stephen Bentley
at @sangerinstitute.bsky.social
; Corin Yeats at CGPS
; Benjamin Metcalf, Yuan Li, Paulina Hawkins, Lesley McGee at @cdcgov.govmirrors.com
; and funded by Gates Foundation

GitHub - GlobalPneumoSeq/gps-pipeline: Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project) Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project) - GlobalPneumoSeq/gps-pipeline

Try it out:
📂 Code: github.com/GlobalPneumo...
✅ Features: QC, serotyping, MLST, GPSC assignment, AMR prediction.
🌍 Built for global use: from powerful HPC clusters to nimble laptops.

Here’s how the pipeline works 👇

Why it matters:
📊 Genomic surveillance is vital for tracking serotypes, AMR, and informing vaccines.
⚡️ GPS Pipeline makes this possible in a reproducible, scalable, and portable way.

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.

🦠🧪🧬 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

Work led by Dr Andrew Balmer, supervised by @lucyweinert.bsky.social and @OlivierRestif at University of Cambridge @cam.ac.uk, collaborated with @gemmamurray.bsky.social at @ucl.ac.uk and @stephlo.bsky.social at @sangerinstitute.bsky.social

Potential new pbp substitutions that link to beta-lactam resistance in S pneumoniae

By linking their shifts in the phenotypic map above with the amino acid changes in PBP protein, we could pinpoint particular substitutions and its impact on resistance.

Some pneumococcal lineages are more resistance to beta-lactams - coincides with our observations in the #GPS_project

AMR cartography to show the MIC values of multiple antibiotics

[New pre-print🚨] When a single genotype (pbp) confer resistance (penicillin, amoxicillin, cephalosporins) to multiple antibiotics, how do we make sense of genetic changes and their impact on AMR?

A new concept - AMR cartography is invented.

www.biorxiv.org/content/10.1...

A collaboration with National Health Research Institute in Taiwan, National Taiwan University, University of Bath and @sangerinstitute.bsky.social

Our findings show how dense population, high vaccine uptake, widespread antibiotic use, and mobility shape a distinct pneumococcal landscape. Sustained genomic surveillance is essential to detect emerging threats, guide vaccine strategy for the ageing population, and monitor AMR in the post-PCV era.

Key findings:
1) Increase in elderly IPD post-PCV13
2) Rapid post-vaccine emergence of GPSC9-serotype 15A.
2) Frequent capsular switching in GPSC6
4) GPSC1-19A are persistent after PCV13

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...

[🚨 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...

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...

[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...

A fantastic collaboration with Shanghai CDC, Fudan University and Children’s Hospital of Soochow University

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...

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...

Last week in #Europneumo2025, the GPS core team presents

1) Database of 26k pneumococcal genomes @harryhung.bsky.social
2) Global population structure of serotype 12F @dralannah.bsky.social
3) SeroBA - WGS-based tool to detect 102 known pneumococcal serotypes @OliverLorenz

Compiled by a global team: Feroze Ganaie (Ph.D, MBA), Anne Wyllie, Sam Manna, Catherine Satzke, Mark van der Linden, Neil Ravenscroft, Hans-Christian Slotved, Lesley McGee, Stephen Bentley, Alannah King, Harry Hung Oliver Lorenz

Wellcome Sanger Institute hashtag#GPS_project

Keeping track on the number of hashtag#pneumococcal serotypes?

SeroBAnk is an atlas of pneumococcal capsule to display its genetics, biochemical structure and serological profiles

www.pneumogen.net/gps/#/serobank

A great collaboration with Feroze Ganaie, Moon Nahm, @sammanna.bsky.social Catherine Satzke, @annewyllie.bsky.social, Mark van der Linden, Neil Ravenscrotf, Hans-Christian Slotved, Lesley McGee, Stephen Bentley, @dralannah.bsky.social @harryhung.bsky.social Oliver Lorenz @stephlo.bsky.social

Issues · GlobalPneumoSeq/seroba A Fork of the Original SeroBA. Contribute to GlobalPneumoSeq/seroba development by creating an account on GitHub.

If you'd like us to add your new serotypes in SeroBA for detection, create an issue on our Github page at github.com/GlobalPneumo...

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...

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...

A great collaboration between @sangerinstitute.bsky.social , @radboudumc.bsky.social , clinical labs in Nijmegen, University of Lausanne, and US CDC
@stephlo.bsky.social @Amelieke Cremers

Key findings
- Paediatric cases declines while adult cases increase
- Serotype 8 (GPSC3) and 12F (GPSC32/26/55) are major drivers
- PCV20 should be considered in children and adults
- Low penicillin resistance

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...

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

More PCV impact studies in the rest of the world see this GPS collection www.microbiologyresearch.org/content/glob...

Collaboration between @sangerinstitute.bsky.social AHRI Ethiopia, and Ghent University @stephlo.bsky.social