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

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.

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

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

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

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

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

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...

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