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GlobalPneumoSeq

@pneumowatch

GPS, the Global Pneumococcal Sequencing project funded by @gatesfoundation is sequencing 50,000 pneumococci to monitor global vaccine implementation and impact.
GlobalPneumoSeq@pneumogen.net pneumogen.net/gps Joined January 2014
434 Following 791 Followers 947 Posts

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GlobalPneumoSeq @pneumowatch
Have you read about our #GPS_project study on how genomic surveillance can have real impact on improving #pneumococcal vaccines? If not, perhaps put it on your reading list now! thelancet.com/journals/lanmi…
www.thelancet.com Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype... Our work reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation...
GlobalPneumoSeq @pneumowatch Aug 17, 2022
We are very excited to share our #GPS_project study out in @LancetMicrobe – showing how genomic surveillance can have real impact on improving #pneumococcal vaccines. thelancet.com/journals/lanmi… 1/14
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GlobalPneumoSeq @pneumowatch
New versions of the GPS Pipeline and the PopPUNK GPS Database are now here!

Get v1.3.0 of GPS Pipeline for better AMR results and more: github.com/GlobalPneumoSe…
Get v12 of the PopPUNK GPS Database (included in GPS Pipeline v1.3.0) to assign more GPSCs: zenodo.org/records/228171…
github.com Release v1.3.0: Better AMR and Longevity · 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 v1.2.0) Changes ARIBA Database Update (#178) The ARIBA database fo...
GlobalPneumoSeq @pneumowatch
New paper! @nicd_sa 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.

microbiologyresearch.org/content/journa…
www.microbiologyresearch.org Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent...
GlobalPneumoSeq @pneumowatch
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/GlobalPneumoSe…
github.com 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 s...
GlobalPneumoSeq @pneumowatch
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/GlobalPneumoSe…
github.com Global Pneumococcal Sequencing (GPS) Project A worldwide genomic survey of the impact of vaccination on the pathogen population - Global Pneumococcal Sequencing (GPS) Project