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.
The reference genomes for common Global Pneumococcal Sequence Clusters (GPSCs) - GlobalPneumoSeq/gpsc-reference-genomes
Key changes in v1.2.0:
- Improved stability
- Reduced ERY resistant false positive
- Updated to the latest PopPUNK GPS Database v11
- MLST database last update date is now viewable
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...
Key findings:
1. GPSC10-24F and GPSC12-3 have significantly increased after PCV13
2. AMR reduced after PCV rolled out
Collaboration between the Center for Infectious Diseases Research at the American University of Beirut and the GPS Project at the @sangerinstitute.bsky.social
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...
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...
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...
