[🚨Data release🚨] The #GPS_project database Monocle is now having 40k pneumococcal genomes and detailed metadata ! Thanks @HarryHung at @sangerinstitute and Simran Utreja at CDC to put them together! data-viewer.monocle.sanger.ac.uk/project/gps
Stephanie Lo
@stephlo.bsky.social
Senior Staff Scientist @ Sanger Institute Senior Lecturer @ University of Bath Leading the Global Pneumococcal Sequencing project, inform vaccine design and promote equality in science
[🚨New Paper 🚨]SeroBA recognised 102/107 known pneumococcal serotypes and its companion resources webpage SeroBAnk are now published on Microbial Genomics @microbiologysociety.org www.microbiologyresearch.org/content/jour...
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...
microbiologyresearch.org
Stephanie Lo@stephlo.bsky.social · last yr.The SeroBA(v2.0) is now available in the GPS pipeline github.com/GlobalPneumo... #GPS_project #pneumococci #serotype #bioinformatics
🦠🧪🧬 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
It's likely the next pandemic will come from wildlife. But how can we prepare for the next spillover event, if we don't understand the diversity of viruses out there? 🦔🦠 Check out our Genomewatch article, where we discuss using meta-genomics to study viral diversity in wild mammals 🖥️🧬 rdcu.be/eHIBl
Zoonotic threats hidden in wildlife
Nature Reviews Microbiology - This Genome Watch article explores how metagenomics can be used to investigate viral diversity and track emerging zoonotic disease threats from wildlife.
urldefense.proofpoint.com
[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...
biorxiv.org
[🚨 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
[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
Our team is hiring an ambitious senior bioinformatician to look into bacterial capsules . This position will closely collaborate with EMBL-EBI Stephen Bentley, John Lees, Steph Lo Closing date: 20 July 2025 sanger.wd103.myworkdayjobs.com/en-GB/Wellco...
Bioinformatician – Bacterial Genomics
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
sanger.wd103.myworkdayjobs.com
It’s my great pleasure to present the Global Pneumoocccal Sequencing project at #LISSSD25 I feel humbled to learn more about Group A and Group B streptococci and other species, and meet great minds to discuss science. #GPS_project
Dr Dorota Jamrozy presents a well-powered GWAS to identify genetic features associated with invasive #GBS disease as compared with carriage at #LISSSD25 Thanks to the >20,000 GBS genomes in the #JUNO_project funded by @gatesfoundation.bsky.social
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
@sophiebelman.bsky.social carried out this spatiotemporal analysis to quantify how fast a pneumococcal lineage can travel across the country, and this work was published on pmc.ncbi.nlm.nih.gov/articles/PMC... #LISSSD25
Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study
Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France ...
pmc.ncbi.nlm.nih.gov
Stuart Campbell@sc345.bsky.social · last yr.@stephlo.bsky.social & global partners describe the extent (worldwide) of intra-country spread (<4 years) of pneumococcus through in silico genotyping, then outlines genotypic methods of predicting vaccine escape (capsules 33F -> 33E) using this in silico data. #LISSSD25 #idsky
@stephlo.bsky.social & global partners describe the extent (worldwide) of intra-country spread (<4 years) of pneumococcus through in silico genotyping, then outlines genotypic methods of predicting vaccine escape (capsules 33F -> 33E) using this in silico data. #LISSSD25 #idsky
Good morning Brisbane! What a nice view to prepare my very first talk at #LISSSD25 ! Looking forward to meeting people at the conference. #GPS_project #pneumococci #Genomics
Society Event Grant – applications for funding to attend EC Summer Conference 2025 are now open until 24 May at 23:59 BST. Check your eligibility and apply now- microb.io/3S9T6cO
Society Events Grant
Funds are available to support eligible members attending the Society Annual Conference or one other Society meeting per year.
microb.io
The SeroBA(v2.0) is now available in the GPS pipeline github.com/GlobalPneumo... #GPS_project #pneumococci #serotype #bioinformatics
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
github.com
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...
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
GPS :: Global Pneumococcal Sequencing Project
Homepage of The Global Pneumococcal Sequencing Project
pneumogen.net
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
Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander www.biorxiv.org/content/10.1...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa
Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but...
biorxiv.org
🆕 Rates of AMR up to 3 times greater in outpatients with cancer compared to those without cancer, suggests USA data. Find out more in @thelancetoncol.bsky.social: tinyurl.com/2uy9ttvv
Do you need a #bioinformatic tool to detect almost all serotypes in #penumococci ? The new SeroBA v2.0 can detect 102 of 107 pneumococcal serotypes github.com/GlobalPneumo...
Issues · GlobalPneumoSeq/seroba
A Fork of the Original SeroBA. Contribute to GlobalPneumoSeq/seroba development by creating an account on GitHub.
github.com
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
An up-to-date review on the evolving landscape of pneumococcal capsule - seroepidemiology -recently recognised novel serotypes -mitis expressed pneumo capsule -future research direction #pneumococcus #vaccine #PCV #NahmLab led by @FerozeGanaie pubmed.ncbi.nlm.nih.gov/39878373/
Update on the evolving landscape of pneumococcal capsule types: new discoveries and way forward - PubMed
SUMMARY<i>Streptococcus pneumoniae</i> (the "pneumococcus") is a significant human pathogen. The key determinant of pneumococcal fitness and virulence is its ability to produce a protective polysaccha...
pubmed.ncbi.nlm.nih.gov
There are four (that's right four!) academic posts open at the School of Biological sciences at Cambridge University. Check them out here: www.jobs.cam.ac.uk/job/?categor... Gr10/11 (AssocProf/Reader; now Prof) Closing 26/1/25. Looking for excellent, collaborative people. Spread the word!
Job Opportunities - University of Cambridge
Current Academic jobs at the University of Cambridge.
jobs.cam.ac.uk
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline https://www.biorxiv.org/content/10.1101/2024.11.27.625679v1
Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomi
biorxiv.org