Sophia David
@sophia-david.bsky.social
Mum to 👦🏻👶🏻. Senior Research Fellow at the Centre for Genomic Pathogen Surveillance, University of Oxford. Bacterial genomes and AMR 🧬 🦠 Love running and the outdoors 🏃🏼♀️🌿
Pinned
Sophia David
@sophia-david.bsky.social
· Jun 12
We’re pleased to share two new preprints with results from a structured survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE), conducted in 37 European countries in 2019.
E. coli: papers.ssrn.com/sol3/papers....
K. pneumoniae: papers.ssrn.com/sol3/papers....
E. coli: papers.ssrn.com/sol3/papers....
K. pneumoniae: papers.ssrn.com/sol3/papers....
Thrilled to see these preprints out after many years of planning, data collection, analysis - and huge efforts from the entire EURGen-Net CCRE Survey Working Group. It's been a pleasure working on these with Anke Kohlenberg @ecdc.europa.eu, Inga Froding & Alma Brolund at Public Health Agency Sweden.
Reposted by Sophia David
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
June 26, 2025 at 7:13 AM
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
Our preprint on using genomic data to explore vaccine target diversity ⬇️ A real pleasure working on this with Khalil Abudahab and the team. We're keen to gather feedback, feel free to get in touch (although I will be a little quiet for a while due to another project arriving soon! 👶)
Pleased to share our latest preprint describing vaccines.watch (vaccines.watch), an interactive platform enabling exploration of vaccine target diversity from global genome data: www.biorxiv.org/content/10.1...
June 19, 2025 at 1:45 PM
Our preprint on using genomic data to explore vaccine target diversity ⬇️ A real pleasure working on this with Khalil Abudahab and the team. We're keen to gather feedback, feel free to get in touch (although I will be a little quiet for a while due to another project arriving soon! 👶)
Thrilled to see these preprints out after many years of planning, data collection, analysis - and huge efforts from the entire EURGen-Net CCRE Survey Working Group. It's been a pleasure working on these with Anke Kohlenberg @ecdc.europa.eu, Inga Froding & Alma Brolund at Public Health Agency Sweden.
We’re pleased to share two new preprints with results from a structured survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE), conducted in 37 European countries in 2019.
E. coli: papers.ssrn.com/sol3/papers....
K. pneumoniae: papers.ssrn.com/sol3/papers....
E. coli: papers.ssrn.com/sol3/papers....
K. pneumoniae: papers.ssrn.com/sol3/papers....
June 12, 2025 at 10:22 AM
Thrilled to see these preprints out after many years of planning, data collection, analysis - and huge efforts from the entire EURGen-Net CCRE Survey Working Group. It's been a pleasure working on these with Anke Kohlenberg @ecdc.europa.eu, Inga Froding & Alma Brolund at Public Health Agency Sweden.
Reposted by Sophia David
We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July
www.training.cam.ac.uk/bioinformati...
Please let anyone who may be interested know.
www.training.cam.ac.uk/bioinformati...
Please let anyone who may be interested know.
Research Informatics - course description: "Working with Bacterial Genomes (IN-PERSON)"
www.training.cam.ac.uk
May 21, 2025 at 1:56 PM
We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July
www.training.cam.ac.uk/bioinformati...
Please let anyone who may be interested know.
www.training.cam.ac.uk/bioinformati...
Please let anyone who may be interested know.
Reposted by Sophia David
🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
GitHub - lskatz/fundamentals-of-bioinformatics
Contribute to lskatz/fundamentals-of-bioinformatics development by creating an account on GitHub.
github.com
May 12, 2025 at 6:00 PM
🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩💻
📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!
#bioinformatics #opensource #STEMeducation
Reposted by Sophia David
🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs - Genome Medicine
Background Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the cli...
genomemedicine.biomedcentral.com
April 30, 2025 at 9:33 AM
🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
@irenlohr.bsky.social @katholt.bsky.social
genomemedicine.biomedcentral.com/articles/10....
Preprint on our new amr.watch tool from @thecgps.bsky.social - this incorporates and analyses genome data of key resistant pathogens from the public archives on an ongoing basis (every 4h) & presents the output via an interactive platform for monitoring AMR trends: www.biorxiv.org/content/10.1...
April 22, 2025 at 11:43 AM
Preprint on our new amr.watch tool from @thecgps.bsky.social - this incorporates and analyses genome data of key resistant pathogens from the public archives on an ongoing basis (every 4h) & presents the output via an interactive platform for monitoring AMR trends: www.biorxiv.org/content/10.1...
Reposted by Sophia David
We’ve just released a public Pathogenwatch collection of the MRSN Diversity Panel comprising 100 diverse K. pneumoniae clinical isolates: pathogen.watch/collection/8... #KlebClub
Pathogenwatch
A global platform for genomic surveillance.
pathogen.watch
February 12, 2025 at 10:08 AM
We’ve just released a public Pathogenwatch collection of the MRSN Diversity Panel comprising 100 diverse K. pneumoniae clinical isolates: pathogen.watch/collection/8... #KlebClub
Reposted by Sophia David
Hi Bluesky! We’re looking forward to engaging with the community and our users on here. Follow this account for updates on the Pathogenwatch platform (pathogen.watch), as well as our sister tools @microreact.bsky.social and @amrwatch.bsky.social developed by @thecgps.bsky.social
Pathogenwatch
A global platform for genomic surveillance.
pathogen.watch
February 12, 2025 at 10:05 AM
Hi Bluesky! We’re looking forward to engaging with the community and our users on here. Follow this account for updates on the Pathogenwatch platform (pathogen.watch), as well as our sister tools @microreact.bsky.social and @amrwatch.bsky.social developed by @thecgps.bsky.social