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Sophia David

@sophia-david.bsky.social
78 followers 80 following 4 posts

Mum to 👦🏻👶🏻. Senior Research Fellow at the Centre for Genomic Pathogen Surveillance, University of Oxford. Bacterial genomes and AMR 🧬 🦠 Love running and the outdoors 🏃🏼‍♀️🌿

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Reposted by Sophia David
Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 02/03/2026
109 participants from 52 countries are convening at Africa CDC Headquarters in Addis Ababa for a focused, experience-led meeting on strengthening routine national antimicrobial resistance (AMR) surveillance systems, including the integration of pathogen genomic data. More at www.amrsurveillance.org
amrsurveillance.org
AMR Convening on Building Sustainable AMR Genomic Surveillance
A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.
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Sophia David @sophia-david.bsky.social · 25/11/2025
Our amr.watch platform now published in PLOS Global Public Health: journals.plos.org/globalpublic...
journals.plos.org
Monitoring antimicrobial resistance trends from global genomics data: amr.watch
Whole genome sequencing (WGS) is increasingly supporting routine pathogen surveillance at local and national levels, providing comparable data that can inform on the emergence and spread of antimicrob...
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Reposted by Sophia David
John Lees @johnlees.bacpop.org · 19/11/2025
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
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Reposted by Sophia David
Rafal Mostowy @rafalmostowy.bsky.social · 26/06/2025
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!
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Sophia David @sophia-david.bsky.social · 19/06/2025
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! 👶)
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Sophia David @sophia-david.bsky.social · 12/06/2025
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.
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Reposted by Sophia David
Andries van Tonder @andriesvt.bsky.social · 21/05/2025
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.
training.cam.ac.uk
Research Informatics - course description: "Working with Bacterial Genomes (IN-PERSON)"
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Reposted by Sophia David
Lee Katz @lskatz.github.io · 12/05/2025
🚨 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
github.com
GitHub - lskatz/fundamentals-of-bioinformatics
Contribute to lskatz/fundamentals-of-bioinformatics development by creating an account on GitHub.
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Reposted by Sophia David
Marit Hetland @genomarit.bsky.social · 30/04/2025
🦠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....
genomemedicine.biomedcentral.com
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...
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Sophia David @sophia-david.bsky.social · 22/04/2025
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...
amr.watch
AMR.watch
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Reposted by Sophia David
Pathogenwatch @pathogenwatch.bsky.social · 12/02/2025
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
pathogen.watch
Pathogenwatch
A global platform for genomic surveillance.
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Reposted by Sophia David
Pathogenwatch @pathogenwatch.bsky.social · 12/02/2025
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
pathogen.watch
Pathogenwatch
A global platform for genomic surveillance.
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