We are very happy to see our study finally appear online @nature.com! This has been work of nearly 10 years in collaboration with the National Institute of Genome Medicine 🇲🇽, the National Cancer Institute 🇲🇽, the @sangerinstitute.bsky.social and others ⬇️ www.nature.com/articles/s41...

Incredible time at #AIR2026 covering breadth of respiratory infection, microbiomes and immunology with some really beautiful biology. Thanks to fellow committee members @resp-micro.bsky.social @drclairesmith.bsky.social @ewanharrison.bsky.social , Alex Kayongo and organisers @eventswcs.bsky.social

Another insightful day of science, discussion and making new friends at #AIR2026 Day 2 Highlights: making sense of big data, spatial transcriptomics and in vitro modelling of respiratory infections @eventswcs.bsky.social @sangerinstitute.bsky.social

Our new preprint which reimplements "the NFDS model" (of Corander et al) to forecast populations after vaccination as a compartmental model, and uses new bioinformatic tools to create and process the pangenome data We look at which surveillance strategies are best to correctly forecast changes

Brilliant news!

Work on respiratory immunology or microbes? Interested in big data, omics or the latest in vitro models?... Treat your lab to a christmas present of AIR 2026 registration! Feb 11th-13th, registration closing soon: coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Great to share the latest work from our group and collaborators. First CARRIAGE study paper led by @drdaggarwal.bsky.social and the heroic efforts of Katie Bellis and Beth Blane in the lab plus all the team at @cambridge-ceu.bsky.social Huge thanks goes to the 22,000 participants of the study

Really pleased to share the first paper to come out of the lab. We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung. The phylogenies indicate that the clones moved from lung->gut www.nature.com/articles/s41...

ICYMI: New online! Unpacking the spread of pathogens

Worried about identification of human samples from microbial sequencing? We were too- this is what we've done about it! www.sciencedirect.com/science/arti...

featuring @duncan-ng.bsky.social @pathogenomenick.bsky.social @emmanuel-saliba.bsky.social @resp-micro.bsky.social @asthmaandlung.org.uk @ewanharrison.bsky.social @ryanthwaites.bsky.social and many many more I can't find on bluesky

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers. 🚨 Submit your abstracts now! 🚨 Please RT coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Samples from 1917 have helped identify the genetic culprits responsible for the spread of treatment-resistant infections 🔎 By mapping plasmid evolution since the pre-antibiotic era, experts found that a minority of plasmids cause most of the multidrug resistance in the world 🧵

Our paper “Global dissemination of npmA mediated pan‑aminoglycoside resistance via a mobile element in Gram‑positive bacteria” is now in @natcomms.nature.com. Part of my freshly defended PhD, so doubly happy! 😄🎉 🧵 (1/14) www.doi.org/10.1038/s414...

More of this kind of thing.

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV. These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response. 1/4

Happy to share our first preprint looking at the nasal microbiome in ~1000 healthy adults from the CARRIAGE study of 20,000 healthy blood donors to understand nasal colonisation by Staphylococcus aureus. Ten years in the making! doi.org/10.21203/rs....

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...

If you can't afford to use a diagnostic test, then its relative performance characteristics become irrelevant. Important issue raised re blood cultures 👇 @lancetmicrobe.bsky.social #ClinMicro #IDSky #AMR www.thelancet.com/journals/lan...

There were more than 125,000 measles cases in the WHO European region in 2024 - the highest number since 1997! 38 deaths have been reported so far, every single one of them preventable. Worth remembering this also as we report on the measles outbreak in the US. 🧪 #IDsky

Weeks ago I highlighted the false balance of “if only scientists could communicate better”. One OpEd writer kindly reached out to me and I want to share my main response to them because I find it remarkable that people still can’t see what we are now all seeing has been under way for years. 🧵👇

Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms rdcu.be/d55l3

Our paper investigating the mutational landscape during Staphylococcus aureus during colonisation is out now rdcu.be//d55l3 @fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social

Certain sublineages of antimicrobial resistant bacteria dominate the surveillance landscape, but what causes them to become resistant? Check out our latest work in Shigella to find out and/or read the thread below www.medrxiv.org/content/10.1101/2024.10.27.24316207v2 1/n

Frustrating - I reviewed a paper that was highly problematic, mainly in scientific rigour undermining most of the conclusions, so I recommend Reject. However the editor decides to Revise presumably due to the more positive comments from reviewer 2... /1

Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7

UK PhD stipends have not been increasing in line with the national minimum wage, and since the generous COVID increase haven’t even bothered to be anchored against an inflation metric. I’m lucky enough to have a spouse to support me but in what world is this not a barrier to entry for others?

Applied Bioinformatics & Public Health Microbiology (21-23 May 2025) is open for registrations! Spread the word - @happykhan.mstdn.science.ap.brid.gy @pathogenomenick.bsky.social @ewanharrison.bsky.social @wvschaik.bsky.social @ksbakes.bsky.social @firefoxx66.bsky.social @katholt.bsky.social

last couple days to apply (for free! from anywhere in the world!) to the Sanger 2025 PhD Programme — Deadline: 28th November 2024 (09:00 GMT) For more info, visit www.sanger.ac.uk/about/study/...

First @bsky.app post! Great session today #FISHIS about the importance of learning from the pandemic for the future. Thanks @hisinfection.bsky.social @marionkoopmans.bsky.social @ewanharrison.bsky.social

Antimicrobial resistance is rapidly rising in Shigella species. How up to date is your treatment guidance? Be sure to read our latest @LancetMicrobe comment to inform your thinking bit.ly/3Z6yNRa 1/10