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...
Other work using the same cohort is in progress looking at the role of human genetics led by @roisinboggan.bsky.social and metagenomics of the nasal microbiome in larger numbers of CARRIAGE study participants by @duncan-ng.bsky.social
We also found some interesting differences in the nasal microbiome between men and women, and between the strains of S. aureus that are present at high abundance. This all now needs evaluation in larger numbers and different human populations.
We found that people less likely to carry S. aureus tended to have more of Dolosigranulum pigrum, Staphylococcus epidermidis and Moraxella catarrhalis. These bacteria may crowd out, kill or compete with S. aureus, but that requires further study.
This confirms previous data and hypothesis that ‘ intermittent carriers’ (people who will sometime be positive for S. aureus and sometimes not) aren’t a distinct biological group - rather they have microbiomes just like persistent or non-carriers.
Combining nasal microbiome data and culture data we show when S. aureus is present, it often dominates. We can group the nasal microbiome into two major patterns:
1. S. aureus dominated with overall low microbial diversity
2. S. aureus is rare, and there is a greater diversity of other bacteria.
This is of important because people who are colonised are at higher risk of S. aureus infection - which is why you get swabbed when you are admitted to hospital.
Over the last 70yrs using nasal swabs and culture it has been established that some people are persistently colonised by Staphylococcus aureus, while others never are - and third group are positive from time to time (intermittent carriers). We investigated the nasal microbiome in these groups
So a few highlights of the study.
Also thanks to the huge contribution and co-leadership of the CARRIAGE study by @julianparkhill.bsky.social John Danesh, Joan Geoghegan, Sharon Peacock and others in the wider CARRIAGE study team at @cam.ac.uk @sangerinstitute.bsky.social and thanks to @wellcometrust.bsky.social for funding
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...
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...
A segregated cycle path and footpath, with a lady and a child walking away from the camera, whilst a group of about six young teenagers in school uniform cycle in the opposite direction.
More of this kind of thing.
Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.
📢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.
🧵👇
