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Josie Bryant

Group Leader at Wellcome Sanger Institute. Using omics to understand chronic lung infections and lung microbiomes in disease

329 подписчиков168 подписок36 постов
Публикации
⟳ Репост от Josie Bryant
Nathan Day

Very pleased to announce that my Crick postdoc work has just been published in Nature Communications: www.nature.com/articles/s41... Big thank you to @bpradel.bsky.social, @jaksonluk.bsky.social, @maxgg.bsky.social and the rest of the host-pathogen interactions in TB lab that made it all possible!

Fast-growing intracellular Mycobacterium tuberculosis populations evade antibiotic treatment - Nature CommunicationsThe slow growth displayed by Mycobacterium tuberculosis has been historically associated with pathogen’s persistence and drug tolerance. Unexpectedly, here the authors identify a rare subpopulation of...www.nature.com
⟳ Репост от Josie Bryant
Jose Bengoechea

Delighted with the publication in @cp-trendsmicrobiol.bsky.social of a concept note where we propose a new framework to capture the complexity of infections in vivo: metapopulation infection biology. Supported by Klebsiella and Cryptococcus research among other pathogens www.cell.com/trends/micro...

Beyond intracellular–extracellular divide toward metapopulation infection biologyThe binary classification of pathogens as intracellular or extracellular fails to capture the complexity of infections in vivo. We propose the metapopulation infection biology framework, in which infe...www.cell.com
⟳ Репост от Josie Bryant
Dr Claire Smith

Delighted to share our new paper, out now in @natureportfolio.nature.com where we show that neutrophil myeloperoxidase (MPO) tracks RSV severity in infants, and can be used as a functional readout of therapeutic efficacy in the lab. 📄 Read it (open access) 👉 rdcu.be/ftx53

Neutrophil myeloperoxidase as a functional biomarker for RSV severity: implications for in vitro therapeutic screeningNature Communications - Preclinical human models are needed to investigate mechanisms and evaluate therapies for severe respiratory syncytial virus (RSV) infection in children. The authors here...rdcu.be
⟳ Репост от Josie Bryant
Wellcome Sanger Institute

Read: 'Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology' in @natcomms.nature.com here 👇 https://www.nature.com/articles/s41467-026-75002-y

Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiologyNature Communications - Whole genome sequencing of pathogens is costly to implement, and partial sequencing sacrifices information. Here, the authors present Phylo-Plex, a method for identifying...www.nature.com
⟳ Репост от Josie Bryant
Kate Baker

👀👇 New work on sexually transmitting Shigella (press-friendly: bit.ly/4bBarEL) From continued collaboration with @clairejenkins2.bsky.social @ukhsa.bsky.social, @pducambridge.bsky.social co-lead @hsalje.bsky.social, a talented student Julia Marshall www.linkedin.com/in/julia--ma..., and others! 🧫🧬💊

The Lancet Infectious Diseases

New Research The spread of sexually transmissible drug-resistant shigellosis in England: a genomic epidemiology study www.thelancet.com/journals/lan...

Josie Bryant

First author is superstar PhD student Cecilia Kyany'a @katungececilia.bsky.social who was profiled here (and is looking for postdoc opportunities): sangerinstitute.blog/2026/06/24/b...

Breathing new life into cystic fibrosis research - Wellcome Sanger Institute BlogCecilia Kyany’a studies the fascinating microbiology of the airway microbiome, especially in people living with cystic fibrosis. As part of her PhD research, Cecilia is uncovering the hidden microbial...sangerinstitute.blog
⟳ Репост от Josie Bryant
John Lees

We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify). On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!

Johanna von Wachsmann

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

⟳ Репост от Josie Bryant
Charles Wei

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies - BMC MicrobiologyBMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...link.springer.com
⟳ Репост от Josie Bryant
John Lees

New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection

Sam Horsfield

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

⟳ Репост от Josie Bryant
John Lees

Some more thoughts on why this outbreak (large, happening quickly, in one place) might be happening: johnlees.me/posts/menb-o... Perhaps strain + immunity + high transmission

menB outbreak in Kent -- more thoughtsPosted some thoughts on the menB outbreak yesterday. Now nine more cases, total at 27. A few more thoughts today, also after discussing with some others. A local factor seems necessary. I think pathog...johnlees.meJohn Lees

I did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely. Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o... I tried to think of factors and their likelihood to explain why this is happening now

⟳ Репост от Josie Bryant
Alan McNally

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysisEscherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…www.sciencedirect.com
⟳ Репост от Josie Bryant
Charlotte Houldcroft

@oldenoughtosay.com I see that your house has recently been visited by the Bad Enterovirus Fairy, aka Hand, foot and mouth disease. I got so het up about baby germs that I wrote a 9.5k word review article on them (800 word version here theconversation.com/if-you-think...). Normal response, right?!

If you think your toddler’s often ill, you’re right – what going to nursery means for catching colds and building immunityHaving an under five in your household increases your risk as an adult of having diarrhoea and vomiting.theconversation.com
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