The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I donβt really like the look of.
Looking forward to sharing our recent work on population metabolism of #klebsiella pneumoniae this week.
Join me to learn about metabolic diversity within species, featuring work by @bananabenana.bsky.social @helena-bethany.bsky.social and a sneak peak at our latest from @kalanip.bsky.social
Thanks @theviin.bsky.social for the invite to join this great meeting, and share our work on Kaptive for capsule typing, and how we can apply it to inform #klebsiella vaccines: tinyurl.com/npaj4vzr
With @tomstantonmicro.bsky.social @shaunkeegan.bsky.social @katholt.bsky.social and many others
𧫠Our publication,βGlobal perspectives on KlebsiellaΒ epidemiology and biology: conference report on the KLEBS 2024 symposium,βΒ is now out!
π Link to paper: www.nature.com/articles/s44...
@kelwyres.bsky.social @katholt.bsky.social @sylvainbrisse.bsky.social @pasteur.fr
Collapsed phylogenetic tree of the Klebsiella pneumoniae Species Complex (top) and the presence of metabolic capabilities (bottom), leading to lineage-specific metabolic networks and traits
Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org π§ͺ plos.io/4qdC2B2
Ditto, ditto, ditto!
We are thrilled this is now available in @plosbiology.org πππ
Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. π¦
Fantastic work by @bananabenana.bsky.social, summarised beautifully below. π€©
π£π¦ Check out our new Editorβs Spotlight! Senior MGEN editor Jesse Shapiro tells us about a recently published paper on the bystander effect on the evolution of Bordetella parapertussis, a non-target species of the pertussis vaccine #MGEN
Read the full blog here: microb.io/48zfOlJ
![figure showing estimated proportion of cases in clusters, for each site. range from 0.04 to 0.93, mean estimate in random effects model is 0.57 [0.46,0.68]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:q5nky4heg5sfix4get4zh2pw/bafkreibshmuvkuafxwd2uk3r42ss6ma2dhmaidbysgvufnbkbv5cn4guai)
figure showing estimated proportion of cases in clusters, for each site. range from 0.04 to 0.93, mean estimate in random effects model is 0.57 [0.46,0.68]
#AMR #Klebsiella cause >100,000 neonatal deaths globally each year.
Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW
doi.org/10.1101/2025...
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread π
Want to learn about #klebsiella genomics?
Check out our free online resource, developed as part of the @klebnet.bsky.social project and in collaboration with ECDC Gen-Epi Bio train.
#genomics #amr #sero-epi #hypervirulence #LINcodes
Registration is open for the Microbial Genomics of Eukaryotes meeting in Glasgow! This event will showcase diverse scientific achievements in eukaryotic genome research. Register now and submit your abstract by 12 August: microb.io/MicroGenomic...
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky π¦ π§¬π₯οΈ /1
www.medrxiv.org/content/10.1...
π¨Β New preprint π¨
My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky
www.biorxiv.org/content/10.1...
AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with deep-learning-based Dark Metabolism Mining https://www.biorxiv.org/content/10.1101/2025.07.21.665674v1
Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social!
Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article)
#MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social
Woohoo Kaptive is now integrated within BIGSdb for #Klebsiella and #Acinetobacter.
Thanks @kjolley.bsky.social!
Also like to acknowledge that the Acineto dbs were developed and maintained by Johanna Kenyon and team at Griffith Uni.
A call to save the date for MicroSeq2025, returning September 3-4. MicroSeq is an online meeting where microbiology meets sequencing, including bacteria, viruses, and fungi.
π¦Hello BlueSky!π¦ Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. πSave the date!π
#MicroSeq2025
First paper on our projects on #Klebsiella transmission in the hospital environment; I'm so lucky to get to work with the wonderful teams@ Malawi Liverpool Wellcome Program, Kamuzu University, Queen Elizabeth Central Hospitalπ²πΌ
#MicroSky #IDSky #GlobalHealth π§¬π»π§ͺ (1/3)
www.medrxiv.org/content/10.1...
So excited that this is now online. It's been a huge collaborative effort to estimate the prevalence of capsule and O antigens associated with #klebsiella neonatal sepsis in Africa and South Asia. The first step to prioritising antigens for a vaccine to protect 1000s of newborns. #MicroSky #AMR
Working on #klebsiella genomes? β
Want to collaborate globally to advance Klebs genomic epi? β
Please join us via the KlebNET-GSP Epidemiology consortium β¬οΈ
#microsky #AMR
Great night at the ASM VIC branch student and ECR awards. Such a high standard of scientific talks, and broad range of science. Congrats to all of the speakers and winners!
πππ
@aussocmic.bsky.social
Interested in a PhD focusing on Streptococcus pneumoniae or pyogenes? Our group is looking for new PhD students to join our lab! Apply here: career10.successfactors.com/sfcareer/job...
Check out our latest Kaptive update for highly sensitive and accurate identification of surface polysaccharide loci from WGS of #AMR pathogens, #Klebsiella and #Acinetobacter baumanii. Led by the awesome @tomstantonmicro.bsky.social
π¦ π§«
π§¬π₯οΈ π¦ 𧫠π§ͺπ¬ Hey BSky Bioinformatics and Genomics!
Some years ago many people were compiling π₯π’π¬ππ¬ π¨π π°π¨π¦ππ§ π’π§ π¬ππ’ππ§ππ as an effort to break biases when looking for reviewers and collaborators...
Is there anything like that for Bioinformatics and Genomics?
#WomenInSTEM
Composite of the paper header showing all authors and an equation showing phylogenetic trees plus plasmids give a complex plasmid picture.
π£Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 𧡠@zaminiqbal.bsky.social
Thanks Andrew- this is just the pack I was hoping for! Please can you add me?
Great thread
This scheme was how Zong and I first established our collaboration. Led to two MRC grants and 33 papers. Canβt encourage people enough to go for this.
What do you think are the critical features pathogen genomic data-sharing platforms require to meet the public health need? Please participate in this public consultation!
