It's out! The LIN code approach for genomic taxonomy of microbial strains and its applications in genomic epidemiology journals.plos.org/plosbiology/...

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...

journals.plos.org

Do you work on Klebsiella oxytoca genomes? Want to know which K and O loci they have? Check out the new Klebs oxy species complex databases here: github.com/klebgenomics... Poster today #ESCMIDGlobal2026 by Naoise McGarry! Papers to follow soon. @klebnet.bsky.social @klebclub.bsky.social

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 don’t really like the look of.

rambaut/figtree

Automatically exported from code.google.com/p/figtree - rambaut/figtree

github.com

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

We will have the pleasure to have Dr. Kelly Wyres in our next webinar talking about: 👉 Metabolic modelling of Klebsiella pneumoniae and strain diversity When: 25.02.206 at 10h00 CET Registration: us06web.zoom.us/webinar/regi... @kelwyres.bsky.social @escmid.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

Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: A meta-analysis of genome-predicted serotype prevalence to inform potential vaccine cover...

Thomas Stanton and colleagues use whole genome sequencing to evaluate the prevalence of Klebsiella pneumoniae K and O antigen types in 13 countries in Africa and South Asia to help inform vaccine desi...

tinyurl.com

Victorian Infection and Immunity Network@theviin.bsky.social · 6mo ago

Next up in the emerging infectious disease threats session we had our invited speaker @kelwyres.bsky.social from @monashuniversity.bsky.social who shared how genomic surveillance can be used to inform anti-Klebsiella pneumoniae vaccines to save babies from neonatal sepsis 🍼🦠💉 #lorneiandi

🧫 Our publication,“Global perspectives on Klebsiella epidemiology and biology: conference report on the KLEBS 2024 symposium,” is now out! 📄 Link to paper: www.nature.com/articles/s44... @kelwyres.bsky.social @katholt.bsky.social @sylvainbrisse.bsky.social @pasteur.fr

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 🧪 plos.io/4qdC2B2

Ditto, ditto, ditto! We are thrilled this is now available in @plosbiology.org 🎉🎉🎉 Our analysis of metabolic diversity in #klebsiella pneumoniae, showing clone specific metabolism. 🦠 Fantastic work by @bananabenana.bsky.social, summarised beautifully below. 🤩

Ben Vezina@bananabenana.bsky.social · 8mo ago

Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊

📣🦠Check out our new Editor’s 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

#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 👇

Life Identification Numbers: A bacterial strain nomenclature approach

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

doi.org

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

Kat Holt@katholt.bsky.social · 9mo ago

The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series! Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more! klebnet.org/2025/11/18/k...

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 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

🚨 New preprint 🚨 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...

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

biorxiv.org

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.

Keith Jolley@kjolley.bsky.social · last yr.

BIGSdb v1.51.4 has been released. This adds a new #Kaptive plugin for surface polysaccharide typing of Acinetobacter baumannii and Klebsiella. github.com/kjolley/BIGS... for details. Kaptive is developed by @tomstantonmicro.bsky.social, @kelwyres.bsky.social , @katholt.bsky.social and colleagues.

🦋Hello BlueSky!🦋 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. 🌟Save the date!🌟 #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 Hospital🇲🇼 #MicroSky #IDSky #GlobalHealth 🧬💻🧪 (1/3) www.medrxiv.org/content/10.1...

High ward-level and within-sample diversity of Klebsiella pneumoniae on a Malawian neonatal unit revealed by single colony whole genome sequencing and post-enrichment metagenomics

Klebsiella pneumoniae is a frequent cause of antimicrobial resistant healthcare associated infections in neonates across sub-Saharan Africa, with multiple lineages associated with neonatal sepsis. How...

medrxiv.org

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

Kat Holt@katholt.bsky.social · last yr.

I'm super happy to share this preprint on ‘Distribution of capsule and O types in #Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage’ doi.org/10.1101/2025...

Working on #klebsiella genomes? ✅ Want to collaborate globally to advance Klebs genomic epi? ✅ Please join us via the KlebNET-GSP Epidemiology consortium ⬇️ #microsky #AMR

KlebNET-GSP@klebnet.bsky.social · last yr.

We are pleased to launch the KlebNET Genomic Epidemiology Consortium! We aim to build a public metadata repository; systematic risk framework for global genomic surveillance; and genomic epi reviews for high-impact #Klebsiella clones. Join us here: klebnet.org/klebnet-gsp-... #ABPHM25

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! 🎉🎉🎉 @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 🦠🧫

Tom Stanton@tomstantonmicro.bsky.social · last yr.

Super excited to finally present the preprint to accompany Kaptive 3 which we released last year! Big thanks to coauthors @kelwyres.bsky.social, @katholt.bsky.social, @genomarit.bsky.social and Iren Löhr. Here's what we did to improve in silico antigen typing 👇🧵 www.biorxiv.org/content/10.1...

🧬🖥️ 🦠🧫 🧪🔬 Hey BSky Bioinformatics and Genomics! Some years ago many people were compiling 𝐥𝐢𝐬𝐭𝐬 𝐨𝐟 𝐰𝐨𝐦𝐞𝐧 𝐢𝐧 𝐬𝐜𝐢𝐞𝐧𝐜𝐞 as an effort to break biases when looking for reviewers and collaborators... Is there anything like that for Bioinformatics and Genomics? #WomenInSTEM

📣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 🧵 @zaminiqbal.bsky.social

Great thread

Rebecca J Hall@drrebeccajhall.bsky.social · 2y ago

Writing lecture slides on 'evolution of AMR' - what are your favourite experimental evolution papers? Bonus points if not E. coli. #microsky

This scheme was how Zong and I first established our collaboration. Led to two MRC grants and 33 papers. Can’t encourage people enough to go for this.

The Royal Society@royalsociety.org · 2y ago

The Royal Society's Newton International Fellowships will open for applications next week on 21 January. These fellowships are for non-UK early career scientists who wish to conduct research in the UK. Find out more on our website: #RSGrants royalsociety.org/grants/newto...