I can’t explain why but reading the news feels like this at the moment

Very interesting to see what amendments were pushed by different parties for this bit of legislation. The One Nation amendment to remove a focus on public health issues caused by climate change (thankfully voted down) was typically 🙄

New online! Microbial genomics for antimicrobial resistance ecology and action

Are you hungry for some Shigella news? Why not come to the 1st International Shigella meeting www.shigella2026.conferences-pasteur.org/home 20-24 April 2026 Paris

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

A great opportunity to attend the #Shigella meeting April 20-24, 2026! Abstract submissions are open! @shigellameeting.bsky.social #Microsky

Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities

Really liked the explanation about human understanding, and what we miss when we use black box models. This has always been my gripe with prediction models for eg AMR - I want to know why that feature is associated with resistance!

Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Topics range from how genomics inform resistance profiling to pathogen surveillance in a #OneHealth framework. 🧬 ✍️ Register: ow.ly/gjOZ50WpOXX 👀 Programme: ow.ly/Whj850WpOXY#OneHealth #IDSky

This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered

Huge amount of work in this paper, very proud of Hugh getting through all these benchmarking tests. We’re much more confident now using ONT-only data for our clinical questions

New preprint where we analysed IS loads in 🦠 #Klebsiella pneumoniae lineages and found they're inversely associated with nutrient usage. We propose an insertional tolerance model, whereby IS can only insert into metabolically-tolerable sites. #IDSky #MicroSky 🧪 www.biorxiv.org/content/10.1...

Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins Structural predictions to improve #phage genome annotation! @hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social www.biorxiv.org/content/10.1...

🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social. Head to our website to register now 👇 www.microseqconference.com/registration...

A periodic table of bacteria?: Mapping bacterial diversity in trait space https://www.biorxiv.org/content/10.1101/2025.07.11.664459v1

The 10th anniversary #ABACBS conference will be held in Adelaide from Nov 24-28. If you're thinking of coming, get in quick, as it's going to be a big week: A fantastic #bioinformatics conference with outstanding national and international speakers, and we're wrapping up the ABACBS week an AC/DC gig

Doesn’t destroy the planet if you use solar energy to power it - in summer our house regularly produces way more solar than we can use, our AC runs entirely off solar during the day with energy to spare

🦋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

🚨Plasmid ALERT – new @eurosurveillance.org rapid comms! @ecdc.europa.eu-led study finds mosaic IncHI1B(pNDM-MAR) plasmid with blaOXA-48 + aerobactin in 492 K. pneumoniae isolates across 8 EU countries (2019–2024). First ESGMAP-backed paper: tinyurl.com/4acezh92 #AMR #plasmids #OneHealth #ESGMAP

Israel: silencing dissent everywhere theshot.net.au/uncategorize...

🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...

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

Explore the important role of #genomics and data-driven technologies for accelerating advances in #AMRresearch, at our Antimicrobial Resistance meeting! #AMR2026 Discover the latest developments informing a dynamic global response to controlling this crisis. 🗓️ 23–25 March 2026 📎 bit.ly/3SWzJUm

Excited to share this preprint focused on the genomic taxonomy of C. diphtheriae #diphtheria ➡️ www.biorxiv.org/content/10.1... Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!

Main character energy is OUT, this summer we’re bringing NPC energy. We’re posted up at the bar dropping lore and suggesting side quests. We’re leaning casually near a locked door and saying “I don’t think you have the key for that” when someone tries the handle. We’re staring at a tree.

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

immem hackthon registration closes 31st May. https://www.escmid.org/congress-events/immem-xiv/12th-microbial-bioinformatics-hackathon/

Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11 www.medrxiv.org/content/10.1...

Happy to share this resource of 568 closed Klebsiella pneumoniae species complex hybrid assemblies, including 1416 plasmids! ⭕️🦠 We hope this will be useful - short reads, long reads, hybrid assembly or all combined - for your own tools/validations 🥳 #Microsky journals.asm.org/doi/10.1128/...

Happy to see this out - please try my code and break it! Also come see me at #ABPHM25 in the showcase today, where I’m presenting AMRGen, an R package for combining and exploring AMR geno pheno data. It was used to help make many of these rules interpretamr.github.io/AMRgen/

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace. Check out the course objectives below and sign up before June 9th to join us! www.futurelearn.com/courses/anti...

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

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads https://www.biorxiv.org/content/10.1101/2025.05.16.654303v1

Has Antony Green called the Eurovision winner yet? #eurovision #auspol #stillwaitingfortheprepolls

Iceland or Sweden for the win #eurovision

Great to see the typeset version of this invited review out. Covers pretty much everything we know about metabolites/peptides produced by Klebsiella spp. and how they interact with the host. #microsky #microbiomesky @microbiotaandhost.bsky.social doi.org/10.1530/MAH-...

🧬 Out today 🧬 - our TyphiNET #AMR surveillance dashboard for #typhoid Use TyphiNET to view genome-derived data on global and national annual trends in AMR and circulating pathogen genotypes via any standard web browser. genomemedicine.biomedcentral.com/articles/10....

Antony Green: Peter Dutton will lose his seat Sarah Ferguson: James McGrath, a massive repudiation of the leader, your response? James McGrath: 🙀

Feeling mildly emotional that this is Green’s last election coverage. He’s covered every Aus election I’ve ever seen, it won’t be the same without him #auspol

🦠Happy to share that our paper studying >3000 Klebsiella pneumoniae genomes in a #OneHealth perspective is now published in Genome Medicine! #MicroSky 🎉 @irenlohr.bsky.social @katholt.bsky.social genomemedicine.biomedcentral.com/articles/10....

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable

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...

Managed to see 9/10 Best Picture nominees this year. My rankings, worst to best: 9. A Complete Unknown - good tunes, didn’t realise Bob Dylan was a bit of a jerk 8. Wicked - can’t believe it was only act 1 7. Conclave - went places I wasn’t expecting for a movie about the Pope