After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research microbiologysociety.org/news/society...

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics We just did that to study the history of #AMR spread @science.org doi.org/10.1126/scie... If you like time travel & biology, this 🧵is for you👇

Avoiding US tech? Some European alts: 🇳🇴 Browser: Vivaldi 🇫🇷 Search: Qwant 🇫🇷 Music: Deezer 🇫🇷 Hosting: OVH 🇫🇮 Mobile OS: Jolla 🇩🇪 Maps: Here WeGo 🇩🇪 Translation: DeepL 🇳🇱 Design: Sketch 🇨🇭 Notes: Standard Notes 🇨🇭 Messenger: Threema 🇨🇭 Dev Tools: Sonar https://proton.me/blog/european-tech-alternatives

sangerinstitute.blog/2025/10/01/t... @sangerinstitute.bsky.social #microsky

Modern plasmids have evolved through complex microevolution and fusion events into a distinct group of highly recombinogenic, multi-replicon, self-transmissible plasmids that now pose the highest risk to resistance dissemination, and therefore to human health. www.science.org/doi/10.1126/...

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 🧵

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

History repeats itself: more disappearing STIs from molecular target mutation 😬 Great 🕵️ work by @sarah1alexander.bsky.social and colleagues!

The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....

The @microbiologysociety.org ‪Journal of Medical Microbiology is looking for a new Editor for One Health - Emerging, Zoonotic and Environmental Diseases. Come join us!

this is pretty much the plot of the movie clear and present danger

Aieeeeeeeeee.

It’s started #stihiv2025 🧪 Fantastic keynote by Henry de Vries His short history of #STI covers changing views of STIs, sexuality, AIDS, queer theory and sex positivity But moves on to where we are now with illiberalism And a shout out ahead of the closing keynote @drjeannem.bsky.social

STI & HIV 2025 World Congress #stihiv2025 starts Montreal Sunday 27th July stihiv2025.org/program/ @stihiv2025.org Absolutely delighted for this to be my first 🧪 feed post The world's biggest conference dedicated to research on sexually transmitted infections #chlamydia #gonorrhoea #syphilis 🧵

Enjoying the beautiful weather in beautiful Montreal ahead of #stihiv2025

Nothing better than talking syphilis! Thanks @ukhsa.bsky.social @thelovetankcic.bsky.social @typemat12.bsky.social @nicolelieberman.bsky.social @manikkohli.bsky.social & others who came to kick off my NIHR Professorship. Looking forward to working with you & communities to improve UK Sexual Health

Terrific news that @robinmay9.bsky.social of @imibirmingham.bsky.social has been appointed CSO of @ukhsa.bsky.social today! www.gov.uk/government/n... A fantastic choice!

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...

Using the antibiotic doxycycline used as post-exposure & pre-exposure prophylaxis (doxyPEP/PrEP) can prevent #STI Even though it's currently not recommended in the Netherlands, 15% of 1,633 survey participants stated recent informal use without prescription #SexualHealth #IDSky #AMR #PublicHealth

Incredible opportunity to work with an excellent team AND undertake a funded PhD on syphilis and STI control in the UK 👇

Lately McSweeneys is a really consistent source of socio-political bangers. www.mcsweeneys.net/articles/i-s...

🚨 We're recruiting! The Journal of Medical Microbiology is seeking two Editors for our Molecular and Microbial Epidemiology section. Help shape the future of microbiology research. 📅 Apply by 20 June 2025 🔗 microb.io/News

Highlighting the importance of access not only to the new gonorrhoea vaccine, but to sexual health services more broadly 👇

A tour de force in investigating and building capacity for a neglected tropical disease through genomics by @chewapreecha.bsky.social

Great on fungal pathogen threats from @chownbioinf.bsky.social (with slides from @drjorhodes.com) #ABPHM25

An exciting new Doctoral Training Programme in Microbial Genomics for Health Protection, in collaboration with the UK Health Security Agency @ukhsa.bsky.social, has just launched, funded by @nihr.bsky.social there are 9 PhD projects available (UK students only) www.birmingham.ac.uk/research/cen...

Super talk from @efosternyarko.bsky.social @lshtmamrcentre.bsky.social on nanopore based sequencing of cholera across Africa, with PulseNet Africa partners #ABPHM25 www.biorxiv.org/content/10.1...

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!

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...

Yesterday was my one-year work anniversary with the @sangerinstitute.bsky.social! One year has flown by. The variety of topics I've gotten to research and write about (🧵), the people I've met and interviewed, and the dino-mini golf that's been played have all made this a memorable year.

High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy. Find out more in #MGen: doi.org/10.1099/mgen...

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

1 week until deadline for this postdoc position. Really key position in my lab working on amazing datasets

If lost there's no going back: "...the lab holds the world’s largest repository of gonorrhea isolates — over 50,000, dating back to 1988 when the CDC began to collect them." www.statnews.com/2025/04/05/c...

Hard to make sense of a lot of the cuts that are happening at #HHS & its agencies. But closing #CDC's STD laboratory at a time when #gonorrhea seems poised to develop resistance to the last reliable drug that can cure it has experts aghast and worried. www.statnews.com/2025/04/05/c...

New preprint, as described by David below. There's been an increase in doxycycline use for prevention and treatment of bacterial STIs. What's happened to resistance in Neisseria gonorrhoeae? Here we track tetM, a tetracycline-resistance gene, looking at both proportion and phylogenetics.

Cecilia Kyany'a will be presenting our very cool work applying spatial transcriptomics to mycobacterial infections at 12.10 in the infection forum #Microbio25

Another fabulous talk in the 'Exploring Hidden Threats: Knowledge Expansion of Understudied Bacterial Pathogens' session from @amberbarton.bsky.social highlighting the challenges on working on non-culturable organisms 👀🦠🧬 @sangerinstitute.bsky.social #MicrobialGenomics #Microbio25 #MicroSky

On my way to #microbio25 for some exciting science! Also a number of cool projects from @sangerinstitute.bsky.social on display, including new approaches to pathogen typing (Vibrio and Treponema), genomic epi of neglected pathogens (cholera, yaws), and developing field-based molecular diagnostics.

Interested in infectious diseases, climate, health, and international collaborations? 🧬 We spoke with Nick Thomson, Head of our Parasites and Microbes programme to cover all those topics and more. Learn more about Nick and his research vision here ⤵️ sangerinstitute.blog/2025/03/21/a...

First paper from my new job 🎉 Removing human reads from viral and microbial metagenomics data. Usually, I want all the human reads I can get, but this was a really interesting project to work on! www.biorxiv.org/content/10.1...

Great to see the latest Genome Watch article on antimicrobial resistance from Sanger scientist Vignesh Shetty (@vignesh-shetty.bsky.social) and Ankur Mutreja! ⤵️

A new preprint from us. Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue. Where high host contamination is still a big issue. We find modest improvements in bacterial yield. But not enough to improve diagnostics www.medrxiv.org/content/10.1...

Very true - but please be especially aware of this if you are organizing meeting in infectious disease, immunity, host pathogens, tropical diseases etc. There were already many complaints from, for example, Africa-based HIV researchers that they couldnt get visas. Now they may simply be disappeared

I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback. github.com/avantonder/b... github.com/avantonder/b...

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KK...

Nature research paper: Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes https://go.nature.com/4igrfC1

#WGS #Bacteria #genomics #variantcalling www.biorxiv.org/content/10.1...