Excited to share some new work on plasmid host specificity and co-occurrence!

Delighted to have played a small part in this great study from colleagues in CaPES: doi.org/10.1038/s414...

There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)

We have a fully funded PhD studentship available @modmedmicro.bsky.social in Oxford to work on a really cool project looking at population heterogeneity in bloodstream infections www.ndm.ox.ac.uk/study/dphil-... Please spread the word/get in touch if you'd like to chat.

Please feel free to message me with any questions! ☺️

🔊 Fully-funded 4yr PhD studentship with the NWB DTP, working on novel regulators of bacterial nitrogen metabolism 🦠 Primary supervisor: @ariannebabina.bsky.social (University of Glasgow) Co-supervisors: myself (Queen’s Belfast)+ Dónal Wall (Glasgow) 🌟 please share 🌟 www.gla.ac.uk/postgraduate...

Come and work with Nicole Stoesser and I in Oxford with the fantastic team @modmedmicro.bsky.social - great opportunity for a postdoc in microbial genomics to do some creative research with great datasets as part of our HPRU. my.corehr.com/pls/uoxrecru...

Now published in @natcomms.nature.com 🎉 www.nature.com/articles/s41... With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!

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

New pre-print from my lab! Plasmids link antibiotic resistance and phage defense. E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!! #microsky#AMR#phage www.biorxiv.org/content/10.1....

Plasmids link antibiotic resistance genes and phage defense systems in E. coli https://www.biorxiv.org/content/10.1101/2025.07.25.666796v1

New Comment—Reinforcing social safety for transgender and non-binary communities amidst global legislative threats tinyurl.com/v3jvjzs5

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

That was fun: 2 days of bacterial genome evolution in beautiful Bath Ta @edfeil.bsky.social @eseb.bsky.social Great to see @craigmaclean.bsky.social @wtmatlock.bsky.social @jpjhall.bsky.social @taylorlabgroup.bsky.social @zaminiqbal.bsky.social @epcrocha.bsky.social @jomcinerney.bsky.social &co

The leading region of many conjugative plasmids is depleted in restriction-modification targets https://www.biorxiv.org/content/10.1101/2025.04.03.647016v1

Deadline in ‼️3 weeks‼️ for this project with me & @paulhoskisson.bsky.social 🦠 🧫

Genomic epidemiology of blaGES-5 integrons www.microbiologyresearch.org/content/jour...

🆕New in @plosbiology.bsky.social: we show compensatory mutations make plasmids play Rock-Paper-Scissors and turn conjugation into a weapon🛡️💫✂️🦠 w/Rosanna Wright, Jamie Wood, @mbottery.bsky.social, @kmudz.bsky.social, @scottishwormboy.bsky.social, Ellie Harrison & @brockhurstlab.bsky.social #MicroSky

Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use! www.biorxiv.org/content/10.1...

Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...

Use it or lose it: Unless we publish papers in our society owned and published journals they will cease to be, along with all the conferences and meetings the proceeds support. Microbiology Society publishes many excellent journals, all edited by experts. #microsky www.microbiologyresearch.org

Cool!

Now updated to include the NCBI accessions for the short- and long-reads and hybrid assemblies… please use them!

Now out in MGen! Daria Frolova's paper on measuring plasmid relatedness using rearrangement distances www.microbiologyresearch.org/content/jour... #microsky

Exciting work from Sam and colleagues!

So exciting to see our piece on the current state of plasmid epidemiology is now out: www.microbiologyresearch.org/content/jour... #microsky

Happy to share the preprint for our strain transmission inference method recently renamed to TRACS! www.biorxiv.org/content/10.1...

Some thoughts on our study… (1/10)

🚨 New preprint! 🚨 We reveal that blaTEM-1 expression varies across the E. coli phylogeny, driving differences in co-amoxiclav resistance: www.biorxiv.org/content/10.1...

First paper from my student Daria Frolova's PhD now on biorxiv: www.biorxiv.org/content/10.1... The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes? 1/n

Our workshop programme is now live! Join us in Merton College or online on 16th May: www.torch.ox.ac.uk/event/commun...

Worth adding that this event is hybrid! You can register for online attendance by following the link 🧑‍💻

Very excited to announce our transdisciplinary AMR workshop 🎉 Join us to hear perspectives and discussion from patient activists, journalists, philosophers, microbiologists, historians, clinicians, policy makers, and artists. More info: www.torch.ox.ac.uk/event/commun...

First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) www.biorxiv.org/content/10.1... #microsky

Very excited to be talking about some new work here… why are plasmids AT-rich compared to the chromosome!?

New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8 www.biorxiv.org/content/10.1...

Our new paper on plasmids and cooperation has been published today in Proceedings B! "Genes for cooperation are not more likely to be carried by plasmids." doi.org/10.1098/rspb... With @lauriebelch.bsky.social Tom Scott @stuwest.bsky.social. Summary thread below... 🧵

It was a pleasure to collaborate with Sam on this massive BSI-associated plasmid surveillance study: www.nature.com/articles/s41...

I had fun using pangenome graphs to explore the global epidemiology of blaGES-5-associated integrons 🔎 The next challenge: can we integrate pangenome graphs into the routine surveillance of integrons? New preprint with #LiamShaw and #NicoleStoesser www.biorxiv.org/content/10.1...

Any suggestions for where a group of students could share/blog/index a short bacterial genomics project? They’ve done some brilliant work and it’d be a shame for it to never see the light of day!

Come do a PhD with me at University of Glasgow. 3-year fully funded PhD for UK students. Friend to Foe: Colonisation as an Entry Point for S. aureus Infectionhttps://www.findaphd.com/phds/project/fully-funded-friend-to-foe-colonisation-as-an-entry-point-for-staphylococcus-aureus-infection/?p166823

The formatted version of our multi-niche, multi-year plasmid genomic epidemiology study is finally available (elifesciences.org/articles/85302), but more importantly, I’d love to see future studies make use of the 1000s of Enterobacterales hybrid assemblies we generated: zenodo.org/records/7948...