Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...

Conjugative plasmids help spread AMR genes. @andrewmatthews.bsky.social @sonjalehtinen.bsky.social & @tatianadimitriu.bsky.social show that #AMR loss in evolving populations involves streamlined #plasmids that gain a transmission advantage by deleting AMR genes @plosbiology.org 🧪 plos.io/48NM0BL

New #MicroSky study showing extensive transmission of #AMR E coli transmission in East Africa under One Health framework, led by Patrick Musicha www.sanger.ac.uk/news_item/an...

📣New preprint alert! We report the alarming finding that stringent response mutations found in clinical isolates increase the frequency of donation of multiresistance plasmids in S. aureus 😱 Great team effort @microclaire.bsky.social @paulrjohnston.bsky.social www.biorxiv.org/content/10.1...

Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...

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👇

📢Our review of the impact of bacterial purine synthesis on antibiotic tolerance and resistance expression is now out! A lot of food for thought and contrasting data from E. coli and S. aureus... 🤔 Read it here: rdcu.be/ezfQ7

Jo Hobbs @hobbslabmicro.bsky.social has a 12 month Postdoc available on mechanisms of antibiotic tolerance. More details here: www.vacancies.st-andrews.ac.uk/Vacancies/W/...

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.

ish is a grep-like CLI tool that uses optimal alignment instead of exact matching. It’s record-type aware, supporting line, FASTA, and FASTQ records. Built in Mojo as a proof of concept for bioinformatics. 🧵1/5

We are still looking for a motivated student to join us in the wonderful world of mosquito microbiome genomies! Funding unfortunately only for UK students for this one. If interested, please send CV & letter of motivation (email in image below) #MicroSky #MicrobiomeSky 💻🧬 🧪Please share widely😊 1/2

Our subclustering and transmission pipeline, PopPIPE has now been published: www.microbiologyresearch.org/content/jour...

📣 The Journal of Medical Microbiology is looking for Editors for the Antimicrobial Resistance section! No prior editor experience required, so it's a great first gig for an ECR. And you get subsidised attendance at the annual meeting. Open to applicants worldwide 🌍 @microbiologysociety.org

My nightmare in #eDNA is to detect a rare or threatened species that turns out to be a false positive, so we set out to evaluate some of the commonly used taxonomic classifiers. The results are finally out: onlinelibrary.wiley.com/doi/full/10.... 1/3

www.findaphd.com/phds/project... A funded PhD studentship is available for a joint project between my lab and @andreashaag.bsky.social @uniofstandrews.bsky.social

Preprint below has been a long time coming, here just in time for #microbio25 ! (if the train wifi lets me) With @andrewmatthews.bsky.social #MicroSky 🧵

Dear #genomics sky 🖥️🧬; does anyone know the earliest reference to the *compacted* de Bruijn graph? I have good initial reference for the de Bruijn graph (both the mathematical and genomics variants), but am having trouble finding an initial source for the compacted de Bruijn graph.

New paper from our group in @pnas.org!! 🚀 Malte Mütter used our amazing liquid-handling robot to test different treatment strategies and found that combination therapy is the most effective to prevent the emergence of plasmid-mediated double resistance www.pnas.org/doi/10.1073/...

PhD opportunity in St Andrews on plasmids, antibiotics and defence systems, in collaboration with Helen Alexander in Edinburgh. Funding via BBSRC EastBio, please share & pass on to anyone interested! #microsky🦠🧫🧬 www.findaphd.com/phds/project...

New paper: We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers. www.sciencedirect.com/science/arti...

Not sure if our recent manuscript made it onto this platform, if not here it is. Re-emerging chloramphenicol susceptibility in ESBL Enterobacterales from Malawi. A good news # AMR story www.nature.com/articles/s41...

Sharing new tools made by Artyom Egorov in my group! 1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1... 2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...

📣 New perspective paper: Insights into durability against resistance from the antibiotic nitrofurantoin We discuss what makes nitrofurantoin robust against resistance evolution, in spite of prolonged and extensive usage against UTIs #MicroSky Open access/CC-BY-4.0: www.nature.com/articles/s44...

Following a suggestion from @benecal.bsky.social I will refer to these threads as "skeetorials" and will use this gif logo. Today's skeetorial is about the NIH Director's New Innovator Award with three different heroes (all in government). 1/n

"I knew a premature VHF diagnosis could cause panic and have profound political implications." – A very strong piece in NEJM by Dr JP Sibomana on the personal and political complexity of diagnosing Rwanda’s first Marburg outbreak. doi.org/10.1056/NEJMp2413951

Are you applying RNA-seq or TraDIS/Tn-seq to antibiotic-treated bacteria? Our paper from earlier this year with @flamycain.bsky.social shows that antibiotic interference with chromosome replication can confound functional genomics analyses! Thread 1/n journals.asm.org/doi/full/10....