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

New paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...

New research article Emergence of carbapenemase-producing #Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey) www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #Ecoli #OpenAccess #OA

What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇

Happy to share our latest work on “In Host Mutational Adaptation of Mycobacterium Tuberculosis Complex Strains During Tuberculosis Infection” published in @jidjournal.bsky.social doi.org/10.1093/infd...

New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵 www.biorxiv.org/content/10.6...

Final version of our last paper is out! www.nature.com/articles/s41...

Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼

Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT. www.uu.nl/en/organisat... Please contact Mathijs Theelen, email address in the link below.

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this www.biorxiv.org/content/10.6...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...

Very happy to share our preprint on a mathematical model for Streptococcus pneumoniae population dynamics after vaccine introductions. It's a reusable model that describes vaccine replacement dynamics and can help to determine strategies for genomic surveillance: doi.org/10.64898/2025.12.18.695090

What drives the K. pneumoniae species complex (KpSC) to thrive from hospitals to soils? In this study, we investigate how pangenome structure and functional diversity shape KpSC adaptability across phylogenetic and ecological contexts. (Thread) www.biorxiv.org/content/10.6...

A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample

Read 'Large-scale characterization of the nasal microbiome redefines Staphylococcus aureus colonization status' from @sangerinstitute.bsky.social, @cam.ac.uk, @imperialcollegeldn.bsky.social and their collaborators in @natcomms.nature.com here ⬇️ www.nature.com/articles/s41...

🧬 A new “Life Identification Number (LIN)” system aims to modernize bacterial classification with a clearer, more stable hierarchy. A step forward for genomic taxonomy! 📖 shorturl.at/vkQuS ✍️ @sylvainbrisse.bsky.social & coll. @pasteur.fr @ox.ac.uk @monashuniversity.bsky.social @lshtm.bsky.social

London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.

🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63

New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...

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

Interesting paper 'Antimicrobial resistance among Gram-positive agents of bacteraemia in the UK and Ireland: trends from 2001 to 2019' TL;DR: - dramatic falls in MRSA - pneumococcal resistance rates low - E. faecium more prevalent (and more vanR) than E. faecalis pubmed.ncbi.nlm.nih.gov/41140273/

New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...

🧬 New #GenEpiBioTrain course! Bacterial Strain Taxonomy for Genomic Surveillance 📅 22–23.10, 09:00–12:00 (CEST) Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering. Info: bit.ly/48qT5df #ECDCTraining #IDsky #EpiSky

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👇

Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)

A plasmid and an ICE teaming up... 🤯😱 www.nature.com/articles/s41...

Now published, our tool to run (almost) all biological models interactively in your web browser Paper: academic.oup.com/bioinformati... Website: biomodels.bacpop.org Code: github.com/bacpop/SBMLt...

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.

Interesting benchmark paper from @dotnagy.bsky.social "Autocycler circularised the most chromosomes (87/92). .. Flye performed worse than other assemblers on almost all metrics. Autocycler + Medaka... was the most accurate long-read only assembler/polisher " www.biorxiv.org/content/10.1...

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

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell

Open PhD position in our lab for starting roughly in September 2026. Cannot recommend this lab enough!!! 🦠🖥️ #MathematicalModelling #BacterialGenomics #Bioinformatics

A little tool I've developed: ExpEvoAnalyzer (github.com/samhorsfield...) - a snakemake pipeline that compares isolate paired-read data from an experimental evolution study to a reference isolate, producing functionally-annotated SNPs in a presence/absence matrix.

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

This work is finally published! 🥳🧬 Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by @jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today: www.microbiologyresearch.org/content/jour...

Oxygen levels can affect how resistance genes work, impacting antibiotic efficacy. This can be relevant for the most used ones: for example, resistance to fosfomycin varies with oxygen. Learn more in our latest paper 👉 bit.ly/3T8sdpp a work led by @jaescudero.bsky.social #AntibioticResistance

#NewResearch 'The food-associated resistome is shaped by processing and production environments' by @nmquijada.bsky.social and co-workers. #MicroSky 🦠 www.nature.com/articles/s41...

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...

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

🚨🚨 New paper in @narjournal.bsky.social! 🍾 Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons). We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín. 👇

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬? In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments! 👇 Check out all the details in Paula’s thread! Hint: 🐇 (most of the time)

New paper alert! 🚨 Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate. We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number. Let's dive in! 🧵👇

Our latest paper explores the factors shaping plasmid-bacteria associations and highlights why studying plasmid-host interactions of clinical relevance is key for understanding the evolution and spread of AMR. Find out more 👉 plasmidlab.es/publications/ #AntibioticResistance