Javier DelaFuente

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/...

!!!!!!!!!!

Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...

Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social
#MicroSky #Mevosky
journals.plos.org/plosbiology/...

Evolved plasmid-carrying clones with high copy number contain a mix of full-length and streamlined plasmids. Left: summary of the initial experimental evolution design and nomenclature used for the evolved plasmid-carrying clones. Host strains had either wildtype (w) or increased (m) mutation rate. Treatment indicates the % of plasmid-free hosts added at each passage during evolution. Right: coverage map of evolved clones. Relative coverage of sequencing reads is shown for all clones across R1 sequence length (only the first 50 kb are shown). The AMR region and copies of IS1 are shown against the ancestral R1 (“anc” treatment) coverage map.

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

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...

New paper out! 🔈🔈📣📣

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.

Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻

www.biorxiv.org/content/10.1...

If you're into plasmid biology, you can't miss this back-to-back by two inspiring teams!

🦠 Nuestro #articulodelmes habla sobre cómo los integrones móviles codifican sistemas de defensa contra fagos de la mano del grupo investigador liderado por el Dr. José Antonio Escudero

📄https://f.mtr.cool/qxwueostwp

Ceftazidime-avibactam use selects multidrug-resistance and prevents designing collateral sensitivity-based therapies against Pseudomonas aeruginosa - Nature Communications Ceftazidime-avibactam is a β-lactam/β-lactamase inhibitor combination restricted for the treatment of multidrug-resistant infections of Pseudomonas aeruginosa non-susceptible to ceftazidime and resist...

Ceftazidime-avibactam (a last resort drug) use selects multidrug-resistance and prevents designing collateral sensitivity based therapies against P. aeruginosa (no robust patterns emerge). Happy to see it published! 🥳 @cnb-csic.bsky.social @idisba.bsky.social
www.nature.com/articles/s41...

enhorabuena Sara!!!

The evolution of antibiotic resistance in Europe, 1998–2019 Author summary Antibiotic resistance is an important public health threat: resistant infections are currently associated with 5 million deaths per year globally. This burden may increase further in th...

New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...

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
🧵

Join us in at #ESEB2025 Barcelona for our symposium on microbial adaptation to changing conditions. Organised by @mtoll8.bsky.social @javierdelafuente.bsky.social and me. Amazing invited speakers @saramitri.bsky.social and Itzik Mizrahi!! @eseb2025.bsky.social

Dissecting pOXA-48 fitness effects in clinical enterobacteria using plasmid-wide CRISPRi screens Conjugative plasmids are the main vehicle for the spread of antimicrobial resistance (AMR) genes in clinical bacteria. AMR plasmids allow bacteria to survive antibiotic treatments, but they also produ...

🚨 New preprint! We know that 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

As of 2025 I am officially a junior PI at the Institute of Functional Biology & Genomics. My lab will focus on building quantitative models of eco-evo dynamics.

There is available funding for PhDs and postdocs — formal job announcements will come soon, but feel free to reach out in the meantime!

Chromosomal plasticity can drive rapid adaptation in bacteria Understanding the molecular mechanisms underlying rapid adaptation to stress is a fundamental question in evolutionary biology. A common mechanism is copy number changes, which can affect single genes...

Chromosomal plasticity can drive rapid adaptation in bacteria by @mtoll8.bsky.social's lab

www.biorxiv.org/content/10.1...

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...

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance - Nature Reviews Microbiology In this Review, Shepherd, Brockhurst and colleagues explore the clinical evidence in support of four major ecological and evolutionary mechanisms of within-patient antimicrobial resistance emergence i...

Thrilled to share our new article now out in Nature Reviews Microbiology! We review how bacterial #AMR evolves within patients during #antibiotic therapy, highlighting the complexity of the problem and how to improve understanding in future work. 1/7 #MicroSky
www.nature.com/articles/s41...

Bacteria can compensate the fitness costs of amplified resistance genes via a bypass mechanism - Nature Communications Antibiotic heteroresistance, in which a susceptible bacterial population includes a small resistant subpopulation, can arise by tandem amplification of resistance genes, which often carry fitness cost...

Excellent paper by Dan Andersson's group

'Bacteria can compensate the fitness costs of amplified resistance genes via a bypass mechanism'

www.nature.com/articles/s41...

Just one week left to apply for this eco-evo PDRA position working in a multidisciplinary team developing synthetic phage therapy 🧫 🧬 🫁 #microsky

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

BBSRC 2-year PDRA position to work on ecology & evolution of phage therapy with synthetically engineered phages. Part of an exciting multi-university consortium & UK’s Engineering Biology priority. Synthetic genomics; experimental evolution; AMR. www.jobs.manchester.ac.uk/Job/JobDetai... #microsky

Exciting chance to join our Wellcome Trust collaborative project understanding AMR evolution in human infections! Genomics, experimental evolution, Pseudomonas. Research Assistant 4-days per week for 2-years, deadline 18.03. www.jobs.manchester.ac.uk/Job/JobDetai... #microsky

Excited to share the first preprint from my lab, collaborating with the fantastic @sanmillan.bsky.social 's lab, led by the amazing Jorge Sastre. We've demonstrated how insertion sequences encoded in plasmids promote bacterial adaptation. This project has been incredibly fun!

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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...

Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons Abstract. Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encod

And its out! New paper for #integron aficionados. We found gene-less cassettes in superintegrons that express/silence other cassettes in the array. Here is a 🧵(if I know how to do this in Bluesky...😆)
academic.oup.com/nar/advance-...

New perspective paper with the amazing @asanchezlab.bsky.social @javierdelafuente.bsky.social and Juan Diaz-Colunga.
Can we use global epistasis patterns to predict/understand plasmid-mediated AMR evolution? www.embopress.org/doi/full/10....