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Alvaro San Millan

@sanmillan.bsky.social

Plasmid biology, antimicrobial resistance plasmidlab.es

86 Posts1664 Follower663 Folgt
Ludo Poiré@ludopoire.bsky.social · 4w ago

Months (years ?) spent on species-wide screens, over 3.000 PCR reactions and an unbelievable amount of 10-uL tips : I'm glad to introduce the novel TAR family of anti-plasmid defenses ! The war between bacteria and their MGEs is far more complex than we expected ⚔️ Read Xavier's 🧵 for more details !

Xavier Charpentier@labxc.bsky.social · 4w ago

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Craig MacLean@craigmaclean.bsky.social · last mo.

New #microsky#AMR Perspective paper with @penamiller.bsky.social rdcu.be/fqBJo ANTIBIOTIC RESISTANCE (IE MIC) AND TOLERANCE ARE NOT BACTERIAL TRAITS! Please read on if you want an explanation for this provocative claim.

Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells

Nature Communications - Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells

rdcu.be

Jerónimo Rodríguez-Beltrán@jerorb.bsky.social · 3mo ago

🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇

Multireplicon plasmids emerge under predictable rules and drive the spread of antimicrobial resistance across bacterial hosts

Plasmids are DNA molecules that replicate independently of the bacterial chromosome and are typically associated with the spread of antimicrobial resistance (AMR) and virulence determinants, among other relevant traits. Fusion events between plasmids generate larger, complex backbones that carry two or more replication systems, known as multireplicon plasmids. Despite decades of study, we are still far from understanding how multireplicon plasmids arise, persist, and shape the evolution of AMR. Here, we analyzed 24,000 non-redundant plasmids across bacterial genera and found that more than 30% of them encoded multiple replicons. Compared to single-replicon plasmids, multireplicon plasmids were larger, were enriched in genes encoding antimicrobial, metal, and biocide resistance as well as virulence factors, and showed higher mobility and a broader host range. We also found that multireplicon assembly is not random. Some replicon pairs repeatedly merge into stable multireplicon plasmids, while other pairs rarely fuse even when they commonly coexist intracellularly. We also show that replicon pairs tend to be localized either in close proximity to one another or on opposite poles of the plasmid. We further highlight that multireplicon plasmids can be broadly classified into two groups: long-term coevolving replicon pairs and transient associations that lack a shared evolutionary history. Finally, we reveal the molecular mechanisms underlying multireplicon formation and highlight the role of insertion sequences in their formation and maintenance. Together, our work sheds light on the abundance, gene content, evolutionary patterns, and formation dynamics of multireplicon plasmids and pinpoints their relevance to bacterial evolution and human health. ### Competing Interest Statement The authors have declared no competing interest. Instituto de Salud Carlos III, https://ror.org/00ca2c886, PI23/01945, PFIS - FI22/00265, Miguel Servet - CP22/00164 European Research Council, https://ror.org/0472cxd90, HorizonGT, 101077809 Fundación Ramón Areces, "Ayudas Fundación Ramón Areces para la realización de Tesis Doctorales en Ciencias de la Vida y de la Materia 2025" Coordenação de Aperfeicoamento de Pessoal de Nível Superior, https://ror.org/00x0ma614, 88881.128025/2025-01

biorxiv.org

Ignacio (Nacho) de Quinto@nachodequinto.bsky.social · 3mo ago

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!🧵👇

David Bikard@dbikard.bsky.social · 4mo ago

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

Raphael Laurenceau@raphael-microb.bsky.social · 4mo ago

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

Ilyas Alav@ilyasalav.bsky.social · 4mo ago

My main postdoc paper is now out in @natureportfolio.nature.com npj Antimicrobials and Resistance! www.nature.com/articles/s44.... Using flow cytometry, we show that the nucleoside analogues azidothymidine, didanosine, stavudine, and trifluridine reduced transfer of AMR plasmids pCT and pKpQIL (1/3)

Mechanistic insights into plasmid transfer inhibition in Enterobacterales by nucleoside analogues - npj Antimicrobials and Resistance

npj Antimicrobials and Resistance - Mechanistic insights into plasmid transfer inhibition in Enterobacterales by nucleoside analogues

nature.com

Centro Nacional de Biotecnología (CNB)@cnb-csic.bsky.social · 4mo ago

En #AGolpeDeBit #RTVE, @sanmillan.bsky.social investigador del #CNB @csic.es habla de este estudio liderado junto a Alfonso Santos López @uam.es y en colaboración con Ayari Fuentes #UNAM_MX centrado en el plásmido pOXA-48 de gran interés clínico 📻 ¡No te lo pierdas! www.rtve.es/play/audios/...

Resistencia a antibióticos: hallada nueva clave en plásmidos

Ponemos el foco en un estudio que identifica un nuevo mecanismo por el que los plásmidos pueden acelerar la aparición de resistencia a los antibióticos

rtve.es

Vaughn Cooper@vscooper.micropopbio.org · 4mo ago

Now out in AEM @asm.org! 🎉🧪 *High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations *We learn how diversity arises quickly and is maintained *EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy journals.asm.org/eprint/FBU9M...

Genetic diversification of Pseudomonas fluorescens maintained by multi-niche selection within biofilms | Applied and Environmental Microbiology

Bacterial biofilms dominate microbial life; however, their evolutionary genetics remain incompletely understood. Extensive replication of biofilm selection experiments by secondary school students can...

journals.asm.org

Vaughn Cooper@vscooper.micropopbio.org · last yr.

Sharing the most significant work from my group, led by the @evolvingstem.bsky.social team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵 www.biorxiv.org/content/10.1...

Teresa M. Coque@tmcoque.bsky.social · 4mo ago

We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇

The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the “robust-yet-fragile” architecture ...

rdcu.be

Alberto HCA@albertohca.bsky.social · 5mo ago

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 👇🏼

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5mo ago

Fitness effects of antimicrobial resistance genes in changing environments https://www.biorxiv.org/content/10.64898/2026.03.06.710025v1

Jesse Shapiro@bjesseshapiro.bsky.social · 6mo ago

Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

doi.org

Allison Lopatkin, PhD@ajlopatkin.bsky.social · 6mo ago

Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!

PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis

Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro

academic.oup.com

Jerónimo Rodríguez-Beltrán@jerorb.bsky.social · 6mo ago

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/...

Cover of PNAS in which we show plasmids as colourful concentric circles, with dots scattered. The image kind of resembles an eye, although it’s visibly a plot.
Paula Ramiro-Martínez@paularamiro.bsky.social · 6mo ago

New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...

Angel Goñi-Moreno@angelgm.eurosky.social · 8mo ago

Preprint out! By controlling growth, via RNAP, we control the entire cellular machinery, and tune the cellular context into distinct, stable states. See how NOT gates behave! Kudos to @angeles-hg.bsky.social and @mirobueno.bsky.social 🔗https://www.biorxiv.org/content/10.64898/2025.12.19.695408v1

Growth control as a central regulator for tuning the cellular context

The cellular context interacts with genetic circuits, decisively defining their performance. However, contextual dependencies (the interplay between the host and the circuit) are often difficult to en...

biorxiv.org

Tatiana Dimitriu@tatianadimitriu.bsky.social · 8mo ago

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/...

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...

journals.plos.org