Alfonso Santos Lopez
@asantoslopez.bsky.social
Evolution of antibiotic resistance. Ramón y Cajal Fellow at Universidad Autónoma de Madrid. https://amrevolution.es/
In 2014, Jason Rosch and I met at a GRC in Tuscany and sketched an idea on a cocktail napkin: what if we evolved S.pneumo in mice, treated them with antibiotics, varied their immune systems and watched what won? 11 years and a huge team effort later, it's out in @cp-cellhostmicrobe.bsky.social 🧵
Our group recently posted 2 new papers! This is the first one where we looked at how anaerobic metabolism in P. aeruginosa alters antibiotic resistance determinants. 1/2
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 4w agoAnoxia selects for high fitness biofilms and increased antibiotic resistance in Pseudomonas aeruginosa https://www.biorxiv.org/content/10.64898/2026.07.09.737528v1
This is our 2nd recently posted paper where we wanted to build off the fantastic 2023 PNAS paper by @prsecor.bsky.social group (www.pnas.org/doi/10.1073/...) 1/3
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
pnas.org
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3w agoLong-term exposure to polyamines leads to bacteriophage resistance in Pseudomonas aeruginosa https://www.biorxiv.org/content/10.64898/2026.07.14.738440v1
To put science in Spain into context, the median project is 50k per year. That's basically doing guerilla science 🧪
Jose A. Esteban@jaestebancbm.bsky.social · 3w agoMuchos ya habréis visto la resolución provisional de los proyectos #PID2025 de la @ageinves.bsky.social Aquí va la distribución. La financiación media por proyecto se ha quedado como el año pasado. Y seguimos con 2/3 de los proyectos con <50 k€ por año. ☹️ www.aei.gob.es/convocatoria...
Rather: small N + strong selection = beneficial mutations linked to DNA repair mutants that ⬆️ mutation supply We tried to be accurate here @catarmbruster.bsky.social www.cell.com/cell-reports... Grateful that evolutionary biology is being used in microbial pathogenesis, now need more pop-gen
Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis
Armbruster et al. find that infection-site biogeography impacts evolution of the opportunistic pathogen, Pseudomonas aeruginosa. In the sinuses of adults with cystic fibrosis, P. aeruginosa residing i...
cell.com
Where are mutations most likely to happen in the genome? @mattjago.bsky.social has answers! This paper is also a masterclass in simple visualizations of complicated ideas. I really enjoyed getting deep into these results as a middle author 🧬
Matt Jago@mattjago.bsky.social · 2mo agoOur work characterizing how mutational bias is influenced by the local sequence context beyond trinucleotides is out now @pnas.org! We also showed which motifs are most prone to mutations caused by strand misalignment, revealing several new hotspots! 🧬 www.pnas.org/doi/10.1073/...
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...
In celebration of good friends and collaborators Erin Gloag @sirmicrobe.bsky.social, Dan Wozniak and @nanamikubota.bsky.social, here's a cool new study about rapid P. aeruginosa adaptation in wounds, with some hidden phage phun as bonus. journals.asm.org/doi/10.1128/...
Pseudomonas aeruginosa biofilm-deficient mutants undergo parallel evolution during chronic infection | Journal of Bacteriology
We demonstrate that in a porcine full-thickness thermal injury wound model, a Pseudomonas aeruginosa mutant deficient in biofilm formation undergoes adaptive evolution by acquiring mutations that alter the outer membrane, either type IV pili (T4P) or lipopolysaccharide (LPS) mutations, that restores the deficient biofilm phenotype. We also observe a striking degree of mutational parallelism, at both the biosynthetic pathway and gene level, indicating the strong selective pressures experienced by these pathways during chronic wound infection.
journals.asm.org
Check it out, this is a truly useful dataset! #mevosky
Paloma Rodera@palomarodera.bsky.social · 3mo agoNew 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 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...
biorxiv.org
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!🧵👇
biorxiv.org
🚨 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 agoWhat 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!🧵👇
Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...
Research Associate in Microbial Evolution:Oxford Road
jobs.manchester.ac.uk
Great article about EvolvingSTEM & Dr. Abigail Matela's leadership to infuse dozens of schools w/ authentic microbiology research experiences that demonstrate evolution in real time. We've engaged more than 11,000 students over 11 years! 😅 🧪 🧫 www.hotmetalcampus.com/news-researc...
EvolvingSTEM Brings Lab Experiments Straight Into the Classroom — Hot Metal Campus
Based out of Bridgeside Point II in Hot Metal Campus, EvolvingSTEM is a science outreach program that brings evolution and microbiology research directly into classrooms across the Pittsburgh region. ...
hotmetalcampus.com
Multiple fully funded PhD/postdoc positions available: experimental evolution of tumour suppression, egalitarian & fraternal ETIs, jumbo phage ecology & genetics. Related EoIs welcome. Email CV/statement of motivation written in own words. Open until filled. Grateful for reposting 🙏
@vscooper.micropopbio.org & @isabelott.bsky.social let me crash their high-school bacteria hunt while I was working on my book "Life's Edge." Their paper's now out, featuring lots of mutants (including my very own CZ1A).
Vaughn Cooper@vscooper.micropopbio.org · 4mo agoNow 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...
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...
So happy to see this finally published in @plosbiology.org! This is the first chapter of @julielebris.bsky.social PhD thesis demonstrating how capsules are exchanged by plug-and-play dynamics w/ @epcrocha.bsky.social #microsky @klebclub.bsky.social Link below- Check out her 🧵 for more details!
Plug-and-play evolution of the Klebsiella pneumoniae capsule locus enables serotype exchange across genetic backgrounds
How complex multi-gene systems evolve across genetic backgrounds without disruptive epistasis remains unclear, particularly in highly exchangeable loci such as the capsule of Klebsiella pneumoniae. Th...
doi.org
Julie Le Bris@julielebris.bsky.social · 11mo agoHow complex functions, with important physiological and evolutionary impacts get repeatedly and efficiently transferred across genomes? That’s what we explored using one of the fastest-evolving loci in Bacteria: the capsule locus. The paper: www.biorxiv.org/content/10.1... Thread👇
Happy to have participated in this beautiful work on the human gut resistome in populations exposed to minimal anthropogenic pollution 🥳. Do not miss it!
Teresa M. Coque@tmcoque.bsky.social · 4mo agoWe 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👇
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
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...
biorxiv.org
Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...
Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis
Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…
sciencedirect.com
Out Now! Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation #MicroSky
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation
Nature Microbiology, Published online: 13 March 2026; doi:10.1038/s41564-026-02290-xInactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
go.nature.com
Check out the latest version of our paper — peer-reviewed, polished, and published. Hope you like it! www.nature.com/articles/s41...
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
nature.com
Alfonso Santos Lopez@asantoslopez.bsky.social · 12mo agoOur new manuscript is out! A bit of everything cool: Plasmids ✅ Insertion Sequences ✅ AMR Evolution ✅ Microbial Communities ✅ Databases analyses ✅ Mathematical modeling ✅ See the scientific thread below of Jorge Sastre, who has brilliantly led this work with @palomarodera.bsky.social
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 agoFitness effects of antimicrobial resistance genes in changing environments https://www.biorxiv.org/content/10.64898/2026.03.06.710025v1
New preprint on the limits of detecting higher-order interactions in microbial communities. www.biorxiv.org/content/10.6... We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.
biorxiv.org
Given that clonal biofilms of single bacterial species rapidly diversify into niche specialists, how do biofilms of multiple species evolve? A 🧵 featuring new collaborative pubs: 1. www.biorxiv.org/content/10.6... 2. www.nature.com/articles/s41...
biorxiv.org
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
biorxiv.org
What a fantastic new addition to my lab! 🚀 Welcome @albertohca.bsky.social to the @uam.es family! Stay tuned for the science we’re going to build together in the coming years!
🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover. 🔗 www.biorxiv.org/content/10.6...
biorxiv.org