Bacterial Mercury Resistance Reveals a Robust Species-Structured Human Antimicrobial Mobilome https://www.biorxiv.org/content/10.64898/2026.06.26.734528v1
Paula Ramiro-Martínez
@paularamiro.bsky.social
Predoctoral researcher at evodynamics lab in Madrid. Bacterial and plasmid evolution 🫧🧬💻
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
🚨 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!🧵👇
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
What happens when Klebsiella's capsule locus is swapped? Unexpectedly little in terms of cell growth. Yet, it does change the bacterium's environment and interactions with it: evolution by seamless plug-and-play capsule swap. Led by @julielebris.bsky.social @olayarendueles.bsky.social
Olaya Rendueles@olayarendueles.bsky.social · 4mo agoSo 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!
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
Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
ecoevorxiv.org
Final version of our last paper is out! 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
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
➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇
biorxiv.org
Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5
Jorge Moura de Sousa@jmouradesousa.bsky.social · 5mo ago➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇
New preprint out on bioRxiv! www.biorxiv.org/content/10.6... Can conjugative plasmids be used to control plasmid and pathogen spread? Follow me down the rabbit hole that led to this story 🧵
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!
A short research stay in 2019 (back in the pre-COVID era) at José R. Penadés lab turned into the third chapter of my PhD and today it finally sees the light.
Targeted elimination of Staphylococcus aureus mastitis infections with synthetic phage-based CRISPR-Cas delivery systems - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Targeted elimination of Staphylococcus aureus mastitis infections with synthetic phage-based CRISPR-Cas delivery systems
nature.com
🧬New paper out! We report the first isolation of viable B. bacteriovorus predators from human gut microbiota. www.frontiersin.org/journals/mic.... Great work of Mario Romero @migueldiezfdz.bsky.social @josete600.bsky.social and @rosacampo.bsky.social
Frontiers | Genome assembly and functional predation analysis of novel Bdellovibrio isolates from human gut microbiota
IntroductionPredatory bacteria of the Bdellovibrio and like organisms (BALOs) have long been postulated as living antimicrobials, yet their occurrence and ec...
frontiersin.org
In this issue: Fresh light on horse evolution, mangrove restoration as coastal flood protection, and the links between aerobic metabolism and planetary oxygenation. In PNAS: https://ow.ly/yB6J50Y5ykK
And what a beautiful @pnas.org cover @paularamiro.bsky.social and @jerorb.bsky.social !!!!!! You should be very proud!
Jerónimo Rodríguez-Beltrán@jerorb.bsky.social · 6mo agoNew 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/...
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/...
Paula Ramiro-Martínez@paularamiro.bsky.social · 6mo agoNew paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
We're thrilled that, in addition, our figure has been chosen as the cover for this issue of PNAS! 🥹🎉
Paula Ramiro-Martínez@paularamiro.bsky.social · 6mo agoNew paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
pnas.org
Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵
Manuel Ares-Arroyo@aresarroyom.bsky.social · 7mo agoBacteria 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...
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...
biorxiv.org
#NewResearch The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles. #MicroSky 🦠 @peterdoug.bsky.social @emggroupucph.bsky.social www.nature.com/articles/s41...
Persistent virulent phages exist across bacterial isolates - Nature Microbiology
The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles.
nature.com
#NewResearch Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle. #MicroSky 🦠 www.nature.com/articles/s41...
Large-scale analysis of bacterial genomes reveals thousands of lytic phages - Nature Microbiology
Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.
nature.com
🎁 Getting a paper acceptance right before Christmas break is one of the best feelings. 100% recommend. Happy holidays, everyone! 🎄✨
A pleasure and an honour to have received this prestigious grant with my admired colleagues and friends @sanmillan.bsky.social and @asanchezlab.bsky.social . More about AMR under plasmid lens!. My sincere gratitude to @caixaresearch.bsky.social @microryc.bsky.social @esgem-sg.bsky.social
caixaresearch.bsky.social
caixaresearch.bsky.social
@caixaresearch.bsky.social · 9mo agoCongratulations to you and your teams, @sanmillan.bsky.social, @asanchezlab.bsky.social and @tmcoque.bsky.social! We are thrilled to support your work and look forward to the impact your project will have. 👏💫
A plasmid golden ratio? 🧬 Plasmid copy number ≈ 2.5% of chromosome size—consistent across bacterial species! pmc.ncbi.nlm.nih.gov/articles/PMC... @jerorb.bsky.social 🧪 #microbesky
Jerónimo Rodríguez-Beltrán@jerorb.bsky.social · last yr.🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...
In episode 337 TWiM explains a study that examines pathogen presence in ancient humans and concludes that zoonoses emerged 6500 years ago with the domestication of livestock, and determination of universal rules that govern plasmid copy number. This week's special guest: @markowenmartin.bsky.social
TWiM 337: Lifestyles of the plasmids
YouTube video by MicrobeTV
youtu.be
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
Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens
Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...
rdcu.be