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...
www.biorxiv.org
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 👇🏼
➡️ 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? 🤔
🧵👇
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👇
🚨 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!👇👇
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
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
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
Final version of our last paper is out!
www.nature.com/articles/s41...
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
➡️ 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? 🤔
🧵👇
Paloma Rodera
www.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!🧵👇
Jorge Moura de Sousa
Jorge Moura de Sousa
Alberto HCA
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!🧵👇
Fitness effects of antimicrobial resistance genes in changing environments https://www.biorxiv.org/content/10.64898/2026.03.06.710025v1
