Ricardo Leon-Sampedro

New paper out 🎆 When an antibiotic-resistant E. coli strain lands in our gut microbiome, whether it will get established or not depends on the ecological context. We studied how other microbes, nutrients, and antibiotic exposure shape its fate.👇

Strain displacement in microbiomes via ecological competition - Nature Microbiology Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

Our paper “Global dissemination of npmA mediated pan‑aminoglycoside resistance via a mobile element in Gram‑positive bacteria” is now in @natcomms.nature.com. Part of my freshly defended PhD, so doubly happy! 😄🎉

🧵 (1/14)

www.doi.org/10.1038/s414...

Great to have worked on this with Alex Hall, @mboum.bsky.social , Markus Reichlin, Katia R. Pfrunder-Cardozo, Nicholas Noll, and Adrian Egli; such a great team!

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...

🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.

Now published in @natcomms.nature.com rdcu.be/eOf63

Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae Competition significantly influences bacterial population dynamics, particularly in how strains interact within and between hosts. This study shows that within-host competition in Streptococcus pneumo...

New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

Do plasmids really move around that much? Well, maybe not always

Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social

This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social

www.cell.com/cell-reports...

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...

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

Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.

Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky

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

Invited speaker Marco La Fortaleza starts the first session of the day talking about epigenetic diversification in bacterial multicellularity. #Multicellverse

Do restriction-modification systems shape plasmid sequence composition? A group of plasmid-aficionados, led by Liam Shaw, started to explore this during the 2023 @embo.org Workshop on Plasmids in Trieste. Happy to have contributed to this work and be part of such a great team!

Really looking forward to this!!

👇

🚨 Seminar at ETH this Thursday! 🚨

Join Dr. Jerónimo Rodríguez-Beltrán (@jerorb.bsky.social) for a talk on how plasmids shape antibiotic resistance.

Plasmid evolution: a (copy) numbers game

🗓 April 3rd | 🕙 10:00–11:00
📍 CHN F42, ETH Zurich

evodynamicslab.com

ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro - Nature Microbiology An extensive experimental analysis of resistance to antibiotics in development or introduced post-2017 in ESKAPE bacteria reveals the dynamics of resistance acquisition, mutational targets and the pre...

🚨 Excited to share that our new study, “ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro” is published in @naturemicrobiol.bsky.social. For details, see the 🧵below and read the paper here: www.nature.com/articles/s41...

Exploring the principles behind antibiotics with limited resistance - Nature Communications This study shows that only those dual-targeting antibiotics limit resistance in Gram-negative pathogens that also target the membrane of the bacteria. This mechanism provides a basis for designing fut...

🚨 Our latest research in @naturecomms.bsky.social shows a promising strategy for less resistance-prone #antibiotics. For details, see the thread below and read the paper “Exploring the principles behind antibiotics with limited resistance” here: #MEvoSky www.nature.com/articles/s41...

We kicked off this semester's #SMEE with two great talks by @dnasaur.bsky.social and @phagemuffin.bsky.social. @usyseth.bsky.social

Really glad I could contribute to this work exploring biofilm formation, mucoidy and tip adhesin diversity in #klebsiella.
For those in #KLEBS2024, I provided a sneak peak of the potential relation between K3 serotype & HMV
This is also my first publication since I joined @cbitoulouse.bsky.social !

Really happy to see this paper out. Extra special for me because it marks my first research publication. Aswin has officially entered the academic world! 📈🦠🧑‍💻

The impact of treatment strategies on the epidemiological dynamics of plasmid-conferred antibiotic resistance | PNAS The issue of antibiotic resistance is a critical concern for public health, prompting numerous investigations into the impact of treatment strategi...

New paper from our group in @pnas.org!! 🚀
Malte Mütter used our amazing liquid-handling robot to test different treatment strategies and found that combination therapy is the most effective to prevent the emergence of plasmid-mediated double resistance www.pnas.org/doi/10.1073/...

Outer membrane changes enable evolutionary escape from bacterial predation To combat antimicrobial resistant pathogens, natural predatory bacteria, like Bdellovibrio bacteriovorus , represent potential alternatives. B. bacteriovorus could be particularly potent as it kills a...

Can E.coli 🦠 escape from predation by ‘living antibiotic’ 💊B.bacteriovorus, a predatory bacterium ?
A first preprint from my lab for people interested in: #MicroSky, #Evolution and new ways to treat #AMR and #Bdellovibrio

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

Some findings in the following thread:

Should I stay or should I go? 🎵

In a new opinion piece, Claudia Igler, Andrina Bernhard and I discuss how conjugative plasmids and temperate bacteriophages balance vertical and horizontal transmission: ecoevorxiv.org/repository/v...

Our framework sheds light on many aspects of MGE biology (1/7)

Next in my To Read list!
Surely great & thorough work from Alex Hall, led by @rleonsampedro.bsky.social Read his thread here 👇🏻👇🏻

Elevated mutation rates in multi-azole resistant Aspergillus fumigatus drive rapid evolution of antifungal resistance Nature Communications - Here, Bottery et al show that resistance to next generation antifungals is more likely to occur within azole resistant Aspergillus fumigatus due to the close linkage between...

New in Nature Comms, we show that azole-resistant Aspergillus fumigatus are more likely to evolve resistance to new antifungals due to variants in their DNA mismatch repair system rdcu.be/d3Iyc @natureportfolio.bsky.social #microsky #fungi #amr

Diverse phage communities are maintained stably on a clonal bacterial host Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...

New preprint by the group I am doing my PhD in: “Chromosomal plasticity can drive rapid adaptation in bacteria”.

This is the first chapter of Ever Vega-Cabrera's thesis and has been in the works for a long time.

https://doi.org/10.1101/2024.12.11.627208 […]

Very glad to see this properly out and open access from my time with @baym.lol We've learnt so much about antibiotic resistance evolution already, and yet so many outstanding and fascinating questions remain, at all levels of selection.
www.annualreviews.org/content/jour...

Possible explains our displacement papers

www.sciencedirect.com/science/arti...

journals.plos.org/plosbiology/...

Thanks for sharing, Alan. Your findings on displacement dynamics align well with what we see: strain-specific competition shapes community composition and resistance dynamics.