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Reposted by Jorge Sastre Domínguez

Adrian Cazares @cazares-adr.bsky.social · 2d

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics

We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...

If you like time travel & biology, this 🧵is for you👇

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance

Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

doi.org

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Reposted by Jorge Sastre Domínguez

Nanami Kubota @nanamikubota.bsky.social · 6d

Published in Current Biology! P. aeruginosa can use its filamentous phage to inhibit competitors but high phage production is susceptible to cheater miniphage invasion. Subsequent phage tragedy of the commons can lower bacteria and phage fitness. Link: authors.elsevier.com/c/1lt5I3QW8S...

Nanami Kubota @nanamikubota.bsky.social · Apr 2

Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...

Filamentous cheater phages drive bacterial and phage populations to lower fitness

Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...

www.biorxiv.org

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Reposted by Jorge Sastre Domínguez

Tami Lieberman @contaminatedsci.bsky.social · 9d

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

www.biorxiv.org

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Reposted by Jorge Sastre Domínguez

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Reposted by Jorge Sastre Domínguez

Didier Mazel @amazeld.bsky.social · 19d

I am so proud to be part of this work, that we initiated Fernando de la Cruz and I, when he was on sabbatical in my lab in 2009... it took so much time for this achievement, 1000 thanks to Raúl Fernández-López! this brought me back to my PhD on cyanobacteria genetics. www.pnas.org/doi/10.1073/...

Mutations in the circadian cycle drive adaptive plasticity in cyanobacteria | PNAS

Circadian clocks allow organisms to anticipate daily fluctuations in light and temperature, but how this anticipatory role promotes adaptation to d...

www.pnas.org

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Reposted by Jorge Sastre Domínguez

Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Reposted by Jorge Sastre Domínguez

Christian Landry @christianlandry.bsky.social · 28d

Really excited to share our latest paper led by @simonaube.bsky.social. Fascinating results examining whether regulatory mutations can lead to adaptation as fast as coding mutations do. #mevosky #evobio #evoSky

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

Adaptation is less accessible through mutations in promoters than in coding sequences when large effect sizes are needed

Mutations within promoters and coding sequences are both involved in adaptation, but their relative contributions remain to be compared directly. Using the fungal enzyme cytosine deaminase, we examine...

www.biorxiv.org

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Reposted by Jorge Sastre Domínguez

Julie Le Bris @julielebris.bsky.social · Sep 5

Delighted to share our recently published work!
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇

Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio

The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major ...

journals.asm.org

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Reposted by Jorge Sastre Domínguez

Olaya Rendueles @olayarendueles.bsky.social · 29d

Check out @julielebris.bsky.social’s thread on our latest manuscript describing phenotypic heterogeneity in capsule production in Klebsiella & Acinetobacter @klebclub.bsky.social

This work started when I was still in @pasteur.fr & got finished in @cbitoulouse.bsky.social
#microsky #phagesky

Julie Le Bris @julielebris.bsky.social · Sep 5

Delighted to share our recently published work!
Ever wondered how Klebsiella (and others) deals with capsule production’s costs ?
The paper: journals.asm.org/doi/10.1128/...
Thread👇

Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio

The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major ...

journals.asm.org

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Reposted by Jorge Sastre Domínguez

Macarena Toll-Riera @mtoll8.bsky.social · 28d

We are hiring a PhD student! Are you fascinated by microbes and evolution? Come join us in Barcelona!

Institut de Biologia Evolutiva (IBE) @ibe-barcelona.bsky.social · 29d

#WeAreHiring

📣 The #IBE_Barcelona is seeking a #PhD Student for the Evolutionary #Microbiology Lab.🔬🧫

⏳ Apply before September 30th and #JoinOurTeam!

#UnravellingEvolution #ConservingBiodiversity

✍ https://www.ibe.upf-csic.es/work-with-us/job-offers

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Reposted by Jorge Sastre Domínguez

Julie Le Bris @julielebris.bsky.social · 28d

How 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👇

Serotype swapping in Klebsiella spp. by plug-and-play

Understanding how complex, multi-gene systems evolve and function across genetic backgrounds is a central question in molecular evolution. While such systems often impose costs through epistatic inter...

www.biorxiv.org

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Reposted by Jorge Sastre Domínguez

Zamin Iqbal @zaminiqbal.bsky.social · Sep 7

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling

Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

www.biorxiv.org

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Reposted by Jorge Sastre Domínguez

Centro Nacional de Biotecnología (CNB) @cnb-csic.bsky.social · Aug 27

El grupo de Álvaro San Millán revela el coste de mantener la resistencia en enterobacterias

El trabajo traza un mapa funcional del plásmido pOXA-48, con potencial para guiar nuevas terapias contra resistencias

bit.ly/4p0fCmY

@sanmillan.bsky.social @aliciapcv.bsky.social @jorgesastred.bsky.social

Identifican el coste fisiológico de mantener la resistencia microbiana en enterobacterias - CNB

bit.ly

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 22

Extremely glad to see this out!!

Wonderful work by all the lab, especially @aliciapcv.bsky.social. Don't miss her thread!!

Alicia Calvo-Villamañán @aliciapcv.bsky.social · Aug 20

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

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Thank you so much!!! 😄

Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Thank you very much!!! 😁😁

Reposted by Jorge Sastre Domínguez

Alfonso Santos Lopez @asantoslopez.bsky.social · Aug 13

Our 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

Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

New paper out! 🔈🔈📣📣

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.

Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻

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

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation

Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...

www.biorxiv.org

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Reposted by Jorge Sastre Domínguez

Allison Lopatkin, PhD @ajlopatkin.bsky.social · Aug 12

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today:

www.microbiologyresearch.org/content/jour...

Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae

The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...

www.microbiologyresearch.org

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Reposted by Jorge Sastre Domínguez

Alvaro San Millan @sanmillan.bsky.social · Aug 13

New paper in collaboration with the @asantoslopez.bsky.social lab!

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

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Kudos to all the authors involved in this work, what a team!!!! @palomarodera.bsky.social @javierdelafuente.bsky.social S. Martinez-Gonzalez, S. Quesada, M. Valencoso-Requena, @aliciapcv.bsky.social C. Costas, @ayari.bsky.social @asantoslopez.bsky.social and @sanmillan.bsky.social

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Summing up, our results indicate that conjugative plasmids not only fuel AMR evolution through gene dissemination, but also through IS-mediated inactivation of chromosomal genes.

Clinically, our study could explain the observed rise of combined AMR phenotypes, such as carbapenems and colistin!

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Finally, we developed a computational model simulating the invasion of a bacterial community by a conjugative plasmid harbouring IS elements.

This allowed us to explore a range of parameters of plasmid dissemination, demonstrating that plasmid invasion can promote the IS-driven evolution of AMR

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Plasmids are the main disseminators of AMR in natural bacterial communities.

Hence, we wondered whether by disseminating, pOXA-48 may also promote the acquisition of further AMR mechanisms.

This was confirmed by simmulating the invasion of a multi-species Enterobacterales community by pOXA-48.

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

Next, we aimed to generalize our results beyond our experimental model of pOXA-48 and IS1 by screening >50.000 genomes from databases.

We linked the presence of plasmid-encoded IS elements with the disruption of chromosomal genes leading to AMR for multiple antibiotics and across diverse taxa.

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

The inactivation of genes is an extended mechanism of AMR. Therefore, we tested the resistance of various clinical isolates of K. pneumoniae against multiple clinically relevant antibiotics.

As expected, the IS encoded in pOXA-48 also increase AMR to kanamycin, ciprofloxacin and chloramphenicol!

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