Célia Souque
@celiasouque.bsky.social
Evolution | Genomics | AMR
ECDC EUPHEM fellow at the Norwegian Institute of Public Health. Previously seen: Harvard Medical School
Currently obsessed with plasmids 🦠
ECDC EUPHEM fellow at the Norwegian Institute of Public Health. Previously seen: Harvard Medical School
Currently obsessed with plasmids 🦠
Reposted by Célia Souque
🚨 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
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
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...
rdcu.be
November 7, 2025 at 9:15 AM
🚨 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
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
Reposted by Célia Souque
✨Célia Souque just showcased the outcomes of the 12th Microbial Bioinformatics Hackathon at IMMEM XIV.
She brilliantly presented the first sneak-peek of PORT – Plasmid Outbreak Reporting Tool! 🧬
Looking forward to continuing this collaboration with PORT!
#IMMEM #Hackathon #Plasmids #ESGEM #ESGMAP
She brilliantly presented the first sneak-peek of PORT – Plasmid Outbreak Reporting Tool! 🧬
Looking forward to continuing this collaboration with PORT!
#IMMEM #Hackathon #Plasmids #ESGEM #ESGMAP
September 18, 2025 at 4:02 PM
✨Célia Souque just showcased the outcomes of the 12th Microbial Bioinformatics Hackathon at IMMEM XIV.
She brilliantly presented the first sneak-peek of PORT – Plasmid Outbreak Reporting Tool! 🧬
Looking forward to continuing this collaboration with PORT!
#IMMEM #Hackathon #Plasmids #ESGEM #ESGMAP
She brilliantly presented the first sneak-peek of PORT – Plasmid Outbreak Reporting Tool! 🧬
Looking forward to continuing this collaboration with PORT!
#IMMEM #Hackathon #Plasmids #ESGEM #ESGMAP
Reposted by Célia Souque
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
September 15, 2025 at 5:26 PM
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
Reposted by Célia Souque
Reposted by Célia Souque
ESGMAP is now on LinkedIn and Bluesky!
We published our first newsletter (lnkd.in/dUe43t8y). It introduces us, our mission, activities, and ways to get involved. Fill out our members' survey, and associate your publications with the group.
Follow us for updates on the mobile elements and plasmids.
We published our first newsletter (lnkd.in/dUe43t8y). It introduces us, our mission, activities, and ways to get involved. Fill out our members' survey, and associate your publications with the group.
Follow us for updates on the mobile elements and plasmids.
June 19, 2025 at 8:56 AM
ESGMAP is now on LinkedIn and Bluesky!
We published our first newsletter (lnkd.in/dUe43t8y). It introduces us, our mission, activities, and ways to get involved. Fill out our members' survey, and associate your publications with the group.
Follow us for updates on the mobile elements and plasmids.
We published our first newsletter (lnkd.in/dUe43t8y). It introduces us, our mission, activities, and ways to get involved. Fill out our members' survey, and associate your publications with the group.
Follow us for updates on the mobile elements and plasmids.
Reposted by Célia Souque
The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
June 3, 2025 at 9:35 PM
The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
Reposted by Célia Souque
(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Prevalence of Group II Introns in Phage Genomes
Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...
www.biorxiv.org
May 24, 2025 at 7:20 PM
(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Célia Souque
New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
May 8, 2025 at 9:24 PM
New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...
Reposted by Célia Souque
🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
www.science.org
May 8, 2025 at 8:27 PM
🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉
Short 🧵
www.science.org/doi/10.1126/...
Reposted by Célia Souque
Cool preprint! The smallest Darwinian entity is a little smarter than we thought...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
RNA-guided nucleases enable a gene drive of insertion sequences in plasmids
Mobile genetic elements (MGEs) and the interactions between them are a major source of evolutionary innovation. Insertion sequences, the simplest MGEs usually encoding only the necessary genes for tra...
www.biorxiv.org
March 24, 2025 at 8:52 AM
Cool preprint! The smallest Darwinian entity is a little smarter than we thought...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Any idea when the abstract submission portal opens for IMMEM XIV? 😊 @esgem-sg.bsky.social
March 3, 2025 at 9:12 AM
Any idea when the abstract submission portal opens for IMMEM XIV? 😊 @esgem-sg.bsky.social
Reposted by Célia Souque
Ground-breaking work by one of the most amazing of scientists. A must read for all plasmids afficionado (and and any evolutionary biologist in general!)
I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics!
(1/n) www.biorxiv.org/content/earl...
(1/n) www.biorxiv.org/content/earl...
Intracellular competition shapes plasmid population dynamics
Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-r...
www.biorxiv.org
February 21, 2025 at 10:17 PM
Ground-breaking work by one of the most amazing of scientists. A must read for all plasmids afficionado (and and any evolutionary biologist in general!)
Reposted by Célia Souque
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
January 17, 2025 at 8:53 PM
This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after
Reposted by Célia Souque
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
January 17, 2025 at 7:03 AM
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1
Reposted by Célia Souque
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology
Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...
www.nature.com
January 10, 2025 at 10:06 AM
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Reposted by Célia Souque
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
A phylogenetic approach to comparative genomics
Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...
rdcu.be
January 8, 2025 at 1:19 PM
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.
These methods must be considered an essential part of the comparative genomics toolkit.
@lauriebelch.bsky.social @stuwest.bsky.social
Reposted by Célia Souque
Sharing three fully funded PhD opportunities to join my lab at Queen’s to work on topics spanning bacterial pathogens, antibiotic resistance, microbial interactions, & mobile genetic elements 🦠. Closing dates in January and February, and open to international candidates 🌍 Projects detailed below ⬇️
December 30, 2024 at 2:27 PM
Sharing three fully funded PhD opportunities to join my lab at Queen’s to work on topics spanning bacterial pathogens, antibiotic resistance, microbial interactions, & mobile genetic elements 🦠. Closing dates in January and February, and open to international candidates 🌍 Projects detailed below ⬇️
Reposted by Célia Souque
In case you missed it: @matthewjshepherd.bsky.social surveyed the clinical literature to reveal how #AMR evolves within patients, why eco/evo mechanisms vary among infections, & what we can do better to improve treatments www.nature.com/articles/s41... #MicroSky
Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance - Nature Reviews Microbiology
In this Review, Shepherd, Brockhurst and colleagues explore the clinical evidence in support of four major ecological and evolutionary mechanisms of within-patient antimicrobial resistance emergence i...
www.nature.com
December 4, 2024 at 2:58 PM
In case you missed it: @matthewjshepherd.bsky.social surveyed the clinical literature to reveal how #AMR evolves within patients, why eco/evo mechanisms vary among infections, & what we can do better to improve treatments www.nature.com/articles/s41... #MicroSky
Gosh parts of me hate the concept of ChatGPT with a passion, but I have to acknowledge it's supremacy when trying to debug a Snakemake pipeline, which I am not convinced are made to be understood by humans 😅
December 3, 2024 at 10:47 AM
Gosh parts of me hate the concept of ChatGPT with a passion, but I have to acknowledge it's supremacy when trying to debug a Snakemake pipeline, which I am not convinced are made to be understood by humans 😅
Reposted by Célia Souque
Volume 2 of the #AMR Starter Pack is here!
go.bsky.app/EUY2FUJ
Follow these amazing people along with those in Vol. 1
go.bsky.app/KkZfvrh
And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place
bsky.app/profile/did:...
go.bsky.app/EUY2FUJ
Follow these amazing people along with those in Vol. 1
go.bsky.app/KkZfvrh
And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place
bsky.app/profile/did:...
December 2, 2024 at 6:52 AM
Volume 2 of the #AMR Starter Pack is here!
go.bsky.app/EUY2FUJ
Follow these amazing people along with those in Vol. 1
go.bsky.app/KkZfvrh
And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place
bsky.app/profile/did:...
go.bsky.app/EUY2FUJ
Follow these amazing people along with those in Vol. 1
go.bsky.app/KkZfvrh
And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place
bsky.app/profile/did:...
Reposted by Célia Souque
Don't know how to do polls in Bluesky, but am very curious to know how what the #microsky thinks.
Genes that increase fitness in natural conditions are:
A. Over-represented on plasmids
B. Over-represented on the chromosome
C. Evenly distributed between plasmids and the chromosome
Genes that increase fitness in natural conditions are:
A. Over-represented on plasmids
B. Over-represented on the chromosome
C. Evenly distributed between plasmids and the chromosome
November 27, 2024 at 9:11 PM
Don't know how to do polls in Bluesky, but am very curious to know how what the #microsky thinks.
Genes that increase fitness in natural conditions are:
A. Over-represented on plasmids
B. Over-represented on the chromosome
C. Evenly distributed between plasmids and the chromosome
Genes that increase fitness in natural conditions are:
A. Over-represented on plasmids
B. Over-represented on the chromosome
C. Evenly distributed between plasmids and the chromosome
That's low-key one of my favorite thing about Oslo - the city center is very often car free, and the few cars are often electric, which makes them much less audible.
Going to back to a 'proper' big city (Stockholm) for a week felt weird!
Going to back to a 'proper' big city (Stockholm) for a week felt weird!
November 27, 2024 at 8:59 AM
That's low-key one of my favorite thing about Oslo - the city center is very often car free, and the few cars are often electric, which makes them much less audible.
Going to back to a 'proper' big city (Stockholm) for a week felt weird!
Going to back to a 'proper' big city (Stockholm) for a week felt weird!
Reposted by Célia Souque
Please sign up, it will be fun!
Open for all with an interest in AMR and genomics (in the UK and elsewhere).
www.targetamr.org.uk
(and please give @target-amr.bsky.social a follow!)
Open for all with an interest in AMR and genomics (in the UK and elsewhere).
www.targetamr.org.uk
(and please give @target-amr.bsky.social a follow!)
October 30, 2024 at 11:56 AM
Please sign up, it will be fun!
Open for all with an interest in AMR and genomics (in the UK and elsewhere).
www.targetamr.org.uk
(and please give @target-amr.bsky.social a follow!)
Open for all with an interest in AMR and genomics (in the UK and elsewhere).
www.targetamr.org.uk
(and please give @target-amr.bsky.social a follow!)
Reposted by Célia Souque
Get ready to dance, our paper – Phage DisCo: targeted discovery of bacteriophages by co-culture – has been pre-printed! 🪩 This has been a really fun project to work on with @sianowen.bsky.social, @baym.lol, @nquinoneso.bsky.social, and our two talented undergrads Kesther and Carmen!
Phage DisCo: targeted discovery of bacteriophages by co-culture https://www.biorxiv.org/content/10.1101/2024.11.22.624878v1
Phage DisCo: targeted discovery of bacteriophages by co-culture https://www.biorxiv.org/content/10.1101/2024.11.22.624878v1
Phages interact with many components of bacterial physiology from the surface to the cytoplasm. Alth
www.biorxiv.org
November 23, 2024 at 6:12 PM
Get ready to dance, our paper – Phage DisCo: targeted discovery of bacteriophages by co-culture – has been pre-printed! 🪩 This has been a really fun project to work on with @sianowen.bsky.social, @baym.lol, @nquinoneso.bsky.social, and our two talented undergrads Kesther and Carmen!