Francesc Coll
@fcic.bsky.social
Computational biologist interested in bacterial genomics, bacterial adaptation and antibiotic resistance. @IBV_CSIC
Reposted by Francesc Coll
The first of some rather chunky papers coming out of Sam Fenn’s work here at @uccmicrobiology.bsky.social
Here we identify and characterise yet another way S. aureus survives life in the bloodstream, but remodelling a major part of its metabolism
Here we identify and characterise yet another way S. aureus survives life in the bloodstream, but remodelling a major part of its metabolism
Metabolic reprogramming promotes Staphylococcus aureus serum resistance during bacteraemia.
Staphylococcus aureus is a leading cause of bloodstream infections causing an estimated 300,000 deaths worldwide. Using a functional genomics approach, our group previously identified that adaptation ...
eur01.safelinks.protection.outlook.com
January 15, 2026 at 1:47 PM
The first of some rather chunky papers coming out of Sam Fenn’s work here at @uccmicrobiology.bsky.social
Here we identify and characterise yet another way S. aureus survives life in the bloodstream, but remodelling a major part of its metabolism
Here we identify and characterise yet another way S. aureus survives life in the bloodstream, but remodelling a major part of its metabolism
Reposted by Francesc Coll
My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
January 15, 2026 at 11:19 AM
My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Reposted by Francesc Coll
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 14, 2026 at 10:14 AM
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...
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Reposted by Francesc Coll
Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)
April 22, 2025 at 9:54 AM
Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)
Reposted by Francesc Coll
Laura Díaz Sáez explicó las actividades que está realizando el Grupo de Trabajo de Difusión (Daniel López, Juan Hermoso, Rafael Molina, Lara Díaz, Sara Hernando-Amado, Jade Rivera, Alberto Marina, Ana de la Torre y Scienseed). Y participaron miembros de otras Conexiones del @CSIC.
November 25, 2025 at 11:02 AM
Laura Díaz Sáez explicó las actividades que está realizando el Grupo de Trabajo de Difusión (Daniel López, Juan Hermoso, Rafael Molina, Lara Díaz, Sara Hernando-Amado, Jade Rivera, Alberto Marina, Ana de la Torre y Scienseed). Y participaron miembros de otras Conexiones del @CSIC.
Reposted by Francesc Coll
Hoy hemos celebrado la Asamblea Anual de la Conexión Resistencias a Antimicrobianos del @csic.es donde nos hemos reunido para hablar sobre este problema de salud y buscar soluciones. Una conexión liderada por @albertomarina.bsky.social y Ana de la Torre. Síguenos para estar informado!
November 24, 2025 at 6:48 PM
Hoy hemos celebrado la Asamblea Anual de la Conexión Resistencias a Antimicrobianos del @csic.es donde nos hemos reunido para hablar sobre este problema de salud y buscar soluciones. Una conexión liderada por @albertomarina.bsky.social y Ana de la Torre. Síguenos para estar informado!
Reposted by Francesc Coll
La otra mesa trató sobre "Adquisición y diseminación de resistencias a los antibióticos: del ecosistema natural al microbioma humano" (Junkal Gramendia, Jaime Villaverde, Pilar Truchado, Carol Ewbank, Francesc Coll, Sara Hernando-Amado, Carles Ubeda).
November 25, 2025 at 10:51 AM
La otra mesa trató sobre "Adquisición y diseminación de resistencias a los antibióticos: del ecosistema natural al microbioma humano" (Junkal Gramendia, Jaime Villaverde, Pilar Truchado, Carol Ewbank, Francesc Coll, Sara Hernando-Amado, Carles Ubeda).
Reposted by Francesc Coll
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted by Francesc Coll
#microsky Pleased to share this work led by Cat Wilson as part of her PhD, tracking Salmonella transmission in low intensity agricultural settings in Malawi. TL;DR - lots of transmission between humans, animals and environment within households. www.nature.com/articles/s41...
Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi - Nature Communications
In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulati...
www.nature.com
November 12, 2025 at 8:36 PM
#microsky Pleased to share this work led by Cat Wilson as part of her PhD, tracking Salmonella transmission in low intensity agricultural settings in Malawi. TL;DR - lots of transmission between humans, animals and environment within households. www.nature.com/articles/s41...
Reposted by Francesc Coll
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
2026-27 Project (Dyson & Mostowy & Knight) - MRC London Intercollegiate Doctoral Training Partnership Studentships
PHACTS: Unravelling PHAge-baCTeria-host immune dynamicS to inform phage therapy SUPERVISORY TEAM Supervisor Dr Zoe Dyson...
mrc-lid.lshtm.ac.uk
November 13, 2025 at 11:11 AM
London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
Reposted by Francesc Coll
We wrapped up #IMMEM XIV over the weekend and it was a fantastic success with over 250 participants from 35 countries. A big thank you to the organisers and specifically @esgem-sg.bsky.social our study group on epidemiological markers! The content will be available on ESCMID media soon. #clinmicro
September 22, 2025 at 6:54 AM
We wrapped up #IMMEM XIV over the weekend and it was a fantastic success with over 250 participants from 35 countries. A big thank you to the organisers and specifically @esgem-sg.bsky.social our study group on epidemiological markers! The content will be available on ESCMID media soon. #clinmicro
Reposted by Francesc Coll
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...
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
September 10, 2025 at 9:12 AM
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...
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...
Reposted by Francesc Coll
“The decision to close the Fleming Fund was not accompanied by an official statement or press release.”
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
UK Government dismantles the Fleming Fund
On July 15, 2025, the UK Government confirmed that it planned to dismantle the country’s
flagship international programme for tackling antimicrobial resistance (AMR). The
Fleming Fund is overseen by t...
www.thelancet.com
September 5, 2025 at 9:18 PM
“The decision to close the Fleming Fund was not accompanied by an official statement or press release.”
www.thelancet.com/journals/lan...
www.thelancet.com/journals/lan...
Reposted by Francesc Coll
Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
Assistant Professor (Research and Education) in Bacterial Genomics at University of Birmingham
Looking for a new job opportunity in academia? Check out this job opening for a Assistant Professor (Research and Education) in Bacterial Genomics on jobs.ac.uk!
www.jobs.ac.uk
September 4, 2025 at 8:22 AM
Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...
Reposted by Francesc Coll
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Reposted by Francesc Coll
Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!
August 14, 2025 at 7:26 AM
Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!
Reposted by Francesc Coll
Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Topics range from how genomics inform resistance profiling to pathogen surveillance in a #OneHealth framework. 🧬
✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY
#IDSky
✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY
#IDSky
August 7, 2025 at 8:14 AM
Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Topics range from how genomics inform resistance profiling to pathogen surveillance in a #OneHealth framework. 🧬
✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY
#IDSky
✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY
#IDSky
Reposted by Francesc Coll
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...
🧵 (1/14)
www.doi.org/10.1038/s414...
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 ...
www.doi.org
July 17, 2025 at 12:13 PM
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...
🧵 (1/14)
www.doi.org/10.1038/s414...
Reposted by Francesc Coll
Researchers at @lshtm.bsky.social, led by @josebengoechea.bsky.social, will conduct a £2.2M study funded by UK MRC to investigate how Klebsiella pneumoniae silently colonises the gut before causing deadly infections. 🔬🦠
Read more 👉 bit.ly/4mNSreh
Read more 👉 bit.ly/4mNSreh
June 5, 2025 at 1:17 PM
Researchers at @lshtm.bsky.social, led by @josebengoechea.bsky.social, will conduct a £2.2M study funded by UK MRC to investigate how Klebsiella pneumoniae silently colonises the gut before causing deadly infections. 🔬🦠
Read more 👉 bit.ly/4mNSreh
Read more 👉 bit.ly/4mNSreh
Reposted by Francesc Coll
Late breaker abstracts for IMMEM conference, to be held in beautiful Portugal this September, close Friday May 23!
Something for the #ABPHM25 crowd to ponder 🤔
www.escmid.org/congress-eve...
Something for the #ABPHM25 crowd to ponder 🤔
www.escmid.org/congress-eve...
Invited & Abstract Programme
Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).
www.escmid.org
May 21, 2025 at 4:57 PM
Late breaker abstracts for IMMEM conference, to be held in beautiful Portugal this September, close Friday May 23!
Something for the #ABPHM25 crowd to ponder 🤔
www.escmid.org/congress-eve...
Something for the #ABPHM25 crowd to ponder 🤔
www.escmid.org/congress-eve...
Reposted by Francesc Coll
🧬Antibiograms have been used during outbreak investigations for decades as a surrogate for genetic relatedness of #MRSA
🦠Authors evaluate the accuracy of antibiograms in detecting transmission, using genomic epidemiology as the reference standard
www.sciencedirect.com/science/arti...
🦠Authors evaluate the accuracy of antibiograms in detecting transmission, using genomic epidemiology as the reference standard
www.sciencedirect.com/science/arti...
February 20, 2025 at 1:50 PM
🧬Antibiograms have been used during outbreak investigations for decades as a surrogate for genetic relatedness of #MRSA
🦠Authors evaluate the accuracy of antibiograms in detecting transmission, using genomic epidemiology as the reference standard
www.sciencedirect.com/science/arti...
🦠Authors evaluate the accuracy of antibiograms in detecting transmission, using genomic epidemiology as the reference standard
www.sciencedirect.com/science/arti...
Reposted by Francesc Coll
📣Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 🧵 @zaminiqbal.bsky.social
January 14, 2025 at 2:20 PM
📣Our latest paper is out now in mSystems: Not quite as it may seem - investigating #plasmid diversity and evolution in #Klebsiella pneumoniae at a single institution over time. A short thread 🧵 @zaminiqbal.bsky.social
Many thanks to all co-authors contributed to this work: Beth Blane, Katie Bellis, Marta Matuszewska, Toska Wonfor, Dorota Jamrozy, Michelle Toleman, Joan Geoghegan, @julianparkhill.bsky.social, Ruth Massey, Sharon Peacock, @ewanharrison.bsky.social
January 14, 2025 at 9:40 AM
Many thanks to all co-authors contributed to this work: Beth Blane, Katie Bellis, Marta Matuszewska, Toska Wonfor, Dorota Jamrozy, Michelle Toleman, Joan Geoghegan, @julianparkhill.bsky.social, Ruth Massey, Sharon Peacock, @ewanharrison.bsky.social
Our study also identified several uncharacterised genes that may be critical for colonisation that warrant further experimental investigation.
January 14, 2025 at 9:40 AM
Our study also identified several uncharacterised genes that may be critical for colonisation that warrant further experimental investigation.
We also found mutations in genes that could influence how S. aureus interact with human cells or the immune system, such as in genes encoding SraP/SasA and TarS.
January 14, 2025 at 9:40 AM
We also found mutations in genes that could influence how S. aureus interact with human cells or the immune system, such as in genes encoding SraP/SasA and TarS.