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Francesc Coll

@fcic.bsky.social
398 followers 119 following 24 posts

Computational biologist interested in bacterial genomics, bacterial adaptation and antibiotic resistance. @IBV_CSIC

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Reposted by Francesc Coll
Paula @paururo.bsky.social · 17/09/2026
Working with bacterial sequencing data and want to get more out of it? ONE-BAG 2026 is a hands-on course covering the full bacterial genomics workflow, from raw reads to phylogenetics. Valencia, 14–17 Dec 2026. Applications close 1 Oct. onebag.uv.es
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Kate Baker @ksbakes.bsky.social · 28/05/2026
Our TARGet AMR genomics-comic is out now - check it out, share it, print it, use it in your lectures, PE events, or maybe even when trying to explain what you do to dinner guests! 🤓 🧬 🧫
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Francesc Coll @fcic.bsky.social · 21/05/2026
Happy to share our recent work on genetic factors and clinical impact of S. aureus adhesion, published in natcomms.nature.com doi.org/10.1038/s414...
doi.org
Genetic determinants of Staphylococcus aureus adhesion shape virulence trade-offs in bacteremia - Nature Communications
To uncover how Staphylococcus aureus strain variation influences adhesion and thus disease outcomes, the authors profile 236 bacteremia isolates, showing that high-adhesion, low-toxicity isolates may ...
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Sara Hernando-Amado @hernando-amado.bsky.social · 14/05/2026
The best results come from diverse minds working together. I´m very happy to share a collaborative work between 3 biologists, 2 mathematicians, a physicist, a chemist, and a physician: www.biorxiv.org/cgi/content/... @the100footpole.bsky.social @omeuxeito.bsky.social @pablolaborda.bsky.social
biorxiv.org
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Francesc Coll @fcic.bsky.social · 01/05/2026
Happy to share our latest work on “In Host Mutational Adaptation of Mycobacterium Tuberculosis Complex Strains During Tuberculosis Infection” published in @jidjournal.bsky.social doi.org/10.1093/infd...
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CSIC @csic.es · 31/03/2026
🦠Los fagos son los virus de las bacterias 🔬Se sabía que se comunicaban, pero se pensaba que solo lo hacían entre los de su especie 👨‍🔬El @ibv-csic.bsky.social revela que distintas especies de virus comparte un 'lenguaje común' para coordinar estrategias de supervivencia 👉 tiny.cc/rdx0101
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Teresa M. Coque @tmcoque.bsky.social · 26/03/2026
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👇
rdcu.be
The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the “robust-yet-fragile” architecture ...
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Antimicrobianos Hub CSIC @amrhubcsic.bsky.social · 25/03/2026
La resistencia a antimicrobianos es una amenaza global. Estos jóvenes talentos ya están trabajando en la solución 🧫✨ Conoce a los finalistas de los Premios CSIC–AEAC y sus proyectos: www.conexion-amr.csic.es/los-premios-...
conexion-amr.csic.es
Los Premios de Investigación en Resistencia a Antimicrobianos CSIC–AEAC ya tienen finalistas | Conexión AMR
La iniciativa está organizada por la Conexión Resistencia Antimicrobianos del CSIC y la Asociación Española para el Avance de la Ciencia.
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Rebecca A. Gladstone @becctococcus.bsky.social · 25/03/2026
Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....
nature.com
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Ewan Harrison @ewanharrison.bsky.social · 11/03/2026
All the data across the different groups is compared. @effkay88.bsky.social @fcic.bsky.social
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Ewan Harrison @ewanharrison.bsky.social · 11/03/2026
Day 3 of AMR of Bacterial Pathogens - Africa course at NICD Johannesburg. Split day into the lab for AMR disk testing, MICs and broth micro-dilution. On the computers and lectures on online and command line AMR tools, MLST and phylogeny. Busy day! @sangerinstitute.bsky.social @engagewcs.bsky.social
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Ewan Harrison @ewanharrison.bsky.social · 11/03/2026
@fcic.bsky.social @effkay88.bsky.social @belamalta10.bsky.social
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Ewan Harrison @ewanharrison.bsky.social · 09/03/2026
Fantastic second day of Antimicrobial Resistance of Bacterial Pathogens - Africa course at NICD Johannesburg. Packed day - covering the basics of genomics, the command line, QC, genotype-to-phenotype, assembly and alignments. @sangerinstitute.bsky.social @engagewcs.bsky.social @fcic.bsky.social
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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 02/03/2026
109 participants from 52 countries are convening at Africa CDC Headquarters in Addis Ababa for a focused, experience-led meeting on strengthening routine national antimicrobial resistance (AMR) surveillance systems, including the integration of pathogen genomic data. More at www.amrsurveillance.org
amrsurveillance.org
AMR Convening on Building Sustainable AMR Genomic Surveillance
A focused convening to identify practical pathways for strengthening routine national AMR surveillance systems, including the integration of genomic data.
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Kate Baker @ksbakes.bsky.social · 04/03/2026
Are you interested in how your genomics work can meaningfully feed into addressing the UK National Action Plan on AMR? 🧬🧫 🦠💊 Then check out our handy personal view out today in Lancet Microbe … 🧵1/n www.sciencedirect.com/science/arti...
sciencedirect.com
The role of microbial genomics in delivering the UK’s national action plan for confronting antimicrobial resistance 2024–29
Antimicrobial resistance (AMR) is a major threat to human and animal health, in addition to environmental resilience. Countries set the agenda on thei…
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Rafal Mostowy @rafalmostowy.bsky.social · 26/02/2026
📢 Hiring a Postdoc in Computational Phage Biology (Kraków, Poland) We study the evolution & structural modularity of prophage-encoded glycan-degrading enzymes in Klebsiella pneumoniae — combining genomics and AlphaFold-based analyses. Details in attached PDF 👇
docs.google.com
Postdoc Ad
Postdoctoral Position in Computational Phage Biology Microbial Genomics Group, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków PL Summary We are seeking a postdoctoral rese...
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Zamin Iqbal @zaminiqbal.bsky.social · 26/02/2026
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...
allthebacteria.readthedocs.io
Overview — AllTheBacteria documentation
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masseylab.bsky.social @masseylab.bsky.social · 11/02/2026
Super cool story from Sam Fenn. He developed a wound model where s. aureus & p. aerunginosa & c. albicans fight it out shows that copper is central to the outcome where Candida and pseudomonas take copper from human tissue to gang up on staph! But staph being staph is as always one step ahead….
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Instituto de Biomedicina de Valencia (IBV), CSIC @ibv-csic.bsky.social · 28/01/2026
Bioinformatician Position Open at the Evolutionary and Functional Genomics Lab @ibb-botanic.bsky.social and Nuria Flames' group @ibv-csic.bsky.social If you are interested, please send a CV and a short motivation letter to nflames@ibv.csic.es with the subject “Bioinfo position 2026” before 27/02/26
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masseylab.bsky.social @masseylab.bsky.social · 15/01/2026
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
eur01.safelinks.protection.outlook.com
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 ...
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Olaya Rendueles @olayarendueles.bsky.social · 15/01/2026
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
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Manuel Ares-Arroyo @aresarroyom.bsky.social · 14/01/2026
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...
biorxiv.org
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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025
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)
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Antimicrobianos Hub CSIC @amrhubcsic.bsky.social · 25/11/2025
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.
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Antimicrobianos Hub CSIC @amrhubcsic.bsky.social · 24/11/2025
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!
Foto de grupoMesa 1Mesa 2Programa
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Antimicrobianos Hub CSIC @amrhubcsic.bsky.social · 25/11/2025
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).
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John Lees @johnlees.bacpop.org · 19/11/2025
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
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Mat Beale @typemat12.bsky.social · 12/11/2025
#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...
nature.com
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...
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Zoe Anne Dyson @msmicrobiocode.bsky.social · 13/11/2025
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.
mrc-lid.lshtm.ac.uk
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...
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ESCMID @escmid.bsky.social · 22/09/2025
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
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Zamin Iqbal @zaminiqbal.bsky.social · 10/09/2025
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...
nature.com
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.
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Onisillos @onisillos.bsky.social · 05/09/2025
“The decision to close the Fleming Fund was not accompanied by an official statement or press release.” www.thelancet.com/journals/lan...
thelancet.com
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...
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Jessica Blair @jessicamablair.bsky.social · 04/09/2025
Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!! @imibirmingham.bsky.social www.jobs.ac.uk/job/DOO184/a...
jobs.ac.uk
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!
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Tami Lieberman @contaminatedsci.bsky.social · 15/08/2025
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.
cell.com
Intraspecies associations from strain-rich metagenome samples
Qu et al. present PHLAME, a method to analyze strain composition in metagenomic samples where many strains of the same species coexist. Using PHLAME, they show relationships between strain abundances ...
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Zamin Iqbal @zaminiqbal.bsky.social · 14/08/2025
Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!
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ESCMID @escmid.bsky.social · 07/08/2025
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
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Carlos Serna @cserna.bsky.social · 17/07/2025
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...
doi.org
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 ...
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LSHTM AMR Centre @lshtmamrcentre.bsky.social · 05/06/2025
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
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Kat Holt @katholt.bsky.social · 21/05/2025
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...
escmid.org
Invited & Abstract Programme
Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).
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Journal of Hospital Infection @thejhi.bsky.social · 20/02/2025
🧬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...
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Sandra Reuter @sandrareuter.bsky.social · 14/01/2025
📣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
Composite of the paper header showing all authors and an equation showing phylogenetic trees plus plasmids give a complex plasmid picture.
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Francesc Coll @fcic.bsky.social · 14/01/2025
Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms rdcu.be/d55l3
rdcu.be
The mutational landscape of Staphylococcus aureus during colonisation
Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...
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Ewan Harrison @ewanharrison.bsky.social · 13/01/2025
Our paper investigating the mutational landscape during Staphylococcus aureus during colonisation is out now rdcu.be//d55l3 @fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social
rdcu.be
The mutational landscape of Staphylococcus aureus during colonisation
Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...
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Gwen Knight @gmknght.bsky.social · 20/11/2024
Three potential PhD positions are now open for applications! - MRCLID: (1) integrated with my fship - AMR prevalence by age&sex (2) long term collab. - AMR gene transfer - Nagasaki: new collaboration comparing UK&Japan AMR rates mrc-lid.lshtm.ac.uk/projects/ www.lshtm.ac.uk/study/resear...
lshtm.ac.uk
Joint PhD Programme for Global Health | LSHTM
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