iiinova — where your digital self keeps evolving

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

113

Reposted by Francesc Coll

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! 🤓 🧬 🧫

1129

Francesc Coll @fcic.bsky.social · 21/05/2026

This has been a very multidisciplinary project led by @Marta Zapotoczna, with major experimental contributions from @Paula Rożen, and valuable input from many collaborators. @ibv-csic.bsky.social @csic.es @Uniwersytet Warszawski

010

Francesc Coll @fcic.bsky.social · 21/05/2026

We suggest that highly-adhesive, α-toxin-defective isolates promote inflammatory but self-limiting infections, whereas weakly adhesive, high-toxicity strains favour immune evasion and severe disease.

100

Francesc Coll @fcic.bsky.social · 21/05/2026

Our findings define adhesion as a polygenic and evolutionarily variable trait with genetic variants in known adhesins and novel loci all affecting adhesion capacity.

100

Francesc Coll @fcic.bsky.social · 21/05/2026

Functional analyses reveal that high levels of SpA limit ClfA-dependent fibrinogen binding, CsbB interferes with ClfA exposure on bacterial surface, and GlcA enhances fibronectin binding via metabolic regulation.

100

Francesc Coll @fcic.bsky.social · 21/05/2026

We applied a bacterial GWAS to identify genetic variants in S. aureus associated with differences in bacterial adhesion. The GWAS identified genetic variants in genes encoding known adhesins (clfA, fnbA, fnbB, ebh), other surface factors (spa, sdrH), MGEs, and other loci (csbB, glcA).

100

Francesc Coll @fcic.bsky.social · 21/05/2026

We found that stronger fibrinogen-binding, particularly in strains lacking α-toxin, correlated with heightened systemic inflammation but lower mortality, linking bacterial adhesion to distinct clinical outcomes.

110

Francesc Coll @fcic.bsky.social · 21/05/2026

We characterised a collection of 236 S. aureus strains isolated from bloodstream infections, profiled for binding to fibrinogen and fibronectin and whole-genome sequencing, with matched patients' clinical data.

100

Reposted by Francesc Coll

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

164

Francesc Coll @fcic.bsky.social · 01/05/2026

Many thanks to everyone involved! @Helen Zhang, @Naomi Medina-Jaudes, @Alicia Forcada-Nadal, and @ewanharrison.bsky.social

000

Francesc Coll @fcic.bsky.social · 01/05/2026

Our study describes the multiplicity and heterogeneity of adaptive genetic changes that M. tuberculosis undergoes during human infection, and provide indirect evidence of the selective pressures that MTBC encounters in host.

100

Francesc Coll @fcic.bsky.social · 01/05/2026

When using available drug treatment data, we found that fluoroquinolone resistance was acquired more frequently than resistance to any other drug, and particularly higher among MDR strains.

100

Francesc Coll @fcic.bsky.social · 01/05/2026

We observed that genes encoding regulators (phoR, whiB6 and mycP1) and effectors (espK and eccE1) of the virulence ESX-1 locus were frequently mutated in host.

100

Francesc Coll @fcic.bsky.social · 01/05/2026

We identified candidate drug resistance loci (prpR, Rv2571c, fadD11, helY, ndhA, Rv0139, fadE5, bioF2, and mce1 operon) identified elsewhere by independent GWAS and functional genomics studies.

100

Francesc Coll @fcic.bsky.social · 01/05/2026

We identified 28 well-known drug resistance loci as hot spots of mutational adaptation in vivo, which demonstrates the robustness of our approach in detecting expected adaptations.

100

Francesc Coll @fcic.bsky.social · 01/05/2026

We used a dataset of 5,900 MTBC genomes from over 1,000 TB patients and applied a convergent evolution approach to identify heavily mutated loci across strains of multiple patients.

100

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...

152

Reposted by Francesc Coll

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

02012

Reposted by Francesc Coll

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 ...

12115

Reposted by Francesc Coll

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.

011

Reposted by Francesc Coll

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

12414

Reposted by Francesc Coll

Ewan Harrison @ewanharrison.bsky.social · 11/03/2026

All the data across the different groups is compared. @effkay88.bsky.social @fcic.bsky.social

111

Reposted by Francesc Coll

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

373

Reposted by Francesc Coll

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

273

Reposted by Francesc Coll

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.

164

Reposted by Francesc Coll

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…

12112

Reposted by Francesc Coll

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...

11012

Reposted by Francesc Coll

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

06629

Reposted by Francesc Coll

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….

2135

Reposted by Francesc Coll

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

022

Reposted by Francesc Coll

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

12854

Reposted by Francesc Coll

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

48453

Reposted by Francesc Coll

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)

13423

Reposted by Francesc Coll

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.

064

Reposted by Francesc Coll

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!

1146

Reposted by Francesc Coll

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).

164

Reposted by Francesc Coll

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

16236

Reposted by Francesc Coll

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...

154

Reposted by Francesc Coll

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

0145

Reposted by Francesc Coll

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.

519099

Reposted by Francesc Coll

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 ...

24726

Reposted by Francesc Coll

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!!

044