Francesc Coll

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

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

@fcic.bsky.social @effkay88.bsky.social @belamalta10.bsky.social

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

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

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…

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...

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...

📢 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 👇

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...

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….

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

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 ...

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

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

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...

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)

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.

Foto de grupo

Mesa 1

Mesa 2

Programa

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!

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).

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

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...

#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...

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.

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

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.

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...

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...

“The decision to close the Fleming Fund was not accompanied by an official statement or press release.”

www.thelancet.com/journals/lan...

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!

Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!

@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...

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.

Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!

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

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 ...

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...

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