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

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

Invited & Abstract Programme Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).

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...

🧬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...

Composite of the paper header showing all authors and an equation showing phylogenetic trees plus plasmids give a complex plasmid picture.

📣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

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.

Nitrogen metabolism showed the strongest evidence of adaptation, with genes encoding sub-units of the assimilatory nitrite reductase (nasD/nirB) and urease (ureG), and a nitrogen regulatory protein (darA/pstA), showing the highest mutational enrichment.

We observed an excess of protein-altering mutations in metabolic genes, in the Agr system and in antibiotic targets; and showed the phenotypic effect of multiple adaptive mutations including changes in haemolytic activity, antibiotic susceptibility, and metabolite utilisation.

We applied a genome-wide mutation enrichment approach to identify genes in the S. aureus genome under parallel and convergent evolution that could represent signals of adaptation during colonisation.

We analysed the genomes of more than 7,000 Staphylococcus aureus isolates obtained from over 1,500 human carriers to identify genetic changes that originated in the bacteria in its host and natural environment.

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...

Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms
rdcu.be/d55l3

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...

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

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...