Carlos Serna

Oxygen levels can affect how resistance genes work, impacting antibiotic efficacy. This can be relevant for the most used ones: for example, resistance to fosfomycin varies with oxygen.

Learn more in our latest paper 👉 bit.ly/3T8sdpp a work led by @jaescudero.bsky.social

#AntibioticResistance

The food-associated resistome is shaped by processing and production environments - Nature Microbiology Whole-metagenome sequencing of 1,780 raw-material, end-product and surface samples from 113 food processing facilities reveals the occurrence of antimicrobial resistance determinants in foods and thei...

#NewResearch

'The food-associated resistome is shaped by processing and production environments' by @nmquijada.bsky.social and co-workers.

#MicroSky 🦠

www.nature.com/articles/s41...

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

ExcludonFinder: mapping transcriptional overlaps between neighboring genes Abstract. Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transc

🚨🚨 New paper in @narjournal.bsky.social! 🍾

Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons).

We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín.

👇

Muchas gracias Ana 😊😊

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Thanks Jose!!!

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?

In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!

👇 Check out all the details in Paula’s thread!

Hint: 🐇 (most of the time)

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...

New paper alert! 🚨

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate.

We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number.

Let's dive in! 🧵👇

Publications - Plasmidlab Take a detailed look at our work Discover our latest results Our story on bacterial evolution research Explore our publication’s archive Browse the list below or enter our PubMed’s repository to…

Our latest paper explores the factors shaping plasmid-bacteria associations and highlights why studying plasmid-host interactions of clinical relevance is key for understanding the evolution and spread of AMR.

Find out more 👉 plasmidlab.es/publications/

#AntibioticResistance

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

Evolutionary hotspots in bacterial genomes Nature Reviews Microbiology, Published online: 21 July 2025; doi:10.1038/s41579-025-01217-3This Genome Watch discusses recent findings in bacterial mutational hotspots, their impact on pathogenesis and antimicrobial resistance, and how we can harness this knowledge to predict pathogen evolution.

New online! Evolutionary hotspots in bacterial genomes

Global emergence and transmission dynamics of carbapenemase-producing Citrobacter freundii sequence type 22 high-risk international clone: a retrospective, genomic, epidemiological study Our study provides evidence to suggest that Citrobacter species are emerging carriers of carbapenem-resistance genes. These findings provide insight into the population structure of CPC species and hi...

Citrobacter freundii ain't ever been a friend of ours... now becoming even more hostile!
#IDSky #ClinMicro #AMR #MedSky
@lancetmicrobe.bsky.social

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

This is a legitimately incredible result that hints at something fundamental about plasmids that we don’t yet understand

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 ...

Aminoglycoside resistance is rising, driven by 16S rRNA methyltransferases like NpmA, which can block ALL drugs in the class

Once rare, the 𝘯𝘱𝘮𝘈2 gene is now spreading via transposons among medically important Gram-positive species including 𝘊𝘭𝘰𝘴𝘵𝘳𝘪𝘥𝘪𝘰𝘪𝘥𝘦𝘴 𝘥𝘪𝘧𝘧𝘪𝘤𝘪𝘭𝘦 and 𝘌𝘯𝘵𝘦𝘳𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘧𝘢𝘦𝘤𝘪𝘶𝘮
⚠️ ‼️

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 ...

Great paper led by @francesccoll.bsky.social and Bruno Gonzalez Zorn

'Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria'

www.nature.com/articles/s41...

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 ...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria
#AntibioticResistance #microSky

www.nature.com/articles/s41...

Totalmente! Aquí os dejo un hilo en el que se explica lo que encontramos principalmente en el trabajo 😉

bsky.app/profile/cser...

Many thanks Zamin 😊

Supercool work on a new variant of the pan-aminoglycoside resistance gene npmA, led by @cserna.bsky.social and @bgzorn.bsky.social.
Really happy to have participated in it with so many friends and collaborators!
Go check it out: www.nature.com/articles/s41...

Coincidentally, Dey et al. have just published the first small‑molecule inhibitors of npmA. The compounds bind a previously untapped “Y‑shaped” pocket on the enzyme (pubs.acs.org/doi/10.1021/...) and could help restore aminoglycoside activity. Perfect timing for our discovery! 😄🧬🚀

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 ...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria www.nature.com/articles/s41...

And special thanks to @fcic.bsky.social and @ewanharrison.bsky.social for hosting most of the work (and for welcoming me so warmly) at @sangerinstitute.bsky.social 😊🍾🥳 (14/14)

Many thanks to Rob Willems and Rogier Jansen for the Dutch E. faecium isolates, @alexmsalmeida.bsky.social for the metagenomic analyses and Bruno Dupuy for his C. difficile expertise 🔬🧪 (13/14)

Grateful to the ARU team @mpulido-vadillo.bsky.social , @josefdelgadoblas.bsky.social (former member), Bosco and PI @bgzorn.bsky.social at @ucm.es @visavet.bsky.social for the many hours that made this study possible 🔬🧬🎊 (12/14)

The worry is obvious ⚠️; one successful jump of npmA2 into a common Gram‑negative pathogen could render aminoglycosides ineffective (11/14)

Putting it all together 🏁:
- npmA2 is located on an ICE that seems to transfer only rarely (lab and database evidence)
- C. diff ST11 has picked it up multiple times, perhaps in pig guts under apramycin pressure (hypothesis)
- One hospital crossover has already moved npmA2 into E. faecium (10/14)

🧪 Lab matings with C. difficile and enterococci failed to transfer the ICE, suggesting horizontal movement is rare (in vitro conditions) and spread could be mainly clonal, a modest relief for the moment 😅 (10/14)

Plot twist 🚨: the very same Tn7734-ICE Tn7740 element turned up in two clonal, vancomycin-resistant E. faecium isolates from a Dutch ICU. This confirms that npmA2 has crossed species lines at least once 🧫⚠️ (9/14)