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Carlos Serna

@cserna.bsky.social

310 followers 330 following 21 posts

Graduate Teaching Assistant at UCM (Madrid). Interested on epidemiology, bacterial genomics, bioinformatics and AMR 🧬💻🐄

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Carlos Serna @cserna.bsky.social · Jul 17

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...

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 ...

www.doi.org

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Reposted by Carlos Serna

European Centre for Disease Prevention and Control @ecdc.europa.eu · 1d

🧬 New #GenEpiBioTrain course!

Bacterial Strain Taxonomy for Genomic Surveillance
📅 22–23.10, 09:00–12:00 (CEST)

Learn how bacterial pathogens are classified & named in genomic surveillance – from #MLST & #cgMLST to SNP-based & k-mer clustering.

Info: bit.ly/48qT5df
#ECDCTraining #IDsky #EpiSky

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Reposted by Carlos Serna

Adrian Cazares @cazares-adr.bsky.social · 3d

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics

We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...

If you like time travel & biology, this 🧵is for you👇

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance

Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

doi.org

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Reposted by Carlos Serna

Oliver Schwengers @oschwengers.bsky.social · 3d

Dear community, Bakta needs your help!

To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-)

(1/2)

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Reposted by Carlos Serna

Pedro Dorado-Morales @doradomoralesp.bsky.social · 6d

A plasmid and an ICE teaming up... 🤯😱

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

The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications

Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin polymerization and biofilm formation in vivo.

www.nature.com

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Reposted by Carlos Serna

John Lees @bacpop.org · 10d

Now published, our tool to run (almost) all biological models interactively in your web browser

Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...

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Reposted by Carlos Serna

Dorottya Nagy @dotnagy.bsky.social · 10d

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Figure 2 from my recently pre-printed manuscript on the completeness and accuracy of Nanopore long-read only bacterial genome assembly for Enterobacterales. a) tile plot of chromosome circularisation, with assembler on the x-axis and sample on the y-axis, shows that the consensus long-read only assembler, Autocycler, circularised more chromosomes at 95% (87/92) than any other long-read or hybrid assembler. b) complex upset plot of plasmid reconstruction, showing that the best plasmid reconstruction was achieved by long-read assemblers incorporating the separate plasmid assembly tool, Plassembler, namely Autocycler and Hybracter, reconstructing >96% of plasmids.

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Reposted by Carlos Serna

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Interesting benchmark paper from @dotnagy.bsky.social

"Autocycler circularised the most chromosomes (87/92). .. Flye performed worse than other assemblers on almost all metrics. Autocycler + Medaka... was the most accurate long-read only assembler/polisher "
www.biorxiv.org/content/10.1...

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

Whole bacterial genome sequence reconstruction using Oxford Nanopore Technologies (“Nanopore”) long-read only sequencing may offer a lower-cost, higher-throughput alternative for pathogen surveillance...

www.biorxiv.org

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Reposted by Carlos Serna

Zamin Iqbal @zaminiqbal.bsky.social · 14d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Reposted by Carlos Serna

John Lees @bacpop.org · 22d

The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...

We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

EMBL International PhD Programme – Unique in the world and waiting for you!

www.embl.org

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Reposted by Carlos Serna

John Lees @bacpop.org · 17d

Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training

And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell

EMBL-EBI Training @training.ebi.embl.org · 20d

Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.

Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫

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Reposted by Carlos Serna

Leonie Lorenz @leonielorenz.bsky.social · 20d

Open PhD position in our lab for starting roughly in September 2026. Cannot recommend this lab enough!!! 🦠🖥️

#MathematicalModelling
#BacterialGenomics
#Bioinformatics

John Lees @bacpop.org · 22d

EMBL International PhD Programme – Unique in the world and waiting for you!

www.embl.org

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Reposted by Carlos Serna

Sam Horsfield @samuelhorsfield.bsky.social · 28d

A little tool I've developed: ExpEvoAnalyzer (github.com/samhorsfield...) - a snakemake pipeline that compares isolate paired-read data from an experimental evolution study to a reference isolate, producing functionally-annotated SNPs in a presence/absence matrix.

GitHub - samhorsfield96/ExpEvoAnalyzer: A workflow to analyse experimental evolution data.

A workflow to analyse experimental evolution data. - samhorsfield96/ExpEvoAnalyzer

github.com

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Reposted by Carlos Serna

Zamin Iqbal @zaminiqbal.bsky.social · Sep 7

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling

Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

www.biorxiv.org

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Reposted by Carlos Serna

Michael Baym @baym.lol · Sep 1

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?

Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics

Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...

www.microbiologyresearch.org

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Reposted by Carlos Serna

Alicia Calvo-Villamañán @aliciapcv.bsky.social · Aug 20

This work is finally published! 🥳🧬
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens

Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...

rdcu.be

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Reposted by Carlos Serna

Allison Lopatkin, PhD @ajlopatkin.bsky.social · Aug 12

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today:

www.microbiologyresearch.org/content/jour...

Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae

The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...

www.microbiologyresearch.org

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Reposted by Carlos Serna

Alvaro San Millan @sanmillan.bsky.social · Aug 4

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

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Reposted by Carlos Serna

Nature Microbiology @natmicrobiol.nature.com · Jul 30

#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...

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...

www.nature.com

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Reposted by Carlos Serna

Hugh Cottingham @hughcottingham.bsky.social · Jul 30

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...

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Reposted by Carlos Serna

Kate Baker @ksbakes.bsky.social · Jul 27

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

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Reposted by Carlos Serna

Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 25

🚨🚨 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.

👇

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

academic.oup.com

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Carlos Serna @cserna.bsky.social · Jul 23

Muchas gracias Ana 😊😊

Reposted by Carlos Serna

Eduardo Rocha @epcrocha.bsky.social · Jul 23

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/...

graphical abstract of the article the extended mobility of plasmids

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Carlos Serna @cserna.bsky.social · Jul 23

Thanks Jose!!!

Reposted by Carlos Serna

Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 22

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)

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