Carlos Serna

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

New paper out in @pnas.org, and it made the cover! 👁️

We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.

‼️Check Paula’s 🧵 and the paper👇

𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...

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...

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions The human pathogen Streptococcus pneumoniae is a major cause of disease, including pneumonia and meningitis. The introduction of Pneumococcal Conjugate Vaccines (PCVs) initially reduced the burden of ...

Very happy to share our preprint on a mathematical model for Streptococcus pneumoniae population dynamics after vaccine introductions. It's a reusable model that describes vaccine replacement dynamics and can help to determine strategies for genomic surveillance: doi.org/10.64898/2025.12.18.695090

What drives the K. pneumoniae species complex (KpSC) to thrive from hospitals to soils? In this study, we investigate how pangenome structure and functional diversity shape KpSC adaptability across phylogenetic and ecological contexts. (Thread)
www.biorxiv.org/content/10.6...

A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample

Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status - Nature Communications Here, using samples from ~1,100 individuals, the authors define the nasal microbiome linked to Staphylococcus aureus colonization, identifying seven communities- either S. aureus-dominated or dominate...

Read 'Large-scale characterization of the nasal microbiome redefines Staphylococcus aureus colonization status' from @sangerinstitute.bsky.social, @cam.ac.uk, @imperialcollegeldn.bsky.social and their collaborators in @natcomms.nature.com here ⬇️
www.nature.com/articles/s41...

🧬 A new “Life Identification Number (LIN)” system aims to modernize bacterial classification with a clearer, more stable hierarchy. A step forward for genomic taxonomy!
📖 shorturl.at/vkQuS
✍️ @sylvainbrisse.bsky.social & coll.

@pasteur.fr @ox.ac.uk @monashuniversity.bsky.social @lshtm.bsky.social

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.

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...

🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.

Now published in @natcomms.nature.com rdcu.be/eOf63

Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae Competition significantly influences bacterial population dynamics, particularly in how strains interact within and between hosts. This study shows that within-host competition in Streptococcus pneumo...

New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...

Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments: a nationwide analysis of closed Enterobacterales genomes - Nature Communications Plasmid-mediated transmission plays a significant role in the spread of carbapenem-resistant Enterobacterales. Here, analyzing 1,115 carbapenemase-producing plasmids from Singapore, the authors sugges...

Delighted to have played a small part in this great study from colleagues in CaPES: doi.org/10.1038/s414...

Antimicrobial resistance among Gram-positive agents of bacteraemia in the UK and Ireland: trends from 2001 to 2019 - PubMed Gram-positive pathogens were the dominant historical pathogens of bacteraemia. The trends seen here-with many near-universally active antibiotics-indicate little hazard of this situation returning. Nevertheless, few treatments exist in some settings, notably multi-resistant E. faecium endocarditis.

Interesting paper

'Antimicrobial resistance among Gram-positive agents of bacteraemia in the UK and Ireland: trends from 2001 to 2019'

TL;DR:
- dramatic falls in MRSA
- pneumococcal resistance rates low
- E. faecium more prevalent (and more vanR) than E. faecalis

pubmed.ncbi.nlm.nih.gov/41140273/

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...

🧬 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

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...

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👇

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 ;-)

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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.

A plasmid and an ICE teaming up... 🤯😱

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

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...

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.

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...

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...

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.
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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

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

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

#MathematicalModelling
#BacterialGenomics
#Bioinformatics

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.

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...

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...

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...

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...

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...

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