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Freya Allen

@freyaallen.bsky.social
171 followers 252 following 3 posts

Postdoc at the University of Birmingham | Evolution and AMR

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Reposted by Freya Allen
Grainger Lab @graingerlab.bsky.social · 21/08/2026
A new pre-print out - we show that promoters and terminators of transcription are frequently coupled, throughout the bacteria, and this is regulatory. www.biorxiv.org/content/10.6...
biorxiv.org
Widespread coupling of promoters and terminators of transcription in bacteria
Transcription underpins the expression of genetic information and is viewed as a series of independent initiation and termination events. In bacteria, promoters and terminators of transcription are th...
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Freya Allen @freyaallen.bsky.social · 05/08/2026
Great first two days at #MEEhubs26 in Manchester, looking forward to the third day of talks!
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Reposted by Freya Allen
Alan McNally @alanmcn1.bsky.social · 19/03/2026
Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...
sciencedirect.com
Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis
Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…
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Reposted by Freya Allen
Willem van Schaik @wvschaik.bsky.social · 18/03/2026
Important study by Chris Connor and Ben Howden (both not on here?) @unimelb.edu.au 'Global dissemination of optrA-mediated linezolid resistance in enterococci', major roles of mobile genetic elements in the dissemination of this important resistance determinant academic.oup.com/jac/article/...
academic.oup.com
Global dissemination of optrA-mediated linezolid resistance in enterococci
AbstractObjectives. Acquired resistance to last-line linezolid has emerged in Enterococcus spp. and can be conferred by the optrA gene. Here, we study the
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Reposted by Freya Allen
Freya Harrison @friendlymicrobe.bsky.social · 05/03/2026
If you check out my lab's recent work, you'll notice how much biofilm structure is destroyed by dehydration & vacuum during standard scanning electron microscopy. These are both images of P. aeruginosa PA14 #biofilm on pig lung tissue at 48h p.i: using cryoSEM retains the biofilm matrix. #MicroSky
In the standard SEM image, aggregates of bacterial cells with no visible matrix sit on top of a network of collagen fibrils. In the cryo image, interconnected aggregates are covered with a smooth coat of matrix, and no collagen is visible - it is under the aggregates, and the only tissue structures visible are patches of elastin fibres.
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Reposted by Freya Allen
Freya Harrison @friendlymicrobe.bsky.social · 05/03/2026
Paper out! We used RNAseq to track changes in P. aeruginosa gene expression over 7 days of #biofilm infection in our #CysticFibrosis lung model. www.microbiologyresearch.org/content/jour... #MicroSky (1/n)
A four-panel figure showing scanning electron micrographs of Pseudomonas biofilm on the surface of pig lung tissue. Aggregates of bacteria sit on top of a network of collagen fibrils, with some bacterial cells penetrating the collagen mesh.
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Reposted by Freya Allen
Lilly Cummins @lillycummins.bsky.social · 02/03/2026
I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts! rdcu.be/e6pHY
rdcu.be
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...
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Reposted by Freya Allen
Rob Fagan @robfagan.bsky.social · 19/02/2026
New paper from us. If you're interested in genetic manipulation of Clostridia, we have a few new tools for you! 36 new plasmids - all available from @addgene.bsky.social www.microbiologyresearch.org/content/jour... #microsky
microbiologyresearch.org
A set of genetic tools for use in Clostridioides difficile and related species
The Clostridia are a phylogenetically diverse group of anaerobic, spore-forming bacteria that include species of medical, veterinary and industrial importance. The last two decades have seen major adv...
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Reposted by Freya Allen
Dr Ross McInnes @roscobacterium.bsky.social · 18/12/2025
Amazing work from @freyaallen.bsky.social and @prob91.bsky.social. I truly believe that Rob is the Sherlock Holmes of MGEs and one of the leaders in the field of artisanal bioinformatics😉!
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Reposted by Freya Allen
Rob Moran @prob91.bsky.social · 18/12/2025
Our new paper in MGen traces the evolution of a plasmid lineage associated with MDR in Enterococcus faecium, primarily driven by IS1216 For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14] @microbiologysociety.org www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium
pRUM-like plasmids are commonly found in multidrug-resistant Enterococcus faecium, but the evolution of these plasmids has not been characterised in detail. When we analysed the genome sequences of tw...
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Reposted by Freya Allen
Willem van Schaik @wvschaik.bsky.social · 08/11/2025
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews academic.oup.com/femsre/advan... (accepted manuscript version) TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com
Resistance to last-resort antibiotics in enterococci
Abstract. The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The
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Reposted by Freya Allen
Willem van Schaik @wvschaik.bsky.social · 06/11/2025
Absolutely delighted (and proud) that @freyaallen.bsky.social passed her viva with minor corrections today. Thanks very much @jessicamablair.bsky.social @robfagan.bsky.social for examining!
From left to right: Willem, Freya, Jess and Rob.

We are standing in front of a wall with a congratulations banner and some left-over Halloween decorations.
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Reposted by Freya Allen
Lilly Cummins @lillycummins.bsky.social · 23/07/2025
🚨New pre-print 🚨 We introduce our new tool GOLD-GWAS and demonstrate its use by digging into the evolution of MRSA facilitated by SCCmec This work was led by talented PhD student @seungwonko.bsky.social who did most of the computational heavylifting 1/n www.biorxiv.org/content/10.1...
biorxiv.org
Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus (MRSA)
Background: Antimicrobial resistance (AMR) in bacterial pathogens is a major threat to global health, rendering standard treatments ineffective and increasing the risk of severe infection or death. Re...
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Reposted by Freya Allen
Cassie Bakshani @cassiebakshani.bsky.social · 18/07/2025
🚨 New preprint klaxon 🚨 We characterised the structure of a PNGaseA superfamily member from Bifidobacterium bifidum LMG13195 and highlight its preference for N-glycan structures attached to a peptide, rather than to a native or denatured protein 💫 @imibirmingham.bsky.social
biorxiv.org
PNGaseA-mediated N-glycan stripping from peptides by infant-derived Bifidobacterium bifidum
N-glycans are highly common sources of nutrition for human colonic-dwelling bacteria. These microbes have evolved a several methods to remove N-glycans from proteins; herein we describe the biochemica...
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Reposted by Freya Allen
Willem van Schaik @wvschaik.bsky.social · 17/07/2025
New manuscript from the group 'IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium' www.biorxiv.org/content/10.1... /1
biorxiv.org
IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium
pRUM-like plasmids are commonly found in multidrug-resistant Enterococcus faecium , but the evolution of these plasmids has not been characterised in detail. When we analysed the genome sequences of t...
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