Freya Allen

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...

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

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...

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

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😉!

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...

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...

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

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.

Thanks Ross!!

Thanks Lisa!

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.

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!

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...

🚨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...

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...

🚨 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

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...

New manuscript from the group

'IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium'

www.biorxiv.org/content/10.1...

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