Hey y’all,
New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae
www.microbiologyresearch.org/content/jour...
Hey y’all,
New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae
www.microbiologyresearch.org/content/jour...
MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI
18.02.2026 12:16 — 👍 39 🔁 28 💬 2 📌 1Shite database shite output. Level of interpretation of output can lead to torrent of shite.
18.02.2026 20:08 — 👍 2 🔁 1 💬 1 📌 0😂 Thanks Ross, too kind!
19.12.2025 05:33 — 👍 1 🔁 0 💬 0 📌 0
Schematic overview of ongoing pRUM-like plasmid evolution. At the centre of the figure is a basic pRUM-like structure, which is surrounded by other genetic elements that can contribute to its evolution. Other elements are linked to the pRUM-like structure by arrows that represent their acquisition or loss, with labels describing the mechanisms involved. These include: small MGEs inserting into the pRUM-like structure, IS1216 from the pRUM-like accessory region mediating adjacent backbone deletions, small plasmids being integrated into pRUM-like structures through IS1216 copy-in cointegrate formation, larger IS1216-containing plasmids or free IS1216 translocatable units being integrated through IS1216 targeted conservative cointegrate formation, and IS1216 translocatable unit loss or cointegrate plasmid resolution via homologous recombination.
[14/14] pRUM-like plasmids continue to diversify through the actions of IS1216 and other small MGEs
These adaptable MDR platforms contribute to the success of CC17 E. faecium, and have the potential to enter other clones, species or genera through cointegrate formation + HGT
Thanks for reading!
Schematic outlining our hypothesis for the evolution of pRUM-like plasmids from a pCANE-like ancestor. In part A, a pCANE like structure acquires an IS1216 translocatable unit to generate an intermediate structure called pMOLASSES. In part B, a pMOLASSES structure undergoes IS1216-mediated deletion events that remove parts of its backbone to generate a pRUM-like structure.
[13/14] We propose a model for the IS1216-mediated evolution of the pRUM-like lineage from pCANE via an intermediate we call pMOLASSES
This seems to have involved an evolutionary trade-off, swapping transfer ability for the plasticity of the IS1216 accessory region 🤔 more on this in the paper!
Alignment of pRUM and pCANE, showing that pCANE includes a near-perfect match to the entire pRUM-like backbone, plus additional backbone instead of the pRUM accessory region. The additional backbone segment includes putative conjugative transfer determinants (for pilus formation, a coupling protein, ATPase, a relaxase) and establishments determinants (anti-resistriction and single-stranded DNA-binding)
[12/14] The 1990s plasmid matched the pRUM backbone almost perfectly, but it was larger and didn’t contain IS1216… instead of an accessory region, it had 44 kb that looked like backbone and contained putative conjugation determinants 🚀
This looked like the ancestor of pRUM, so we called it pCANE
[11/14] At this point the story strays into a bit of plasmid archaeology…
For her PhD, @freyaallen.bsky.social was working on a ST17 vancomycin-sensitive E. faecium from the 1990s, and she wondered, does it have a pRUM-like plasmid?
It does, but what we found surprised us! 😮
[10/14] Since 2019 I'd wondered, what did the pRUM-like lineage emerge from?
The accessory region wasn’t flanked by a target site duplication, which suggested some backbone had been lost in old IS1216-mediated deletions… but how much? What was lost, and what would an ancestral plasmid look like? 🤔
Overview of pRUM-like plasmid structures showing notable variants generated by IS1216 activity, including the acquisition of entire small plasmids, or parts of larger plasmids (most notably examples usually found in species or genera other than E. faecium)
[9/14] Importantly, we saw lots of cointegrate formation, generating structures comprised of parts from usually distinct plasmids
IS26 family elements are great at this!
Several small plasmids have been rolled into pRUM-like structures, including pCOLA and pDRY, named after popular rum mixers 🍹
Map of a representative pRUM-like plasmid backbone with variation marked across it, including insertions in the backbone, antibiotic resistane genes and plasmid replicons found in the accessory region, and backbone deletions extending out from the IS1216 at the boundaries of the accessory region
[8/14] Examining plasmid structures revealed enormous variation!
Most was in the accessory region, which ranged in size from 809 bp (a lone IS1216) to 285 kb, and included all sorts of acquired genes
Multiple IS1216-mediated deletions have also removed adjacent parts of the backbone
Bar chart showing the numbers of pRUM like plasmids found in Enterococcus faecium of various sequence types - the bars are coloured to show the sources of isolation for E. faecium hosts, which include various human clinical samples, human or animal faeces, pet food, or marine sediment
[7/14] We screened GenBank and found 150 complete pRUM-like plasmid sequences
Their mostly E. faecium hosts were isolated from various sources around the world, and represented an array of STs… though all but one were E. faecium CC17
[6/14] Over the years I spoke a lot about wanting to finish this, but the reality of side projects is it’s just hard to find the time…
This one revived in 2023 when @freyaallen.bsky.social, always interested in evolution, wanted to learn about these MGEs, giving the project the kickstart it needed!
[5/14] The pHHEf1/pHHEf2 variation had all the hallmarks of IS1216 activity, but was this the extent of it? Or was there more variation in this accessory region?
We’d need to examine more pRUM-like plasmid structures, which I started in 2019, but this project soon fell behind a lot of others…
[4/14] Why is IS1216 important? It’s part of the IS26 family!
IS26 is a major driver of MDR in Gram-negative pathogens, and I’ve worked on it or structures impacted by it across various projects since 2012...
Check out Harmer and Hall’s review to learn more: journals.asm.org/doi/10.1128/...
Two circular plasmid maps - their backbone is the same, but they have accessory regions that contain different things - vancomycin resistance genes in pHHEf1, and ertythromycin/aminglycoside resistance genes + the integrated small plasmid pCOLA in pHHEf2.... below the circular maps is a linear alignment of the plasmid sequences that confirms their backbones are the same, but their accessory regions, although located in the same backbone position, are completely different
[3/14] Two plasmids caught my eye: pHHEf1 and pHHEf2
Their pRUM-like backbones were identical, with ARG-bearing accessory regions in exactly the same position, but the content of those regions was totally different!
Strikingly, both were bounded by copies of the insertion sequence IS1216…
[2/14] @roscobacterium.bsky.social and @wvschaik.bsky.social introduced me (a Gram-negative person) to the world of enterococci when I joined UoB in 2019…
They asked if I was interested in looking at plasmids in local clinical isolate genomes, and of course I was keen to explore Gram-positive MGEs
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...
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
16.12.2025 19:52 — 👍 12 🔁 9 💬 0 📌 0Maybe I am being grumpy, but can people please stop using poorly curated databases of antibiotic resistance genes (I am looking at you, DeepARG) on shotgun metagenomic data and then present these results without any reflection on their validity, or shortcomings of databases?
20.08.2025 10:27 — 👍 54 🔁 10 💬 4 📌 0
Happy Noodlococcus day to all those who celebrate! 🍜🧫🦠
We’re in 3 different continents now but all celebrating the 6th anniversary of the discovery of our noodle-y friend by eating some delicious noodles @prob91.bsky.social @biostan.bsky.social @gemccallum.bsky.social
🚨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...
Thanks David!
18.07.2025 14:25 — 👍 1 🔁 0 💬 0 📌 0
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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