Rob Moran
@prob91.bsky.social
co-founder of ContamClub • plasmid fan • purveyor of artisanal bioinformatics
😂 Thanks Ross, too kind!
December 19, 2025 at 5:33 AM
😂 Thanks Ross, too kind!
[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!
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!
December 18, 2025 at 7:46 AM
[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!
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!
[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!
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!
December 18, 2025 at 7:46 AM
[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!
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!
[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
This looked like the ancestor of pRUM, so we called it pCANE
December 18, 2025 at 7:46 AM
[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
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! 😮
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! 😮
December 18, 2025 at 7:46 AM
[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! 😮
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? 🤔
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? 🤔
December 18, 2025 at 7:46 AM
[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? 🤔
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? 🤔
[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 🍹
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 🍹
December 18, 2025 at 7:46 AM
[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 🍹
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 🍹
[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
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
December 18, 2025 at 7:46 AM
[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
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
[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
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
December 18, 2025 at 7:46 AM
[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
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!
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!
December 18, 2025 at 7:46 AM
[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!
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…
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…
December 18, 2025 at 7:46 AM
[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…
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/...
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/...
IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers | Microbiology and Molecular Biology Reviews
SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and sup...
journals.asm.org
December 18, 2025 at 7:46 AM
[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/...
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/...
[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…
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…
December 18, 2025 at 7:46 AM
[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…
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
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
December 18, 2025 at 7:46 AM
[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
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...
For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14]
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
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...
www.microbiologyresearch.org
December 18, 2025 at 7:46 AM
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...
For anyone interested in plasmid structures and the smaller MGEs that shape them 🧵👇 [1/14]
@microbiologysociety.org
www.microbiologyresearch.org/content/jour...
Reposted by Rob Moran
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
Genomic rearrangement of the capsule operon in a phylogenetically distinct cluster of the multi-drug resistant Escherichia coli lineage ST131 https://www.biorxiv.org/content/10.64898/2025.12.15.689991v1
December 16, 2025 at 7:52 PM
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
Reposted by Rob Moran
Maybe 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?
August 20, 2025 at 10:27 AM
Maybe 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?
Reposted by Rob Moran
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
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
August 9, 2025 at 2:44 PM
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
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
Reposted by Rob Moran
🚨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...
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...
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...
www.biorxiv.org
July 23, 2025 at 10:50 AM
🚨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...
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...
Reposted by Rob Moran
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
'IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium'
www.biorxiv.org/content/10.1...
/1
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...
www.biorxiv.org
July 17, 2025 at 8:39 AM
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
'IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium'
www.biorxiv.org/content/10.1...
/1