Rob Moran

Rob Moran

@prob91.bsky.social

co-founder of ContamClub • plasmid fan • purveyor of artisanal bioinformatics

61 followers71 following16 posts

Rob Moran reposted

Dave Baltrus 🦦
@surtlab.bsky.social

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...

microbiologyresearch.orgIndependent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringaeInsertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strain...
Rob Moran
@prob91.bsky.social

[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!

Rob Moran
@prob91.bsky.social

[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!

Rob Moran
@prob91.bsky.social

[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! 😮

Rob Moran
@prob91.bsky.social

[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

Rob Moran
@prob91.bsky.social

[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 🍹

Rob Moran
@prob91.bsky.social

[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? 🤔

Rob Moran
@prob91.bsky.social

[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

Rob Moran
@prob91.bsky.social

[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

Rob Moran
@prob91.bsky.social

[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…

Rob Moran
@prob91.bsky.social

[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!

Rob Moran
@prob91.bsky.social

[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…

Rob Moran
@prob91.bsky.social

[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/...

journals.asm.orgIS26 and the IS26 family: versatile resistance gene movers and genome reorganizers | Microbiology and Molecular Biology ReviewsSUMMARYIn 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...

Rob Moran reposted

Willem van Schaik
@wvschaik.bsky.social

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?

Rob Moran reposted

Lilly Cummins
@lillycummins.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...

biorxiv.orgGenome 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...

Rob Moran reposted

Willem van Schaik
@wvschaik.bsky.social

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.orgIS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faeciumpRUM-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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