How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
Super-excited to be organising the first in-person meeting of the @target-amr.bsky.social network today and tomorrow.
We will be launching an initiative for pump-priming and an amazing comic by Eddie Ross on AMR Genomics
Happy to share that our latest research on the eco-evolutionary dynamics of MDR plasmids and PDPs is now out (open access vAuthor) in The ISME Journal doi.org/10.1093/isme...
Here, we explored how plasmid-dependent phages (PDPs) act as a selective pressure against the spread of multidrug resistance
Less than 1 week to apply for this postdoc!
If you want to find out more about the project have a look at our recent preprint: www.biorxiv.org/content/10.6...#mevosky
Why does antibiotic resistance evolution vary between patients?
Come to @officialuom.bsky.social@mermanchester.bsky.social to help us find out!
2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution
Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...
Bacterial immune proteins have repeatedly evolved to become parts of eukaryotic immunity. But how?
Our new preprint uncovers a recent horizontal transfer event & shows how eukaryotes co-opted a toxic bacterial immune protein 🦠🧪🧵 1/
Interested in working on the evolution of photosynthetic endosymbioses? Come join us!
I have 2 open positions in my new group @cemess.bsky.social in Vienna
3yr postdoc info: tinyurl.com/4emkjpn4
4yr PhD info: tinyurl.com/mtxmsjpy
Apply by 1st June!
Please share/repost
#Protists#Symbiosis#PhD
Here’s the latest preprint from my work on evolved resistance to Type VI Secretion system (T6SS) weaponry, funded by a @wellcometrust.bsky.social Sir Henry Wellcome Fellowship. So happy to see this out!
www.biorxiv.org/content/10.6...
Very excited to announce that we are hiring for three faculty positions at @universityofleeds.bsky.social in @bioscienceleeds.bsky.social: A/Prof Plant Science, A/Prof Animal Biology and Lecturer in Ecology, Zoology, Biodiversity or Ecosystem Management. Please do get in touch to chat. Links below:
🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process.
www.biorxiv.org/content/10.6...
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).
A brief 🧵 (carried over from the old place)
A study in Nature shows that the single-celled form of a tiny, aquatic organism can turn into a multicellular version by three different routes. The discovery adds insight to the possible origins of multicellular life, suggesting a previously unrecognized degree of flexibility. 🧪
Pleased to finally share this fun collab that began at #Ento23@cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun).
Horizontal transfer of an #AntimicrobialPeptide across insects
bit.ly/DrsHGT
1/🧵
CBASS is a cyclic nucleotide-based antiviral system in bacteria that is related to cGAS-STING signaling in animals. One of the big questions is how CBASS is activated during phage infection? We made some progress on this during my final year in the Kranzusch lab.
www.biorxiv.org/content/10.6...
Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes
www.science.org/doi/10.1126/...
Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!
Linking below previous thread on our findings
📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!
We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.
Found 3 new families targeting immune signaling!
#MicroSky Please RT
@erc.europa.eu-funded postdoc position in my lab to identify the molecular basis of prey-predator interactions using our favorite micro-vampire Bdellovibrio exovorus as a model.
Let's find what the bite is made of! 🧛
Flexible start date.
Info: euraxess.ec.europa.eu/jobs/415877
New post-doctoral research position in my phage-host interactions (Phi) laboratory in @otagomicroimmuno.bsky.social at @universityofotago.bsky.social New Zealand. The project is focused on defences against jumbo phages. Please share and if interested apply using the link in the comments.
Phage therapy offers a powerful tool against AMR infections—but only if we move from isolated cases to coordinated systems. The first initiative of the ASM Health Unit, led by Colleen Kraft and Dev Mittar, will tackle this. Delighted by this scientific leadership, join us!
asm.org/about-asm/as...
New preprint out on bioRxiv!
www.biorxiv.org/content/10.6...
Can conjugative plasmids be used to control plasmid and pathogen spread?
Follow me down the rabbit hole that led to this story 🧵
Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...
New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!
Thank you Mike! I encourage your colleagues to join the new initiative from ASM Health to develop and execute on synergies with phage therapy. Would be great to involve multiple societies and NGO's here as appropriate, as we share common goals.
asm.org/about-asm/as...
Out now in @plosbiology.org : our big joint effort on the role of #CRISPR in plasmid competition. Read on for a really fun (I’m biased ok) analysis of how a defence system has new selective pressures when it’s mobile
journals.plos.org/plosbiology/... 1/6
Excited to share our new preprint exploring how Paramecium achieves diverse flow functions, i.e. feeding and swimming, simultaneously. This work was spearheaded by our ExM expert, PhD student Daphne Laan @daphnelaan.bsky.social :
www.biorxiv.org/content/10.6...
Up to what degree of interspecific genetic distance is it possible to form viable and fertile hybrids? A strange species of paramecium breaks the record:
www.biorxiv.org/content/10.6...
Alita Burmeister (@aburmeister.bsky.social) is looking to hire a postdoc (or potentially a PhD student) for projects on phage resistance and evolution. The position description is posted to the Eco-Evo Jobs wiki and also available on her lab's website (arburmeister.weebly.com).
Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution...
www.biorxiv.org/content/10.6...
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
Continuing to treat already resistant infections tends to drive ever higher resistance: evolution doesn’t stop at the breakpoint folks!
www.biorxiv.org/content/10.6...
Key take-aways:
There are lots of insights here for how to diagnose and manage resistance more effectively… but most important #1 for chronic infections is finding out if resistance is there BEFORE you start to treat! - doable, cheap, likely to delay resistance
www.biorxiv.org/content/10.6...
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
Key take-aways:
Resistance is costly. In some patients with high diversity this leads to oscillating resistance levels as susceptible and resistant subpopulations alternate driven by antibiotic selection on a resistance:growth trade off.
www.biorxiv.org/content/10.6...
But, in low diversity infections costs pose no barrier to increasing resistance, driven by recurrent selective sweeps of costly resistance mutations. As such, fitness trade-offs can be leveraged to reduce resistance provided there is ecological competition.
www.biorxiv.org/content/10.6...
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
Key take-aways:
Cipro resistance emerged by 3 main eco/evo mechanisms
1. Selection for pre-existing resistance
2. Spontaneous mutations
3. Immigration of resistant strains
OR complex combinations of multiple of these mechanisms
www.biorxiv.org/content/10.6...
Key take-aways:
Selection of pre-existing resistance predominated and accelerated emergence of breakpoint resistance relative to more stochastic processes of spontaneous mutations or strain immigration
www.biorxiv.org/content/10.6...
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
Fascinating and important study on Klebsiella plasmid diversity
'Plasmids from human, animal and marine [Klebsiella pneumoniae complex] isolates formed shared genetic clusters spanning ecological boundaries'
www.microbiologyresearch.org/content/jour...
Hoping to return to bluesky after a social media hiatus! Nice to start it off with some career updates - I've just started as a College for Life Sciences Fellow @wiko-berlin.bsky.social. Really excited to live+work in Berlin! Read about what i'll be up to here:
www.wiko-berlin.de/en/fellows/a...
📢📢📢Lectureships at Bristol!📢📢📢
We're hiring 3 x lecturers (=assistant professor) in Biological Sciences, across the discipline.
Great department, great colleagues, great building, great city
Details here:
www.bristol.ac.uk/jobs/find/de...
🚨 New preprint 🚨
How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence?
A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship!
www.biorxiv.org/content/10.6...
Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...
🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover.
🔗 www.biorxiv.org/content/10.6...
A short research stay in 2019 (back in the pre-COVID era) at José R. Penadés lab turned into the third chapter of my PhD and today it finally sees the light.