New Essay: 'Resistance potentiators: Evolutionary catalysts of antibiotic resistance' To understand the evolutionary drivers of #AMR we need to move beyond resistance genes to thinking about the ability of genomes to generate AMR variants. #microsky journals.plos.org/plosbiology/...

Resistance potentiators: Evolutionary catalysts of antibiotic resistance

How do bacteria evolve resistance to antibiotics? Drawing on evidence from experimental evolution, pathogen genomics, and molecular microbiology, this Essay argues that the evolution of antibiotic res...

journals.plos.org

New #microsky#AMR Perspective paper with @penamiller.bsky.social rdcu.be/fqBJo ANTIBIOTIC RESISTANCE (IE MIC) AND TOLERANCE ARE NOT BACTERIAL TRAITS! Please read on if you want an explanation for this provocative claim.

Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells

Nature Communications - Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells

rdcu.be

Evolutionary rescue in a phage community! New paper from former PhD student, Sam Greenrod, with brilliant colleague @craigmaclean.bsky.social : academic.oup.com/ismej/advanc...

Rapid adaptation accelerates competitive suppression in a parasite community

Abstract. Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites

academic.oup.com

Excited to share this new paper from the lab: academic.oup.com/ismej/articl...! See thread below

Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug-resistance plasmids

Abstract. Phage therapy offers an alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are promising the

academic.oup.com

Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6 cjm.sb-roscoff.fr/en/conferenc...

I have been reading through papers on evolution and microbes from the 1940s to 1960s. I have found some amazing work, but I am sure that there is much more that I haven’t found. Can you send me links to classic evolution+microbiology papers from pre Levin era?

And the preprint is out! www.biorxiv.org/content/10.6... We compared plasmid conjugation in liquid and on solid across 13 AMR plasmids with different types of conjugative pili.

Tatiana Dimitriu@tatianadimitriu.bsky.social · 4mo ago

First paper submitted fully from the lab!

Final version of our last paper is out! www.nature.com/articles/s41...

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology

Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.

nature.com

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…

Matthew J Shepherd@matthewjshepherd.bsky.social · 6mo ago

🚨 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)

Happy 38th birthday to the #LTEE! #BOTD in 1988. Keep on evolving! #science #evolution #microbiology

New #AMR pre-print Combining antibiotics with genotoxins can efficiently suppress bacterial in high throughput experimental models. www.biorxiv.org/content/10.6... Fun collaboration with Nassos Typas lab led by @mulkern.bsky.social

🧵 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...

New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

biorxiv.org

New pre-print with @wtmatlock.bsky.social!!! www.biorxiv.org/content/10.6... What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

🚨 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...

A four-year postdoc focusing on "plant growth-promoting bacteriophages" available in my group. Skills in metaviromics and metagenomics essential. Application deadline: 2.2.2026. For more info, see the link.

Postdoctoral Researcher in discovering the benefits of plant growth-promoting bacteriophages

Postdoctoral Researcher in discovering the benefits of plant growth-promoting bacteriophages

jobs.helsinki.fi

We've come full circle! I began my postdoctoral career by identifying the peptidyl deformylase gene. Today, we show that half of bacterial species harbor multiple PDF genes (up to 7, for always a single Met-tRNA transformylase), and while the role of these PDFs ... academic.oup.com/mbe/article/...

Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance

Abstract. Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despit

academic.oup.com

Good news for Canada and Canadian science. It is the right time to aggressively target top international and expatriate scientific talent. Although I am a blue skies scientist, I think that it is right to focus on research with societal and economic impact ... www.canada.ca/en/innovatio...

Just wrote my last grant review of 2025. UKRI: if you ask me to review another grant next week I will give it a 0 out of principle!

Back in Oxford, but still buzzing with excitement from #MicroEvo25 ! Great science, friendly and relaxed atmosphere, and a brilliant opportunity to catch up with friends and colleagues. Liverpool is a good place for scientific meetings.

Just finished reading this amazing history of biology by #massivelegendofscience Francois Jacob. Some of the evolutionary biology and microbiology is outdated, but the perspective is compelling and the breadth of scientific scholarship is amazing.

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Intracellular competition shapes plasmid population dynamics

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

science.org

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️ Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Liverpool on Fin...

PhD Project - MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Li...

findaphd.com

New paper: www.sciencedirect.com/science/arti... Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.

mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae

Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pne…

sciencedirect.com

I can't wait for the day that I see a paper entitled "One health papers on AMR are a major source of AMR"

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

rdcu.be

New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester) #phagesky#microsky www.biorxiv.org/content/10.1...

Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome

Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...

biorxiv.org

DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol... Nicolás Rascovan & colleagues @currentbiology.bsky.social

Three Bicentenary research fellowships on offer at @officialuom.bsky.social @fbmh-uom.bsky.social for exceptional ECRs with <3y postdoc experience 3yrs salary + £30k pa research expenses Do you have a great idea & want to join @mermanchester.bsky.social? www.bmh.manchester.ac.uk/research/sup...

New pre-print www.biorxiv.org/content/10.1... Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social! #phagesky#microsky

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage

Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...

biorxiv.org