Craig MacLean
@craigmaclean.bsky.social
Scientist working on antibiotic resistance, evolution, and mobile genetic elements. Prof at U.Oxford and Fellow of All Souls College
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 Some of the evolutionary biology and microbiology is outdated, but the perspective is compelling and the breadth of scientific scholarship is amazing.
November 25, 2025 at 7:28 PM
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 Some of the evolutionary biology and microbiology is outdated, but the perspective is compelling and the breadth of scientific scholarship is amazing.
Reposted by Craig MacLean
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/...
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...
www.science.org
November 20, 2025 at 9:42 PM
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/...
www.science.org/doi/10.1126/...
Reposted by Craig MacLean
🚨#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...
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...
www.findaphd.com
November 18, 2025 at 9:38 AM
🚨#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...
Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...
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.
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…
www.sciencedirect.com
November 6, 2025 at 12:13 PM
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.
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.
I can't wait for the day that I see a paper entitled "One health papers on AMR are a major source of AMR"
October 29, 2025 at 9:58 PM
I can't wait for the day that I see a paper entitled "One health papers on AMR are a major source of AMR"
Reposted by Craig MacLean
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
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
January 8, 2025 at 1:19 PM
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
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
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...
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...
www.biorxiv.org
October 27, 2025 at 8:19 AM
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...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Reposted by Craig MacLean
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
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
October 24, 2025 at 3:00 PM
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
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Reposted by Craig MacLean
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...
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...
Bicentenary Early Career Research Fellowships | Biology, Medicine and Health | University of Manchester
Find out about and apply for a Bicentenary Early Career Research Fellowship.
www.bmh.manchester.ac.uk
October 9, 2025 at 8:48 PM
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...
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
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 ...
www.biorxiv.org
October 9, 2025 at 10:07 AM
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
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
Reposted by Craig MacLean
hosting.northumbria.ac.uk/nu-omics/vom...
#phagesky #phage #microsky
Come and join us for Viruses of Microbes UK 2026 at @northumbriauni.bsky.social ! Fantastic chance for ECRs to showcase their work 🙂
#phagesky #phage #microsky
Come and join us for Viruses of Microbes UK 2026 at @northumbriauni.bsky.social ! Fantastic chance for ECRs to showcase their work 🙂
VOM-UK Conferences - NU-OMICS
Viruses of Microbes UK (VoM-UK) Conference The Virus of Microbes UK (VoM-UK) Conference is hosted by Microbiome Excellence Peak of Excellence at Northumbria University. This two-day conference takes place annually at the end of January/beginning of February and is a chance for researchers to gather and share their knowledge. The VoM-UK conference is designed to […]
hosting.northumbria.ac.uk
October 9, 2025 at 9:21 AM
hosting.northumbria.ac.uk/nu-omics/vom...
#phagesky #phage #microsky
Come and join us for Viruses of Microbes UK 2026 at @northumbriauni.bsky.social ! Fantastic chance for ECRs to showcase their work 🙂
#phagesky #phage #microsky
Come and join us for Viruses of Microbes UK 2026 at @northumbriauni.bsky.social ! Fantastic chance for ECRs to showcase their work 🙂
Interesting job opportunity:
duunitori.fi/tyopaikat/ty...
duunitori.fi/tyopaikat/ty...
Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori
Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!
duunitori.fi
October 2, 2025 at 6:49 AM
Interesting job opportunity:
duunitori.fi/tyopaikat/ty...
duunitori.fi/tyopaikat/ty...
Reposted by Craig MacLean
Now published in @natcomms.nature.com 🎉
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
September 30, 2025 at 4:21 PM
Now published in @natcomms.nature.com 🎉
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
www.nature.com/articles/s41...
With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
New pre-print
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky
www.biorxiv.org/content/10.1...
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky
www.biorxiv.org/content/10.1...
www.biorxiv.org
September 30, 2025 at 3:16 PM
New pre-print
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky
www.biorxiv.org/content/10.1...
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky
www.biorxiv.org/content/10.1...
Reposted by Craig MacLean
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV
Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...
www.biorxiv.org
September 29, 2025 at 7:45 PM
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
New pre-print: Eco-evolutionary responses of phage to different thermal regimes.
Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2
www.biorxiv.org/content/10.1...
Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2
www.biorxiv.org/content/10.1...
Evolutionary rescue accelerates competitive exclusion in a parasite community
Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...
www.biorxiv.org
September 29, 2025 at 1:54 PM
New pre-print: Eco-evolutionary responses of phage to different thermal regimes.
Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2
www.biorxiv.org/content/10.1...
Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
1/2
www.biorxiv.org/content/10.1...
Reposted by Craig MacLean
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Craig MacLean
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
royalsocietypublishing.org
September 25, 2025 at 1:55 PM
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
September 25, 2025 at 2:31 PM
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...
my.corehr.com/pls/uoxrecru...
Reposted by Craig MacLean
Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
September 10, 2025 at 3:40 PM
Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
Reposted by Craig MacLean
Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
By solving a previously unsolved biological question, the AI co-scientist predicted
a complex mechanism of gene transfer and generated hypotheses that opened new research
directions, illustrating AI's...
www.cell.com
September 9, 2025 at 5:23 PM
Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
Reposted by Craig MacLean
Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization
Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails
from unrelated species to transfer their DNA across bacterial hosts. This tail piracy
enables broad dissemination and ...
www.cell.com
September 9, 2025 at 5:05 PM
Thrilled to share our two latest papers with the @tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
This looks like a must read …
August 13, 2025 at 10:19 PM
This looks like a must read …
Reposted by Craig MacLean
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
August 13, 2025 at 10:41 AM
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance genes and phage defense systems in E. coli
Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...
www.biorxiv.org
July 29, 2025 at 1:28 PM
New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....