Paul Johnston
@paulrjohnston.bsky.social
School of Medicine, University of St Andrews
https://scholar.google.de/citations?hl=en&user=YKzmUT8AAAAJ&view_op=list_works&sortby=pubdate
https://scholar.google.de/citations?hl=en&user=YKzmUT8AAAAJ&view_op=list_works&sortby=pubdate
Reposted by Paul Johnston
📣New preprint alert! We report the alarming finding that stringent response mutations found in clinical isolates increase the frequency of donation of multiresistance plasmids in S. aureus 😱 Great team effort @microclaire.bsky.social @paulrjohnston.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 13, 2025 at 12:41 PM
📣New preprint alert! We report the alarming finding that stringent response mutations found in clinical isolates increase the frequency of donation of multiresistance plasmids in S. aureus 😱 Great team effort @microclaire.bsky.social @paulrjohnston.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Paul Johnston
Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...
Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients - Cell Death Discovery
Cell Death Discovery - Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients
www.nature.com
October 28, 2025 at 6:22 PM
Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...
Reposted by Paul Johnston
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance
Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...
doi.org
October 6, 2025 at 10:42 AM
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Reposted by Paul Johnston
📢Our review of the impact of bacterial purine synthesis on antibiotic tolerance and resistance expression is now out! A lot of food for thought and contrasting data from E. coli and S. aureus... 🤔
Read it here: rdcu.be/ezfQ7
Read it here: rdcu.be/ezfQ7
The impact of bacterial purine metabolism on antibiotic efficacy
npj Antimicrobials and Resistance - The impact of bacterial purine metabolism on antibiotic efficacy
rdcu.be
August 5, 2025 at 5:53 AM
📢Our review of the impact of bacterial purine synthesis on antibiotic tolerance and resistance expression is now out! A lot of food for thought and contrasting data from E. coli and S. aureus... 🤔
Read it here: rdcu.be/ezfQ7
Read it here: rdcu.be/ezfQ7
Reposted by Paul Johnston
Jo Hobbs @hobbslabmicro.bsky.social has a 12 month Postdoc available on mechanisms of antibiotic tolerance. More details here: www.vacancies.st-andrews.ac.uk/Vacancies/W/...
July 16, 2025 at 10:44 AM
Jo Hobbs @hobbslabmicro.bsky.social has a 12 month Postdoc available on mechanisms of antibiotic tolerance. More details here: www.vacancies.st-andrews.ac.uk/Vacancies/W/...
Reposted by Paul Johnston
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Dropbox
tinyurl.com
June 12, 2025 at 11:26 AM
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Reposted by Paul Johnston
ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
Ish: SIMD and GPU Accelerated Local and Semi-Global Alignment as a CLI Filtering Tool https://www.biorxiv.org/content/10.1101/2025.06.04.657890v1
June 9, 2025 at 1:05 PM
ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
Reposted by Paul Johnston
We are still looking for a motivated student to join us in the wonderful world of mosquito microbiome genomies! Funding unfortunately only for UK students for this one. If interested, please send CV & letter of motivation (email in image below) #MicroSky #MicrobiomeSky 💻🧬 🧪Please share widely😊 1/2
#PhD alert, here @unistrathclyde.bsky.social in the very friendly, diverse, artsy & welcoming city of Glasgow 🏴
Disentangling the functional modules of #mosquito #microbiomes - what puzzle pieces build our #holobionts?
#MicroSky #MicrobiomeSky 💻🧬🧪
More here 😊 www.strath.ac.uk/studywithus/...
Disentangling the functional modules of #mosquito #microbiomes - what puzzle pieces build our #holobionts?
#MicroSky #MicrobiomeSky 💻🧬🧪
More here 😊 www.strath.ac.uk/studywithus/...
June 5, 2025 at 9:34 AM
We are still looking for a motivated student to join us in the wonderful world of mosquito microbiome genomies! Funding unfortunately only for UK students for this one. If interested, please send CV & letter of motivation (email in image below) #MicroSky #MicrobiomeSky 💻🧬 🧪Please share widely😊 1/2
Reposted by Paul Johnston
Our subclustering and transmission pipeline, PopPIPE has now been published:
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Integrated population clustering and genomic epidemiology with PopPIPE
Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission...
www.microbiologyresearch.org
April 30, 2025 at 4:36 PM
Our subclustering and transmission pipeline, PopPIPE has now been published:
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Paul Johnston
📣 The Journal of Medical Microbiology is looking for Editors for the Antimicrobial Resistance section! No prior editor experience required, so it's a great first gig for an ECR. And you get subsidised attendance at the annual meeting. Open to applicants worldwide 🌍 @microbiologysociety.org
April 30, 2025 at 9:42 AM
📣 The Journal of Medical Microbiology is looking for Editors for the Antimicrobial Resistance section! No prior editor experience required, so it's a great first gig for an ECR. And you get subsidised attendance at the annual meeting. Open to applicants worldwide 🌍 @microbiologysociety.org
Reposted by Paul Johnston
My nightmare in #eDNA is to detect a rare or threatened species that turns out to be a false positive, so we set out to evaluate some of the commonly used taxonomic classifiers.
The results are finally out: onlinelibrary.wiley.com/doi/full/10....
1/3
The results are finally out: onlinelibrary.wiley.com/doi/full/10....
1/3
A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies
Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic app...
onlinelibrary.wiley.com
April 23, 2025 at 1:27 AM
My nightmare in #eDNA is to detect a rare or threatened species that turns out to be a false positive, so we set out to evaluate some of the commonly used taxonomic classifiers.
The results are finally out: onlinelibrary.wiley.com/doi/full/10....
1/3
The results are finally out: onlinelibrary.wiley.com/doi/full/10....
1/3
Reposted by Paul Johnston
www.findaphd.com/phds/project...
A funded PhD studentship is available for a joint project between my lab and @andreashaag.bsky.social @uniofstandrews.bsky.social
A funded PhD studentship is available for a joint project between my lab and @andreashaag.bsky.social @uniofstandrews.bsky.social
Harnessing Bacterial Viruses to Combat Antibiotic-Resistant Infections at University of St Andrews on FindAPhD.com
PhD Project - Harnessing Bacterial Viruses to Combat Antibiotic-Resistant Infections at University of St Andrews, listed on FindAPhD.com
www.findaphd.com
March 31, 2025 at 2:08 PM
www.findaphd.com/phds/project...
A funded PhD studentship is available for a joint project between my lab and @andreashaag.bsky.social @uniofstandrews.bsky.social
A funded PhD studentship is available for a joint project between my lab and @andreashaag.bsky.social @uniofstandrews.bsky.social
Reposted by Paul Johnston
Preprint below has been a long time coming, here just in time for #microbio25 ! (if the train wifi lets me)
With @andrewmatthews.bsky.social
#MicroSky
🧵
With @andrewmatthews.bsky.social
#MicroSky
🧵
Stealth plasmids: rapid evolution of deleted plasmids can displace antibiotic resistance plasmids under selection for horizontal transmission. https://www.biorxiv.org/content/10.1101/2025.03.30.646151v1
March 31, 2025 at 1:10 PM
Preprint below has been a long time coming, here just in time for #microbio25 ! (if the train wifi lets me)
With @andrewmatthews.bsky.social
#MicroSky
🧵
With @andrewmatthews.bsky.social
#MicroSky
🧵
Reposted by Paul Johnston
Dear #genomics sky 🖥️🧬; does anyone know the earliest reference to the *compacted* de Bruijn graph? I have good initial reference for the de Bruijn graph (both the mathematical and genomics variants), but am having trouble finding an initial source for the compacted de Bruijn graph.
March 26, 2025 at 8:59 PM
Dear #genomics sky 🖥️🧬; does anyone know the earliest reference to the *compacted* de Bruijn graph? I have good initial reference for the de Bruijn graph (both the mathematical and genomics variants), but am having trouble finding an initial source for the compacted de Bruijn graph.
Reposted by Paul Johnston
New paper from our group in @pnas.org!! 🚀
Malte Mütter used our amazing liquid-handling robot to test different treatment strategies and found that combination therapy is the most effective to prevent the emergence of plasmid-mediated double resistance www.pnas.org/doi/10.1073/...
Malte Mütter used our amazing liquid-handling robot to test different treatment strategies and found that combination therapy is the most effective to prevent the emergence of plasmid-mediated double resistance www.pnas.org/doi/10.1073/...
The impact of treatment strategies on the epidemiological dynamics of plasmid-conferred antibiotic resistance | PNAS
The issue of antibiotic resistance is a critical concern for public health, prompting
numerous investigations into the impact of treatment strategi...
www.pnas.org
December 18, 2024 at 4:08 PM
New paper from our group in @pnas.org!! 🚀
Malte Mütter used our amazing liquid-handling robot to test different treatment strategies and found that combination therapy is the most effective to prevent the emergence of plasmid-mediated double resistance www.pnas.org/doi/10.1073/...
Malte Mütter used our amazing liquid-handling robot to test different treatment strategies and found that combination therapy is the most effective to prevent the emergence of plasmid-mediated double resistance www.pnas.org/doi/10.1073/...
Reposted by Paul Johnston
PhD opportunity in St Andrews on plasmids, antibiotics and defence systems, in collaboration with Helen Alexander in Edinburgh. Funding via BBSRC EastBio, please share & pass on to anyone interested! #microsky🦠🧫🧬
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
December 11, 2024 at 5:00 PM
PhD opportunity in St Andrews on plasmids, antibiotics and defence systems, in collaboration with Helen Alexander in Edinburgh. Funding via BBSRC EastBio, please share & pass on to anyone interested! #microsky🦠🧫🧬
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Reposted by Paul Johnston
New paper:
We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers.
www.sciencedirect.com/science/arti...
We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers.
www.sciencedirect.com/science/arti...
Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli
Biomedical research has implicated the bacterial metabolite colibactin as a causal risk factor for several cancer types, in particular, colorectal can…
www.sciencedirect.com
December 5, 2024 at 9:04 AM
New paper:
We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers.
www.sciencedirect.com/science/arti...
We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers.
www.sciencedirect.com/science/arti...
Reposted by Paul Johnston
Not sure if our recent manuscript made it onto this platform, if not here it is. Re-emerging chloramphenicol susceptibility in ESBL Enterobacterales from Malawi. A good news # AMR story
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase-producing Enterobacterales - Nature Communications
In this work, authors probe the molecular mechanism of re-emerging CHL susceptibility in Malawian Enterobacterales isolates, where they identify a stable truncation of resistance genes by insertion se...
www.nature.com
December 3, 2024 at 11:48 AM
Not sure if our recent manuscript made it onto this platform, if not here it is. Re-emerging chloramphenicol susceptibility in ESBL Enterobacterales from Malawi. A good news # AMR story
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Paul Johnston
Sharing new tools made by Artyom Egorov in my group!
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
October 24, 2024 at 11:12 AM
Sharing new tools made by Artyom Egorov in my group!
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
Reposted by Paul Johnston
📣 New perspective paper: Insights into durability against resistance from the antibiotic nitrofurantoin
We discuss what makes nitrofurantoin robust against resistance evolution, in spite of prolonged and extensive usage against UTIs #MicroSky
Open access/CC-BY-4.0: www.nature.com/articles/s44...
We discuss what makes nitrofurantoin robust against resistance evolution, in spite of prolonged and extensive usage against UTIs #MicroSky
Open access/CC-BY-4.0: www.nature.com/articles/s44...
Insights into durability against resistance from the antibiotic nitrofurantoin - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Insights into durability against resistance from the antibiotic nitrofurantoin
www.nature.com
November 25, 2024 at 8:41 AM
📣 New perspective paper: Insights into durability against resistance from the antibiotic nitrofurantoin
We discuss what makes nitrofurantoin robust against resistance evolution, in spite of prolonged and extensive usage against UTIs #MicroSky
Open access/CC-BY-4.0: www.nature.com/articles/s44...
We discuss what makes nitrofurantoin robust against resistance evolution, in spite of prolonged and extensive usage against UTIs #MicroSky
Open access/CC-BY-4.0: www.nature.com/articles/s44...
Reposted by Paul Johnston
Following a suggestion from @benecal.bsky.social I will refer to these threads as "skeetorials" and will use this gif logo.
Today's skeetorial is about the NIH Director's New Innovator Award with three different heroes (all in government).
1/n
Today's skeetorial is about the NIH Director's New Innovator Award with three different heroes (all in government).
1/n
a cartoon of homer simpson holding a card
ALT: a cartoon of homer simpson holding a card
media.tenor.com
November 23, 2024 at 1:05 PM
Following a suggestion from @benecal.bsky.social I will refer to these threads as "skeetorials" and will use this gif logo.
Today's skeetorial is about the NIH Director's New Innovator Award with three different heroes (all in government).
1/n
Today's skeetorial is about the NIH Director's New Innovator Award with three different heroes (all in government).
1/n
Reposted by Paul Johnston
"I knew a premature VHF diagnosis could cause panic and have profound political implications." – A very strong piece in NEJM by Dr JP Sibomana on the personal and political complexity of diagnosing Rwanda’s first Marburg outbreak. doi.org/10.1056/NEJMp2413951
Fight or Flight — Facing the Marburg Outbreak in Rwanda | NEJM
Having diagnosed two ICU patients with the first known cases of Marburg virus disease
in Rwanda, a physician must prioritize limiting spread, despite pleas for transfer
from the patients’ families.
doi.org
November 21, 2024 at 4:23 PM
"I knew a premature VHF diagnosis could cause panic and have profound political implications." – A very strong piece in NEJM by Dr JP Sibomana on the personal and political complexity of diagnosing Rwanda’s first Marburg outbreak. doi.org/10.1056/NEJMp2413951
Reposted by Paul Johnston
Are you applying RNA-seq or TraDIS/Tn-seq to antibiotic-treated bacteria? Our paper from earlier this year with @flamycain.bsky.social shows that antibiotic interference with chromosome replication can confound functional genomics analyses! Thread 1/n journals.asm.org/doi/full/10....
A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria | mSystems
Altered gene dosage due to changes in DNA replication has been observed under a variety
of stresses with a variety of experimental techniques. However, the implications of
changes in gene dosage for s...
journals.asm.org
November 19, 2024 at 3:39 PM
Are you applying RNA-seq or TraDIS/Tn-seq to antibiotic-treated bacteria? Our paper from earlier this year with @flamycain.bsky.social shows that antibiotic interference with chromosome replication can confound functional genomics analyses! Thread 1/n journals.asm.org/doi/full/10....