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Paul Johnston

@paulrjohnston.bsky.social
469 followers 2.5K following 12 posts

School of Medicine, University of St Andrews "Cynical and scathing" scholar.google.de/citations?hl=en&u…

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Reposted by Paul Johnston
Shreya Vichare @shreyavichare.bsky.social · 02/10/2026
It’s finally starting to feel real 🧬🌾 Preprint's out! @daganlab.bsky.social we asked: when does a plasmid stop being “accessory”? In Pantoea agglomerans, LPP1 promotes wheat-root colonization and is deeply integrated with chromosomal gene regulation and metabolism. www.biorxiv.org/content/10.6...
biorxiv.org
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Tatiana Dimitriu @tatianadimitriu.bsky.social · 20/08/2026
New paper led by Liam Shaw, with Arancha Peñil Celis, @aresarroyom.bsky.social, @adalijuanluo.bsky.social & Fernando de la Cruz. academic.oup.com/nar/article/... This is very much Liam’s story, but I loved playing a small part in it 🧵
academic.oup.com
The leading region of many plasmids is adapted for translational efficiency
Abstract. To successfully transfer, conjugative plasmids must overcome a recipient cell’s defence mechanisms. The leading region of many plasmids—the first
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Shaun Keegan @shaunkeegan.bsky.social · 22/07/2026
Additionally we explicitly explored the impact of a large scale change in behaviour (COVID-19 restrictions) on invasive meningococcal disease dynamics, exploring the pre-, during- and post-COVID eras. A pleasure to work on this study! Thank you to all involved! #EpiSky #IDSky #MicroSky #MedSky 🧪
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The Lancet Microbe @lancetmicrobe.bsky.social · 10/06/2026
New comment Genotype-based antimicrobial resistance tests need a new regulatory framework www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #OpenAccess #OA
Principles of genotype-based AMR diagnostic regulation
1.	
Contextualise performance claims: require stratified performance, where feasible, by geography, time window, and phylogenetic lineage, and transparent isolate sampling frames. Intended-use claims should match demonstrated coverage.
2.	
Make representativeness an evidentiary criterion: treat representativeness like sample size—as a formal element of evidentiary sufficiency. For broad indications, requirement of minimum coverage across regions, lineages, or demographic groups. When gaps remain, either narrow labelling or use staged indication expansion tied to new data.
3.	
Mandate prespecified post-market monitoring and re-evaluation: approval should be contingent on minimum confirmatory phenotyping rates among susceptible calls (potentially risk-stratified and geography-stratified), sentinel networks for intensive culture or phenotyping, and predefined triggers (eg, rising very major errors, detection of novel determinants) that prompt modification and review.
4.	
Create pathways for iterative updates: because rules or models should evolve, regulators should provide streamlined mechanisms for updating genotype–phenotype rules and algorithms, with clear expectations for evidence and re-evaluation. These pathways for iterative updates could reduce disincentives to improve tests rapidly.
5.	
Integrate with AMR surveillance systems: these diagnostics are at the intersection of clinical care and surveillance. Regulatory requirements should align with national and global AMR surveillance to support data sharing, standardised definitions, and rapid recognition of emerging mechanisms.
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Reposted by Paul Johnston
Alvaro San Millan @sanmillan.bsky.social · 13/03/2026
Final version of our last paper is out! www.nature.com/articles/s41...
nature.com
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.
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Yanying Yu @yanyingyu.bsky.social · 16/12/2025
Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...
dx.plos.org
Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance
Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...
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Reposted by Paul Johnston
PLOS Biology @plosbiology.org · 12/12/2025
Conjugative plasmids help spread AMR genes. @andrewmatthews.bsky.social @sonjalehtinen.bsky.social & @tatianadimitriu.bsky.social show that #AMR loss in evolving populations involves streamlined #plasmids that gain a transmission advantage by deleting AMR genes @plosbiology.org 🧪 plos.io/48NM0BL
 Evolved plasmid-carrying clones with high copy number contain a mix of full-length and streamlined plasmids. Left: summary of the initial experimental evolution design and nomenclature used for the evolved plasmid-carrying clones. Host strains had either wildtype (w) or increased (m) mutation rate. Treatment indicates the % of plasmid-free hosts added at each passage during evolution. Right: coverage map of evolved clones. Relative coverage of sequencing reads is shown for all clones across R1 sequence length (only the first 50 kb are shown). The AMR region and copies of IS1 are shown against the ancestral R1 (“anc” treatment) coverage map.
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Mat Beale @typemat12.bsky.social · 26/11/2025
New #MicroSky study showing extensive transmission of #AMR E coli transmission in East Africa under One Health framework, led by Patrick Musicha www.sanger.ac.uk/news_item/an...
sanger.ac.uk
Antimicrobial resistant bacteria and genes move freely between people, animals and the environment
By analysing Escherichia coli (E. coli) genomes, researchers have shown that antimicrobial resistant bacteria and the genes that confer resistance move between bacterial hosts and across ecological co...
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hobbslabmicro.bsky.social @hobbslabmicro.bsky.social · 13/11/2025
📣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...
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Tim De Pooter @timdepooter.bsky.social · 28/10/2025
Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...
nature.com
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
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Adrian Cazares @cazares-adr.bsky.social · 06/10/2025
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👇
doi.org
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...
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hobbslabmicro.bsky.social @hobbslabmicro.bsky.social · 05/08/2025
📢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
rdcu.be
The impact of bacterial purine metabolism on antibiotic efficacy
npj Antimicrobials and Resistance - The impact of bacterial purine metabolism on antibiotic efficacy
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Malcolm White @mfwhite2.bsky.social · 16/07/2025
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/...
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Paul Medvedev @pashadag.bsky.social · 12/06/2025
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.
tinyurl.com
Dropbox
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Seth Stadick @ducktapeprogrammer.bsky.social · 09/06/2025
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
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Eva Heinz @evaheinz7.bsky.social · 05/06/2025
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
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John Lees @johnlees.bacpop.org · 30/04/2025
Our subclustering and transmission pipeline, PopPIPE has now been published: www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
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...
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hobbslabmicro.bsky.social @hobbslabmicro.bsky.social · 30/04/2025
📣 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
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Philipp Bayer @philippbayer.bsky.social · 23/04/2025
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
onlinelibrary.wiley.com
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...
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Malcolm White @mfwhite2.bsky.social · 31/03/2025
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
findaphd.com
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
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Tatiana Dimitriu @tatianadimitriu.bsky.social · 31/03/2025
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 🧵
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Rob Patro @robp.bsky.social · 26/03/2025
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.
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Ricardo León-Sampedro @rleonsampedro.bsky.social · 18/12/2024
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/...
pnas.org
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...
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Tatiana Dimitriu @tatianadimitriu.bsky.social · 11/12/2024
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...
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Tommi Mäklin @themaklin.bsky.social · 05/12/2024
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...
sciencedirect.com
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…
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Adam P. Roberts @gcagatgcaatg.bsky.social · 03/12/2024
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...
nature.com
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...
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Gemma C. Atkinson @gemmaatkinson.bsky.social · 24/10/2024
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...
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Danna Gifford @dannagifford.bsky.social · 25/11/2024
📣 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...
nature.com
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
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Jeremy Berg @jeremymberg.bsky.social · 23/11/2024
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
media.tenor.com
a cartoon of homer simpson holding a card
ALT: a cartoon of homer simpson holding a card
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Maarten van der Heijden @mrvanderheijden.bsky.social · 21/11/2024
"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
doi.org
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.
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Lars Barquist @lbarquist.bsky.social · 19/11/2024
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....
journals.asm.org
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...
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