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Paul Johnston

@paulrjohnston.bsky.social

410 followers 2.5K following 10 posts

School of Medicine, University of St Andrews https://scholar.google.de/citations?hl=en&user=YKzmUT8AAAAJ&view_op=list_works&sortby=pubdate

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Environmental science 47%

Geology 20%

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Reposted by Paul Johnston

Adrian Cazares @cazares-adr.bsky.social · 10d

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👇

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

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Reposted by Paul Johnston, Alan McNally

hobbslabmicro.bsky.social @hobbslabmicro.bsky.social · Aug 5

📢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

The impact of bacterial purine metabolism on antibiotic efficacy

npj Antimicrobials and Resistance - The impact of bacterial purine metabolism on antibiotic efficacy

rdcu.be

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Reposted by Paul Johnston

Malcolm White @mfwhite2.bsky.social · Jul 16

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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Reposted by Paul Johnston

Paul Medvedev @pashadag.bsky.social · Jun 12

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

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Reposted by Paul Johnston

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 9

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

Reposted by Paul Johnston

Eva Heinz @evaheinz7.bsky.social · Feb 8

#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/...

Schematic overview of the PhD; combining bacterial genomes from a large collection to analyse adhesins, metabolic potential, bacterial warfare; and compare to other arthropod symbiontes and design a minimal microbiome.

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Reposted by Paul Johnston

John Lees @bacpop.org · Apr 30

Our subclustering and transmission pipeline, PopPIPE has now been published:
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

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Reposted by Paul Johnston

hobbslabmicro.bsky.social @hobbslabmicro.bsky.social · Apr 30

📣 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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Reposted by Paul Johnston

Philipp Bayer @philippbayer.bsky.social · Apr 23

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....

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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

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Reposted by Paul Johnston

Malcolm White @mfwhite2.bsky.social · Mar 31

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

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

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Reposted by Paul Johnston

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Mar 31

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

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Reposted by Paul Johnston

Rob Patro @robp.bsky.social · Mar 26

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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Paul Johnston @paulrjohnston.bsky.social · Feb 27

me please

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Reposted by Paul Johnston

Ricardo Leon-Sampedro @rleonsampedro.bsky.social · Dec 18

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/...

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

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Reposted by Paul Johnston

Tatiana Dimitriu @tatianadimitriu.bsky.social · Dec 11

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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Reposted by Paul Johnston

Tommi Mäklin @themaklin.bsky.social · Dec 5

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...

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

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Reposted by Paul Johnston

Adam P. Roberts @gcagatgcaatg.bsky.social · Dec 3

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...

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

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Paul Johnston @paulrjohnston.bsky.social · Dec 2

“The only kind of writing is rewriting.”

Paul Johnston @paulrjohnston.bsky.social · Nov 27

Had some T5 (>100kb) data from PlasmidsNG. Would send several aliquots per genome to get a bit more coverage. But otherwise fine. DTRs notwithstanding

Paul Johnston @paulrjohnston.bsky.social · Nov 27

I use archive.ph

archive.ph

Reposted by Paul Johnston

Danna Gifford @dannagifford.bsky.social · Nov 25

📣 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...

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

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Reposted by Paul Johnston

Jeremy Berg @jeremymberg.bsky.social · Nov 23

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

a cartoon of homer simpson holding a card

ALT: a cartoon of homer simpson holding a card

media.tenor.com

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Reposted by Paul Johnston

Maarten van der Heijden @mrvanderheijden.bsky.social · Nov 21

"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

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Paul Johnston @paulrjohnston.bsky.social · Nov 20

Hoffentlich wird es sequenziert

Paul Johnston @paulrjohnston.bsky.social · Nov 20

CPE?

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Reposted by Paul Johnston

Lars Barquist @lbarquist.bsky.social · Nov 19

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

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Paul Johnston @paulrjohnston.bsky.social · Nov 19

less than 20h elapsed time with 3x a100-sxm4-80g, plus a few hours demultiplexing

Paul Johnston @paulrjohnston.bsky.social · Nov 18

*GPU

Paul Johnston @paulrjohnston.bsky.social · Nov 18

We do it on our HPC you nodes (36x A100)

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Paul Johnston @paulrjohnston.bsky.social · Nov 17

Thanks for putting this together