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H-index: 17
Environmental science 47%
Geology 20%
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Reposted by Paul Johnston

cazares-adr.bsky.social
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
3 34 73

Reposted by Paul Johnston, Alan McNally

hobbslabmicro.bsky.social
📢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
14 22

Reposted by Paul Johnston

mfwhite2.bsky.social
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/...
1 6 6

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
1 16 25

Reposted by Paul Johnston

biorxiv-bioinfo.bsky.social
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
9

Reposted by Paul Johnston

evaheinz7.bsky.social
#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.
17 19

Reposted by Paul Johnston

bacpop.org
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
2 3 4

Reposted by Paul Johnston

hobbslabmicro.bsky.social
📣 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
2 19 11

Reposted by Paul Johnston

philippbayer.bsky.social
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
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
2 12 28

Reposted by Paul Johnston

mfwhite2.bsky.social
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
12 5

Reposted by Paul Johnston

biorxiv-microbiol.bsky.social
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
5 13

Reposted by Paul Johnston

robp.bsky.social
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.
2 3 12

by Paul Johnston

paulrjohnston.bsky.social
me please
1 1

Reposted by Paul Johnston

rleonsampedro.bsky.social
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
12 13

Reposted by Paul Johnston

tatianadimitriu.bsky.social
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...
47 28

Reposted by Paul Johnston

themaklin.bsky.social
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
5 50 85

Reposted by Paul Johnston

gcagatgcaatg.bsky.social
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
2 2

by Paul Johnston

paulrjohnston.bsky.social
“The only kind of writing is rewriting.”
1

by Paul Johnston

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

by Paul Johnston

paulrjohnston.bsky.social
I use archive.ph
archive.ph

Reposted by Paul Johnston

dannagifford.bsky.social
📣 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
7 37 71

Reposted by Paul Johnston

jeremymberg.bsky.social
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
10 41 130

Reposted by Paul Johnston

mrvanderheijden.bsky.social
"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
1 5

by Paul Johnston

paulrjohnston.bsky.social
Hoffentlich wird es sequenziert
1

by Paul Johnston

paulrjohnston.bsky.social
CPE?
1 1

Reposted by Paul Johnston

lbarquist.bsky.social
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
1 12 27

by Paul Johnston

paulrjohnston.bsky.social
less than 20h elapsed time with 3x a100-sxm4-80g, plus a few hours demultiplexing
2

by Paul Johnston

paulrjohnston.bsky.social
*GPU
1

by Paul Johnston

paulrjohnston.bsky.social
We do it on our HPC you nodes (36x A100)
1 1

by Paul Johnston

paulrjohnston.bsky.social
Thanks for putting this together

References

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Updated 1m