Paul Johnston

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

Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...

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...

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👇

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

📢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

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/...

1/4 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.

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

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

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...

Our subclustering and transmission pipeline, PopPIPE has now been published:
www.microbiologyresearch.org/content/jour...

📣 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

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...

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

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/phds/project...
A funded PhD studentship is available for a joint project between my lab and @andreashaag.bsky.social @uniofstandrews.bsky.social

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
🧵

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.

me please

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...

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/...

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...

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…

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...

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...

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...

“The only kind of writing is rewriting.”

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

I use archive.ph

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...

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

📣 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...

a cartoon of homer simpson holding a card ALT: a cartoon of homer simpson holding a card

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

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.

"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

Hoffentlich wird es sequenziert

CPE?

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...

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....

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

*GPU