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Sam Lipworth @samlipworth.bsky.social · 7h

We have a fully funded PhD studentship available @modmedmicro.bsky.social in Oxford to work on a really cool project looking at population heterogeneity in bloodstream infections www.ndm.ox.ac.uk/study/dphil-... Please spread the word/get in touch if you'd like to chat.

DPhil project themes

www.ndm.ox.ac.uk

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Reposted by Sam Lipworth

The Lancet Microbe @lancetmicrobe.bsky.social · 18h

New research article

Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #AMR #WGS #OpenAccess #OA

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Sam Lipworth @samlipworth.bsky.social · 20h

Pleased to see this out today in @lancetmicrobe.bsky.social www.sciencedirect.com/science/arti.... We estimate the independent effects of AMR genes on MIC at a drug-bug level and challenge the idea that resistance is a binary phenomenon.

Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study

Surveillance and prediction of antibiotic resistance in Escherichia coli relies on curated databases of genes and mutations. We aimed to quantify the …

www.sciencedirect.com

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Reposted by Sam Lipworth

Bash the bug @bashthebug.net · 8d

From Pipettes to Pipelines: Greening a Multidisciplinary Research Lab.

@dotnagy.bsky.social writes about the experiences from the Modernising Medical Microbiology (MMM) research group on engaging wet lab, computer lab, and office teams on the #sustainability agenda.

#GreenLab #SustainableScience

From Pipettes to Pipelines — Oxford Climate Society

Dorottya Nagy writes about the experiences from the Modernising Medical Microbiology (MMM) Unit research group on engaging wet lab, computer lab, and office teams on the sustainability agenda.

oxfordclimatesociety.com

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Reposted by Sam Lipworth

Will Matlock @wtmatlock.bsky.social · 8d

Now published in @natcomms.nature.com 🎉

www.nature.com/articles/s41...

With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!

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Reposted by Sam Lipworth

Justine Rudkin @scousemicrobe.bsky.social · 8d

PhD opportunity to come and work in Glasgow, developing advanced tissue culture models to study Staphylococcus aureus colonisation and infection #microsky #PhD #DTPprogram

Enquiries from potential applicants are welcome.

www.gla.ac.uk/postgraduate...

www.findaphd.com/phds/program...

University of Glasgow - Postgraduate study - Centres for Doctoral Training - NorthWest Biosciences - Our Projects - Understanding Pathogens, from Molecules to Phenotypes - Justine Rudkin

www.gla.ac.uk

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Reposted by Sam Lipworth

John Lees @bacpop.org · 9d

Now published, our tool to run (almost) all biological models interactively in your web browser

Paper: academic.oup.com/bioinformati...
Website: biomodels.bacpop.org
Code: github.com/bacpop/SBMLt...

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Reposted by Sam Lipworth

Dorottya Nagy @dotnagy.bsky.social · 9d

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Figure 2 from my recently pre-printed manuscript on the completeness and accuracy of Nanopore long-read only bacterial genome assembly for Enterobacterales. a) tile plot of chromosome circularisation, with assembler on the x-axis and sample on the y-axis, shows that the consensus long-read only assembler, Autocycler, circularised more chromosomes at 95% (87/92) than any other long-read or hybrid assembler. b) complex upset plot of plasmid reconstruction, showing that the best plasmid reconstruction was achieved by long-read assemblers incorporating the separate plasmid assembly tool, Plassembler, namely Autocycler and Hybracter, reconstructing >96% of plasmids.

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Reposted by Sam Lipworth

Zamin Iqbal @zaminiqbal.bsky.social · 13d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Reposted by Sam Lipworth

Dorottya Nagy @dotnagy.bsky.social · 13d

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1...

Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

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Reposted by Sam Lipworth

We Are R-Ladies @weare.rladies.org · 15d

Ever run `install.packages()` and wish it were faster, smarter, and more reliable?

The {pak} package speeds things up with parallel downloads, dependency solving, and reproducible installs.

📦 pak.r-lib.org

#RStats

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Sam Lipworth @samlipworth.bsky.social · 15d

Come and work with Nicole Stoesser and I in Oxford with the fantastic team @modmedmicro.bsky.social - great opportunity for a postdoc in microbial genomics to do some creative research with great datasets as part of our HPRU.

my.corehr.com/pls/uoxrecru...

Job Details

my.corehr.com

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Reposted by Sam Lipworth

bioRxiv Genomics @biorxiv-genomic.bsky.social · 23d

Identification of specific metabolic capacities associated with major extraintestinal pathogenic Escherichia coli lineages https://www.biorxiv.org/content/10.1101/2025.09.14.675865v1

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Sam Lipworth @samlipworth.bsky.social · 20d

Great collaboration with @ukhsa.bsky.social #HPRU colleagues #nicolestoesser and the NEKSUS consortium of 9 NHS trusts in England

Sam Lipworth @samlipworth.bsky.social · 20d

Overall, using R10.4.1, super-high accuracy basecalling and autocycler, we can reliably infer marker geens (MLST/ARGs etc) and feel that performance was good enough to drop Illumina sequencing for the NEKSUS study (more to follow in due course!)

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Sam Lipworth @samlipworth.bsky.social · 20d

Dot showed that overall, @rrwick.bsky.social Autocycler appears to outperform other long read assemblers and long read only assemblies are extremely accurate (median Q-score of 67). Long read polishing helps small amount + benefits from short read polishing are very small (only for worst assemblies)

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Sam Lipworth @samlipworth.bsky.social · 20d

Great new work from #DotNagy @modmedmicro.bsky.social - she tool 96 clinical isolates from the NEKSUS study and sequenced with both Illumina and Nanopore - question was, can we do away with hybrid sequencing for the rest of the study?
www.biorxiv.org/content/10.1...

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

Whole bacterial genome sequence reconstruction using Oxford Nanopore Technologies ('Nanopore') long-read only sequencing may offer a lower-cost, higher-throughput alternative for pathogen surveillance...

www.biorxiv.org

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Reposted by Sam Lipworth

Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Reposted by Sam Lipworth

Alicia Calvo-Villamañán @aliciapcv.bsky.social · Aug 13

Very happy to be a (small) part of this story!
The role of plasmid-encoded ISs in the acceleration of AMR evolution, through inactivation of different bacterial genes.

Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

New paper out! 🔈🔈📣📣

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.

Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻

www.biorxiv.org/content/10.1...

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation

Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...

www.biorxiv.org

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Reposted by Sam Lipworth

nstoesser.bsky.social @nstoesser.bsky.social · Jul 26

New analysis from Kevin Chau @modmedmicro.bsky.social for the SinkBug Consortium (a collaboration with teams across 29 UK hospitals, NITCAR, UKHSA): Pathogen and AMR gene burden in 287 hospital sink-trap metagenomes and factors associated with high burdens.

medRxivpreprint @medrxivpreprint.bsky.social · Jul 25

The hospital Sink-ome: Pathogen and antimicrobial resistance gene burden in sink-traps across 29 UK hospitals and associations with sink characteristics https://www.medrxiv.org/content/10.1101/2025.07.25.25332191v1

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Reposted by Sam Lipworth

Kate Baker @ksbakes.bsky.social · Jul 27

There are half a million cases of invasive non-Typhoidal Salmonella (iNTS) every year and while you might know S. Typhimurim and Enteritidis, you may not have heard of S. Panama 💩 🩸 🧫 💊 Check out our latest in @lancetmicrobe.bsky.social doi.org/10.1016/j.la... and the 🧵 below to find out more 1/n

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Sam Lipworth @samlipworth.bsky.social · Jul 14

Great figure, I'm sure this is a dim question but why does it seem to have a cyclical pattern with outliers every ten years or so?

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Sam Lipworth @samlipworth.bsky.social · Jul 4

Interesting but then why doesn't famotidine have the same risk? (Or does it!)

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Reposted by Sam Lipworth

Andrew Rambaut @arambaut.bsky.social · Jul 2

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...

Details and instructions for installing on the BEAST website: beast.community

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Reposted by Sam Lipworth

Zamin Iqbal @zaminiqbal.bsky.social · May 19

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well
www.biorxiv.org/content/10.1...

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