TLDR: Dual-arm protocol provides comparable, if slightly improved performance, at the cost of longer turn-around times and higher sample failure rates and so is not currently suitable for a clinical setting.
04.02.2026 13:25 β π 1 π 0 π¬ 0 π 0
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
19.11.2025 12:27 β π 62 π 36 π¬ 1 π 0
Two men having a conversation
A panel of speakers answering a question
A woman wearing a grey blazer and blue lanyard answering a question
A grand hall with large windows and chandeliers. All audiences members facing a screen that displays 'Welcome to the NHS Respiratory Metagenomics Network Day'.
What an inspiring day! Last week we hosted our second Network Day, bringing together over 120 people. We explored the development of the national pilot metagenomic service, which is improving detection & treatment of respiratory infections. Thank you to all who joined and to our fantastic speakers!
13.11.2025 16:52 β π 3 π 2 π¬ 2 π 0
Possibly one of the biggest changes in microbiology has been going on quietly over the past decade. Whilst this remains a diagnostic in development- and we have much to learn about how to use it- it represents a step change in how we manage infections.
07.11.2025 14:35 β π 11 π 5 π¬ 0 π 0
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
08.10.2025 08:28 β π 5 π 5 π¬ 0 π 0
New research article
Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #OpenAccess #OA
02.10.2025 08:47 β π 21 π 6 π¬ 2 π 3
Efficient detection and typing of phage-plasmids
Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...
π¨ New preprint! π§¬
ππ‘ππ π-π©π₯ππ¬π¦π’ππ¬ (π-ππ¬) are fascinating elements: both πππ¦π©ππ«πππ π©π‘ππ ππ¬ and π©π₯ππ¬π¦π’ππ¬ β‘οΈ tricky to detect.
We present ππ²πππ’π§π β the first π’πππ§ππ’ππ’ππππ’π¨π§ ππ§π ππ₯ππ¬π¬π’ππ’ππππ’π¨π§ ππ¨π¨π₯ π οΈdesigned specifically for P-Ps:
β
Accurate
β
Sensitive
β
Easy to use
π www.biorxiv.org/content/10.1...
03.09.2025 13:02 β π 31 π 17 π¬ 2 π 2
the treasure trove of all sequencing datasets
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
22.07.2025 21:58 β π 72 π 38 π¬ 1 π 5
myloasm - metagenomic assembly with (noisy) long reads
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
28.05.2025 17:53 β π 132 π 78 π¬ 5 π 3
Same-day pan-microbial metagenomics for personalised therapy and pathogen surveillance on the intensive care unit: a single-centre prospective study
Next speaker was Luke Blagdon Snell with Same-day pan-microbial metagenomics for personalized therapy and pathogen surveillance on the intensive care unit: a single-centre prospective study (escmid.reg.key4events.com/AbstractList...).
13.04.2025 04:03 β π 1 π 2 π¬ 1 π 0
Implementing same-day respiratory metagenomic diagnostics in paediatric intensive care
Robbie Hammond presented next with Implementing same-day respiratory metagenomic diagnostics in paediatric intensive care (escmid.reg.key4events.com/AbstractList...). Their method had a turnaround time of 6 hours.
13.04.2025 04:03 β π 1 π 2 π¬ 1 π 0
Pan-microbial metagenomics protocol v1.2Public workspaceCritical
This is the updated metagenomics protocol for respiratory samples
search.app/V491AEp3tmB7...
04.02.2025 21:28 β π 5 π 3 π¬ 4 π 0
β οΈ BREAKING:
The suspected H5N1 bird flu infected child in Marin county drank raw milk, according to Marin HHS.
The child presented to a local emergency department with fever and vomiting. No other family members became sick, indicating no person-to-person transmission.
11.12.2024 06:10 β π 152 π 39 π¬ 7 π 9
@UKHSA latest respiratory surveillance released.
1.flu positivity and hospitalisations rising fast - earlier than last year and exponential growth
2. RSV remains high but looks like it is close to peak - highest rates in children under 5.
3. COVID at low levels and stable.
05.12.2024 14:11 β π 41 π 21 π¬ 2 π 5
Letter sent in to the Editor of the Guardian on brain microbiome nonsense.
03.12.2024 10:01 β π 352 π 92 π¬ 21 π 30
Itβs remarkable that the events of the 2019 Samoa measles outbreak arenβt more widely known: www.telegraph.co.uk/news/measles...
05.11.2024 17:05 β π 59 π 21 π¬ 1 π 0
Results 10 yrs metagenomic sequencing for CNS infections www.nature.com/articles/s41...
Impressive.
Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.
13.11.2024 17:15 β π 41 π 17 π¬ 2 π 1
Gonna need to get a round in
13.11.2024 11:22 β π 3 π 0 π¬ 1 π 0
Professor at UC Davis
Work: phylogenomics & evolvability of host-microbiome systems; #openscience;
Other: #birds; baseball; T1D
Lab phylogenomics.me
Pics jonathaneisen.smugmug.com
Links linktr.ee/jonathaneisen
TED go.ted.com/6WPm
Research fellow in clinical metagenomics at University College London
Research scientist interested in mosquitoes, infectious disease, nanopore seq and metagenomics. Views are my own.
Computational Biology PhD Student at the University of Birmingham. (Meta)genomic pathogen surveillance, infectious disease modelling, and BW disarmament. π¬π§/πΈπ¬
Computational biologist interested in bacterial genomics, bacterial adaptation and antibiotic resistance. @IBV_CSIC
Virology with a side-order of human evolution.
Consultant Medical Microbiologist (UK)
Consultant Medical Biopathologist (Greece)
Views my own
Transforming infection detection and patient care
Bioinformatician at UCLH and UCL.
Pathogens + Computing!
https://bookshop.org/p/books/a-heart-that-works-rob-delaney/3f4398e419f2db84
Microbiologist-activist, in-between microbes & public health, fighting for equity. Deputy Executive Director @chrfbd. Science by & for the many, not the few.
Clinical Lecturer and ID/Micro registrar in Oxford
Journalist and broadcaster. Brixton via Birr.
Running London Landmarks half-marathon in April for charidee, not that I like to wang on about it. Please donate at my Just Giving page
Postdoc at Dana-Farber and Harvard Med with Heng Li (@lh3lh3.bsky.social). Prev: UBC / UofT.
I like thinking about biological sequence analysis and its applications to metagenomics / microbial genomics.
https://jim-shaw-bluenote.github.io
And all this science I don't understand, it's just my job five days a week.
Professor of Microbiome and Systems Biology @ Nottingham Trent University. π³οΈβπ
Working predominantly on the human gut microbiota.
All views my own.
Head of Bioinformatics at Broken String Biosciences.
https://www.brokenstringbio.com/
Still love microbial bioinformatics. Now working in the cell and gene therapy space. Keen Python and Nextflow coder
Livestreams: twitch.tv/Limmy
Blog: https://brianlimond.substack.com/
