New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

Have you ever wondered why children starting nursery/daycare pick up so many germs? I certainly did, and with a crack team of parent-scientists/clinicians, we set out to answer that question. Is childcare a germ factory or an immune bootcamp? journals.asm.org/doi/10.1128/...

Germ factories or immune boot camps? Infection and immunity in childcare settings | Clinical Microbiology Reviews

SUMMARYChildcare outside the home is a common experience for many children in high-income countries. It is associated with an increase in the incidence of infectious diseases—not just for the child bu...

journals.asm.org

Apply by 11th May to do a PhD @lshtm.bsky.social Work with epidemiologists, social scientists & modellers to understand quality of life measures in Syphilis and develop evidence on cost-effectiveness of interventions & public health strategies. @thelovetankcic.bsky.social @joetucker.bsky.social

Our latest preprint compares the dual-arm nanopore workflow with the respiratory metagenomics protocol currently implemented across the NHS, using clinical samples. 👉 www.researchsquare.com/article/rs-8... @nhsmetagenomicsnet.bsky.social @lukebsnell.bsky.social @ronandoyle.bsky.social

As part of the @nhsmetagenomicsnet.bsky.social we have compared the current in-service nanopore metagenomics protocol with ONT's own dual-arm protocol. The results are published in the following preprint: www.researchsquare.com/article/rs-8...

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

EMBL-EBI@ebi.embl.org · 10mo ago

Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care. EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform. #WAAW2025 #ActOnAMR www.ebi.ac.uk/about/news/t... 🧬💻

#microsky Pleased to share this work led by Cat Wilson as part of her PhD, tracking Salmonella transmission in low intensity agricultural settings in Malawi. TL;DR - lots of transmission between humans, animals and environment within households. www.nature.com/articles/s41...

Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi - Nature Communications

In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulati...

nature.com

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!

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.

The Lancet Microbe@lancetmicrobe.bsky.social · 11mo ago

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

Our new preprint covering the improvements we made to our respiratory metagenomic assay is out now: www.medrxiv.org/content/10.1... ✅ Now implemented in 6 NHS hospitals ✅ Increased sensitivity ✅ Increased pathogen genome coverage (1/3)

Optimisation of whole cell human depletion provides increased sensitivity and microbial genome coverage from respiratory metagenomic assays

Metagenomics is being adopted worldwide as a laboratory developed test. We have previously reported a unified metagenomic method for the direct detection of microorganisms from respiratory samples, de...

medrxiv.org

Our new preprint covering the improvements we made to our respiratory metagenomic assay is out now: www.medrxiv.org/content/10.1... ✅ Now implemented in 6 NHS hospitals ✅ Increased sensitivity ✅ Increased pathogen genome coverage (1/3)

Optimisation of whole cell human depletion provides increased sensitivity and microbial genome coverage from respiratory metagenomic assays

Metagenomics is being adopted worldwide as a laboratory developed test. We have previously reported a unified metagenomic method for the direct detection of microorganisms from respiratory samples, de...

medrxiv.org

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

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

A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...

PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools

Abstract. Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They co

academic.oup.com

🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...

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 ...

biorxiv.org

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/

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

1 hour lab-in-tube assay for TB! "point-of-care single-tube assay...to attain single-nucleotide specificity and high sensitivity within 1 hour of sample application, without a conventional DNA isolation procedure" www.science.org/doi/10.1126/...

Rapid tuberculosis diagnosis from respiratory or blood samples by a low cost, portable lab-in-tube assay

A low complexity, portable lab-in-tube tuberculosis assay for resource-limited areas analyzes blood, saliva, and sputum with a handheld device.

science.org

"Importantly, the metagenomic tests provide results within 6–8 h" That's quick! #metagenomics #IDSky #ClinMicro #medsky @lancetmicrobe.bsky.social www.thelancet.com/journals/lan...

UK launch metagenomic pathogen surveillance programme

On Jan 30, 2025, the UK Health Security Agency (UKHSA) announced the launch of the metagenomics Surveillance Collaboration and Analysis Programme (mSCAPE)—the world’s first biosecurity surveillance sy...

thelancet.com

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...).

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.

This is the updated metagenomics protocol for respiratory samples search.app/V491AEp3tmB7...

Microbiome science needs more microbiologists- A new commentary authored by myself and @abaumler.bsky.social www.nature.com/articles/s41...

Do you make core genome alignments for phylogenomics? Mona Taouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. www.microbiologyresearch.org/content/jour... (1/4)

Exploring SNP filtering strategies: the influence of strict vs soft core

Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental ...

microbiologyresearch.org

⚠️ 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.

@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.

Letter sent in to the Editor of the Guardian on brain microbiome nonsense.

It’s remarkable that the events of the 2019 Samoa measles outbreak aren’t more widely known: www.telegraph.co.uk/news/measles...

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%.