David Cleary
@bacterioskeptic.bsky.social
Assistant Professor in Microbial Genomics (#microbiome, #pneumococci, #haemophilus). My views not UoB. Husband, dad, music miserablist and egg chasing.
Delighted to share our new paper, out now in @natureportfolio.nature.com where we show that neutrophil myeloperoxidase (MPO) tracks RSV severity in infants, and can be used as a functional readout of therapeutic efficacy in the lab. 📄 Read it (open access) 👉 rdcu.be/ftx53
Neutrophil myeloperoxidase as a functional biomarker for RSV severity: implications for in vitro therapeutic screening
Nature Communications - Preclinical human models are needed to investigate mechanisms and evaluate therapies for severe respiratory syncytial virus (RSV) infection in children. The authors here...
rdcu.be
An interesting and unexpectedly comforting piece on neutral theory substack.com/@profmcinern...
James McInerney (@profmcinerney)
You kinda have to stick with this one to the end before I get to my point. I hope that one the way you find it interesting. It is about how a lot of decisions mean nothing.
substack.com
the FT has two pieces on the slow-motion collapse of UK higher ed. 4/5ths of unis are doing voluntary layoffs; 38% are doing compulsory. Meanwhile Britain and its flatlined productivity growth sleepwalks through its unprecedented loss of advanced capabilities www.ft.com/content/8097...
Useful article: How to deal with disappointment – by an expert in this misunderstood emotion theconversation.com/how-to-deal-...
How to deal with disappointment – by an expert in this misunderstood emotion
In our professional and personal lives, disappointment is an emotional signal worth learning to read.
theconversation.com
A little write up of Uzal's (Lecturer and Research Associate at University of Jos Plateau State in Nigeria) @bactivac.bsky.social supported visit to learn pneumococcal genomics with me and biofilms with @allan-lab.bsky.social www.birmingham.ac.uk/news/2026/sp...
Spotlight on BactiVac Network training opportunities - University of Birmingham
Uzal shares his story of resilience, which features a successful training opportunity in the UK, awarded and funded by the BactiVac Network.
birmingham.ac.uk
New preprint! The first first-author work of my postdoc at the Baker! So, babies' airways are colonised from birth, and our group has shown that early colonisers shape respiratory health. 1/7 www.biorxiv.org/content/10.6...
Question: anyone struggle with Streptococcus pneumoniae growth in plasticware? Eliminated almost every other variable and it's lovely in glass but terrible in polystyrene plates. Anyone observed, got a mechanism or a fix? Driving us potty!
Rapid release of multiplex PCR amplicon scheme for Andes hantavirus whole genome sequencing validated on control material: www.biorxiv.org/content/10.6... @scalene.bsky.social @stevepullan.bsky.social @ukhsa.bsky.social output from HPRU in Public Health Genomics
biorxiv.org
However you dice it, it’s been a great night for Thai-based cryptocurrency billionaires & Vladimir Putin - who, incredibly, is currently getting more good news from the UK than Ukraine.
Immunogenicity and safety of co-administration of adjuvanted respiratory syncytial virus prefusion F protein vaccine with 20-valent pneumococcal conjugate vaccine in adults aged ≥60 years: a randomized, non-inferiority trial academic.oup.com/cid/article/...
Immunogenicity and safety of co-administration of adjuvanted respiratory syncytial virus prefusion F protein vaccine with 20-valent pneumococcal conjugate vaccine in adults aged ≥60 years: a randomize...
AbstractBackground. Respiratory syncytial virus (RSV) illness and pneumococcal disease present high disease burden and health risks to older adults. Vaccin
academic.oup.com
As a scientist, I am here to report that this headline is indeed accurate as I am in fact STUNNED!! Wow. This is incredible. 🧪 "Newly discovered bacterial defense system challenges genetic code’s central dogma.": www.science.org/content/arti...
Very interesting read. www.asimov.press/p/bioinforma... (Thanks to @torstenseemann.bsky.social for sharing over on the #ABACBS slack)
A Brief History of Bioinformatics Software
How computer scientists on the fringes of biology made sense of sequencing data.
asimov.press
How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...
Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study
The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it
merenlab.org
Postdoctoral Position (Please re-post) A funded postdoctoral position for a recent graduate to study aspects of Neisseria gonorrhoeae pathogenesis, antigenic variation, genetics, or physiology. Please contact Hank Seifert h-seifert@northwestern.edu #Microsky, #Microbiology, #MicrobialEvolution
#pneumococci continue to be the leading cause of LRI deaths globally: Global burden of lower respiratory infections and aetiologies, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023 - The Lancet Infectious Diseases www.thelancet.com/journals/lan...
Global burden of lower respiratory infections and aetiologies, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023
This comprehensive analysis underscores both the gains achieved through vaccination and the challenges that remain in controlling the LRI burden globally. Furthermore, it demonstrates persistent dispa...
thelancet.com
Here I would like to introduce a genome downloading tool: GenomeFetch 👇🧬 This is a Linux tool written in pure Shell/Bash for downloading bacterial genomes (genome assemblies) from RefSeq or GenBank 🧫
GitHub - raymondkiu/GenomeFetch: GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank.
GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank. - raymondkiu/GenomeFetch
github.com
I had the opportunity to present my research at #AIR2026 (Wellcome Genome Campus), focusing on how lactate shapes host-microbe interactions in the lung It was a great experience to share this work, receive valuable feedback, and engage with researchers across microbiology and immunology. #microbiome
Here we go then, lab website at last! Still some gaps to fill and I've definitely not caught all the broken links yet but here we are. www.lungmicrobiome.org Hellow world!
Respiratory Microbiome Group — University of Birmingham
Investigating the role of microbial communities in respiratory health and disease.
lungmicrobiome.org
Minor update on genomics of the menB outbreak. UKHSA have updated with four more outbreak isolates, and a high quality assembly of the earlier genome. tl;dr ran ska+gubbins again, same results, all of these genomes look basically identical www.bacpop.org/blog/menb_up...
Updated genomic analysis of the 2026 menB outbreak in Kent, UK
This is a brief update to the previous menB analysis we’d posted here. UKHSA have released a technical briefing and further data which includes four further isolates from the outbreak, and a high qual...
bacpop.org
Thought provoking article: Improving scientific mentoring with history and philosophy of science url: royalsocietypublishing.org/rspb/article...
Improving scientific mentoring with history and philosophy of science
Abstract. Mentoring graduate students and postdoctoral researchers shapes the development of future scientists and, by extension, the progress of science i
royalsocietypublishing.org
Back at my old stomping ground @uniofsurrey.bsky.social with my eldest for an offer holder day. Forgotten how nice the campus was …
Some provisional analysis on one of the genomes from the menB outbreak detailed below: johnlees.me/posts/menb-o...
menB outbreak in Kent -- first genome
Previous posts on menB: First thoughts and summary Working hypothesis for outbreak UKHSA have sequenced one of the isolates from the outbreak, which is on PubMLST (190637). This is excellent and UKHSA...
johnlees.me
John Lees@johnlees.bacpop.org · 5mo agoSome more thoughts on why this outbreak (large, happening quickly, in one place) might be happening: johnlees.me/posts/menb-o... Perhaps strain + immunity + high transmission