Joe Wanford

Thanks so much, Lesley :)

Thanks, Julie! The pain of the mocks was worth it 😂

I will shortly be advertising multiple PDRA positions – if you love molecular microbiology and bacterial pathogenesis, please get in touch for a chat!

Now that it’s official, I’m delighted to announce I’ve been awarded a Wellcome Trust Career Development Award to fund my lab’s work on K. pneumoniae pathogenesis for the next 8 years! Very grateful to many fantastic mentors and collaborators who’ve helped throughout this process.

Bifidobacteria support optimal infant vaccine responses - Nature Neonatal antibiotic use is shown to reduce immune response to infant vaccines, accompanied by reduced abundance of Bifidobacteria in the gut microbiota, with experiments in mice indicating that probio...

Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...

I am recruiting a research assistant. Please send to anyone you know who is interested in gaining more lab experience in host:pathogen interactions of bacterial infections.

www.jobs.cam.ac.uk/job/50738/

Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice - Nature Microbiology InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantificati...

OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice

#microsky 🧪

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

New in Nat Comm

A rapid evolution-tracking system for 𝘒𝘭𝘦𝘣𝘴𝘪𝘦𝘭𝘭𝘢 𝘱𝘯𝘦𝘶𝘮𝘰𝘯𝘪𝘢𝘦 that experimentally tests how this leading MDR threat resists antibiotics and adapts to serum to invade the bloodstream

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

Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition Nature Communications - Acute systemic immune activation may affect gut-luminal colonisation dynamics. Here, the authors show that LPS exposure in mice elevates gut-luminal oxygen species levels,...

I am very excited to share our latest publication on the effect of systemic #endotoxin on intestinal #microbiota spearheaded by the brilliant Sanne Kroon at the Hardt lab @eth-dbiol.bsky.social @ethzurich.bsky.social @naturecomms.bsky.social

👉🏼 rdcu.be/eelLn

🚨 Join us at King's College London for all things cellular microbiology! Super friendly meeting with cool science and great opportunity for ECRs to present their work!

What do Pablo Picasso and Charles Janeway have in common? Both were interested in patterns of life. Janeway was focused on pathogen associated molecular patterns (PAMPs) that are detected by our immune system. But what are these patterns he refers to?

100+ years of phase variation: the premier bacterial bet-hedging phenomenon Stochastic, reversible switches in the expression of Salmonella flagella variants were first described by Andrewes in 1922. Termed phase variation (PV), subsequent research found that this phenomenon ...

New paper alert! Thoughtful review of phase variation, including current controversies. @microbiologysociety.org www.microbiologyresearch.org/content/jour...

Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses - Nature Phagocytosed bacteria can serve as an alternative nutrient source for macrophages, influencing their metabolic and immune responses through the recycling of microbial components, with the process regulated by nutrient-sensing mechanisms and bacterial viability.

Nature research paper: Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses

https://go.nature.com/3XmyOPD

The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response to Mycobacterium tuberculosis (Mtb) infection and support bacterial persistence. We prev...

Happy to share a preprint from the Angelo lab many years in the making. Read on for a saga of multiplexed imaging, immunometabolism, and TB granulomas with some fun side quests into the realms of geographical information sciences and transcriptomics… (1/20) doi.org/10.1101/2025...

Base-modified nucleotides mediate immune signaling in bacteria Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. While cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of other ...

Base-modified nucleotides mediate immune signaling in bacteria www.science.org/doi/abs/10.1... #jcampubs

Save the date:2/3 June: UK Cellular Micro is coming back to London! We have two amazing keynotes and all other talks will be selected from abstracts. Submissions opening soon

Diabetes potentiates the emergence and expansion of antibiotic resistance Diabetic infections are a reservoir for the emergence and proliferation of antibiotic resistance in Staphylococcus aureus.

Delighted to share our new study. A collaboration with the Thurlow lab. Antibiotic resistance rapidly emerges and thrives in diabetic mice. A worrying coming together of two major and growing health problems worldwide www.science.org/doi/10.1126/...

New research article

Antibody responses in #Klebsiella pneumoniae bloodstream infection: a prospective cohort study

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

#IDSky #ClinMicro #BSI #OpenAccess #OA

Fast and Accurate in silico Antigen Typing with Kaptive 3 Surface polysaccharides are common antigens in priority pathogens and therefore attractive targets for novel control strategies such as vaccines, monoclonal antibody and phage therapies. Distinct serotypes correspond to diverse polysaccharide structures that are encoded by distinct biosynthesis gene clusters, e.g. the Klebsiella pneumoniae species complex (KpSC) K- and O- loci encode the synthesis machinery for the capsule (K) and outer-lipopolysaccharides (O), respectively. We previously presented Kaptive and Kaptive 2, programs to identify K and O-loci directly from KpSC genome assemblies (later adapted for Acinetobacter baumannii), enabling sero-epidemiological analyses to guide vaccine and phage therapy development. However, for some KpSC genome collections, Kaptive (v≤2) was unable to type a high proportion of K-loci. Here we identify the cause of this issue as assembly fragmentation, and present a new version of Kaptive (v3) to circumvent this problem, reduce processing times and simplify output interpretation. We compared the performance of Kaptive v2 and Kaptive v3 for typing genome assemblies generated from subsampled Illumina read sets (decrements of 10x depth), for which a corresponding high quality completed genome was also available to determine the 'true' loci (n=549 KpSC, n=198 A. baumannii). Both versions of Kaptive showed high rates of agreement to the matched true locus among 'typeable' locus calls (≥96% for ≥20x read depth), but Kaptive v3 was more sensitive, particularly for low depth assemblies (at <40x depth, v3 ranged 0.85-1 vs v2 0.09-0.94) and/or typing KpSC K-loci (e.g. 0.97 vs 0.82 for non-subsampled assemblies). Overall, Kaptive v3 was also associated with a higher rate of optimal outcomes i.e. loci matching those in the reference database were correctly typed and genuine novel loci were reported as untypeable (73-98% for v3 vs 7-77% for v2 for KpSC K-loci). Kaptive v3 was >1 order of magnitude faster than Kaptive v2 making it easy to analyse thousands of assemblies on a desktop computer, facilitating broadly accessible in silico serotyping that is both accurate and sensitive. The Kaptive v3 source code is freely available on GitHub (https://github.com/klebgenomics/Kaptive), and has been implemented in Kaptive Web (https://kaptive-web.erc.monash.edu). ### Competing Interest Statement The authors have declared no competing interest.

Super excited to finally present the preprint to accompany Kaptive 3 which we released last year!

Big thanks to coauthors @kelwyres.bsky.social, @katholt.bsky.social, @genomarit.bsky.social and Iren Löhr.

Here's what we did to improve in silico antigen typing 👇🧵
www.biorxiv.org/content/10.1...

Klebsiella pneumoniae disrupts vasodilation by targeting eNOS post translational modifications via the type VI secretion system and the capsule polysaccharide Vasodilation is a crucial protective response to inflammation and infection. Endothelial cells control vasodilation through the bioavailability of eNOS-produced nitric oxide (NO), and the generation o...

New pre print! We establish an ex vivo blood vessel model to investigate the effect of infection on vascular physiology in real time. We show Klebsiella inhibits vasodilation in a T6SS-dependent manner by targeting eNOs. Superb work by @safimicro.bsky.social www.biorxiv.org/content/10.1...

Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11 - Nature Microbiology HD5 induces filopodial extensions in epithelial cells that the pathogen Shigella exploits to facilitate invasion and infection.

OUT NOW: Human enteric α-defensin 5 interacts with colonic epithelial receptor P2Y11 to induce filopodia and promote Shigella infection

by Kai Ye & co

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

Klebsiella pneumoniae emerging anti-immunology paradigms: from stealth to evasion Klebsiella pneumoniae (KP) is a global threat to human health due to the isolation of multidrug-resistant strains. Despite advancements in understandi…

Last work from the lab in @cp-trendsmicrobiol.bsky.social !
We review the most recent evidence on the strategies deployed by Klebsiella to counteract host defences. www.sciencedirect.com/science/arti... The co-evolution with the immune system has taught the bug a couple of tricks!!!

Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems

CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems

Congrats Tana Wein! Thank you Kranzusch lab!
www.nature.com/articles/s41...

Funding for AIDS relief program to stop after foreign aid pause ordered The President's Emergency Plan for AIDS Relief, or PEPFAR, provides billions in funding to organizations to combat HIV.

Unconscionable

Perhaps the most disgusting announcement of a week full of disgusting announcements.

The impact PEPFAR has played in global fight against HIV/AIDS is a shining example of how investing in global health is in the national interest.

www.cbsnews.com/news/funding...

microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a us...

Our new preprint "microGalaxy: A gateway to tools, workflows, and training for accessible, reproducible, and FAIR microbial data analysis" is live! 🎉

📝 Read it here: www.biorxiv.org/content/10.1...

#Microbiome #FAIRdata #usegalaxy @galaxyproject.bsky.social

Simulating 500 million years of evolution with a language model

"An AI model developed to design proteins simulates 500 million years of protein evolution in developing new fluorescent protein"

www.science.org/doi/10.1126/...

ESKAPE pathogens are outsmarting us. Our latest paper in @naturemicrobiol.bsky.social reveals alarming ease of resistance evolution to antibiotics in development. Collaborative work with @csabapallab.bsky.social‬
and Kintses Lab

Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11

wellcomeopenresearch.org/articles/9-3...

Early childhood infections do NOT strengthen your immune system...they only make you sicker throughout childhood Data from a new study unambiquous SCIENCE

A new longitudinal cohort study found that children who were sick more often in early childhood were more likely to continue being sick in later childhood with more moderate to severe infections and require more antibiotic therapies.
/1

A phylogenetic approach to comparative genomics - Nature Reviews Genetics Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The authors review the application ...

Comparative genomics needs to use phylogenetic methods: why, how and common questions www.nature.com/articles/s41... @annadewar.bsky.social @lauriebelch.bsky.social