Polymicrobial infections can involve co-colonizing #pathogens, but how do they interact across host environments? This study shows that phenazines from #Pseudomonas aeruginosa drive strain- & O2-dependent inhibition of #Klebsiella pneumoniae @plosbiology.org 🧪 plos.io/4tQlYX4

🆕🔥🟢RAPID-TEST RCT N=552 Among patients with RTIs being considered for antibiotic treatment in primary care, use of an rapid multiplex microbiological point-of-care test (RM-POCT) DID NOT reduce same-day antibiotic prescribing or worsen symptom severity #idsky jamanetwork.com/journals/jam...

And now it's out! Happy that PNAS selected for the cover this SEM image snapped by @samjlord.bsky.social, one of the most evocative visualizations of Euplotes that I have ever encountered. www.pnas.org/doi/10.1073/... Stay tuned for what is shaping up to be some fascinating follow-up in the lab...

I think we're gonna genuinely resolve antibiotic resistance. This inventive paper uses a light-tunable conjugated polymer called P3, which absolutely shreds #Klebsiella and its #biofilms. They even used it to improve infected wound healing - scifi shit #AMR #MicroSky🧪 doi.org/10.3389/fcim...

Really interesting idea explored here in this preprint. Codon usage is subtle but important

It seems to me that this is a systemic failure of journals failing do the bare minimum and charging $ for it, not peer reviewers. Peer review is a FREE service provided by academics who cannot be expected to also check every ref. Journals should automate ref screening upon submission.

wow — the preprint host, arxiv, is banning authors for a year if they submit papers with hallucinated citations 🤖

For 40 years the 8-nt ‘Kozak Sequence’ was thought to mark sites of translation initiation. In a new study, we revise this model by identifying an ~80-nt sequence—the extended Translation Initiation Sequence (eTIS)— that guides ribosomes to correct start sites. 🧵 www.biorxiv.org/content/10.6...

Oh my. This is spectacular. sinceyouarrived.world/taken

Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.

Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.

Wow, this biotechnology is a work of art. Impressively designed and presented. Very exciting biotech. Figure 1 is also striking in it's design and use of colour

Direct #AMR diagnostics of patient samples works - Reduces diagnosis by >80 hours - Saves $2400–$3900/per 100 ICU beds/week They screened patient samples for #carbapenem resistant organisms in a hospital setting: - Immunochromatographic test - PCR www.journalofhospitalinfection.com/article/S019...

This work was co-led by myself and Peter Yoon. Structure was led by Peter, @terryzzy.bsky.social , and Trevor Docter. Many thanks to our intrepid collaborators and special thanks to Jennifer for supporting us through this project. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...

🚨 Final session alert! 🚨 Join us this Thursday for the last #KlebClub Virtual Seminar Series 2026 session! 🗓 April 30 ⏰ 9–10:30 AM EDT 🎤 Theme: KlebClub Community Flash Talks ✨Insights on #Klebsiella pneumoniae—from stress resistance and telomere #phages, phage defense to metabolism. #microsky

Excited to finally share our new preprint on bioRxiv describing Verticall (github.com/rrwick/Verti...), a robust & efficient tool for building recombination-free bacterial phylogenies. Huge thanks to @rrwick.bsky.social & @katholt.bsky.social for this incredible work! www.biorxiv.org/content/10.6...

New rapid, colorimetric #carbapenemase diagnostic method that's cheap and smart. 1) Take potential CPE and incubate with imipenem disk 2) Take disk and incubate with known carb sensitive isolate 3) Add resazurin as a live/dead indicator #AMR #IDSky journals.asm.org/doi/10.1128/...

This preprint on #Shigella flexneri covers a new genotyping scheme + tool, #AMR and analysis of 13k genomes from ~1925-current day 🦠 #MicroSky #microbiology 🧪 www.biorxiv.org/content/10.6...

🔬 How can genomics transform the fight against antimicrobial resistance? 💡 Find out at the TARGetAMR Conference 2026! 📅 14–15 May, Birmingham 🧬 Two days of collaboration, innovation and real world solutions 🎟️ Secure your FREE place: www.targetamr.org.uk/hdrevents/ta... #TARGetAMR26

Study from my Lab detailing how Aerobactin-mediated iron acquisition is critical for hypervirulent Klebsiella to disseminate from the gut to cause invasive disease. Tour de Force work led by my wonderful Grad student, Giovanna Hernandez! #PLoSPathogens #Klebsiella journals.plos.org/plospathogen...

Answering emails after a week off work is a full-Monday job. It makes me want to take the week off. Recursively, I can see where this is headed.

Do you work on Klebsiella oxytoca genomes? Want to know which K and O loci they have? Check out the new Klebs oxy species complex databases here: github.com/klebgenomics... Poster today #ESCMIDGlobal2026 by Naoise McGarry! Papers to follow soon. @klebnet.bsky.social @klebclub.bsky.social

Another win for antibiotic stewardship 💊 Fig 2b shows a reduction of metagenomic resistance gene loads to beta-lactams, aminoglycosides and tetracycline when a multi-site stewardship program is implemented across ~23 months 🦠 Love the use of #metagenomics here 🧬 #AMR #AntibioticResistance 🧪

When my intrusive thoughts win while in the lab. A reminder that experiments could always be going worse.

Really great article which measures the optimal outcomes for routine Nanopore seq in a clinical setting 🧬🧫 Check this out for: - Rapid sequence typing 🌿 - Antibiotic resistance gene detection 💊 - SNPs 🦠 #MicroSky #microbiology #IDSky #EpiSky #AMR 🧪 www.microbiologyresearch.org/content/jour...

New paper from Hugh Cottingham, @katholt.bsky.social , @yekwah.bsky.social @nenadmacesic.bsky.social and co. Great to see the speed/accuracy tradeoff info here, I don't think I've seen it laid out like this before. www.microbiologyresearch.org/content/jour...

What happens when you use a strain-resolved assembler on 720 Gbp of Nanopore metagenome sequence? Simultaneous strain-level resolution of multiple co-occurring lineages from hundreds of single contig high-quality genomes, including 78 Pelagibacter. @tnn1.bsky.social and myself:

Bioinformaticians of Melbourne, the next ABACBS-Melbourne Bioinformatics Coffee Catch Up is this Thursday, 2 April. (Please note the new time/day for 2026!) Everyone is welcome. Details in the attached image. See you there!

When Australian universities do the right thing and clean house of all top execs for this colossally embarrassing blunder, and still need to find savings, I'm happy to take a PVC-level role for 600k p/a less than they currently pay. www.abc.net.au/news/2026-03...

🚨 New paper🚨 from PhD student Rilla Tammi and collaborators! Using FINRISK/FINDIET 2002 datasets (n=1,228) a novel "CRC lifestyle index" was calculated from 9 CRC-related factors (incl. diet) and investigated for associations with gut microbial diversity and taxa 🔗 link.springer.com/article/10.1...

#CSIRO, Australia's fed scientific research organisation is yet again being cut: 102 jobs in climate, 110 in health/biosecurity, 55 in agriculture/food + 35 in minerals [1, 2]. CSIRO has an ROI of 8.8 since 2023 ($8.80 return for every $1 invested) [3, 4]. Cuts are ideological not evidence-based.

Hey fellow scientists, I'm just letting you know that if you're promoting something with some junky AI image, I'm not gonna click. You've got a workshop, a conference, a new paper? Just not gonna bother. You want a bespoke image? Hire an illustrator.

Most of the academic research workforce is performance managed to the max, simply by the nature of the funding landscape. Flexibility is the only perk we have, don’t rip it from us because HR depts don’t understand the nature of the work.

Very happy to see our microphysiological human mini-bladder published! 🎉 We show how urine composition affects tissue health and thus invasivness of UPEC, and how cell wall-deficient UPEC from the tissue reactive UTIs. 🦠 Check it out here: www.nature.com/articles/s41... #UTISky

Surveyed misconceptions around #AntibioticResistance are fascinating: • 66% believe they aren't at risk of resistance when taking antibiotics • ~70% assume ‘antibiotic resistance’ refers to the body gaining resistance • ~25% expect antibiotics for viral infections #AMR #SciComm Sources below:

Amazing vis in this thread. And science too!

Have you wondered if some E. clones are so successful because of their plasmids? www.biorxiv.org/content/10.1... A combination of bioinf and lab work showed that some plasmids have coexisted for centuries, and that a specific colicin gene is able to kill other clones paving their way for success!

Looking forward to sharing our recent work on population metabolism of #klebsiella pneumoniae this week. Join me to learn about metabolic diversity within species, featuring work by @bananabenana.bsky.social @helena-bethany.bsky.social and a sneak peak at our latest from @kalanip.bsky.social

See you this Wedneday 😀 Join us for an evening of cutting-edge microbiology, industry insights, and great conversation! 📅 Wednesday, 25 February 2026 ⏰ 6:00–7:30pm 📍 The Burrow (Beer Garden Room), West End 🍕 Free pizza provided! 👉 Register via the QR code on the poster.

The language we use in science is important. Repeatedly, the public understands 'antibiotic resistance' over 'antimicrobial resistance' Clarity > correctness. #AMR will continue until messaging improves #AntibioticResistance #SciComm www.nature.com/articles/s43... www.nature.com/articles/s43...

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

We will have the pleasure to have Dr. Kelly Wyres in our next webinar talking about: 👉 Metabolic modelling of Klebsiella pneumoniae and strain diversity When: 25.02.206 at 10h00 CET Registration: us06web.zoom.us/webinar/regi... @kelwyres.bsky.social @escmid.bsky.social

Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky

I usually accept most requests, but I think getting paid would help when motivation to accept is low. For-profit journals should pay reviewers. Non-profit journals should offer publishing discounts. Anti-LLM screening would need to be implemented as well.

How would you design a *multithreaded*, *concurrent* & *dynamic* hash table if you are focused specifically on common k-mer workloads, where streaming query & insertion are common? Jamshed, Prashant and I explore this in kache-hash, a cache-friendly k-mer hash table! www.biorxiv.org/content/10.6...

What #Ecoli 🦠 genes enable environmental persistence? Incredibly layered work in this study, spanning: - Environmental meta-transcriptomics 📊 - Isolate culturing 🧫 - #metabolism ♻️ - Mouse survivability experiments 🐁 - TraDIS 🧬 - Isogenic mutant validation ∆ 🧪 www.biorxiv.org/content/10.6...

🎉 Almost 3 months to go! 🧬 Join us at the TARGetAMR Annual Conference 2026, 14–15 May, Birmingham 🔎 Collaborate, learn & lead the fight against AMR. 👉 Register today: www.targetamr.org.uk/now-open-cal... #TARGetAMR26

New research article The effect of pneumococcal conjugate vaccine and pneumococcal polysaccharide vaccine on nasopharyngeal colonisation following human infection challenge with serotype 3 and serotype 6B (PREVENTING PNEUMO 2) www.thelancet.com/journals/lan... #IDSky #ClinMicro #OpenAccess #OA

Mixotricha paradoxa "is composed of five different organisms: three bacterial ectosymbionts on its surface for locomotion and at least one endosymbiont lives inside to...digest cellulose in wood to produce acetate for its host(s)" Single-celled eukaryotes are wild en.wikipedia.org/wiki/Mixotri...

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