iiinova — where your digital self keeps evolving

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Patrick S. Mitchell @psmitchej.bsky.social · 25/05/2026

Thrilled to announce that the Department of Microbiology at the University of Washington, School of Medicine is hiring at the Assistant Professor level (tenure-track)! The Pacific Northwest is an awesome place to live and do science 🧪🦠. Join us! apply.interfolio.com/185622 Applications due 8/1.

apply.interfolio.com

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

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Keith Jolley @kjolley.bsky.social · 14/05/2026

BIGSdb v1.53.2 has been released and is now live on @pubmlst.org. This adds functionality to the LINvis plugin. This includes annotation of nodes representing specific LIN prefixes entered as a list.

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The Lancet Microbe @lancetmicrobe.bsky.social · 13/05/2026

New research article Persistent spread of carbapenemase-producing #Klebsiella pneumoniae in acute care hospitals in 36 European countries (the CCRE survey) www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #OpenAccess #OA

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Onisillos @onisillos.bsky.social · 13/05/2026

"A major European survey marks a significant milestone in the effort to control antimicrobial resistance ( #AMR), providing the most comprehensive genomic picture to date of carbapenem- and/or colistin-resistant Enterobacterales (CCRE) across hospitals in Europe." www.ecdc.europa.eu/en/news-even...

ecdc.europa.eu

Europe advances genomic surveillance of CCRE with landmark multi-country study

A major European survey marks a significant milestone in the effort to control antimicrobial resistance (AMR), providing the most comprehensive genomic picture to date of carbapenem- and/or colistin-r...

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The Lancet Microbe @lancetmicrobe.bsky.social · 13/05/2026

New research article Emergence of carbapenemase-producing #Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey) www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #Ecoli #OpenAccess #OA

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Robert Petit @rpetit3.bsky.social · 30/04/2026

Howdy! Happy to announce that Bactopia v4 is finally out! 🥳 This release supports the latest from @seqera.io Nextflow v26 (strict syntax, static types, and records! oh my!) It also open's the doors to start doing some fun things with Bactopia. To learn more, check out: bactopia.io/blog/bactopi...

bactopia.io

Bactopia v4 Updates and Improvements | Bactopia

Learn about the new features and improvements in Bactopia version 4.

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Natacha Couto @natachacouto.bsky.social · 13/05/2026

It’s still funny to look at students’ faces at the registration desk when I say I’m an invited speaker 😄

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 26/03/2026

Been working on a browser version of BRIG. No install. Interactive. Looking for beta testers; message me if you're interested.

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nstoesser.bsky.social @nstoesser.bsky.social · 24/02/2026

Are you a post-doctoral microbiologist interested in characterising bacterial resistance evolution and want to apply your knowledge and expertise to developing new therapeutics for Klebsiella (and other Enterobacterales) infections? Then we need you! Apply now bit.ly/3MX39Ce close date March 13th 👀

my.corehr.com

Job Details

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Natacha Couto @natachacouto.bsky.social · 19/11/2025

If you weren’t able to join #IMMEMXIV in Porto this year, don’t miss this chance to hear the poster presentations made available by @escmid.bsky.social on their YouTube channel. @esgem-sg.bsky.social

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Natacha Couto @natachacouto.bsky.social · 10/11/2025

Join us tomorrow if you like plasmids and clones! @sandrareuter.bsky.social will be talking about a particular intriguing outbreak 🤓. @escmid.bsky.social

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Natacha Couto @natachacouto.bsky.social · 27/09/2025

Com and join us in Groningen for an update on metagenomics 😊

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Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

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ESCMID @escmid.bsky.social · 22/09/2025

We wrapped up #IMMEM XIV over the weekend and it was a fantastic success with over 250 participants from 35 countries. A big thank you to the organisers and specifically @esgem-sg.bsky.social our study group on epidemiological markers! The content will be available on ESCMID media soon. #clinmicro

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Natacha Couto @natachacouto.bsky.social · 20/09/2025

This has been an incredible week, one I will hardly forget. It started with a hackathon with a brilliant group of people. Followed by a cutting-edge meeting, #IMMEMXIV organized by @esgem-sg.bsky.social and @escmid.bsky.social which turned out to be one of my highest points this year.

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 19/09/2025

Come see my poster at IMMEM Poster 151. 🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq). ⚙️ SpecCheck – an open-source command-line tool that applies these standards […] [Original post on mstdn.science]

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ESCMID @escmid.bsky.social · 16/09/2025

🧠 Straight from one of the programme committee members, Angela offers what she is looking forward to most at #IMMEMXIV starting tomorrow in Porto, Portugal! You can review the programme and follow along during the conference days on social media. ow.ly/ucIc50WNoeA

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ESCMID @escmid.bsky.social · 07/09/2025

🧠 Straight from the programme committee treasurer, Sylvain offers what he is looking forward to most at #IMMEM XIV. Review the programme: ow.ly/ucIc50WNoeA 🚀 With only 10 days left, secure your spot at this conference today! Register now: ow.ly/rLhU50WNoeC #IDSky #clinmicro

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ESCMID @escmid.bsky.social · 23/08/2025

📣 Nominate exceptional candidates for the ballot by next Sunday, 31 Aug 2025! ⏰ Elections will be held among the membership at the end of 2025. 🗳️More info: ow.ly/3c5A50Wtjhs #IDSky #clinmicro #MedSky

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ESCMID @escmid.bsky.social · 13/08/2025

🚨New Epi Alert this week: Mongolia reporting over 13K measles cases; Italy is experiencing its worst West Nile virus season w/ 173 human cases & 11 deaths in the last weeks; cholera in N. Darfur, melioidosis in Thailand, malaria in Namibia & more. ow.ly/OytK50WEl6u #IDSky #clinmicro #MedSky

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ESCMID @escmid.bsky.social · 07/08/2025

Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Topics range from how genomics inform resistance profiling to pathogen surveillance in a #OneHealth framework. 🧬 ✍️ Register: ow.ly/gjOZ50WpOXX 👀 Programme: ow.ly/Whj850WpOXY #IDSky

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Dr Emma Hodcroft @firefoxx66.bsky.social · 25/07/2025

📢New job posting!📢 Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬 My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on! 1/5

An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"

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ESCMID @escmid.bsky.social · 15/07/2025

Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Session topics range from how genomics inform resistance profiling to pathogen surveillance in a One Health framework. Learn more: ow.ly/lBGs50WpOZs #IDSky #MedSky #clinmicro

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Natacha Couto @natachacouto.bsky.social · 11/07/2025

Don't miss the chance to be a part of this exciting conference on microbial typing & genomics #IMMEMXIV. The theme this year is Microbial typing: from fundamental to daily microbiology. @escmid.bsky.social @esgem-sg.bsky.social Register today and see you in Porto! www.escmid.org/congress-eve...

escmid.org

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 19/06/2025

Pleased to share our latest preprint describing vaccines.watch (vaccines.watch), an interactive platform enabling exploration of vaccine target diversity from global genome data: www.biorxiv.org/content/10.1...

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ESCMID @escmid.bsky.social · 16/06/2025

🚨TODAY IS THE LAST DAY to apply for a new fellowship opportunity! Train the Trainers Fellowship is designed to support individuals to attend selected events & then organise a follow-up activity in their own country. ⏰ Due today! 💡 Learn more & apply: ow.ly/Z5Ro50VYLzl #IDSky #MedSky #clinmicro

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ESCMID @escmid.bsky.social · 28/05/2025

ESCMID's Emerging Infections Subcommittee comments on the rise in MERS-CoV cases As of 12 May 2025, 9 new MERS-CoV cases - including 2 deaths - have been reported by health authorities in Saudi Arabia. Read the statement including links to further reports: ow.ly/ST6L50VZeT2 #IDSky #clinmicro

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Moritz Kraemer @mugkraemer.bsky.social · 28/05/2025

Write-up of our open-source software tool, Grapevne, enabling rapid construction of multi-data type workflows for enhanced pandemic preparedness. It was born out of the need to repeat analyses during the invasion of multiple Variants of Concern. wellcomeopenresearch.org/articles/10-...

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@ESGEM_ESCMID @esgem-sg.bsky.social · 26/05/2025

We invite you all to our next webinar on "Carbapenemases in Enterobacterales in the food chain in the EU/EFTA" Speaker: Beatriz Guerra When: 16th June 12h00 CET Ling for registration (Open but mandatory): us06web.zoom.us/webinar/regi... See you there!

us06web.zoom.us

Welcome! You are invited to join a webinar: Carbapenemases in Enterobacterales in the food chain in the EU/EFTA. After registering, you will receive a confirmation email about joining the webinar.

Organised by: ESGEM & EFWISG

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Robert Petit @rpetit3.bsky.social · 06/05/2025

At #APHL annual conference? Check out poster 212 to learn more about Bactopia and all the fun things it can do! Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉 @bactopia.com @nextflow.io @aphl.org Full PDF: datasets.bactopia.com/media/2025-b...

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Kate Baker @ksbakes.bsky.social · 23/05/2025

Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n www.biorxiv.org/content/10.1...

biorxiv.org

Defence systems drive accessory genome interactions in Pseudomonas aeruginosa

As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassin...

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Kate Baker @ksbakes.bsky.social · 23/05/2025

Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11 www.medrxiv.org/content/10.1...

medrxiv.org

The natural history of the emergence of sexually transmissible shigellosis

Shigellosis is a gastrointestinal illness caused by bacteria belonging to one of four species of Shigella . Sexually transmissible shigellosis was first reported in 1974, but recently there has been a...

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Pathoplexus @pathoplexus.org · 22/05/2025

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV. These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response. 1/4

Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.

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Conor (Conchúr) Meehan @conmeehan.bsky.social · 22/05/2025

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace. Check out the course objectives below and sign up before June 9th to join us! www.futurelearn.com/courses/anti...

futurelearn.com

Antimicrobial Databases and Genotype Prediction - Online Course - FutureLearn

Transform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with Wellcome Connecting Science.

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Marit Hetland @genomarit.bsky.social · 22/05/2025

Happy to share this resource of 568 closed Klebsiella pneumoniae species complex hybrid assemblies, including 1416 plasmids! ⭕️🦠 We hope this will be useful - short reads, long reads, hybrid assembly or all combined - for your own tools/validations 🥳 #Microsky journals.asm.org/doi/10.1128/...

journals.asm.org

Complete genomes of 568 diverse Klebsiella pneumoniae species complex isolates from humans, animals, and marine sources in Norway from 2001 to 2020 | Microbiology Resource Announcements

Klebsiella pneumoniae species complex are opportunistic pathogens that can transmit between humans, animals, and the environment (1). Here, we report hybrid genome assemblies of 578 (568 complete) gen...

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Natacha Couto @natachacouto.bsky.social · 22/05/2025

This has been an amazing journey and I’ve learnt a lot from it! Take a look at @katholt.bsky.social thread to know more!

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Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

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Craig MacLean @craigmaclean.bsky.social · 08/05/2025

New Research Assistant position available in my lab to work on a project testing the efficacy of pills dependent #phage against clinical isolates of enteric bacteria . Part of a growing phage research theme in my lab my.corehr.com/pls/uoxrecru...

my.corehr.com

Job Details

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Sandra Reuter @sandrareuter.bsky.social · 24/04/2025

@esgem-sg.bsky.social Webinar coming up 6th May with @ameliabarberphd.bsky.social "Candida parapsilosis: sequencing for clinical microbiology" together with ESCMID Fungal Infection Study Group. Register here: us06web.zoom.us/webinar/regi... I'm looking forward to learning about fungal sequencing!

us06web.zoom.us

Welcome! You are invited to join a webinar: Candida parapsilosis: sequencing for clinical microbiology. After registering, you will receive a confirmation email about joining the webinar.

Organised by ESGEM, EFISG

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Centre for Genomic Pathogen Surveillance @thecgps.bsky.social · 22/04/2025

Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)

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Eduardo Rocha @epcrocha.bsky.social · 16/04/2025

New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!

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Nabil-Fareed Alikhan @happykhan.mstdn.science.ap.brid.gy · 11/04/2025

here's a recording of a seminar i gave today. Using containers (docker) for bioinformatics software youtu.be/eBy-W2bUklw?si=A1mNYiKSe3k… I cover. ✅ What is containerisation and how it helps make analyses reproducible and portable ✅ Key differences between Docker and Singularity ✅ […]

mstdn.science

Original post on mstdn.science

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Sheppard Lab @sheppardlab.bsky.social · 07/04/2025

TWO postdoc positions in Computational Microbiology and/or biochemistry. Join our interdisciplinary group in the new Life and Mind Building @OxfordBiology, @UniofOxford, @IneosOxford Please apply and share this post: www.jobs.ac.uk/job/DMP641/p...

jobs.ac.uk

Postdoctoral Research Associate at University of Oxford

Discover Postdoctoral Research Associate jobs and more in higher education on jobs.ac.uk. Apply for further details on the top job board.

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Gytis Dudas @evogytis.bsky.social · 03/04/2025

We're looking for a PhD student to join us at Vilnius University in Lithuania. We work on RNA virus evolution computationally but we'd like to generate more mosquito RNA virus sequence data. Official ad: www.gmc.vu.lt/en/doctoral-.... Please share & continue reading if interested.

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Natacha Couto @natachacouto.bsky.social · 03/04/2025

I’ve travelled to Bucharest to join the Bioinformatics Horizons meeting (rsbi.ro/evenimente/b...) organized by the Romanian Society of Bioinformatics. I’ll be talking about plasmid typing and AMR genotyping. Looking forward to all the other talks. 🤓

rsbi.ro

Bioinformatics Horizons – Romanian Society of Bioinformatics

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Natacha Couto @natachacouto.bsky.social · 27/03/2025

I had a wonderful time doing this workshop with you @sandrareuter.bsky.social. Thanks to @escmid.bsky.social Programme Director Jacob Moran-Gilad for inviting us to do this!

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Plasmid Society @plasmidsociety.bsky.social · 11/03/2025

The International Society for Plasmid Biology and other Mobile Genetic Elements are finally in Bluesky!! 😎😎😎

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