Natacha Couto

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

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

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

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.
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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

Thanks to everyone who contributed to this amazing meeting, faculty, program committee members, @escmid.bsky.social @esgem-sg.bsky.social and to audience for the valuable interventions. See you at #IMMEMXV

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.

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]

🧠 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

One week to go! 🤓👏🏼

Looking forward to reading this one!

🧠 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

📣 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

🚨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

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

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"

📢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!

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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

IMMEM XIV ESCMID in collaboration with ESGEM, is organising the 14th International Meeting on Microbial Epidemiological Markers. Discover microbial typing, from fundamental to daily microbiology in Porto, Portu...

You are absolutely right, apologies for that here is the link again www.escmid.org/congress-eve...

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...

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...

🚨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

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

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-...

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

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!

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...

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...

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...

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...

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...

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.

📢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.

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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...

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...

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/...