Natacha Couto
@natachacouto.bsky.social
Scientist, One Health, AMR, Genomics
Join us tomorrow if you like plasmids and clones! @sandrareuter.bsky.social will be talking about a particular intriguing outbreak 🤓. @escmid.bsky.social
We invite you to the joint ESGEM & ESGMAP webinar:
👉 Dr. Sandra Reuter, University of Freiburg
“Tracking clonal and plasmid transmission in carbapenem- and colistin-resistant Klebsiella pneumoniae.”
📅 Date & Time: November 11, 2025, 12:00 PM CEST
🔗 Register here: us06web.zoom.us/webinar/regi...
👉 Dr. Sandra Reuter, University of Freiburg
“Tracking clonal and plasmid transmission in carbapenem- and colistin-resistant Klebsiella pneumoniae.”
📅 Date & Time: November 11, 2025, 12:00 PM CEST
🔗 Register here: us06web.zoom.us/webinar/regi...
Welcome! You are invited to join a webinar: ESGEM & ESGMAP: Tracking clonal and plasmid transmission in carbapenem- and colistin-resistant Klebsiella pneumoniae. After registering, you will receive a ...
Chairs: Natacha Couto & Elisabeth Grohmann
Speaker: Sandra Reuter
us06web.zoom.us
November 10, 2025 at 2:54 PM
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 😊
New Course Alert: Rapid #diagnostics & #surveillance of critical pathogens in the hospital are essential for patient treatment and hospital outbreak detection. Learn more & sign up today for this 3-day course! ow.ly/xUyq50X1iWQ
#IDSky #clinmicro #MedSky
#IDSky #clinmicro #MedSky
September 27, 2025 at 11:04 AM
Com and join us in Groningen for an update on metagenomics 😊
Reposted by Natacha Couto
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
Thread 1/n
September 25, 2025 at 9:29 PM
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
Thread 1/n
Reposted by Natacha Couto
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
September 22, 2025 at 6:54 AM
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
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.
September 20, 2025 at 6:39 PM
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.
Reposted by Natacha Couto
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]
🔬 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]
September 19, 2025 at 8:15 AM
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]
🔬 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]
Reposted by Natacha Couto
🧠 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
ow.ly/ucIc50WNoeA
September 16, 2025 at 3:40 PM
🧠 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
ow.ly/ucIc50WNoeA
One week to go! 🤓👏🏼
🧠 Straight from the conference chair, Natacha offers what she is looking forward to most at #IMMEM XIV. Review the programme: ow.ly/ucIc50WNoeA
🚀 With only one week left, secure your spot at this conference today! Register now: ow.ly/rLhU50WNoeC
#IDSky #clinmicro
🚀 With only one week left, secure your spot at this conference today! Register now: ow.ly/rLhU50WNoeC
#IDSky #clinmicro
September 10, 2025 at 1:11 PM
One week to go! 🤓👏🏼
Reposted by Natacha Couto
🧠 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
🚀 With only 10 days left, secure your spot at this conference today! Register now: ow.ly/rLhU50WNoeC
#IDSky #clinmicro
September 7, 2025 at 11:05 AM
🧠 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
🚀 With only 10 days left, secure your spot at this conference today! Register now: ow.ly/rLhU50WNoeC
#IDSky #clinmicro
Reposted by Natacha Couto
📣 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
🗳️More info: ow.ly/3c5A50Wtjhs
#IDSky #clinmicro #MedSky
August 23, 2025 at 8:01 AM
📣 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
🗳️More info: ow.ly/3c5A50Wtjhs
#IDSky #clinmicro #MedSky
Reposted by Natacha Couto
🚨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
#IDSky #clinmicro #MedSky
August 13, 2025 at 4:47 PM
🚨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
#IDSky #clinmicro #MedSky
Reposted by Natacha Couto
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
✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY
#IDSky
August 7, 2025 at 8:14 AM
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
✍️ Register: ow.ly/gjOZ50WpOXX
👀 Programme: ow.ly/Whj850WpOXY
#IDSky
Reposted by Natacha Couto
📢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
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
July 25, 2025 at 10:44 AM
📢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
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
Reposted by Natacha Couto
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
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
July 15, 2025 at 1:25 PM
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
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
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.bsky.social @esgem-sg.bsky.social
Register today and see you in Porto!
www.escmid.org/congress-eve...
www.escmid.org
July 11, 2025 at 3:57 PM
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.bsky.social @esgem-sg.bsky.social
Register today and see you in Porto!
www.escmid.org/congress-eve...
Reposted by Natacha Couto
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...
June 19, 2025 at 8:44 AM
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...
Reposted by Natacha Couto
🚨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
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
June 16, 2025 at 7:16 AM
🚨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
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
Reposted by Natacha Couto
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
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
May 28, 2025 at 7:57 AM
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
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
Reposted by Natacha Couto
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-...
It was born out of the need to repeat analyses during the invasion of multiple Variants of Concern.
wellcomeopenresearch.org/articles/10-...
May 28, 2025 at 8:08 AM
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-...
It was born out of the need to repeat analyses during the invasion of multiple Variants of Concern.
wellcomeopenresearch.org/articles/10-...
Reposted by Natacha Couto
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!
Speaker: Beatriz Guerra
When: 16th June 12h00 CET
Ling for registration (Open but mandatory): us06web.zoom.us/webinar/regi...
See you there!
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
us06web.zoom.us
May 26, 2025 at 8:19 AM
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!
Speaker: Beatriz Guerra
When: 16th June 12h00 CET
Ling for registration (Open but mandatory): us06web.zoom.us/webinar/regi...
See you there!
Reposted by Natacha Couto
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...
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...
May 6, 2025 at 3:52 PM
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...
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...
Reposted by Natacha Couto
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
May 23, 2025 at 6:33 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Natacha Couto
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...
www.medrxiv.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...
www.medrxiv.org
May 23, 2025 at 12:44 PM
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...
www.medrxiv.org/content/10.1...
Reposted by Natacha Couto
📢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
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
May 22, 2025 at 4:06 PM
📢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
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
Reposted by Natacha Couto
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...
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...
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.
www.futurelearn.com
May 22, 2025 at 11:39 AM
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...
Check out the course objectives below and sign up before June 9th to join us!
www.futurelearn.com/courses/anti...