A novel version of diphtOscan is available at gitlab.pasteur.fr/BEBP/diphtos.... v2.2.0 makes it easy to install on local computers. diphtOscan scans genomes and extracts information including #diphtheria toxin and antimicrobial resistance genes, biovar, species and subtyping information.

Life Identification Numbers: A bacterial strain nomenclature approach Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

🧫 Our publication,“Global perspectives on Klebsiella epidemiology and biology: conference report on the KLEBS 2024 symposium,” is now out!

📄 Link to paper: www.nature.com/articles/s44...

@kelwyres.bsky.social @katholt.bsky.social @sylvainbrisse.bsky.social @pasteur.fr

🚨 Last few days to register for our Nanopore Users Day 2026!
Registration is free but mandatory, as places are limited, don’t miss out!

Join us for a day of scientific exchanges and networking focused on ONT sequencing and its applications!

@chloebaum.bsky.social @pasteur.fr @nanoporetech.com

🔷 Mais quel rapport entre l'Institut Pasteur et les popcorn ?

C'est le nom de l'étude à laquelle vous pouvez participer de façon anonyme !

What drives the K. pneumoniae species complex (KpSC) to thrive from hospitals to soils? In this study, we investigate how pangenome structure and functional diversity shape KpSC adaptability across phylogenetic and ecological contexts. (Thread)
www.biorxiv.org/content/10.6...

📢 Save the Date!

The 2nd Nanopore Users Day will take place 🗓️10 March 2026 at the Duclaux Amphitheater, Institut Pasteur (Paris). This edition will be open to external participants!

👉 More details and registration info coming soon!

@chloebaum.bsky.social @pasteur.fr @nanoporetech.com

Bacterial strain Taxonomy for Genomic Surveillance - GenEpi-BioTrain Webinar - Research This workshop aims to provide participants with a comprehensive understanding of bacterial classification and nomenclature approaches used in genomic surveillance. Participants will gain insight into ...

Almost there! Starting tomorrow morning (Paris time), the webinar on Bacterial strain Taxonomy for Genomic Surveillance organized within the ECDC sponsored GenEpi-BioTrain programme; registration is free; see more here: research.pasteur.fr/en/event/bac...

#diphtheria strain taxonomy: Life identification number (LIN) codes for the genomic taxonomy of Corynebacterium diphtheriae strains, by @josefdelgadoblas.bsky.social, Martin Rethoret-Pasty and myself, @biorxivpreprint.bsky.social al @biorxiv-microbiol.bsky.social

Identification of Corynebacteria of the diphtheriae Species Complex and detection of the diphtheria toxin g... This protocol describes a quadruplex real-time PCR (Dip4plex), performed with the Qiagen QuantiNova™ Multiplex PCR Kit, for simultaneous identification of Corynebacteria of th...

qPCR diagnosis of #diphtheria: you may be interested by our procedure, which is now widely used across European reference laboratories: www.protocols.io/view/identif... @EURLdiphtheriaPertussis thanks @chcrestani.bsky.social for releasing on protocols.io

Corynebacterium diphtheriae Outbreak in Migrant Populations in Europe | NEJM A surge of cases of Corynebacterium diphtheriae infection was observed in reception centers for migrants in Europe beginning in the summer of 2022. Most of the cases were cutaneous, although some r...

A new report describes the genetic epidemiology and antimicrobial-resistance patterns of a surge of cases of 𝘊𝘰𝘳𝘺𝘯𝘦𝘣𝘢𝘤𝘵𝘦𝘳𝘪𝘶𝘮 𝘥𝘪𝘱𝘩𝘵𝘩𝘦𝘳𝘪𝘢𝘦 infection that was identified in migrant populations in Europe. Read the full report: nej.md/3HEF3ZS

#MedSky #IDSky

Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans - Nature Communications This study reveals prior undetected transmission events of Corynebacterium ulcerans, suggesting pets play an intermediary role between wildlife and humans. Two main sublineages were identified, showin...

Thrilled to share our new @natcomms.nature.com paper “Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans” with @sylvainbrisse.bsky.social!

Read more ▶️ www.nature.com/articles/s41...

@pasteur.fr #GenomicEpidemiology #Zoonoses #OneHealth

Had a great time in Luxembourg at the first Network meeting of the EURLs for Public Health! Huge thanks to @ecdc.europa.eu for making it possible for our EURL-PH on #diphtheria and #pertussis to meet in person and to connect with fellow EURLs! Looking forward to the next meeting! @pasteur.fr

Significant respiratory virus activity in the EU/EEA, with #influenza & #RSV epidemics ongoing.

Vaccination campaigns against respiratory pathogens continue in many EU/EEA countries, and people who are eligible for vaccination are encouraged to get vaccinated.

More info: erviss.org
#IDsky #EpiSky

Spotlight on Klebsiella pneumoniae

In this blog @katholt.bsky.social sheds light on Klebsiella pneumoniae, a major cause of hospital-acquired infections 🦠 and a key player in the global antimicrobial resistance crisis.

📖 Read more: bit.ly/41gOzKF

@lshtm.bsky.social @megancarey.bsky.social @cmcrodrigues.bsky.social

Back in Argentina after the #KlebsiellaSymposium at @pasteur.fr. Grateful to the organizers @sylvainbrisse.bsky.social and @chcrestani.bsky.social for the opportunity to present my work on #Klebsiella in #Wastewater and to connect with brilliant researchers. Inspired and honored!

PubMLST - Public databases for molecular typing and microbial genome diversity Public databases for molecular typing and microbial genome diversity

BIGSdb v1.49.1 has been released. This version improves the layout of user registration and admin pages, and provides the option to export LIN code prefixes of specified length in the Export plugin. BIGSdb powers the databases on pubmlst.org and bigsdb.pasteur.fr.

github.com/kjolley/BIGS...

Microscopic photograph of the RSV virus.

Coming up next week - another part of our #GenEpiBioTrain online trainings!

This time we will focus on #RSV with the help of #InstitutePasteur.

The aim is to provide participants with in-depth knowledge of RSV, its genomic diversity, evolution, available treatments, & emerging vaccine strategies.

Thanks @sylvainbrisse.bsky.social for involving me in KlebNET-GSP as project manager 3y ago, it was a very enriching experience! Thanks to all the attendees of #KLEBS2024 for making this a great success, it was our best reward! And thanks to the @gatesfoundation.bsky.social for making it possible!

Will do the same soon! 😉