sylvain Brisse

Mid-career Group Leader position in AI in genomics at Institut Pasteur, Paris - Research Institut Pasteur and the CNRS are launching a call for a mid-career group leader position in AI in genomics. We are looking for an experienced researcher (typically with > 8 years of research experien...

Opening of a Group Leader position in AI in genomics at Institut Pasteur @pasteur.fr , Paris research.pasteur.fr/en/call/mid-...

📣🦠Check out our new Editor’s Spotlight! Senior MGEN editor Jesse Shapiro tells us about a recently published paper on the bystander effect on the evolution of Bordetella parapertussis, a non-target species of the pertussis vaccine #MGEN

Read the full blog here: microb.io/48zfOlJ

The potential for large outbreaks of pertussis highlights the importance of maintaining or increasing vaccine coverage in pregnancy and in infants and children.

Global Incidence of #Pertussis after the COVID-19 Pandemic - A large collaborative effort under the auspices of the International #Bordetella Society, led by Andrew Gorringe, from the UK Health Security Agency. jamanetwork.com/journals/jam...

And a big thanks to our funders @gatesfoundation.bsky.social @pasteur.fr @ibeidlabex.bsky.social @wellcometrust.bsky.social @klebnet.bsky.social

Thanks to @kjolley.bsky.social @chcrestani.bsky.social @kelwyres.bsky.social @margaretlam.bsky.social Martin Maiden @pubmlst.org @daanensen.bsky.social @katholt.bsky.social Federica Palma, Melanie Hennart and Alexis Criscuolo @giphy-ip.bsky.social and other co-authors

The wide adoption of cgMLST LIN code strain taxonomies has the potential to result in a universal approach for standardized bacterial genotyping that could greatly enhance microbial biodiversity studies, international genomic epidemiology and infectious disease surveillance

Data confidentiality is an important barrier to rapid response to outbreaks. As LIN codes are sufficient to define strain identity across countries, they provide a solution for cross-border collaborative genomic surveillance investigations, without the need to share genomic sequences themselves

The recognition of sub-populations associated with distinct phenotypes is an important “raison d’être” of taxonomies. cgMLST LIN codes strain taxonomies will advance our understanding of the links between genotypes and clinical phenotypes, vaccine coverage and antimicrobial resistance

LIN codes provide clear definitions of sublineages, can help track dissemination at fine genetic scales within sublineages, and can subdivide isolates from single long-term outbreaks

To make the LIN code taxonomy broadly accessible, its components (alleles, profiles, cgSTs, LIN codes and nicknames) can be extracted using an application programming interface, and used with external tools and analysis platforms, such as @pathogenwatch.bsky.social

A taxonomic system needs to be created and updated in a coordinated manner. The cgMLST LIN code strain taxonomy is implemented in @kjolley.bsky.social 's BIGSdb, and is deployed at two main sites, PubMLST (at Oxford University) and BIGSdb-Pasteur (at Institut Pasteur, Paris)

LIN code diversity within a bacterial species can be summarized using circular packing plots, which illustrate the diversity of populations at each classification level. These representations also enable the identification of the most epidemiologically represented populations

LIN codes can be nicknamed with simple denominations, to enable easy communication. Nicknames can be assigned to LIN code prefixes based on prior denominations. For example, Klebsiella pneumoniae sublineages (SL) and clonal groups (CG) were nicknamed using the popular MLST identifiers

Core genome multilocus sequence typing (cgMLST) enables standardized high-resolution strain genotyping. Life Identification Number (LIN) codes are series of numeric codes that reflect genomic similarity between organisms, from left to right down to strain identity.

« cgMLST LIN codes » These strange acronyms hide an important advance in the standardization of bacterial strains taxonomy, enabling harmonized global surveillance of bacterial pathogens and more efficient multi-country outbreak investigations

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 👇

IMMEM XIV Poster presentations Explore the different post presentations that were recorded as part of the 14th edition of the International Meeting on Microbial Epidemiological Markers (IM...

The next five videos from our #IMMEM XIV poster presentations are available on our YouTube channel and cover topics like #plasmids, #genomics, #sequencing and more. Stay tuned for more videos every Wednesday!

https://youtube.com/playlist?list=PLBG53xT7PX7v-C3XcKHnKeVP1NxsrLqBU&si=tpFqDe_obR6LZLtx

Great work by @armovse.bsky.social with help from @josefdelgadoblas.bsky.social and colleagues at @institutpasteur.bsky.social and @flebreton.bsky.social ‘s group

We show nearly equal discrimination when compared to whole-genome single nucleotide polymorphisms analysis. The cumulative cgMLST strategy combines broad phylogenetic applicability and nearly complete genotyping resolution, expanding the utility of this harmonized approach for genomic epidemiology.

Compared to the KpSC scheme used alone, pairwise allelic distances among isolates increased on average 5.6-fold using the Kpn scheme. Schemes are easy to combine using BIGSdb’s interface or APIs developed by @kjolley.bsky.social

As a use case, we created non-redundant cgMLST schemes for the individual species K. pneumoniae sensu stricto (Kpn-cgMLST scheme), and its multidrug resistant sublineages (SLs) SL147 and SL307.

We illustrate this approach using the Klebsiella pneumoniae species complex (KpSC). I have been asked for ages, «When will you develop a more resolutive scheme ?». Here is it ! … with a systematic approach applicable to all broadly diverse bacterial species, and all sublineages thereof.

To overcome this trade-off, we conceptualizaed and developed the cumulative cgMLST approach, where sets of core loci conserved within nested phylogenetic entities are added.

Core genome multilocus sequence typing (cgMLST) is a powerful method for bacterial strain genotyping. However, the size of the core genome decreases as the phylogenetic breadth of the target group increases, reducing discriminatory power. We call this the discrimination/applicability tradeoff

Cumulative cgMLST provides increased discrimination of nested phylogenetic groups Background Core genome multilocus sequence typing (cgMLST) is a powerful method for bacterial strain genotyping. However, the size of the core genome decreases as the phylogenetic breadth of the targe...

Cumulative cgMLST : Our novel preprint is out @biorxiv doi.org/10.1101/2025...

YouTube video by Drugs for Neglected Diseases initiative (DNDi) Beni: Surviving Sleeping Sickness

Great video on the impact of the magic bullet developed by @dndi.org against human african trypanosomiasis youtu.be/GcIx32MDdkU?...

The @klebnet.bsky.social team are pleased to share slides from our “Klebsiella pneumoniae Genomic Epidemiology & Antimicrobial Resistance” lecture series!

Topics include Kleb diversity, lineages, AMR, hypervirulence, how to use Kaptive & Kleborate for typing, and more!

klebnet.org/2025/11/18/k...

Great collaboration between @institutpasteur (Thanks to Valerie Bouchez and others in my group), @vallhebron.com (team of Juanjo Gonzalez) and #CDC (Mike Weigand @mikeyweigand), and @anisabelBento

The most recent common ancestor of all sequenced Bpp isolates was estimated around the year 1877, making it one of the youngest human pathogens. We retraced the adaptation of #parapertussis to humans via key mutations in the master regulator bvgA-fhaB intergenic region around year 1900.