The BIGSdb website Policy concerning the platform & data use agreement and the privacy notice of BIGSdb-Pasteur was updated on March 25, 2024. Please consult it before using the platform and the data.

The procedure for submitting data for curation were updated on Mai 03, 2024. Please consult them before making a new submission. If any questions, contact us.

Corynebacterium diphtheriae outbreak

Large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe - phenotypic and genomic analysis - Hoefer et al. has been published in medRxiv!

A pan-European consortium was created to assess the clinical, epidemiological and microbiological features of this outbreak - BIGSdb Corynebacterium diphtheriae complex was used for sharing data between collaborators and analysing genome data.

The isolate-genome collection is avavailable in BIGSdb@Pasteur and accessible at the public project 2022_EuropeanWideReemergence_collection

Upgraded to 1.42.6

BIGSdb pasteur is now in 1.42.6:

More information are available here

ReporTree plugin

ReporTree added to BIGSdb-Pasteur

ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters developed by Mixão et al. (Genome Med, 2023)

This plugin creates the required input files for ReporTree and runs the tool to identify and characterize genetic clusters. A full description of the ReporTree plugin can be found in the BIGSdb manual.


Corynebacterium diphtheriae reemergence, genomic framework and bioinformatics tool to detect antimicrobial resistance and virulence - Hennart et al. preprint has been published in biorXiv!

The bioinformatics pipeline DIPHTOSCAN hepls to extract from genomes resistance and virulence genes, and medically relevant features including the toxin gene presence and disruption. The code source is available at

Genomic taxonomy of K. pneumoniae

A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae - Hennart et al. 2022 has been published on Molecular Biology and Evolution!

LINcodes are now being defined in BIGSdb_Klebsiella based on the 629-loci cgMLST scheme. Find out more about LIN codes in BIGSdb here.

Upgraded to 1.35.1

BIGSdb pasteur is now in 1.35.1:

  • Version 1.34 provides support for LINcodes based on cgMLST schemes. See for more information about LINcodes.
  • Version 1.35 adds support for alternative codon tables.

More information are available here

Rss feed available

You can now follow the latest news posted in BIGSdb pasteur with your favorite news/rss feed aggregator.

KlebNET Genomic Surveillance Platform

Website for the #KlebNET Genomic Surveillance Platform is now live!

KlebNET-GSP provides the scientific community with a unified genomic surveillance platform with tailored analytics for the Klebsiella pneumoniae species complex (KpSC) wihle developing an international network of scientists involved in Klebsiella research and building capacity in genomics.

Check it out at

Don't forget to explore the News section for coming up events and training workshops, and to subscribe to the klebnet Google Group

Genomic library of Bordetella

Genomic library of Bordetella - Bridel et al. preprint has been published in biorXiv!

A unified library of Bordetella genomes has been set-up by merging previously existing Oxford and Pasteur databases, importing genomes from public repositories, and developing harmonized genotyping schemes. A genus-wide cgMLST genotyping scheme was developed and 18 putative novel species found. Specific schemes were developed to define antigenic, virulence and macrolide resistance profiles.

Access the Bordetella genomic library at

The genomic platform provides an expandable resource for unified genotyping of Bordetella strains and will hopefully facilitate collective evolutionary and epidemiological understanding of the reemergence of whooping cough and other Bordetella infections.

A new website

A new website is welcoming you, we hope you appreciate. Don't forget to star your favorite bacterias !

If you find any issue, do not hesitate to contact us.

Diphtheria MLST strain nomenclature

The MLST strain nomenclature service for diphtheriae/ulcerans strains is now available. This nomenclature has been earlier mantained by Martin Maiden and Keith Jolley at the University of Oxford, and now migrated by Sebastien Bridel to BIGSdb-Pasteur

Upgraded to 1.32.2

BIGSdb pasteur is now in 1.32.2:

  • a customizable dashboard allows you to visualize key information such as geographical distribution, or number of isolates available in the database
  • the Microreact plugin have been updated following breaking changes introduced on the Microreact website

More information are available here

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