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 https://doi.org/10.1101/2021.07.26.453808 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 klebnet.org

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 https://bigsdb.pasteur.fr/bordetella/

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 https://bigsdb.pasteur.fr/diphtheria/.

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

Genomic taxonomy of K. pneumoniae

A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae - Hennart et al. preprint has been published on bioRxiv!

A proposal to build genomic taxonomies of bacterial strains using a dual approach combining single linkage clustering and life identification numbers into a single cgMLST-based multilevel classification system.

Here, the 634-loci strict core genome MLST (scgMLSTv1) initially identified in Bialek-Davenet et al, 2014 was reassessed, and an improved cgMLST scheme of 629-loci (scgMLST629_S) for K. pneumoniae Species Complex genotyping was provided.

This Hennart et al. 629-loci cgMLST scheme has been incorporated into the BIGSdb-Klebsiella nomenclature server.

Upgraded to 1.30.0

BIGSdb pasteur is now in 1.30.0:

  • enabling support of iTOL

More information are available here

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