Hoefer et al. has been published in medRxiv!Large-scale Corynebacterium diphtheriae outbreak among migrant populations in Europe - phenotypic and genomic analysis -
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
BIGSdb pasteur is now in 1.42.6:
- This release introduces a new plugin that provides a wrapper for ReporTree - Mixão et al. 2023 Genome Med 15:43. See https://bigsdb.readthedocs.io/en/latest/data_analysis/reportree.html for details.
- Version 1.42 improves web-based sequence scanning by showing the position of the first in-frame stop codon for loci defined as 'complete CDS' and adds an option to separate the search for start and stop codons.
More information are available here
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.
Hennart et al. preprint has been published in biorXiv!Corynebacterium diphtheriae reemergence, genomic framework and bioinformatics tool to detect antimicrobial resistance and virulence -
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 https://gitlab.pasteur.fr/BEBP/diphtoscan
Hennart et al. 2022 has been published on Molecular Biology and Evolution!A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae -
LINcodes are now being defined in BIGSdb_Klebsiella based on the 629-loci cgMLST scheme. Find out more about LIN codes in BIGSdb here.
#KlebNET Genomic Surveillance Platform is now live!Website for the
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
Bridel et al. preprint has been published in biorXiv!Genomic library of Bordetella -
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.
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