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