KlebNET-GSP
A global genomic surveillance platform for Klebsiella pneumoniae
The aim of KlebNET-GSP is to provide the scientific community with a unified genomic surveillance platform with tailored analytics for the Klebsiella pneumoniae species complex (KpSC). We also aim to develop an international network of scientists involved in Klebsiella research and build capacity in genomics.
News
What is Klebsiella pneumoniae?
Klebsiella pneumoniae is a Gram-negative bacterium and a major human pathogen. It is part of a species complex which also comprises other disease-causing species including Klebsiella quasipneumoniae and Klebsiella variicola.
K. pneumoniae and the related species cause a wide range of infections that can be hospital-acquired (HA) such as sepsis, pneumonia, urinary tract and wound infections. These occur most commonly among neonates, the elderly and immunocompromised patients. HA isolates are often resistant to multiple antibiotics, leading to the classification of K. pneumoniae by the World Health Organisation as a “critical” priority pathogen for which new antibiotics are urgently needed. Of particular concern are the increasing rates of resistance to carbapenems, a class of antibiotics that are vital for the treatment of severe infections.
K. pneumoniae is also responsible for community-acquired (CA) infections, including pneumonia, endophthalmitis and pyogenic liver abscess. These infections are often severe and can occur in otherwise healthy individuals. CA isolates commonly carry a repertoire of virulence genes such as siderophores. Moreover, infections involving strains with high levels of both resistance and virulence have now also been reported, leading to concern over a potential rise of serious untreatable infections.
Members of the species complex, including K. pneumoniae, are also important agents of disease in animals, particularly in livestock (e.g. bovine mastitis). They are isolated at high rates from environmental and water samples. It is therefore pivotal to apply a One Health approach to Klebsiella research and genomic surveillance in order to fully understand the ecology of these pathogens.
What is genomic surveillance?
Genomic surveillance has become fundamental to our understanding of pathogen ecology and disease dynamics. In K. pneumoniae, genomic surveillance is a useful tool to monitor which lineages are causing disease in different countries and settings (HA or CA), and how these lineages are emerging and evolving, particularly with regards to acquisition of antimicrobial resistance and virulence genes. It can also be used to assess the diversity of serological markers, including K (capsule) and O antigens (LPS), which are potential vaccine candidates.
The availability of harmonised platforms for global genomic surveillance is key to developing a common understanding of pathogen evolution and emerging risks, and to informing control strategies.
What are the aims of KlebNET-GSP?
The primary aim of this project is to develop a comprehensive platform for global surveillance of the Klebsiella pneumoniae species complex that supports analysis of genomic data by the community. We will be developing the different analytics and features of this platform with a key objective of informing vaccine development. In particular, we will further develop and integrate existing tools including Pathogenwatch, Kleborate and BIGSdb (see below for more details), linking these also with the public sequence archives (e.g. the European Nucleotide Archive) for easy exchange of data. We also aim to improve the analytics available for Klebsiella surveillance, for example by improving our ability to predict key phenotypes such as resistance, virulence and serotype from the genotype, and developing genome-based nomenclature schemes.
We envisage that our combined scientific and technical advances will facilitate reporting of Klebsiella for public health surveillance at local, national and global scales, enabling crucial development and monitoring of interventions (e.g., vaccines).
Principal Investigators
David Aanensen
Professor, Oxford
Andrew McArthur
David Braley Chair, McMaster
Angela Dramowski
Professor, Stellenbosch
Sascha Ott
Professor, Warwick
Andrew Whitelaw
Professor, Stellenbosch
KlebNET Team
K. pneumoniae Genomes
The geographical origin of the K. pneumoniae genomic data in our integrated platform (Dec 2021). Note that K. pneumoniae is taken in the broad sense, i.e., the K. pneumoniae Species Complex (including K. variicola and other related taxa).
The Tools
Kleborate is a tool to screen genome assemblies of the K. pneumoniae species complex for genotypic markers that are of clinical and public health importance. It can be run on the command-line or via the Pathogenwatch application, and its AMR and virulence gene schemes are integrated within BIGSdb-Pasteur.
Further details can be found in the associated publication and user documentation.
Pathogenwatch is a web application that provides tailored genome analytics for a range of bacterial (and other) species, including those from the Klebsiella pneumoniae species complex, as well as visualisation tools for the integration of these analytics with epidemiological data.
Further details can be found in the associated publication and user documentation.
BIGSdb-Pasteur is a web-based platform that hosts a collection of curated databases of genome sequences and genotypes and provides universally accessible nomenclatures for referencing and comparing bacterial strains.
The platform is built on the BIGSdb software developed by Keith Jolley. Further information can be found in the associated publication and user documentation.
Please refer to Kaptive for capsule and LPS locus typing of Klebsiella, further information can be found in the associated publication and user documentation.
LIN codes, a novel approach for Genomic Taxonomy of Bacterial strains
LIN codes are numerical codes given to bacteria based on genomic fingerprinting With LIN codes, every bacterial strain has its own identifier (a short code similar to a barcode) which is easy to share and use and also indicates how much different strains are related to each other. Using LIN codes is a great way to make epidemiological surveillance simpler, more flexible and more reactive.
For full LIN codes concept, please watch a general public video at: https://www.youtube.com/watch?v=xRqydUyLcr8
please visit the genomic taxonomy platform BIGSb-Pasteur: https://bigsdb.pasteur.fr/
(see also : Preprint by Palma et al., bioRxiv, 2024 doi: https://doi.org/10.1101/2024.03.11.58….
Collaborative Consortium Projects
We coordinate collaborative consortia and meta-analyses related to Klebsiella genomics, aiming to strengthen the evidence base for interpreting genomic surveillance data. This includes the KlebNET-GSP AMR Genotype/Phenotype Consortium exploring the interpretation of antimicrobial resistance genotypes; as well as groups focused on developing a genomic risk framework, neonatal sepsis antigen distributions, and neonatal sepsis transmission dynamics
Workshops and bioinformatics training
We will hold symposia and workshops with project partners and researchers conducting clinical, public health and environmental surveillance of Klebsiella. These will seek input into the platform development to enhance its utility and adoption. We will also offer bioinformatic training. Online workshops will aim to improve participants’ understanding of key principles and methods in genomic epidemiology, and provide hands-on practical guidance on the use of bioinformatic tools for data analysis and visualisation.
Links & Contacts
Supported by the University of Oxford, Institut Pasteur and the London School of Hygiene & Tropical Medicine
Funded in part by the Gates Foundation
