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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
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Journal Article
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
2021
Overview
Klebsiella pneumoniae
is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of
K. pneumoniae
genome data. Here we introduce Kleborate, a tool for analysing genomes of
K. pneumoniae
and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available
Klebsiella
genomes, including clinical isolates from a pan-European study of carbapenemase-producing
Klebsiella
, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type
K. pneumoniae
from gut metagenomes.
Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ 45/23
/ Anti-Bacterial Agents - pharmacology
/ Anti-Bacterial Agents - therapeutic use
/ Bacterial Proteins - genetics
/ Cross Infection - drug therapy
/ Cross Infection - epidemiology
/ Cross Infection - microbiology
/ Drug Resistance, Multiple, Bacterial - genetics
/ Gastrointestinal Microbiome - genetics
/ Genomes
/ Genomics
/ Humanities and Social Sciences
/ Humans
/ Infant
/ Klebsiella Infections - diagnosis
/ Klebsiella Infections - drug therapy
/ Klebsiella Infections - epidemiology
/ Klebsiella Infections - microbiology
/ Klebsiella pneumoniae - genetics
/ Klebsiella pneumoniae - isolation & purification
/ Klebsiella pneumoniae - pathogenicity
/ Molecular Epidemiology - methods
/ Mutation
/ Neonates
/ Science
/ Sepsis
/ Software
