A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

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 interp...

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Bibliographic Details
Published in:Nature communications Vol. 12; no. 1; pp. 4188 - 16
Main Authors: Lam, Margaret M. C., Wick, Ryan R., Watts, Stephen C., Cerdeira, Louise T., Wyres, Kelly L., Holt, Kathryn E.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 07.07.2021
Nature Publishing Group
Nature Portfolio
Subjects:
45
45/23
631/114/1314
631/326/325/2482
631/326/41/2530
692/700/478/174
Anti-Bacterial Agents - pharmacology
Anti-Bacterial Agents - therapeutic use
Antibiotics
Antimicrobial agents
Antimicrobial resistance
Associated species
Bacterial Proteins - genetics
beta-Lactamases - genetics
Carbapenemase
Clinical isolates
Cross Infection - diagnosis
Cross Infection - drug therapy
Cross Infection - epidemiology
Cross Infection - microbiology
Datasets as Topic
Drug resistance
Drug Resistance, Multiple, Bacterial - genetics
Epidemiological Monitoring
Epidemiology
Gastrointestinal Microbiome - genetics
Genome, Bacterial
Genomes
Genomics
Genotyping
Health surveillance
Humanities and Social Sciences
Humans
Infant
Infant, Newborn
Interrogation
Klebsiella
Klebsiella Infections - diagnosis
Klebsiella Infections - drug therapy
Klebsiella Infections - epidemiology
Klebsiella Infections - microbiology
Klebsiella pneumoniae
Klebsiella pneumoniae - genetics
Klebsiella pneumoniae - isolation & purification
Klebsiella pneumoniae - pathogenicity
Metagenome - genetics
Molecular Epidemiology - methods
Molecular Typing - methods
multidisciplinary
Mutation
Neonates
Phylogeny
Population structure
Public health
Science
Science (multidisciplinary)
Sepsis
Software
Virulence
Virulence - genetics
Virulence Factors - genetics
Whole Genome Sequencing
ISSN:2041-1723, 2041-1723
Online Access:Get full text
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Summary: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.
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ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-021-24448-3