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

TLDR

Klebsiella pneumoniae is a leading cause of antimicrobial‑resistant healthcare‑associated infections, neonatal sepsis, community‑acquired liver abscess, and chronic intestinal diseases, yet its diverse and complex population structure complicates genomic analysis. The authors present Kleborate, a tool that consolidates interrogation of clinically relevant genomic features of K. pneumoniae and its related species complex. Kleborate offers a framework for genomic surveillance and epidemiology across research, clinical, and public health settings, enabling analysis of publicly available genomes—including a pan‑European carbapenemase‑producing Klebsiella study—and detection and typing of K.

Abstract

Abstract 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.