RT Journal Article SR Electronic T1 Genomic surveillance framework and global population structure for Klebsiella pneumoniae JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.12.14.422303 DO 10.1101/2020.12.14.422303 A1 Margaret M. C. Lam A1 Ryan R. Wick A1 Stephen C. Watts A1 Louise T. Cerdeira A1 Kelly L. Wyres A1 Kathryn E. Holt YR 2021 UL http://biorxiv.org/content/early/2021/02/05/2020.12.14.422303.abstract AB K. 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.Competing Interest StatementThe authors have declared no competing interest.