Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones

Klebsiella pneumoniae is characterised by a large number of distinct, deep-branching phylogenetic lineages (clonal groups). Individual K. pneumoniae genomes contain approximately 5500 genes, including <2000 common genes shared among most strains and 3500 drawn from an extensive pool of ≥30 000 protein-coding sequences with hundreds of antimicrobial resistance (AMR) genes. A small number of globally distributed K. pneumoniae clonal groups appear to be particularly adept at acquiring AMR genes. Genomic analyses revealed the most widely recognised AMR clone (CG258), which is associated with the dissemination of the K. pneumoniae carbapenemase gene, has evolved via a series of large-scale genomic recombination events, and shows extensive capsular antigen and AMR gene diversity. Comparatively little is known about the many other common AMR clones or those that acquire transient resistance. Antimicrobial-resistant Klebsiella pneumoniae (Kp) has emerged as a major global public health problem. While resistance can occur across a broad range of Kp clones, a small number have become globally distributed and commonly cause outbreaks in hospital settings. Here we describe recent comparative genomics investigations that have shed light on Kp population structure and the evolution of antimicrobial-resistant clones. These studies provide the basic framework within which genomic epidemiology and evolution can be understood, but have merely scratched the surface of what can and should be explored. We assert that further large-scale comparative and functional genomics studies are urgently needed to better understand the biology of this clinically important bacterium. Antimicrobial-resistant Klebsiella pneumoniae (Kp) has emerged as a major global public health problem. While resistance can occur across a broad range of Kp clones, a small number have become globally distributed and commonly cause outbreaks in hospital settings. Here we describe recent comparative genomics investigations that have shed light on Kp population structure and the evolution of antimicrobial-resistant clones. These studies provide the basic framework within which genomic epidemiology and evolution can be understood, but have merely scratched the surface of what can and should be explored. We assert that further large-scale comparative and functional genomics studies are urgently needed to better understand the biology of this clinically important bacterium.