Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

• DOI: 10.1038/s41467-022-30717-6
• Publication Date: 2022-05-31T10:03:42Z
• Authors: Claire L. Gorrie; Mirjana Mirčeta; Ryan R. Wick; Louise M. Judd; Margaret M. C. Lam; Ryota Gomi; Iain J. Abbott; Nicholas R. Thomson; Richard A. Strugnell; Nigel F. Pratt; Jill S. Garlick; Kerrie M. Watson; Peter C. Hunter; David V. Pilcher; Steve A. McGloughlin; Denis W. Spelman; Kelly L. Wyres; Adam W. J. Jenney; Kathryn E. Holt
• Keywords: Aerobactin

Abstract Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted year-long prospective surveillance study K. clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals diverse pathogen population, including other species within complex (18%). Several infections were caused variicola/K. hybrids, one shows evidence nosocomial transmission. A wide range antimicrobial resistance (AMR) phenotypes observed, genetic mechanisms identified (mainly plasmid-borne genes). ESBLs correlated with acquired AMR genes (median n = 10). Bacterial genomic features associated onset (OR 2.34, p 0.015) rhamnose-positive capsules 3.12, < 0.001). Virulence plasmid-encoded (aerobactin, hypermucoidy) observed at low-prevalence (<3%), mostly community-onset cases. WGS-confirmed transmission implicated just 10% cases, but strongly 21, 1 × 10 −11 ). estimate 28% risk onward for ESBL-positive strains vs 1.7% ESBL-negative strains. These indicate that hospitalised patients due largely to strains, an additional burden from nosocomially-transmitted community-acquired hypervirulent