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

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 and Kathryn E. Holt ()
Additional contact information
Claire L. Gorrie: The University of Melbourne
Mirjana Mirčeta: Microbiology Unit, Alfred Pathology Service, The Alfred Hospital
Ryan R. Wick: Monash University
Louise M. Judd: Monash University
Margaret M. C. Lam: Monash University
Ryota Gomi: Monash University
Iain J. Abbott: Microbiology Unit, Alfred Pathology Service, The Alfred Hospital
Nicholas R. Thomson: Wellcome Sanger Institute
Richard A. Strugnell: The University of Melbourne
Nigel F. Pratt: Infectious Diseases Clinical Research Unit, The Alfred Hospital
Jill S. Garlick: Infectious Diseases Clinical Research Unit, The Alfred Hospital
Kerrie M. Watson: Monash University
Peter C. Hunter: Aged Care, Caulfield Hospital, Alfred Health
David V. Pilcher: Intensive Care Unit, The Alfred Hospital
Steve A. McGloughlin: Intensive Care Unit, The Alfred Hospital
Denis W. Spelman: Microbiology Unit, Alfred Pathology Service, The Alfred Hospital
Kelly L. Wyres: Monash University
Adam W. J. Jenney: The University of Melbourne
Kathryn E. Holt: Monash University

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals a diverse pathogen population, including other species within the K. pneumoniae species complex (18%). Several infections were caused by K. variicola/K. pneumoniae hybrids, one of which shows evidence of nosocomial transmission. A wide range of antimicrobial resistance (AMR) phenotypes are observed, and diverse genetic mechanisms identified (mainly plasmid-borne genes). ESBLs are correlated with presence of other acquired AMR genes (median n = 10). Bacterial genomic features associated with nosocomial onset are ESBLs (OR 2.34, p = 0.015) and rhamnose-positive capsules (OR 3.12, p

Date: 2022
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DOI: 10.1038/s41467-022-30717-6

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