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

Author

Listed:
  • 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
    The University of Melbourne)

  • Margaret M. C. Lam

    (Monash University)

  • Ryota Gomi

    (Monash University
    Kyoto University)

  • Iain J. Abbott

    (Microbiology Unit, Alfred Pathology Service, The Alfred Hospital
    Monash University)

  • Nicholas R. Thomson

    (Wellcome Sanger Institute
    London School of Hygiene & Tropical Medicine)

  • 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
    Monash University)

  • Steve A. McGloughlin

    (Intensive Care Unit, The Alfred Hospital
    Monash University)

  • Denis W. Spelman

    (Microbiology Unit, Alfred Pathology Service, The Alfred Hospital
    Monash University)

  • Kelly L. Wyres

    (Monash University)

  • Adam W. J. Jenney

    (The University of Melbourne
    Microbiology Unit, Alfred Pathology Service, The Alfred Hospital
    Monash University)

  • Kathryn E. Holt

    (Monash University
    London School of Hygiene & Tropical Medicine)

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

Suggested Citation

  • 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 & , 2022. "Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30717-6
    DOI: 10.1038/s41467-022-30717-6
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    Cited by:

    1. Kai Zhou & Chun-Xu Xue & Tingting Xu & Ping Shen & Sha Wei & Kelly L. Wyres & Margaret M. C. Lam & Jinquan Liu & Haoyun Lin & Yunbo Chen & Kathryn E. Holt & Yonghong Xiao, 2023. "A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Tommi Mäklin & Harry A. Thorpe & Anna K. Pöntinen & Rebecca A. Gladstone & Yan Shao & Maiju Pesonen & Alan McNally & Pål J. Johnsen & Ørjan Samuelsen & Trevor D. Lawley & Antti Honkela & Jukka Corande, 2022. "Strong pathogen competition in neonatal gut colonisation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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