Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

Margaret M. C. Lam, Kelly L. Wyres, Sebastian Duchêne, Ryan R. Wick, Louise M. Judd, Yunn-Hwen Gan, Chu-Han Hoh, Sophia Archuleta, James S. Molton, Shirin Kalimuddin, Tse Hsien Koh, Virginie Passet, Sylvain Brisse and Kathryn E. Holt ()
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Margaret M. C. Lam: University of Melbourne
Kelly L. Wyres: University of Melbourne
Sebastian Duchêne: University of Melbourne
Ryan R. Wick: University of Melbourne
Louise M. Judd: University of Melbourne
Yunn-Hwen Gan: National University of Singapore
Chu-Han Hoh: National University of Singapore
Sophia Archuleta: National University of Singapore
James S. Molton: National University of Singapore
Shirin Kalimuddin: Singapore General Hospital
Tse Hsien Koh: Singapore General Hospital
Virginie Passet: Biodiversity and Epidemiology of Bacterial Pathogens
Sylvain Brisse: Biodiversity and Epidemiology of Bacterial Pathogens
Kathryn E. Holt: University of Melbourne

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract Severe liver abscess infections caused by hypervirulent clonal-group CG23 Klebsiella pneumoniae have been increasingly reported since the mid-1980s. Strains typically possess several virulence factors including an integrative, conjugative element ICEKp encoding the siderophore yersiniabactin and genotoxin colibactin. Here we investigate CG23’s evolutionary history, showing several deep-branching sublineages associated with distinct ICEKp acquisitions. Over 80% of liver abscess isolates belong to sublineage CG23-I, which emerged in ~1928 following acquisition of ICEKp10 (encoding yersiniabactin and colibactin), and then disseminated globally within the human population. CG23-I’s distinguishing feature is the colibactin synthesis locus, which reportedly promotes gut colonisation and metastatic infection in murine models. These data show circulation of CG23 K. pneumoniae decades before the liver abscess epidemic was first recognised, and provide a framework for future epidemiological and experimental studies of hypervirulent K. pneumoniae. To support such studies we present an open access, completely sequenced CG23-I human liver abscess isolate, SGH10.

Date: 2018
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DOI: 10.1038/s41467-018-05114-7

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