Genomic characteristics of clinically important ST11 Klebsiella pneumoniae strains worldwide

Jiankang Zhao; Chao Liu; Yingmei Liu; Yulin Zhang; Zhujia Xiong; Yanyan Fan; Xiaohui Zou; Binghuai Lu; Bin Cao

Journal of Global Antimicrobial Resistance (Sep 2020)

Genomic characteristics of clinically important ST11 Klebsiella pneumoniae strains worldwide

Jiankang Zhao,
Chao Liu,
Yingmei Liu,
Yulin Zhang,
Zhujia Xiong,
Yanyan Fan,
Xiaohui Zou,
Binghuai Lu,
Bin Cao

Affiliations

Jiankang Zhao: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Chao Liu: Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
Yingmei Liu: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Yulin Zhang: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Zhujia Xiong: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Yanyan Fan: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Xiaohui Zou: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Binghuai Lu: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
Bin Cao: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China; Tsinghua University–Peking University Joint Center for Life Sciences, Beijing, China; Corresponding author at: Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan Friendship Hospital, National Clinical Research Centre for Respiratory Disease, No. 2, East Yinghua Street, Chaoyang District, Beijing 100029, China.

Journal volume & issue: Vol. 22
pp. 519 – 526

Abstract

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Objectives: ST11 Klebsiella pneumoniae is among the most important clinical pathogens in China, and KL47 and KL64 are the dominant K types of these strains. Understanding the genomic characteristics of these strains would be critical to their anti-infection treatment. Methods: There were 364 genome sequences of ST11 K. pneumoniae strains isolated and collected from 13 countries from 2003 to 2018. These genome sequences included 338 downloaded from the National Center for Biotechnology Information (NCBI) database and 26 newly sequenced. Phylogenetic analyses of pan-genome and unique genes, and resistance and virulence gene analyses, were carried out to elucidate the molecular characteristics of these strains. Results: A total of 19 732 genes were identified from the 364 ST11 strains, and the pan-genome was open, indicating the genetic diversity of ST11 K. pneumoniae. These strains were clustered into three clades. Clade 1 contained the most various K types (14/15, 93.3%) and unique genes. KL47 and KL64 were the dominant K types of clades 2 and 3, accounting for 100% and 99.4% of strains in each clade, respectively. KL64 strains contained the most virulence genes, including iucA and rmpA, and the two genes tend to coexist. In addition, strains in clade 1 were isolated from all 13 countries; the strains in clades 2 and 3 were isolated mainly from China. Conclusions: The ST11 K. pneumoniae strain of KL64 is a newly emerging superbug, with more resistance and virulence genes in China; this was significantly different from other countries, and we should be alert to the dissemination of this subclone.

Published in Journal of Global Antimicrobial Resistance

ISSN: 2213-7165 (Print); 2213-7173 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Science: Microbiology
Website: https://www.journals.elsevier.com/journal-of-global-antimicrobial-resistance

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