Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395

Genome Medicine

Research

Andrey A. Shelenkov¹  Vasiliy G. Akimkin¹  Yulia V. Mikhaylova¹  Ruth Bouganim²  German A. Shipulin³  Alina D. Matsvay³  Yuliya A. Savochkina³  Valeria V. Shapovalova³  Marina S. Dyachkova³  Karsten Becker⁴  Jürgen A. Bohnert⁴  Evgeny A. Idelevich⁵  Dror Marchaim⁶  Roman S. Kozlov⁷  Mikhail V. Edelstein⁷  Elvira R. Shaidullina⁷  Michael Lalk⁸  Ayslu M. Mardanova⁹  Katharina J. Hoff^1,10  Andreas E. Zautner^1,11  François Lebreton^1,12  Sebastian Guenther^1,13  Stefan E. Heiden^1,14  Michael Schwabe^1,14  Katharina Sydow^1,14  Thomas Rohde^1,14  Katharina Schaufler^1,15 

[1] Central Research Institute of Epidemiology, Moscow, Russia;Department of Internal Medicine A, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel;Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia;Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany;Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany;Institute of Medical Microbiology, University Hospital Münster, Münster, Germany;Infection Control Unit, Shamir (Assaf Harofeh) Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel;Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia;Institute of Biochemistry, University of Greifswald, Greifswald, Germany;Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia;Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany;Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany;Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, USA;Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany;Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany;Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany;Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany;

关键词: Klebsiella pneumoniae;    Recombination;    Plasmid;    Hypervirulence;    Multidrug-resistance;    Whole genome sequencing;    Carbapenem resistance;    ESBL;   

DOI  :  10.1186/s13073-023-01159-6

 received in 2022-06-23, accepted in 2023-01-20,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundKlebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage.MethodsWe computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features.ResultsClustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of “hybrid” resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype.ConclusionsTo the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.

【 授权许可】

CC BY   
© The Author(s) 2023

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