Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions. / Pei, Na; Li, Yanming; Liu, Chunjiao; Jian, Zijuan; Liang, Tianzhu; Zhong, Yiming; Sun, Wanying; He, Jingxuan; Cheng, Xinyi; Li, Hongling; Lei, Xiaole; Liu, Xin; Deng, Ziqing; Liu, Qingxia; Chen, Xia; Yan, Qun; Kristiansen, Karsten; Li, Junhua; Liu, Wenen.

In: Microbiology Spectrum, Vol. 10, No. 2, e02698-21, 2022.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Pei, N, Li, Y, Liu, C, Jian, Z, Liang, T, Zhong, Y, Sun, W, He, J, Cheng, X, Li, H, Lei, X, Liu, X, Deng, Z, Liu, Q, Chen, X, Yan, Q, Kristiansen, K, Li, J & Liu, W 2022, 'Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions', Microbiology Spectrum, vol. 10, no. 2, e02698-21. https://doi.org/10.1128/spectrum.02698-21

APA

Pei, N., Li, Y., Liu, C., Jian, Z., Liang, T., Zhong, Y., Sun, W., He, J., Cheng, X., Li, H., Lei, X., Liu, X., Deng, Z., Liu, Q., Chen, X., Yan, Q., Kristiansen, K., Li, J., & Liu, W. (2022). Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions. Microbiology Spectrum, 10(2), [e02698-21]. https://doi.org/10.1128/spectrum.02698-21

Vancouver

Pei N, Li Y, Liu C, Jian Z, Liang T, Zhong Y et al. Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions. Microbiology Spectrum. 2022;10(2). e02698-21. https://doi.org/10.1128/spectrum.02698-21

Author

Pei, Na ; Li, Yanming ; Liu, Chunjiao ; Jian, Zijuan ; Liang, Tianzhu ; Zhong, Yiming ; Sun, Wanying ; He, Jingxuan ; Cheng, Xinyi ; Li, Hongling ; Lei, Xiaole ; Liu, Xin ; Deng, Ziqing ; Liu, Qingxia ; Chen, Xia ; Yan, Qun ; Kristiansen, Karsten ; Li, Junhua ; Liu, Wenen. / Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions. In: Microbiology Spectrum. 2022 ; Vol. 10, No. 2.

Bibtex

@article{1667f5e3a9ed4e7ea751615678b51511,
title = "Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions",
abstract = "Global dissemination of K. pneumoniae clones poses health hazards to the public. Genomic epidemiology studies with comprehensive data set further revealed clone divergence, showing a high complexity in evolution. Moreover, clones carrying both acquired virulent and antimicrobial-resistant genes emerged and might replace the carbapenem-resistant clones. Co-occurrence of virulence and resistance is emerging. An unbiased collection of 3,061 clinical K. pneumoniae isolates (January 5, 2013 to July 24, 2018) underwent whole-genome sequencing. Pairwise core-genome single-nucleotide polymorphism (cgSNP) distances identified clone divergence and transmission events. A sum of 2,193 nonduplicated genomes clustered into four phenotypically indistinguishable species complexes. 93% (n = 2,035) were KpI with its largest clonal group (CG) being CG11 (n = 406). Three hundred ninety-three were ST11 and three hundred seventy-four carried blaKPC-2. Noticeably, CG11 is divided into two main subclones based on the capsule synthesis K loci (KL). CG11-KL64 showed a clear hypervirulent plus antimicrobial-resistant (hv+AMR) characteristic. Besides, the phylogenetic structure revealed the clone divergence of CG25, and this is the first report with sufficient CG25 genomes to identify the divergence. The outcomes of the hv+AMR CG25 cluster 1 affected patients were poorer (P < 0.05). Moreover, two episodes of strain transmissions were associated with CG25 cluster 1. Other transmissions were associated with ST20 and ST307. Genomic epidemiology identified clone divergence of CG11 and CG25. The hv+AMR subclones pose greater threats on a global scale. Nosocomial transmissions of the high-risk clones raised our concerns about the evolution and transmission of emerging clones among newborns and critically ill patients. IMPORTANCE The convergence of AMR and acquired virulence posing higher risks to the public is a focusing point. With sufficient genomes and genotypes, we successfully identify the convergence in two subclones, the previously reported CG11-KL64, and the newly reported CG25 cluster 1. The novel finding of the CG25 divergence was not only revealed by the phylogenetic tree but also confirmed by the clinical outcome data and the accessory genome patterns. Moreover, the transmission subclones circulated in two clinically important wards highlights the deficiency of infection control program using conventional methods. Without the assistance of whole-genome sequencing, the transmissions of high-risk clones could not be identified.",
keywords = "Anti-Bacterial Agents/pharmacology, Clone Cells, Drug Resistance, Multiple, Bacterial/genetics, Genomics, Humans, Infant, Newborn, Klebsiella Infections/epidemiology, Klebsiella pneumoniae/genetics, Microbial Sensitivity Tests, Phylogeny, beta-Lactamases/genetics",
author = "Na Pei and Yanming Li and Chunjiao Liu and Zijuan Jian and Tianzhu Liang and Yiming Zhong and Wanying Sun and Jingxuan He and Xinyi Cheng and Hongling Li and Xiaole Lei and Xin Liu and Ziqing Deng and Qingxia Liu and Xia Chen and Qun Yan and Karsten Kristiansen and Junhua Li and Wenen Liu",
year = "2022",
doi = "10.1128/spectrum.02698-21",
language = "English",
volume = "10",
journal = "Microbiology spectrum",
issn = "2165-0497",
publisher = "American Society for Microbiology",
number = "2",

}

RIS

TY - JOUR

T1 - Large-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions

AU - Pei, Na

AU - Li, Yanming

AU - Liu, Chunjiao

AU - Jian, Zijuan

AU - Liang, Tianzhu

AU - Zhong, Yiming

AU - Sun, Wanying

AU - He, Jingxuan

AU - Cheng, Xinyi

AU - Li, Hongling

AU - Lei, Xiaole

AU - Liu, Xin

AU - Deng, Ziqing

AU - Liu, Qingxia

AU - Chen, Xia

AU - Yan, Qun

AU - Kristiansen, Karsten

AU - Li, Junhua

AU - Liu, Wenen

PY - 2022

Y1 - 2022

N2 - Global dissemination of K. pneumoniae clones poses health hazards to the public. Genomic epidemiology studies with comprehensive data set further revealed clone divergence, showing a high complexity in evolution. Moreover, clones carrying both acquired virulent and antimicrobial-resistant genes emerged and might replace the carbapenem-resistant clones. Co-occurrence of virulence and resistance is emerging. An unbiased collection of 3,061 clinical K. pneumoniae isolates (January 5, 2013 to July 24, 2018) underwent whole-genome sequencing. Pairwise core-genome single-nucleotide polymorphism (cgSNP) distances identified clone divergence and transmission events. A sum of 2,193 nonduplicated genomes clustered into four phenotypically indistinguishable species complexes. 93% (n = 2,035) were KpI with its largest clonal group (CG) being CG11 (n = 406). Three hundred ninety-three were ST11 and three hundred seventy-four carried blaKPC-2. Noticeably, CG11 is divided into two main subclones based on the capsule synthesis K loci (KL). CG11-KL64 showed a clear hypervirulent plus antimicrobial-resistant (hv+AMR) characteristic. Besides, the phylogenetic structure revealed the clone divergence of CG25, and this is the first report with sufficient CG25 genomes to identify the divergence. The outcomes of the hv+AMR CG25 cluster 1 affected patients were poorer (P < 0.05). Moreover, two episodes of strain transmissions were associated with CG25 cluster 1. Other transmissions were associated with ST20 and ST307. Genomic epidemiology identified clone divergence of CG11 and CG25. The hv+AMR subclones pose greater threats on a global scale. Nosocomial transmissions of the high-risk clones raised our concerns about the evolution and transmission of emerging clones among newborns and critically ill patients. IMPORTANCE The convergence of AMR and acquired virulence posing higher risks to the public is a focusing point. With sufficient genomes and genotypes, we successfully identify the convergence in two subclones, the previously reported CG11-KL64, and the newly reported CG25 cluster 1. The novel finding of the CG25 divergence was not only revealed by the phylogenetic tree but also confirmed by the clinical outcome data and the accessory genome patterns. Moreover, the transmission subclones circulated in two clinically important wards highlights the deficiency of infection control program using conventional methods. Without the assistance of whole-genome sequencing, the transmissions of high-risk clones could not be identified.

AB - Global dissemination of K. pneumoniae clones poses health hazards to the public. Genomic epidemiology studies with comprehensive data set further revealed clone divergence, showing a high complexity in evolution. Moreover, clones carrying both acquired virulent and antimicrobial-resistant genes emerged and might replace the carbapenem-resistant clones. Co-occurrence of virulence and resistance is emerging. An unbiased collection of 3,061 clinical K. pneumoniae isolates (January 5, 2013 to July 24, 2018) underwent whole-genome sequencing. Pairwise core-genome single-nucleotide polymorphism (cgSNP) distances identified clone divergence and transmission events. A sum of 2,193 nonduplicated genomes clustered into four phenotypically indistinguishable species complexes. 93% (n = 2,035) were KpI with its largest clonal group (CG) being CG11 (n = 406). Three hundred ninety-three were ST11 and three hundred seventy-four carried blaKPC-2. Noticeably, CG11 is divided into two main subclones based on the capsule synthesis K loci (KL). CG11-KL64 showed a clear hypervirulent plus antimicrobial-resistant (hv+AMR) characteristic. Besides, the phylogenetic structure revealed the clone divergence of CG25, and this is the first report with sufficient CG25 genomes to identify the divergence. The outcomes of the hv+AMR CG25 cluster 1 affected patients were poorer (P < 0.05). Moreover, two episodes of strain transmissions were associated with CG25 cluster 1. Other transmissions were associated with ST20 and ST307. Genomic epidemiology identified clone divergence of CG11 and CG25. The hv+AMR subclones pose greater threats on a global scale. Nosocomial transmissions of the high-risk clones raised our concerns about the evolution and transmission of emerging clones among newborns and critically ill patients. IMPORTANCE The convergence of AMR and acquired virulence posing higher risks to the public is a focusing point. With sufficient genomes and genotypes, we successfully identify the convergence in two subclones, the previously reported CG11-KL64, and the newly reported CG25 cluster 1. The novel finding of the CG25 divergence was not only revealed by the phylogenetic tree but also confirmed by the clinical outcome data and the accessory genome patterns. Moreover, the transmission subclones circulated in two clinically important wards highlights the deficiency of infection control program using conventional methods. Without the assistance of whole-genome sequencing, the transmissions of high-risk clones could not be identified.

KW - Anti-Bacterial Agents/pharmacology

KW - Clone Cells

KW - Drug Resistance, Multiple, Bacterial/genetics

KW - Genomics

KW - Humans

KW - Infant, Newborn

KW - Klebsiella Infections/epidemiology

KW - Klebsiella pneumoniae/genetics

KW - Microbial Sensitivity Tests

KW - Phylogeny

KW - beta-Lactamases/genetics

U2 - 10.1128/spectrum.02698-21

DO - 10.1128/spectrum.02698-21

M3 - Journal article

C2 - 35416698

VL - 10

JO - Microbiology spectrum

JF - Microbiology spectrum

SN - 2165-0497

IS - 2

M1 - e02698-21

ER -

ID: 304784463