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

BACKGROUND: Klebsiella 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...

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Autores principales: Shaidullina, Elvira R., Schwabe, Michael, Rohde, Thomas, Shapovalova, Valeria V., Dyachkova, Marina S., Matsvay, Alina D., Savochkina, Yuliya A., Shelenkov, Andrey A., Mikhaylova, Yulia V., Sydow, Katharina, Lebreton, François, Idelevich, Evgeny A., Heiden, Stefan E., Becker, Karsten, Kozlov, Roman S., Shipulin, German A., Akimkin, Vasiliy G., Lalk, Michael, Guenther, Sebastian, Zautner, Andreas E., Bohnert, Jürgen A., Mardanova, Ayslu M., Bouganim, Ruth, Marchaim, Dror, Hoff, Katharina J., Schaufler, Katharina, Edelstein, Mikhail V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9926764/
https://www.ncbi.nlm.nih.gov/pubmed/36782220
http://dx.doi.org/10.1186/s13073-023-01159-6
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author Shaidullina, Elvira R.
Schwabe, Michael
Rohde, Thomas
Shapovalova, Valeria V.
Dyachkova, Marina S.
Matsvay, Alina D.
Savochkina, Yuliya A.
Shelenkov, Andrey A.
Mikhaylova, Yulia V.
Sydow, Katharina
Lebreton, François
Idelevich, Evgeny A.
Heiden, Stefan E.
Becker, Karsten
Kozlov, Roman S.
Shipulin, German A.
Akimkin, Vasiliy G.
Lalk, Michael
Guenther, Sebastian
Zautner, Andreas E.
Bohnert, Jürgen A.
Mardanova, Ayslu M.
Bouganim, Ruth
Marchaim, Dror
Hoff, Katharina J.
Schaufler, Katharina
Edelstein, Mikhail V.
author_facet Shaidullina, Elvira R.
Schwabe, Michael
Rohde, Thomas
Shapovalova, Valeria V.
Dyachkova, Marina S.
Matsvay, Alina D.
Savochkina, Yuliya A.
Shelenkov, Andrey A.
Mikhaylova, Yulia V.
Sydow, Katharina
Lebreton, François
Idelevich, Evgeny A.
Heiden, Stefan E.
Becker, Karsten
Kozlov, Roman S.
Shipulin, German A.
Akimkin, Vasiliy G.
Lalk, Michael
Guenther, Sebastian
Zautner, Andreas E.
Bohnert, Jürgen A.
Mardanova, Ayslu M.
Bouganim, Ruth
Marchaim, Dror
Hoff, Katharina J.
Schaufler, Katharina
Edelstein, Mikhail V.
author_sort Shaidullina, Elvira R.
collection PubMed
description BACKGROUND: Klebsiella 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. METHODS: We 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. RESULTS: Clustering 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. CONCLUSIONS: To 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-023-01159-6.
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spelling pubmed-99267642023-02-15 Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395 Shaidullina, Elvira R. Schwabe, Michael Rohde, Thomas Shapovalova, Valeria V. Dyachkova, Marina S. Matsvay, Alina D. Savochkina, Yuliya A. Shelenkov, Andrey A. Mikhaylova, Yulia V. Sydow, Katharina Lebreton, François Idelevich, Evgeny A. Heiden, Stefan E. Becker, Karsten Kozlov, Roman S. Shipulin, German A. Akimkin, Vasiliy G. Lalk, Michael Guenther, Sebastian Zautner, Andreas E. Bohnert, Jürgen A. Mardanova, Ayslu M. Bouganim, Ruth Marchaim, Dror Hoff, Katharina J. Schaufler, Katharina Edelstein, Mikhail V. Genome Med Research BACKGROUND: Klebsiella 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. METHODS: We 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. RESULTS: Clustering 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. CONCLUSIONS: To 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-023-01159-6. BioMed Central 2023-02-13 /pmc/articles/PMC9926764/ /pubmed/36782220 http://dx.doi.org/10.1186/s13073-023-01159-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Shaidullina, Elvira R.
Schwabe, Michael
Rohde, Thomas
Shapovalova, Valeria V.
Dyachkova, Marina S.
Matsvay, Alina D.
Savochkina, Yuliya A.
Shelenkov, Andrey A.
Mikhaylova, Yulia V.
Sydow, Katharina
Lebreton, François
Idelevich, Evgeny A.
Heiden, Stefan E.
Becker, Karsten
Kozlov, Roman S.
Shipulin, German A.
Akimkin, Vasiliy G.
Lalk, Michael
Guenther, Sebastian
Zautner, Andreas E.
Bohnert, Jürgen A.
Mardanova, Ayslu M.
Bouganim, Ruth
Marchaim, Dror
Hoff, Katharina J.
Schaufler, Katharina
Edelstein, Mikhail V.
Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
title Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
title_full Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
title_fullStr Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
title_full_unstemmed Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
title_short Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
title_sort genomic analysis of the international high-risk clonal lineage klebsiella pneumoniae sequence type 395
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9926764/
https://www.ncbi.nlm.nih.gov/pubmed/36782220
http://dx.doi.org/10.1186/s13073-023-01159-6
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