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Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014

BACKGROUND: By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. METHODS: We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinic...

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Autores principales: Becker, Laura, Kaase, Martin, Pfeifer, Yvonne, Fuchs, Stephan, Reuss, Annicka, von Laer, Anja, Sin, Muna Abu, Korte-Berwanger, Miriam, Gatermann, Sören, Werner, Guido
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930415/
https://www.ncbi.nlm.nih.gov/pubmed/29744043
http://dx.doi.org/10.1186/s13756-018-0352-y
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author Becker, Laura
Kaase, Martin
Pfeifer, Yvonne
Fuchs, Stephan
Reuss, Annicka
von Laer, Anja
Sin, Muna Abu
Korte-Berwanger, Miriam
Gatermann, Sören
Werner, Guido
author_facet Becker, Laura
Kaase, Martin
Pfeifer, Yvonne
Fuchs, Stephan
Reuss, Annicka
von Laer, Anja
Sin, Muna Abu
Korte-Berwanger, Miriam
Gatermann, Sören
Werner, Guido
author_sort Becker, Laura
collection PubMed
description BACKGROUND: By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. METHODS: We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae. RESULTS: NGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of bla(OXA-48) via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany. CONCLUSIONS: Our study results suggest prevalence of “classical” K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13756-018-0352-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-59304152018-05-09 Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014 Becker, Laura Kaase, Martin Pfeifer, Yvonne Fuchs, Stephan Reuss, Annicka von Laer, Anja Sin, Muna Abu Korte-Berwanger, Miriam Gatermann, Sören Werner, Guido Antimicrob Resist Infect Control Research BACKGROUND: By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. METHODS: We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae. RESULTS: NGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of bla(OXA-48) via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany. CONCLUSIONS: Our study results suggest prevalence of “classical” K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13756-018-0352-y) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-02 /pmc/articles/PMC5930415/ /pubmed/29744043 http://dx.doi.org/10.1186/s13756-018-0352-y Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Becker, Laura
Kaase, Martin
Pfeifer, Yvonne
Fuchs, Stephan
Reuss, Annicka
von Laer, Anja
Sin, Muna Abu
Korte-Berwanger, Miriam
Gatermann, Sören
Werner, Guido
Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
title Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
title_full Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
title_fullStr Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
title_full_unstemmed Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
title_short Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
title_sort genome-based analysis of carbapenemase-producing klebsiella pneumoniae isolates from german hospital patients, 2008-2014
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930415/
https://www.ncbi.nlm.nih.gov/pubmed/29744043
http://dx.doi.org/10.1186/s13756-018-0352-y
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