Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014
Abstract 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...
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| Language: | English |
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BMC
2018-05-01
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| Series: | Antimicrobial Resistance and Infection Control |
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| Online Access: | http://link.springer.com/article/10.1186/s13756-018-0352-y |
| _version_ | 1818444316276686848 |
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| author | Laura Becker Martin Kaase Yvonne Pfeifer Stephan Fuchs Annicka Reuss Anja von Laer Muna Abu Sin Miriam Korte-Berwanger Sören Gatermann Guido Werner |
| author_facet | Laura Becker Martin Kaase Yvonne Pfeifer Stephan Fuchs Annicka Reuss Anja von Laer Muna Abu Sin Miriam Korte-Berwanger Sören Gatermann Guido Werner |
| author_sort | Laura Becker |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-14T19:14:00Z |
| format | Article |
| id | doaj.art-bd75abadb9e24fc9b519da30dd251b20 |
| institution | Directory Open Access Journal |
| issn | 2047-2994 |
| language | English |
| last_indexed | 2024-12-14T19:14:00Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
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| series | Antimicrobial Resistance and Infection Control |
| spelling | doaj.art-bd75abadb9e24fc9b519da30dd251b202022-12-21T22:50:40ZengBMCAntimicrobial Resistance and Infection Control2047-29942018-05-017111210.1186/s13756-018-0352-yGenome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014Laura Becker0Martin Kaase1Yvonne Pfeifer2Stephan Fuchs3Annicka Reuss4Anja von Laer5Muna Abu Sin6Miriam Korte-Berwanger7Sören Gatermann8Guido Werner9Robert Koch InstituteNational Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr-University BochumRobert Koch InstituteRobert Koch InstituteRobert Koch InstituteRobert Koch InstituteRobert Koch InstituteNational Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr-University BochumNational Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr-University BochumRobert Koch InstituteAbstract 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.http://link.springer.com/article/10.1186/s13756-018-0352-yKPCOXA-48ST258HypermucoviscousHypervirulentST23 |
| spellingShingle | Laura Becker Martin Kaase Yvonne Pfeifer Stephan Fuchs Annicka Reuss Anja von Laer Muna Abu Sin Miriam Korte-Berwanger Sören Gatermann Guido Werner Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014 Antimicrobial Resistance and Infection Control KPC OXA-48 ST258 Hypermucoviscous Hypervirulent ST23 |
| 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 | KPC OXA-48 ST258 Hypermucoviscous Hypervirulent ST23 |
| url | http://link.springer.com/article/10.1186/s13756-018-0352-y |
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