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

• Published in: Antimicrobial resistance & infection control Vol. 7; no. 1; p. 62
• Main Authors: Becker, Laura, Kaase, Martin, Pfeifer, Yvonne, Fuchs, Stephan, Reuss, Annicka, von Laer, Anja, Sin, Muna Abu, Korte-Berwanger, Miriam, Gatermann, Sören, Werner, Guido
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 02.05.2018; BioMed Central; BMC
• Subjects: Anti-Bacterial Agents - therapeutic use; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; beta-Lactamases - genetics; beta-Lactamases - metabolism; Genetic aspects; Genome, Bacterial - genetics; Genotypes; Germany - epidemiology; Health aspects; Humans; Hypermucoviscous; Hypervirulent; Klebsiella; Klebsiella Infections - drug therapy; Klebsiella Infections - epidemiology; Klebsiella Infections - microbiology; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - isolation & purification; Klebsiella pneumoniae - metabolism; KPC; Microbial drug resistance; Multilocus Sequence Typing; OXA-48; Polymorphism, Single Nucleotide - genetics; ST23; ST258; Whole Genome Sequencing; Germany; Hypermucoviscous; K1 capsule; ST23; Hypervirulent; OXA-48; ST258; KPC
• ISSN: 2047-2994; 2047-2994
• DOI: 10.1186/s13756-018-0352-y

By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing isolated from hospitalized patients in Germany between 2008 and 2014. We selected a representative subset of 107 carbapenemase-producing 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, gene/ type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on 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 strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European 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. Our study results suggest prevalence of "classical" 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 isolates outside Asia is highly worrisome and requires intense molecular surveillance.