Abstract
BackgroundBy 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.MethodsWe 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.ResultsNGS-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 blaOXA-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.ConclusionsOur 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.
Highlights
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
We selected a comprehensive subset of 107 strains including only carbapenemase-producing K. pneumoniae possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1)
The number of carbapenemase-producing K. pneumoniae isolates sent to the National Reference Centre (NRC) and Robert Koch Institute (RKI) increased continuously until 2014; we tried to balance the selection of isolates over the collection period appropriately (2010, n = 20; 2011, n = 20; 2012, n = 25; 2013, n = 22; 2014, n = 13)
Summary
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. Third-generation cephalosporin-resistant and carbapenemresistant Klebsiella pneumoniae are important health-care pathogens associated with increased morbidity and mortality among high-risk patients. Recent data from the European Antimicrobial Resistance Surveillance network (EARS-Net) for health-care associated pathogens (from invasive infections) constitute a rising number of thirdgeneration cephalosporin-resistant and carbapenem-. The National Reference Centre (NRC) for Gram-negative nosocomial pathogens in Germany is challenged by analysing an increasing number of several thousand carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter each year, starting with only a few hundred isolates back in 2008/2009. The most frequent carbapenemase type in these isolates was OXA-48, followed by KPC-2/− 3 and NDM-1. The most common specified carbapenemases were OXA-48-like (53%), KPC-2/− 3 (17%) and NDM-1 (12%)(A.R., A.v.L., M.A.S., unpublished data)
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