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 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.

Keywords: Hypermucoviscous; Hypervirulent; K1 capsule; KPC; OXA-48; ST23; ST258.

Fig. 1

Distribution of Klebsiella-MLST and carbapenemase types. The columns show the relative amount of corresponding sequence type (ST) within the group of carbapenemase-producing isolates (KPC-2, KPC-3, OXA-48, NDM-1)

Fig. 2

Identified plasmid replicons in 107 carbapenemase-producing K. pneumoniae isolates using NGS data and PlasmidFinder software. The inc groups were presented at the y axis and the color code refers to the corresponding carbapenemase genes (see legend)

Fig. 3

Phylogeny of 103 carbapenemase-producing K. pneumoniae isolates from German hospital patients, 2008-2014. The image shows a ML tree based on 159.154 SNPs of the core genome. A K. variicola isolate (ST906, OXA-48) served as an outgroup to root the tree (the corresponding branch is shortened 1/100). Clades of three or more isolates received an alternating colour code grey/blue. The clades are labelled with the corresponding MLST type. The outer ring corresponds to the four different carbapenemase (see Figure legend for colour code). The colour of the branches correlate with the corresponding boostrap value (light red (0) to black (100))

Fig. 4

Phylogeny of carbapenemase-producing isolates from Germany, 2008-2014 in relation to an international K. pneumoniae isolate collection. The image shows a ML tree based on 126.347 SNPs for 99 carbapenemase-producing isolates from Germany and 238 international K. pneumoniae isolates. The tree was rooted midpoint. Clades represented by two or more isolates were colour-coded/shaded (grey/blue) and the MLST type is listed. The outer ring corresponds to the origin of the strains given as a colour code (see Figure legend). The colours of the branches correlate with the corresponding boostrap value (light red (0) to black (100))