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Figure S1. Origin of the 107 German carbapenemase-producing K. pneumoniae isolates. Regions are shown, where isolates originated from. Isolates from Saxony could not be elucidated further due to the lack of additional geographic information. Number of isolates is given by the size of the circle (see legend). Image is from: © Bundesamt für Kartographie und Geodäsie, Frankfurt am Main, Germany. Figure S2. Virulence gene content in 107 carbapenemase-producing K. pneumonaie isolates from Germany. Data are given in % of isolates showing possession of the corresponding gene cluster. The graph shows four most frequent virulence genes identified in more than one single isolate. Figure S3. Detailed view of the ML tree concerning ST258/ST512 – carbapenemase-producing K. pneumoniae isolates from Germany, 2008-2014. The image shows a subtree of Fig. 3 containing 52 isolates of ST258 (light violett) and ST512 (grey). Colour codes of the inner ring designate the corresponding carbapenemase type, the outer designates the wzi allele (see legend). Figure S4. ML tree of NGS-based analysis of German K. pneumoniae isolates and isolates from an international collection - detailed view of the cluster ST258/ST512 isolates. The image shows a subtree of Fig. 4 containing 66 isolates of ST258 and ST512. Colour codes of the inner ring correspond to the origin of strains, the middle ring to the carbapenemase KPC-2 or KPC-3, and the outer ring demonstrates the wzi allele type. (PPTX 1367 kb)

Table S2. Names and sequences of used primers for MLST and PCR amplification of virulence genes and β-lactamase genes. Table S3. Identified virulence genes in K. pneumoniae isolate no. 316/15 (ST23, OXA-48). Table S4. Identified wzi alleles from NGS data of 107 carbapenemase-producing K. pneumoniae from Germany. (DOCX 35 kb)

Additional file 1: Fig. S1. Long-read alignment for plasmid 1 (pPBIO1953_NDM-1). Fig. S2. Assembly graphs of the reference isolate PBIO1953 and the putative plasmid recipient isolates. Fig. S3. Plasmidogram of different bacterial isolates. Fig. S4. Global core SNP phylogeny of K. pneumoniae ST307 isolates. Fig. S5. Single-nucleotide polymorphism (SNP) distribution of K. pneumoniae ST307 isolates. Fig. S6. Missense variants in genes putatively related to colistin resistance. Fig. S7. Comparison of the closed genome of PBIO1953 (PT18) with the other isolates.

Table S2. Names and sequences of used primers for MLST and PCR amplification of virulence genes and β-lactamase genes. Table S3. Identified virulence genes in K. pneumoniae isolate no. 316/15 (ST23, OXA-48). Table S4. Identified wzi alleles from NGS data of 107 carbapenemase-producing K. pneumoniae from Germany. (DOCX 35 kb)

Figure S1. Origin of the 107 German carbapenemase-producing K. pneumoniae isolates. Regions are shown, where isolates originated from. Isolates from Saxony could not be elucidated further due to the lack of additional geographic information. Number of isolates is given by the size of the circle (see legend). Image is from: © Bundesamt für Kartographie und Geodäsie, Frankfurt am Main, Germany. Figure S2. Virulence gene content in 107 carbapenemase-producing K. pneumonaie isolates from Germany. Data are given in % of isolates showing possession of the corresponding gene cluster. The graph shows four most frequent virulence genes identified in more than one single isolate. Figure S3. Detailed view of the ML tree concerning ST258/ST512 – carbapenemase-producing K. pneumoniae isolates from Germany, 2008-2014. The image shows a subtree of Fig. 3 containing 52 isolates of ST258 (light violett) and ST512 (grey). Colour codes of the inner ring designate the corresponding carbapenemase type, the outer designates the wzi allele (see legend). Figure S4. ML tree of NGS-based analysis of German K. pneumoniae isolates and isolates from an international collection - detailed view of the cluster ST258/ST512 isolates. The image shows a subtree of Fig. 4 containing 66 isolates of ST258 and ST512. Colour codes of the inner ring correspond to the origin of strains, the middle ring to the carbapenemase KPC-2 or KPC-3, and the outer ring demonstrates the wzi allele type. (PPTX 1367 kb)