Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type-specific adaptation.
Health-care-associated infections by multi-drug-resistant bacteria constitute one of the greatest challenges to modern medicine. Bacterial pathogens devise various mechanisms to withstand the activity of a wide range of antimicrobial compounds, among which the acquisition of carbapenemases is one of the most concerning. In Klebsiella pneumoniae, the dissemination of the K. pneumoniae carbapenemase is tightly connected to the global spread of certain clonal lineages. Although antibiotic resistance is a key driver for the global distribution of epidemic high-risk clones, there seem to be other adaptive traits that may explain their success. Here, we exploited the power of deep transcriptome profiling (RNA-seq) to shed light on the transcriptomic landscape of 37 clinical K. pneumoniae isolates of diverse phylogenetic origins. We identified a large set of 3346 genes which was expressed in all isolates. While the core-transcriptome profiles varied substantially between groups of different sequence types, they were more homogenous among isolates of the same sequence type. We furthermore linked the detailed information on differentially expressed genes with the clinically relevant phenotypes of biofilm formation and bacterial virulence. This allowed for the identification of a diminished expression of biofilm-specific genes within the low biofilm producing ST258 isolates as a sequence type-specific trait.
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Sebastian
S
Bruchmann
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Uthayakumar
U
Muthukumarasamy
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Sarah
S
Pohl
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Matthias
M
Preusse
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Agata
A
Bielecka
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
Tanja
T
Nicolai
Medizinisches Labor Ostsachsen, Mikrobiologie, Görlitz, Germany.
Isabell
I
Hamann
Medizinisches Labor Ostsachsen, Mikrobiologie, Görlitz, Germany.
Roger
R
Hillert
Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany.
Axel
A
Kola
Institute of Hygiene and Environmental Medicine, Charité University Medicine Berlin, Berlin, Germany.
Petra
P
Gastmeier
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Denitsa
D
Eckweiler
Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.|Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, A Joint Venture of the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany.
Susanne
S
Häussler
D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D018441:Biofilms / Q000254:growth & development*; D003428:Cross Infection / Q000382:microbiology*; D003430:Cross-Sectional Studies; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D020869:Gene Expression Profiling; D014644:Genetic Variation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007711:Klebsiella pneumoniae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D007814:Larva / Q000382:microbiology; D008969:Molecular Sequence Data; D009036:Moths / Q000382:microbiology; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D001618:beta-Lactamases / Q000235:genetics* / Q000378:metabolism
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001618:beta-Lactamases; C063912:carbapenemase