GEO DataSets

(Submitter supplied) Klebsiella pneumoniae poses a significant global health threat primarily attributable to its pronounced resistance. Here, we report an in vitro acquired resistance analyses of K. pneumoniae to the combination of amikacin and polymyxin B. We found some differentially expressed genes associated with the resistome of K. pneumoniae. The main differences were found in the genes aphA, asmA, phoP, and in the arn operon. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32198

6 Samples

Download data: CSV

(Submitter supplied) Purpose: This study aims to compare the transcriptome profiling (RNA-seq) of ompR mutant to that of WT and to evaluate the transcrptional regulation of OmpR in K. pneumoniae in exponential phase.

Organism:

Klebsiella pneumoniae ATCC 43816

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31955

4 Samples

Download data: XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Klebsiella pneumoniae subsp. pneumoniae

Type:

Other

Platforms:

GPL33821 GPL33822

20 Samples

Download data

(Submitter supplied) The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress-resistance, however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq, and to monitor Hfq-mediated RNA-RNA interactions. more...

Organism:

Klebsiella pneumoniae subsp. pneumoniae

Type:

Other

Platform:

GPL33821

8 Samples

Download data: XLSX

(Submitter supplied) The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress-resistance, however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq, and to monitor Hfq-mediated RNA-RNA interactions. more...

Organism:

Klebsiella pneumoniae subsp. pneumoniae

Type:

Other

Platform:

GPL33822

4 Samples

Download data: XLSX

(Submitter supplied) The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress-resistance, however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq, and to monitor Hfq-mediated RNA-RNA interactions. more...

Organism:

Klebsiella pneumoniae subsp. pneumoniae

Type:

Other

Platform:

GPL33821

8 Samples

Download data: XLSX

(Submitter supplied) Carbapenem-resistantKlebsiella pneumoniae(CR-Kp) is significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract, where the bacterium is usually present at low density, but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28669

23 Samples

Download data: TXT

(Submitter supplied) Compared with HKE9, HKE9-M-rpoS (rpoS knockout in hypervirulent Klebsiella pneumoniae strain HKE9) had 624 genes expressed significantly different, among which 148 genes were significantly up-regulated and 476 genes were significantly down-regulated, 586 genes on chromosomes, 10 genes on circular plasmid and 28 genes on linear plasmid; HKE9-C-M-rpoS had 746 genes expressed significantly different, among which 286 genes were significantly up-regulated and 460 genes were significantly down-regulated, 727 genes on chromosomes, 11 genes on circular plasmid and 8 genes on linear plasmid. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28669

9 Samples

Download data: TXT

(Submitter supplied) hvKP ATCC43816 and its lytic phage H5 were employed as a phage-antibiotic combination model. Based on the comprehensive characterization of phages, including cryo-electron microscopy, we evaluated the synergic effect of H5 on bacterial killing in vitro when combined with multiple antibiotics, and analyzed the advantages of phage-antibiotic combinations from an evolutionary perspective and proposes a novel PAS mechanism by using ceftazidime as an example.

Organism:

Klebsiella pneumoniae subsp. pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30661

15 Samples

Download data: TXT

(Submitter supplied) Determination of the effect of the mutation in PhoQ on global gene expression of Kp209

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25165

6 Samples

Download data: XLSX

(Submitter supplied) CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials against multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae. Comparing different Cas nucleases, we found that AsCas12a exhibited robust targeting across different strains. more...

Organism:

Klebsiella pneumoniae; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL25165

20 Samples

Download data: TSV

(Submitter supplied) To investigate of phenotypic effects of antibacterial synergy and gene expression analysis

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32198

4 Samples

Download data: TXT

(Submitter supplied) The increasing antibiotic resistance of Klebsiella pneumoniae poses a serious threat to global public health. To investigate the antibiotic resistance mechanism of Klebsiella pneumonia, we performed gene expression profiling analysis using RNA-seq data for clinical isolates of Klebsiella pneumonia, KPN16 and ATCC13883. Our results showed that mutant strain KPN16 is likely to act against the antibiotics through increased increased butanoate metabolism and lipopolysaccharide biosynthesis, and decreased transmembrane transport activity.

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28669

6 Samples

Download data: TXT

(Submitter supplied) Purpose: This study aims to compare the transcriptome profiling (RNA-seq) of ompR mutant to that of WT and to evaluate the transcrptional regulation of OmpR in K. pneumoniae.

Organism:

Klebsiella pneumoniae ATCC 43816

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31955

4 Samples

Download data: XLS

(Submitter supplied) In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations.

Organism:

Escherichia coli; Enterococcus faecalis; Pseudomonas aeruginosa; Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

5 related Platforms

35 Samples

Download data: TSV, TXT

(Submitter supplied) The transcriptional, epigenomic, and genomic profiles of K. pneumoniae isolates were characterised to identify novel colistin and carbapenem resistance mechanisms. The genomic DNA and total RNA of the isolates were isolated and sequenced on PacBio.

Organism:

Enterobacter cloacae; Klebsiella pneumoniae; Enterobacter bugandensis; Enterobacter cloacae complex sp. R_G8; Acinetobacter baumannii; Enterobacter asburiae

Type:

Expression profiling by high throughput sequencing; Other

12 related Platforms

22 Samples

Download data: CSV, DIFF, GFF, PDF

(Submitter supplied) Carbapenem-resistant Klebsiella pneumoniae classified as multilocus sequence type 258 (ST258)are a problem in healthcare settings in many countries globally. ST258 isolates are resistant tomultiple classes of antibiotics and can cause life-threatening infections, such as pneumonia andsepsis, in susceptible individuals. Treatment strategies for such infections are limited. Hence,understanding the response of K. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32198

18 Samples

Download data: TXT

(Submitter supplied) Multispecies biofilms are the predominant form of bacterial growth in natural and human-associated environments. Although the pathways involved in monospecies biofilm have been well characterized, less is known about the metabolic pathways and emergent traits of a multispecies biofilm community. Here, we performed a transcriptome survey of the developmental stages of a 3-species biofilm community and combined it with quantitative imaging and growth experiments. more...

Organism:

Klebsiella pneumoniae KP-1; Pseudomonas protegens Pf-5; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

4 related Platforms

48 Samples

Download data: TXT

(Submitter supplied) Metabolites generated in response to infection have a major role in shaping the nature of the immune response. We predicted that the metabolic response to the highly prevalent Klebsiella pneumoniae sequence type 258 (Kp ST258) strains is responsible for their ability to persist in the lungs, despite the expected proinflammatory signaling evoked by LPS. By combining in situ metabolic imaging and comprehensive transcriptional analyses, we demonstrate that Kp ST258 activates host glutaminolysis and fatty acid oxidation (FAO), generating an oxidant-rich microenvironment predisposed to the accumulation of anti-inflammatory monocyte populations. more...

Organism:

Mus musculus; Klebsiella pneumoniae subsp. pneumoniae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30661 GPL30662 GPL24247

15 Samples

Download data: H5, TSV, TXT

(Submitter supplied) This study aims to determine the epidemiology of Enterobacteriaceae resistant to antibiotics of last resort in pregnant women in labour at a tertiary hospital, Pretoria, South Africa. Rectal swabs shall be used to screen for colonisation with CRE and colistin-resistant Enterobacteriales in pregnant women during labour. Carbapenem and colistin-resistant Enterobacterales can cause the following infections: bacteraemia; nosocomial pneumonia; urinary tract infections, and intra-abdominal infections. more...

Organism:

Enterobacter cloacae; Klebsiella pneumoniae; Enterobacter roggenkampii

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL27625 GPL32492 GPL32493

5 Samples

Download data: GFF, XLSX