GEO DataSets

(Submitter supplied) Antibiotic use can lead to expansion of multi-drug resistant pathobionts within the gut microbiome that can cause life-threatening infections. Selective alternatives to conventional antibiotics are in dire need. Here, we describe a Klebsiella PhageBank that enables the rapid design of antimicrobial bacteriophage cocktails to treat multi-drug resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34705

4 Samples

Download data: CSV

(Submitter supplied) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...

Organism:

Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae; Salmonella enterica; Serratia marcescens; Citrobacter rodentium

Type:

Expression profiling by high throughput sequencing

6 related Platforms

64 Samples

Download data: TXT

(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:

Escherichia coli; Klebsiella pneumoniae

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:

Pseudomonas aeruginosa; Klebsiella pneumoniae; Enterococcus faecalis; Escherichia coli

Type:

Expression profiling by high throughput sequencing

5 related Platforms

35 Samples

Download data: TSV, 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:

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

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:

Klebsiella pneumoniae subsp. pneumoniae; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30661 GPL24247 GPL30662

15 Samples

Download data: H5, TSV, TXT

(Submitter supplied) Transcriptomic analysis of Aspergillus fumigatus and Klebsiella pneumoniae grown as single and mixed biofilms.

Organism:

Klebsiella pneumoniae; Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23160 GPL25164 GPL32070

9 Samples

Download data: XLSX

(Submitter supplied) Klebsiella pneumoniae poses significant threat to global health. Detailed investigation to the nature of its interaction to human epithelial cells is still lacking. OmpR is an important regulator to the expression of major outer membrane protein genes, ompF and ompC. Here, we exploited the recently described dual RNA-seq to simultaneously measure genome-wide expression of host and pathogen two hours into infection. more...

Organism:

Homo sapiens; Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25943

5 Samples

Download data: TXT

(Submitter supplied) The inappropriate use of antibiotics is a severe public health problem worldwide, contributing to the emergence of multidrug-resistant (MDR) bacteria. To explore the possible impacts of the inappropriate use of antibiotics on the immune system, we use Klebsiella pneumoniae (K. pneumoniae) infection as an example and show that imipenem increases the mortality of mice infected by MDR K. pneumoniae. Further studies demonstrate that imipenem enhances the secretion of outer membrane vesicles (OMVs) with significantly elevated presentation of GroEL, which promotes the phagocytosis of OMVs by macrophages that depends on the interaction between GroEL and its receptor LOX-1. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28669

6 Samples

Download data: TXT

(Submitter supplied) In bacteria the defence system to counter oxidative stress is orchestrated by three transcriptional factors – SoxS, SoxR and OxyR. Although the transcriptional regulon of these factors are known in many bacteria, similar data is not available for K. pneumoniae. To address this data gap, oxidative stress was induced in K. pneumoniae MGH 78578 using paraquat and the corresponding regulon was identified using RNA-seq. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25164

6 Samples

Download data: TXT