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) The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, and the E. coli Keio single-gene deletion library is often regarded as a gold standard for gene essentiality studies. more...

Organism:

Enterobacter cloacae; Escherichia coli; Salmonella enterica subsp. enterica serovar Typhimurium; Klebsiella pneumoniae; Citrobacter rodentium; Salmonella enterica subsp. enterica serovar Enteritidis

Type:

Other

8 related Platforms

13 Samples

Download data: TXT, XLSX

(Submitter supplied) Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging human pathogen causing invasive infection in immune-competent hosts. The hypervirulence is strongly linked to the overproduction of hypermucovisous capsule, but the underlining regulatory mechanism of hypermucoviscosity (HMV) has been elusive, especially at the post-transcriptional level mediated by small RNAs (sRNAs). Using a recently developed RNA interactome profiling approach, we have investigated the Hfq-associated sRNA regulatory network and established the first in vivo RNA-RNA interactome in HvKP. more...

Organism:

Klebsiella pneumoniae subsp. pneumoniae ATCC 43816

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33764

14 Samples

Download data: TXT

(Submitter supplied) To map the Hfq-mediated RNA regulatory network in HvKP, we harnessed the LiRIP-seq approach recently established in our lab, which enabled global profiling of RNA-RNA interactomes in live bacteria. Transformation of the pBAD-t4rnl1 plasmid into Klebsiella allowed us to express T4 RNA ligase 1 for proximity-ligation of RNAs in vivo, followed by co-immunoprecipitation (coIP) to enrich the Hfq-bound RNA transcripts (singleton reads) and ligated RNA fragments (chimeras: sRNA-mRNA, sRNA-sRNA, etc).

Organism:

Klebsiella pneumoniae subsp. pneumoniae ATCC 43816

Type:

Other

Platform:

GPL33764

6 Samples

Download data: TXT

(Submitter supplied) Conjugative plasmids are the main vehicle for the horizontal spread of antimicrobial resistance (AMR). Although AMR plasmids provide advantages to their hosts under antibiotic pressure, they can also disrupt the cell’s regulatory network, impacting the fitness of their hosts. Despite the importance of plasmid-bacteria interactions on the evolution of AMR, the effects of plasmid carriage on host physiology has remained underexplored, and most studies have focused on model bacteria and plasmids that lack clinical relevance. more...

Organism:

Klebsiella variicola; Citrobacter freundii; Klebsiella pneumoniae; Escherichia coli

Type:

Expression profiling by high throughput sequencing

6 related Platforms

78 Samples

Download data: TSV

(Submitter supplied) Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. more...

Organism:

Citrobacter freundii; Klebsiella pneumoniae; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25368 GPL34185 GPL28669

55 Samples

Download data: TSV

(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:

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

Type:

Expression profiling by high throughput sequencing

6 related Platforms

64 Samples

Download data: TXT

(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) In this study we investigate and compare DEGs of K. aerogenes macrocolonies during temperature entrainment (12:12, 35°C:36°C) and subsequent free running conditions (35°C). The goal of this experiment was to identify rhythmically expressed genes in K. aerogenes, the first human gut commensal bacterium with described circadian clock (Paulose et al. 2016). K. aerogenes circadian clock is sensitive to temperature entrainment (Paulose et al. more...

Organism:

Klebsiella aerogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30826

12 Samples

Download data: XLSX

(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