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ABSTRACT: Whole-genome analysis of extended spectrum Beta-lactamase (ESBL)-producing Klebsiella pneumonia isolated from carriers admitted at orthopedic wards in Uganda and Tanzania

PROVIDER: PRJNA951629 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24046068_1.fastq.gz	Fastqsanger.gz
	SRR24046068_2.fastq.gz	Fastqsanger.gz
	SRR24046069_1.fastq.gz	Fastqsanger.gz
	SRR24046069_2.fastq.gz	Fastqsanger.gz
	SRR24046070_1.fastq.gz	Fastqsanger.gz

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Transcriptional alterations of virulence-associated genes in extended spectrum beta-lactamase (ESBL)-producing uropathogenic Escherichia coli during morphologic transitions induced by ineffective antibiotics

Project description:The present study examines changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic and in the presence of human primary bladder epithelial cells. The morphological shifts induced by ineffective antibiotics are associated with significant transcriptional virulence alterations in ESBL-producing UPEC, which may affect survival and persistence in the urinary tract.

2017-06-06 | GSE99661 | GEO

Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 E. coli to Carbapenem Exposure

Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.

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RNAseq transcriptome analysis of K. pneumoniae MS6671 and E. coli MS8345 treated with PBT2

Project description:The emergence of colistin resistance in carbapenem-resistant and extended-spectrum ß-lactamase (ESBL)-producing bacteria is a significant threat to human health, and new treatment strategies are urgently required. Here we investigated the ability of the safe-for-human use ionophore PBT2 to restore antibiotic sensitivity in several polymyxin-resistant, ESBL-producing, carbapenem resistant Gram-negative human pathogens. PBT2 was observed to resensitize Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa to last-resort polymyxin class antibiotics, including a ‘next generation’ polymyxin derivative, FADDI-287. To gain additional insight into the potential mechanism of action of PBT2, we analyzed the transcriptome of K. pneumoniae and E. coli in the presence of sub-inhibitory concentrations of PBT2. Treatment with PBT2 was associated with multiple stress responses in both K. pneumoniae and E. coli. Significant changes in the transcription of transition metal ion homeostasis genes were observed in both strains.

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Fecal Microbiota Transplantation for Extended-Spectrum Beta Lactamase Carriers.

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RNAseq transcriptome analysis of K. pneumoniae MS6671 with PBT2 and colistin

Project description:The emergence of polymyxin resistance in carbapenem-resistant and extended-spectrum -lactamase (ESBL)-producing bacteria is a critical threat to human health, and new treatment strategies are urgently required. Here, we investigated the ability of the safe-for-human use ionophore PBT2 to restore antibiotic sensitivity in polymyxin-resistant, ESBL-producing, carbapenem-resistant Gram-negative human pathogens. PBT2 was observed to resensitize Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Pseudomonas aeruginosa to last-resort polymyxin class antibiotics, including the less-toxic next-generation polymyxin derivative, FADDI-287. We were unable to select for mutants resistant to PBT2 + FADDI-287 in polymyxin resistant E. coli containing a plasmid-borne mcr-1 gene or K. pneumoniae carrying a chromosomal mgrB mutation. Using a highly invasive K. pneumoniae strain engineered for polymyxin resistance through mgrB mutation, we successfully demonstrated the efficacy of PBT2 + FADDI-287 in vivo for the treatment of Gram-negative sepsis. These data present a new treatment modality to break antibiotic resistance in high priority polymyxin-resistant Gram-negative pathogens.

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Project description:Within-host genetic diversity of extended spectrum beta-lactamase (ESBL)-producing Enterobacterales

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Extended-Spectrum Beta-Lactamase(ESBL)-producing E.coli from raw meats in Singapore markets

Project description:Extended-Spectrum Beta-Lactamase(ESBL)-producing E.coli from raw meats in Singapore markets

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Identification, synthesis, and in vitro activity of antimicrobial peptide from African catfish against the Extended-Spectrum Beta-Lactamase (ESBL) producing Escherichia coli.

Project description:The global surge in multi-drug resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has led to a growing need for new antibacterial compounds. Despite being promising, the potential of fish-derived antimicrobial peptides (AMPs) in combating ESBL-E. coli is largely unexplored. In this study, native peptides were extracted from the skin mucus of farmed African Catfish, Clarias gariepinus, using a combination of 10 % acetic acid solvent hydrolysis, 5 kDa ultrafiltration, and C18 hydrophobic interactions. Peptides were then sequenced using Orbitrap Fusion Lumos Tribrid Mass Spectrometry. The identified peptides were screened for potential antibacterial activity using Random Forest and AdaBoost machine learning algorithms. The most promising peptide was then chemically synthesized and evaluated in vitro for safety on Rabbit red blood cells and activity against ESBL-E. coli (ATCC 35218) utilizing the spot-on-lawn and broth dilution methods. Eight short peptides were identified with 13 - 22 amino acid residues and molecular weight range of 968.42 to 2434.11 Da. Peptide, FACAP-II was non-hemolytic to rabbit erythrocytes (p>0.05), with Zone of Inhibition (ZOI) of 22.7 mm and Minimum Inhibitory concentration (MIC) of 91.3 μg/mL. The peptide is thus a candidate antibacterial compound with enormous potential applications in the pharmaceutical industry. However, further studies are still required to establish the upscale production strategy and optimize its activity and safety in vivo.

2024-06-25 | PXD049239 | Pride

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