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Bacteriophage

ABSTRACT: Natural phages isolated from holy rivers of Kathmandu against multi-drug resistant human pathogen (Escherichia coli, Klebsiella and Salmonella) collected from hospital. Genome sequencing

PROVIDER: PRJNA383466 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5460624_1.fastq.gz	Fastqsanger.gz
	SRR5460624_2.fastq.gz	Fastqsanger.gz
	SRR5460625_1.fastq.gz	Fastqsanger.gz
	SRR5460625_2.fastq.gz	Fastqsanger.gz
	SRR5460626_1.fastq.gz	Fastqsanger.gz

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Bacteriophage sp.

Project description:Lytic phages against MDR strains

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Project description:Phages against multi drug resistant bacteria

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Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae

Project description: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. pneumoniae, we identified host factors required for phage infection in major Klebsiella phage families. Leveraging the diversity of the PhageBank and experimental evolution strategies, we formulated combinations of phages that minimize the occurrence of phage resistance in vitro. Optimized bacteriophage cocktails selectively suppressed the burden of multi-drug resistant K. pneumoniae in the mouse gut microbiome and drove bacterial populations to lose key virulence factors that act as phage receptors. Further, phage-mediated diversification of bacterial populations in the gut enabled co-evolution of phage variants with higher virulence and a broader host range. Altogether, the Klebsiella PhageBank represents a roadmap for both phage researchers and clinicians to enable phage therapy against a critical multidrug-resistant human pathogen.

2024-10-01 | GSE272297 | GEO

The PA3040-PA3042 operon influences biofilm formation and bacteriophage survival in Pseudomonas aeruginosa

Project description:Bacteriophages (hereafter “phages”) are ubiquitous predators of bacteria in the natural world, but interest is growing in their development into antibacterial therapy as complement or replacement for antibiotics. However, bacteria have evolved a huge variety of anti-phage defense systems allowing them to resist phage lysis to a greater or lesser extent, and in pathogenic bacteria these inevitably impact phage therapy outcomes. In addition to dedicated phage defense systems, some aspects of the general stress response also impact phage susceptibility, but the details of this are not well known. In order to elucidate these factors in the opportunistic pathogen Pseudomonas aeruginosa, we used the laboratory-conditioned strain PAO1 as host for phage infection experiments as it is naturally poor in dedicated phage defense systems. Screening by transposon insertion sequencing indicated that the uncharacterized operon PA3040-PA3042 was potentially associated with resistance to lytic phages. However, we found that its primary role appeared to be in regulating biofilm formation. Its expression was highly growth-phase dependent and responsive to phage infection and cell envelope stress.

2023-10-30 | GSE246284 | GEO

Bacteriophage sp.

Project description:Aeromonas phages genome analysis

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Bacteriophage sp.

Project description:Non-O157 STEC phages

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The component parts of bacteriophage virions accurately defined by a new machine-learning approach built on evolutionary features.

Project description:Klebsiella pneumoniae has risen to prominence as a major threat to human health, with hypervirulent and drug-resistant lineages spreading globally. Given their antimicrobial resistant phenotypes, new therapies are required for the treatment of these infections, and bacteriophages (phages) that kill Klebsiella are being identified for use in phage therapy. In order to circumvent the evolution of phage-resistance taking hold the way that drug-resistance has, clear and considered actions are needed in selecting the phages that would be used in therapeutic cocktails. It is known that annotation of phage genomes is poor, potentially obscuring those phages with the most therapeutic potential. Here we show that phages isolated from infrequently sampled environments have features of therapeutic potential and developed a computational tool called STEP3 to understand the evolutionary features that distinguish the component parts of diverse phages, features that proved particularly suitable to detection of virion proteins with only distantly related homologies. These features were integrated into an ensemble framework to achieve a stable and robust prediction performance by STEP3. Proteomics-based analysis of two phages validated the prediction accuracy of STEP3 and revealed the virions contain component parts that include DNA-binding factors, otherwise unrecognizable capsule degradation enzymes and membrane translocation factors.

2021-04-30 | PXD020607 | Pride

Bacteriophage sp.

Project description:E. coli lysis phages genome analysis

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Bacteriophage sp.

Project description:Whole genome analysis of kk-collection phages

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Urinary bacteriophage cooperation with bacterial pathogens during human urinary tract infections supports lysogenic phage therapy

Project description:Despite much promise to overcome drug-resistant infections, clinical studies of bacteriophage anti-bacterial therapy have failed to show durable effectiveness. Although lysogeny plays an important role in bacterial physiology, its significance in diverse microbiomes remains under-studied. Here, we tested the hypotheses that 1) urinary microbiome phage populations switch to a higher relative proportion of temperate phages and 2) the activity of the phage recombination machinery (integration / excision / transposition) is higher during human urinary tract infections (UTIs) than in non-infected urinary tracts. Using human urine, model organisms, mass spectrometry, gene expression analysis, and the phage phenotype prediction model BACPHLIP, the results support our hypotheses at the functional protein and gene level. From a human health perspective, are temperate phages part of the problem and not the defenders we wished them to be? These data support the use of lysogenic phages as a therapeutic Trojan Horses.

2025-01-17 | PXD059932 | Pride

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