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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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Project description:Lytic phages against MDR strains

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Project description:Phages against multi drug resistant bacteria

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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

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.

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Bacteriophage sp.

Project description:Aeromonas phages genome analysis

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Bacteriophage sp.

Project description:E. coli lysis phages genome analysis

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Proteomic characterization of bacteriophage peptides from mastitis producer Staphylococcus aureus by LC-ESI-MS/MS and their bacteriophage phylogenomic analysis

Project description:The present work describes LC-ESI-MS/MS analyses of tryptic digestion peptides from phages that infect Staphylococcus aureus-causing mastitis, and isolated from dairy products. A total of 1935 non-redundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 80 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, of the phage origin peptides found, eighteen of them were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides which are present in closely related phages, and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.

2021-03-25 | PXD023530 | Pride

Transcriptional, Proteomic, and Metabolic Adaptations of Gut Bacteroides and Parabacteroides Hosts to Persistent Bacteriophage Infection In Vitro

Project description:The mechanisms underlying the coexistence of crAss-like phages and other types of phages infecting Bacteroidales are not well understood. This study examines potential mechanisms that promote phage coexistence in the Bacteroidales order through RNA-seq and proteomic analysis. The analysis was performed on anaerobic bacterial cultures co-cultured with phages over a period of 5 days and corresponding control cultures without phage, with daily subculturing into FAB (Fastidious Anaerobe Broth) fresh media. The study focuses on four individual phage-bacteria pairs: Bacteroides intestinalis APC919/174-crAss001, Bacteroides xylanisolvens APCS1/XY-crAss002, Bacteroides thetaiotaomicron VPI-5482 tdk-acapsular mutant (cps) - DAC15, and Parabacteroides distasonis APCS2/PD-PDS1. Each phage-host pair used had 4 biological replicates. The samples for the analysis were collected during the bacterial mid-log phase (OD600= ~0.3) on the fifth day of co-culture, which occurred between 5-7 hours after subculture. Bacterial cultures were centrifuged at 4,500 x g for 15 min at 4 °C. Immediately after centrifugation, the supernatant was transfer to a new tube and stored at -80 °C and the pellet was carefully dried to remove any remaining liquid and also stored at -80 °C. All samples were processed for proteomics analysis in which proteins differentially expressed in control or infected sample conditions were of interest due to their potential involvement during crAss-like phage infection.

2024-12-09 | PXD057336 | Pride

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