Genetic mining of newly isolated Salmophages for phage therapy

Salmophages for phage therapy

Antibiotics have long been the treatment of choice for bacterial infections, but the emergence of antibiotic resistance in many species has led to renewed interest in phage therapy.

Phages, or viruses that specifically target and infect bacteria, can be an effective means of treating bacterial infections – and they do not carry the same risk of developing resistance.

In this study, the authors set out to isolate and characterize 10 novel phages that specifically infect Salmonella enterica, a Gram-negative bacterium responsible for foodborne illness.

Using bioinformatics tools, they were able to assemble and annotate the genomes of these newly isolated phages.

The results provide valuable insights into the potential use of these phages for phage therapy against Salmonella infections.

With the growing threat of antibiotic resistance, studies such as these offer exciting possibilities for novel treatments for infectious diseases.

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On 10 August 2022, the authors Julia Gendre, Mireille Ansaldi, David R Olivenza, Yann Denis, Josep Casadesús, and Nicolas Ginet published their article: Genetic mining of newly isolated Salmophages for phage therapy.

Topics:

• Nine virulent and one moderate Salmonella phages were genetically characterized and annotated for potential use in phage therapy.
• The study used a bioinformatics pipeline to assemble genomes de novo and perform syntactic annotation.
• Genome-wide analyses were performed for taxonomic annotation using vContact2 and VICTOR.
• Functional annotation was improved by detecting distant homologies and comparisons with the PHROG database.
• Anti-CRISPR proteins were identified as putative functions relevant to phage cocktail formulation for Salmonella biocontrol.

Abstract

Salmonella enterica, a Gram-negative zoonotic bacterium, is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide.

The main reservoirs are found in poultry farms, but they are also found in wild birds.

The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections.

Here, we aimed to decipher and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy.

We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR.

We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database.

Finally, we searched for useful functions for phage therapy, such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRISPR proteins.

We, thus, were able to genetically characterize nine virulent phages and one temperate phage and identify putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.

Keywords: PHROG database; Salmonella; bacteriophages; biocontrol; functional annotation; genomic analysis; phage therapy.

Copyright: the authors.

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