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Viruses 2017, 9(11), 328; https://doi.org/10.3390/v9110328

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014

1
Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
2
GoSeqIt ApS, Ved Klædebo 9, 2970 Hørsholm, Denmark
3
Department of Biotechnology and Biomedicine, Technical University of Denmark, Matematiktorvet, Building 301, 2800 Kongens Lyngby, Denmark
4
Instituto de Investigaciones Biotecnológicas, Universidad de San Martín, 1650 San Martín, Buenos Aires, Argentina
*
Author to whom correspondence should be addressed.
Received: 13 October 2017 / Revised: 31 October 2017 / Accepted: 2 November 2017 / Published: 3 November 2017
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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Abstract

Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory agencies requiring a thorough characterization of the drug. Here, DNA sequencing of constituent biological entities constitutes a first step. The pyophage (PYO) cocktail is one of the main commercial products of the Georgian Eliava Institute of Bacteriophage, Microbiology and Virology and is used to cure skin infections. Since its first production in the 1930s, the composition of the cocktail has been periodically modified to add phages effective against emerging pathogenic strains. In this paper, we compared the composition of three PYO cocktails from 1997 (PYO97), 2000 (PYO2000) and 2014 (PYO2014). Based on next generation sequencing, de novo assembly and binning of contigs into draft genomes based on tetranucleotide distance, thirty and twenty-nine phage draft genomes were predicted in PYO97 and PYO2014, respectively. Of these, thirteen and fifteen shared high similarity to known phages. Eleven draft genomes were found to be common in the two cocktails. One of these showed no similarity to publicly available phage genomes. Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. aeruginosa and S. aureus were found in both cocktails. Finally, we estimated larger overlap of the PYO2000 cocktail to PYO97 compared to PYO2014. Using next generation sequencing and metagenomics analysis, we were able to characterize and compare the content of PYO cocktails separated by 17 years in time. Even though the cocktail composition is upgraded every six months, we found it to remain relatively stable over the years. View Full-Text
Keywords: PYO phage cocktail; metagenomics; human phage therapy PYO phage cocktail; metagenomics; human phage therapy
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Villarroel, J.; Larsen, M.V.; Kilstrup, M.; Nielsen, M. Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014. Viruses 2017, 9, 328.

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