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Open AccessArticle

Characterizing Phage Genomes for Therapeutic Applications

1
Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
2
Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA
3
Leidos, Reston, VA 20190, USA
*
Author to whom correspondence should be addressed.
Viruses 2018, 10(4), 188; https://doi.org/10.3390/v10040188
Received: 13 March 2018 / Revised: 6 April 2018 / Accepted: 9 April 2018 / Published: 10 April 2018
(This article belongs to the Special Issue Hurdles for Phage Therapy (PT) to Become a Reality)
Multi-drug resistance is increasing at alarming rates. The efficacy of phage therapy, treating bacterial infections with bacteriophages alone or in combination with traditional antibiotics, has been demonstrated in emergency cases in the United States and in other countries, however remains to be approved for wide-spread use in the US. One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates. We present the phage characterization workflow used by our team to generate data for submitting phages to the Federal Drug Administration (FDA) for authorized use. Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination. This workflow has been developed in accordance with community standards for high-throughput sequencing of viral genomes as well as principles for ideal phages used for therapy. The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria. We propose these guidelines as a minimum standard for phages being submitted to the FDA for review as investigational new drug candidates. View Full-Text
Keywords: phage therapy; viral genomes; best practices; IND; high-throughput sequencing phage therapy; viral genomes; best practices; IND; high-throughput sequencing
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Philipson, C.W.; Voegtly, L.J.; Lueder, M.R.; Long, K.A.; Rice, G.K.; Frey, K.G.; Biswas, B.; Cer, R.Z.; Hamilton, T.; Bishop-Lilly, K.A. Characterizing Phage Genomes for Therapeutic Applications. Viruses 2018, 10, 188.

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