Characterizing Phage Genomes for Therapeutic Applications
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 ap...
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Published in | Viruses Vol. 10; no. 4; p. 188 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Switzerland
MDPI AG
10.04.2018
MDPI |
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Abstract | 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. |
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AbstractList | 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. |
Author | Voegtly, Logan J Biswas, Biswajit Frey, Kenneth G Bishop-Lilly, Kimberly A Lueder, Matthew R Hamilton, Theron Long, Kyle A Philipson, Casandra W Rice, Gregory K Cer, Regina Z |
AuthorAffiliation | 1 Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; casandra.w.philipson.civ@mail.mil 2 Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA; logan.j.voegtly.ctr@mail.mil (L.J.V.); matthew.r.lueder.ctr@mail.mil (M.R.L.); kyle.a.long8.ctr@mail.mil (K.A.L.); gregory.k.rice.ctr@mail.mil (G.K.R.); kenneth.g.frey4.civ@mail.mil (K.G.F.); biswajit.biswas.civ@mail.mil (B.B.); regina.z.cer.ctr@mail.mil (R.Z.C.); theron.c.hamilton.mil@mail.mil (T.H.) 3 Leidos, Reston, VA 20190, USA |
AuthorAffiliation_xml | – name: 1 Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA; casandra.w.philipson.civ@mail.mil – name: 2 Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA; logan.j.voegtly.ctr@mail.mil (L.J.V.); matthew.r.lueder.ctr@mail.mil (M.R.L.); kyle.a.long8.ctr@mail.mil (K.A.L.); gregory.k.rice.ctr@mail.mil (G.K.R.); kenneth.g.frey4.civ@mail.mil (K.G.F.); biswajit.biswas.civ@mail.mil (B.B.); regina.z.cer.ctr@mail.mil (R.Z.C.); theron.c.hamilton.mil@mail.mil (T.H.) – name: 3 Leidos, Reston, VA 20190, USA |
Author_xml | – sequence: 1 givenname: Casandra W surname: Philipson fullname: Philipson, Casandra W email: casandra.w.philipson.civ@mail.mil, casandra.w.philipson.civ@mail.mil organization: Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA. casandra.w.philipson.civ@mail.mil – sequence: 2 givenname: Logan J surname: Voegtly fullname: Voegtly, Logan J email: logan.j.voegtly.ctr@mail.mil, logan.j.voegtly.ctr@mail.mil organization: Leidos, Reston, VA 20190, USA. logan.j.voegtly.ctr@mail.mil – sequence: 3 givenname: Matthew R surname: Lueder fullname: Lueder, Matthew R email: matthew.r.lueder.ctr@mail.mil, matthew.r.lueder.ctr@mail.mil organization: Leidos, Reston, VA 20190, USA. matthew.r.lueder.ctr@mail.mil – sequence: 4 givenname: Kyle A surname: Long fullname: Long, Kyle A email: kyle.a.long8.ctr@mail.mil, kyle.a.long8.ctr@mail.mil organization: Leidos, Reston, VA 20190, USA. kyle.a.long8.ctr@mail.mil – sequence: 5 givenname: Gregory K surname: Rice fullname: Rice, Gregory K email: gregory.k.rice.ctr@mail.mil, gregory.k.rice.ctr@mail.mil organization: Leidos, Reston, VA 20190, USA. gregory.k.rice.ctr@mail.mil – sequence: 6 givenname: Kenneth G surname: Frey fullname: Frey, Kenneth G email: kenneth.g.frey4.civ@mail.mil organization: Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA. kenneth.g.frey4.civ@mail.mil – sequence: 7 givenname: Biswajit surname: Biswas fullname: Biswas, Biswajit email: biswajit.biswas.civ@mail.mil organization: Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA. biswajit.biswas.civ@mail.mil – sequence: 8 givenname: Regina Z surname: Cer fullname: Cer, Regina Z email: regina.z.cer.ctr@mail.mil, regina.z.cer.ctr@mail.mil organization: Leidos, Reston, VA 20190, USA. regina.z.cer.ctr@mail.mil – sequence: 9 givenname: Theron surname: Hamilton fullname: Hamilton, Theron email: theron.c.hamilton.mil@mail.mil organization: Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA. theron.c.hamilton.mil@mail.mil – sequence: 10 givenname: Kimberly A surname: Bishop-Lilly fullname: Bishop-Lilly, Kimberly A email: kimberly.a.bishop-lilly.civ@mail.mil organization: Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD 21702, USA. kimberly.a.bishop-lilly.civ@mail.mil |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29642590$$D View this record in MEDLINE/PubMed |
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ContentType | Journal Article |
Copyright | 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2018 by the authors. 2018 |
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Keywords | viral genomes IND high-throughput sequencing best practices phage therapy |
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SubjectTerms | Alcohol Antibiotics Antimicrobial agents Bacterial infections Bacteriophages - classification Bacteriophages - genetics Bacteriophages - isolation & purification Bacteriophages - physiology best practices Contamination Drug development Drug resistance Enzymes FDA approval Genes Genetic engineering Genome, Viral - genetics Genomes Genomics Guidelines as Topic high-throughput sequencing Humans IND Infections Laboratories Lifestyles Multidrug resistance Next-generation sequencing phage therapy Phage Therapy - standards Phages Phenols Phylogeny Pipelines Reproducibility of Results Safety Therapeutic applications Toxins viral genomes Virulence Workflow |
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Title | Characterizing Phage Genomes for Therapeutic Applications |
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