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Characterization of a Novel Bacteriophage Henu2 and Evaluation of the Synergistic Antibacterial Activity of Phage-Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10020174. [PMID: 33572473 PMCID: PMC7916345 DOI: 10.3390/antibiotics10020174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus phage Henu2 was isolated from a sewage sample collected in Kaifeng, China, in 2017. In this study, Henu2, a linear double-stranded DNA virus, was sequenced and found to be 43,513 bp long with 35% G + C content and 63 putative open reading frames (ORFs). Phage Henu2 belongs to the family Siphoviridae and possesses an isometric head (63 nm in diameter). The latent time and burst size of Henu2 were approximately 20 min and 7.8 plaque forming unit (PFU)/infected cells. The Henu2 maintained infectivity over a wide range of temperature (10–60 °C) and pH values (4–12). Phylogenetic and comparative genomic analyses indicate that Staphylococcus aureus phage Henu2 should be a new member of the family of Siphoviridae class-II. In this paper, Phage Henu2 alone exhibited weak inhibitory activity on the growth of S. aureus. However, the combination of phage Henu2 and some antibiotics or oxides could effectively inhibit the growth of S. aureus, with a decrease of more than three logs within 24 h in vitro. These results provide useful information that phage Henu2 can be combined with antibiotics to increase the production of phage Henu2 and thus enhance the efficacy of bacterial killing.
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Serwer P, Wright ET. In-Gel Isolation and Characterization of Large (and Other) Phages. Viruses 2020; 12:v12040410. [PMID: 32272774 PMCID: PMC7232213 DOI: 10.3390/v12040410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.
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Hyman P. Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth. Pharmaceuticals (Basel) 2019; 12:E35. [PMID: 30862020 PMCID: PMC6469166 DOI: 10.3390/ph12010035] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 01/21/2023] Open
Abstract
For a bacteriophage to be useful for phage therapy it must be both isolated from the environment and shown to have certain characteristics beyond just killing strains of the target bacterial pathogen. These include desirable characteristics such as a relatively broad host range and a lack of other characteristics such as carrying toxin genes and the ability to form a lysogen. While phages are commonly isolated first and subsequently characterized, it is possible to alter isolation procedures to bias the isolation toward phages with desirable characteristics. Some of these variations are regularly used by some groups while others have only been shown in a few publications. In this review I will describe (1) isolation procedures and variations that are designed to isolate phages with broader host ranges, (2) characterization procedures used to show that a phage may have utility in phage therapy, including some of the limits of such characterization, and (3) results of a survey and discussion with phage researchers in industry and academia on the practice of characterization of phages.
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Affiliation(s)
- Paul Hyman
- Department of Biology/Toxicology, Ashland University, 401 College Ave., Ashland, OH 44805, USA.
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Serwer P, Wright ET, Chang JT, Liu X. Enhancing and initiating phage-based therapies. BACTERIOPHAGE 2014; 4:e961869. [PMID: 26713220 PMCID: PMC4588221 DOI: 10.4161/21597073.2014.961869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/29/2014] [Accepted: 08/29/2014] [Indexed: 02/02/2023]
Abstract
Drug development has typically been a primary foundation of strategy for systematic, long-range management of pathogenic cells. However, drug development is limited in speed and flexibility when response is needed to changes in pathogenic cells, especially changes that produce drug-resistance. The high replication speed and high diversity of phages are potentially useful for increasing both response speed and response flexibility when changes occur in either drug resistance or other aspects of pathogenic cells. We present strategy, with some empirical details, for (1) using modern molecular biology and biophysics to access these advantages during the phage therapy of bacterial infections, and (2) initiating use of phage capsid-based drug delivery vehicles (DDVs) with procedures that potentially overcome both drug resistance and other present limitations in the use of DDVs for the therapy of neoplasms. The discussion of phage therapy includes (a) historical considerations, (b) changes that appear to be needed in clinical tests if use of phage therapy is to be expanded, (c) recent work on novel phages and its potential use for expanding the capabilities of phage therapy and (d) an outline for a strategy that encompasses both theory and practice for expanding the applications of phage therapy. The discussion of DDVs starts by reviewing current work on DDVs, including work on both liposomal and viral DDVs. The discussion concludes with some details of the potential use of permeability constrained phage capsids as DDVs.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry; The University of Texas Health Science Center; San Antonio, TX USA
| | - Elena T Wright
- Department of Biochemistry; The University of Texas Health Science Center; San Antonio, TX USA
| | - Juan T Chang
- Department of Biochemistry and Molecular Biology; Baylor College of Medicine; Houston, TX USA
| | - Xiangan Liu
- Department of Biochemistry and Molecular Biology; Baylor College of Medicine; Houston, TX USA
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Wright EE, Elliman JR, Owens L. Induction and characterization of lysogenic bacteriophages from Streptococcus iniae. J Appl Microbiol 2013; 114:1616-24. [PMID: 23490045 DOI: 10.1111/jam.12192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/04/2013] [Accepted: 03/07/2013] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the presence of prophage in Streptococcus iniae, a highly problematic fish pathogen. METHODS AND RESULTS Cross-spotting assays and mitomycin C inductions were conducted to screen for prophage in 48 Strep. iniae isolates. Bacteriophages were characterized by plaque assays, transmission electron microscopy and DNA restriction enzyme digestion. Plaque assays confirmed prophages in 14·6% of isolates. Phages vB_SinS-44, vB_SinS-45, vB_SinS-46 and vB_SinS-48 lysed 78·5% of Strep. iniae isolates and displayed distinctive host ranges. Microscopy revealed virions exhibiting long, non-contractile tails and isometric heads consistent with phages from the family Siphoviridae. Restriction digests revealed genome sizes ranging from 27·5 to 66·3 kbp, with distinct cutting patterns that indicate the presence of related prophages in bacteria isolated from different geographic regions. CONCLUSIONS The rate of prophage carriage found is comparably low and induction rates varied between phages. The four characterized Siphoviridae phages have broad host ranges within the Strep. iniae isolates. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first description and characterization of lysogenic phages from Strep. iniae. These phages are candidates for research and diagnosis of the bacterium and their identification should accelerate the discovery of lytic phages to be trialled against Strep. iniae infections in fish.
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Affiliation(s)
- E E Wright
- Department of Microbiology and Immunology, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Qld, Australia.
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Kahánková J, Spanová A, Pantůcek R, Horák D, Doskar J, Rittich B. Extraction of PCR-ready DNA from Staphylococcus aureus bacteriophages using carboxyl functionalized magnetic nonporous microspheres. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:599-602. [PMID: 19188099 DOI: 10.1016/j.jchromb.2009.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 01/06/2009] [Accepted: 01/07/2009] [Indexed: 10/21/2022]
Abstract
Magnetic microspheres P(HEMA-co-EDMA) were used for PCR-ready phage DNA isolation from lysogenic strains of Staphylococcus aureus, including two new clinical isolates. The conditions of phage particle lysis were optimized. The quality of eluted phage DNA was evaluated by PCR. It was demonstrated that PCR-ready phage DNA can be isolated from small volumes of phage lysates (150 microl) by magnetic microspheres. The reported method is very expeditious without using toxic compounds such as phenol or chloroform. It can be used for phage identification and phage gene detection.
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Affiliation(s)
- Jana Kahánková
- Masaryk University, Faculty of Science, Institute of Experimental Biology, Tvrdého 14, CZ-602 00 Brno, Czech Republic
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Research Spotlight: J. Sep. Sci. 18/2008. J Sep Sci 2008. [DOI: 10.1002/jssc.200890067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Thomas JA, Rolando MR, Carroll CA, Shen PS, Belnap DM, Weintraub ST, Serwer P, Hardies SC. Characterization of Pseudomonas chlororaphis myovirus 201varphi2-1 via genomic sequencing, mass spectrometry, and electron microscopy. Virology 2008; 376:330-8. [PMID: 18474389 DOI: 10.1016/j.virol.2008.04.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 01/28/2008] [Accepted: 04/02/2008] [Indexed: 10/22/2022]
Abstract
Pseudomonas chlororaphis phage 201varphi2-1 is a relative of Pseudomonas aeruginosa myovirus phiKZ. Phage 201 phi2-1 was examined by complete genomic sequencing (316,674 bp), by a comprehensive mass spectrometry survey of its virion proteins and by electron microscopy. Seventy-six proteins, of which at least 69 have homologues in phiKZ, were identified by mass spectrometry. Eight proteins, in addition to the major head, tail sheath and tail tube proteins, are abundant in the virion. Electron microscopy of 201 phi2-1 revealed a multitude of long, fine fibers apparently decorating the tail sheath protein. Among the less abundant virion proteins are three homologues to RNA polymerase beta or beta' subunits. Comparison between the genomes of 201 phi2-1 and phiKZ revealed substantial conservation of the genome plan, and a large region with an especially high rate of gene replacement. The phiKZ-like phages exhibited a two-fold higher rate of divergence than for T4-like phages or host genomes.
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Affiliation(s)
- Julie A Thomas
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
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Serwer P, Hayes SJ, Lieman K. Aggregates of bacteriophage 0305phi8-36 seed future growth. Virol J 2007; 4:131. [PMID: 18053210 PMCID: PMC2222632 DOI: 10.1186/1743-422x-4-131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/04/2007] [Indexed: 11/12/2022] Open
Abstract
Lytic bacteriophage 0305φ8-36 forms visually observed aggregates during plaque formation. Aggregates intrinsically lower propagation potential. In the present study, the following observations indicate that lost propagation potential is regained with time: (1) Aggregates sometimes concentrate at the edge of clear plaques. (2) A semi-clear ring sometimes forms beyond the plaques. (3) Formation of a ring is completely correlated with the presence of aggregates at the same angular displacement along the plaque edge. To explain this aggregate-derived lowering/raising of propagation potential, the following hypothesis is presented: Aggregation/dissociation of bacteriophage of 0305φ8-36 is a selected phenomenon that evolved to maintain high host finding rate in a trade-off with maintaining high rate of bacteriophage progeny production. This hypothesis explains ringed plaque morphology observed for other bacteriophages and predicts that aggregates will undergo time-dependent change in structure as propagation potential increases. In support, fluorescence microscopy reveals time-dependent change in the distance between resolution-limited particles in aggregates.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA.
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SERWER PHILIP, HAYES SHIRLEYJ, LIEMAN KAREN, GRIESS GARYA. In situ fluorescence microscopy of bacteriophage aggregates. J Microsc 2007; 228:309-21. [DOI: 10.1111/j.1365-2818.2007.01855.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Thomas JA, Hardies SC, Rolando M, Hayes SJ, Lieman K, Carroll CA, Weintraub ST, Serwer P. Complete genomic sequence and mass spectrometric analysis of highly diverse, atypical Bacillus thuringiensis phage 0305phi8-36. Virology 2007; 368:405-21. [PMID: 17673272 PMCID: PMC2171028 DOI: 10.1016/j.virol.2007.06.043] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 06/09/2007] [Accepted: 06/30/2007] [Indexed: 10/23/2022]
Abstract
To investigate the apparent genomic complexity of long-genome bacteriophages, we have sequenced the 218,948-bp genome (6479-bp terminal repeat), and identified the virion proteins (55), of Bacillus thuringiensis bacteriophage 0305phi8-36. Phage 0305phi8-36 is an atypical myovirus with three large curly tail fibers. An accurate mode of DNA pyrosequencing was used to sequence the genome and mass spectrometry was used to accomplish the comprehensive virion protein survey. Advanced informatic techniques were used to identify classical morphogenesis genes. The 0305phi8-36 genes were highly diverged; 19% of 247 closely spaced genes have similarity to proteins with known functions. Genes for virion-associated, apparently fibrous proteins in a new class were found, in addition to strong candidates for the curly fiber genes. Phage 0305phi8-36 has twice the virion protein coding sequence of T4. Based on its genomic isolation, 0305phi8-36 is a resource for future studies of vertical gene transmission.
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Affiliation(s)
- Julie A. Thomas
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Stephen C. Hardies
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Mandy Rolando
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Shirley J. Hayes
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Karen Lieman
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Christopher A. Carroll
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Susan T. Weintraub
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
| | - Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900
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Hardies SC, Thomas JA, Serwer P. Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage. Virol J 2007; 4:97. [PMID: 17919320 PMCID: PMC2147016 DOI: 10.1186/1743-422x-4-97] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 10/05/2007] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The recently sequenced 218 kb genome of morphologically atypical Bacillus thuringiensis phage 0305phi8-36 exhibited only limited detectable homology to known bacteriophages. The only known relative of this phage is a string of phage-like genes called BtI1 in the chromosome of B. thuringiensis israelensis. The high degree of divergence and novelty of phage genomes pose challenges in how to describe the phage from its genomic sequences. RESULTS Phage 0305phi8-36 and BtI1 are estimated to have diverged 2.0 - 2.5 billion years ago. Positionally biased Blast searches aligned 30 homologous structure or morphogenesis genes between 0305phi8-36 and BtI1 that have maintained the same gene order. Functional clustering of the genes helped identify additional gene functions. A conserved long tape measure gene indicates that a long tail is an evolutionarily stable property of this phage lineage. An unusual form of the tail chaperonin system split to two genes was characterized, as was a hyperplastic homologue of the T4gp27 hub gene. Within this region some segments were best described as encoding a conservative array of structure domains fused with a variable component of exchangeable domains. Other segments were best described as multigene units engaged in modular horizontal exchange. The non-structure genes of 0305phi8-36 appear to include the remnants of two replicative systems leading to the hypothesis that the genome plan was created by fusion of two ancestral viruses. The case for a member of the RNAi RNA-directed RNA polymerase family residing in 0305phi8-36 was strengthened by extending the hidden Markov model of this family. Finally, it was noted that prospective transcriptional promoters were distributed in a gradient of small to large transcripts starting from a fixed end of the genome. CONCLUSION Genomic organization at a level higher than individual gene sequence comparison can be analyzed to aid in understanding large phage genomes. Methods of analysis include 1) applying a time scale, 2) augmenting blast scores with positional information, 3) categorizing genomic rearrangements into one of several processes with characteristic rates and outcomes, and 4) correlating apparent transcript sizes with genomic position, gene content, and promoter motifs.
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Affiliation(s)
- Stephen C Hardies
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
| | - Julie A Thomas
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
| | - Philip Serwer
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, USA
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