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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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2
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Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood. Viruses 2017; 9:v9060144. [PMID: 28604602 PMCID: PMC5490821 DOI: 10.3390/v9060144] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/25/2017] [Accepted: 06/06/2017] [Indexed: 01/18/2023] Open
Abstract
For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types.
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Farlow J, Filippov AA, Sergueev KV, Hang J, Kotorashvili A, Nikolich MP. Comparative whole genome analysis of six diagnostic brucellaphages. Gene 2014; 541:115-22. [PMID: 24530704 DOI: 10.1016/j.gene.2014.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/04/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022]
Abstract
Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages.
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Affiliation(s)
| | - Andrey A Filippov
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kirill V Sergueev
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Adam Kotorashvili
- Richard G. Lugar Center for Public Health Research, Tbilisi, Georgia
| | - Mikeljon P Nikolich
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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Flores V, López-Merino A, Mendoza-Hernandez G, Guarneros G. Comparative genomic analysis of two brucellaphages of distant origins. Genomics 2012; 99:233-40. [PMID: 22300630 DOI: 10.1016/j.ygeno.2012.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/20/2011] [Accepted: 01/03/2012] [Indexed: 10/14/2022]
Abstract
Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb) and compared it with that of Pr, a broad host-range brucellaphage recently isolated in Mexico. The genomes consist of 41,148 bp (Tb) and 38,253 bp (Pr), they differ mainly in the region encoding structural proteins, in which the genome of Tb shows two major insertions. Both genomes share 99.87% nucleotide identity, a high percentage of identity among phages isolated at so globally distant locations and temporally different occasions. Sequence analysis revealed 57 conserved ORFs, three transcriptional terminators and four putative transcriptional promoters. The co-occurrence of an ORF encoding a putative DnaA-like protein and a putative oriC-like origin of replication was found in both brucellaphages genomes, a feature not described in any other phage genome. These elements suggest that DNA replication in brucellaphages differs from other phages, and might resemble that of bacterial chromosomes.
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Affiliation(s)
- Victor Flores
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México Distrito Federal, Mexico.
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Turse JE, Pei J, Ficht TA. Lipopolysaccharide-Deficient Brucella Variants Arise Spontaneously during Infection. Front Microbiol 2011; 2:54. [PMID: 21833310 PMCID: PMC3153030 DOI: 10.3389/fmicb.2011.00054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 02/10/2011] [Indexed: 12/22/2022] Open
Abstract
Lipopolysaccharide-deficient mutants of smooth Brucella species (rough mutants) have been shown to arise spontaneously in culture. However, in situ analysis of Brucella infected macrophages using antibody directed against O-polysaccharide suggested a loss of reactivity of Brucella consistent with the appearance of rough organisms, and a potential contribution to infection. The experiments reported describe the direct recovery of Brucella from macrophages infected in vitro and from the spleens of infected mice at a frequency similar to that described in vitro, suggesting that Brucella dissociation is not simply an in vitro artifact. The frequency of appearance of spontaneous rough organisms deficient in O-polysaccharide expression measured in vitro is approximately 2–3 logs higher than the appearance of mutation to antibiotic resistance, purine auxotrophy, or reversion of erythritol sensitive ΔeryC mutants to tolerance. Genetic trans-complementation using a plasmid-based expression of Brucella manBA successfully restored O-polysaccharide expression in only one-third of O-polysaccharide deficient spontaneous mutants. Suggesting that the appearance of rough mutants is caused by mutation at more than one locus. In addition, Sanger sequencing of the manBA structural genes detected multiple sequence changes that may explain the observed phenotypic differences. The presence of O-polysaccharide resulted in macrophage and neutrophil infiltration into the peritoneal cavity and systemic distribution of the organism. In contrast, rough organisms are controlled by resident macrophages or by extracellular killing mechanisms and rapidly cleared from this compartment consistent with the inability to cause disease. Loss of O-polysaccharide expression appears to be stochastic giving rise to organisms with biological properties distinct from the parental smooth organism during the course of infection.
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Affiliation(s)
- Joshua E Turse
- Veterinary Pathobiology and Faculty of Genetics, Texas A&M University and Texas AgriLife Research College Station, TX, USA
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6
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Reservoir of bacterial exotoxin genes in the environment. Int J Microbiol 2011; 2010:754368. [PMID: 21318166 PMCID: PMC3026987 DOI: 10.1155/2010/754368] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 12/12/2010] [Indexed: 12/03/2022] Open
Abstract
Many bacteria produce secreted virulence factors called exotoxins. Exotoxins are often encoded by mobile genetic elements, including bacteriophage (phage). Phage can transfer genetic information to the bacteria they infect. When a phage transfers virulence genes to an avirulent bacterium, the bacterium can acquire the ability to cause disease. It is important to understand the role played by the phage that carry these genes in the evolution of pathogens. This is the first report of an environmental reservoir of a bacterial exotoxin gene in an atypical host. Screening bacterial isolates from the environment via PCR identified an isolate with a DNA sequence >95% identical to the Staphylococcus aureus enterotoxin A gene (sea). 16S DNA sequence comparisons and growth studies identified the environmental isolate as a psychrophilic Pseudomonas spp. The results indicate that the sea gene is present in an alternative bacterial host, providing the first evidence for an environmental pool of exotoxin genes in bacteria.
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7
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Segondy M, Allardet-Servent A, Caravano R, Ramuz M. Common physical map of fourBrucellabacteriophage genomes. FEMS Microbiol Lett 1988. [DOI: 10.1111/j.1574-6968.1988.tb03173.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Corbel MJ. Brucella phages: advances in the development of a reliable phage typing system for smooth and non-smooth Brucella isolates. ANNALES DE L'INSTITUT PASTEUR. MICROBIOLOGY 1987; 138:70-5. [PMID: 3606876 DOI: 10.1016/0769-2609(87)90056-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Corbel M. 2 Phage Typing of Brucella. METHODS IN MICROBIOLOGY 1984. [DOI: 10.1016/s0580-9517(08)70387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Corbel MJ, Scott AC, Ross HM. Properties of a cell-wall-defective variant of Brucella abortus of bovine origin. J Hyg (Lond) 1980; 85:103-13. [PMID: 6820027 PMCID: PMC2134006 DOI: 10.1017/s002217240002711x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The properties of an atypical Brucella strain isolated from lymph node tissue of a cow slaughtered as a brucellosis reactor were examined. The organism was Gram negative and highly pleomorphic, existing as cocci, coccobacilli, rods, branched and irregular forms which stained with fluorescent antibody conjugates prepared against rough and smooth Brucella abortus strains. It produced lecithinase and required at least 15% v/v equine or bovine serum for growth. It did not need supplementary CO2 for growth, produced H2S and was inhibited by brucella dyes and partially by i-erythritol. Growth inhibition or lysis was produced by brucella-phages. The organism was not pathogenic for guinea-pigs or mice but evoked antibodies mainly to rough Brucella antigens.
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Corbel MJ, Morris JA. Investigation of the effect of brucella-phage on the course of experimental infection with Brucella abortus. THE BRITISH VETERINARY JOURNAL 1980; 136:278-89. [PMID: 6770960 DOI: 10.1016/s0007-1935(17)32293-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Corbel MJ. Isolation and properties of a phage lytic for non-smooth Brucella organisms. JOURNAL OF BIOLOGICAL STANDARDIZATION 1979; 7:349-60. [PMID: 536378 DOI: 10.1016/s0092-1157(79)80009-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A phage for non-smooth cells of Brucella abortus was isolated from a mixture of three brucella-phages incubated with rough brucella cells in the presence of N-methyl-N'-nitro-N-nitrosoguanidine. It did not lyse smooth cells of Br. abortus strains nor those of other Brucella species, but during the course of its replication in rough organisms a small proportion of phage mutants were produced which were similar in properties to smooth-specific phages. The rough-specific phage, R, itself resembled Weybridge phage in its morphological and serological properties. Phage R was found to contain DNA and segregated into high and low density fractions, both with plaque-forming activity, on ultra-centrifugation in CsSO4 gradients. Unlike the smooth-specific phages it attached to heat-labile receptors present on non-smooth brucella cells.
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Thomas EL, Corbel MJ. Isolation of a phage lytic for several Brucella species following propagation of Tbilisi phage in the presence of mitomycin C. Arch Virol 1977; 54:259-61. [PMID: 70199 DOI: 10.1007/bf01314793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new brucella-phage, designated D, was isolated from a batch of Tbilisi phage grown on Brucella abortus strain 544 in the presence of mitomycin C. Although resembling Tbilisi phage in morphology, it differed in its host range, adsorption properties, chemical stability and antigenic specificity.
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