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Wang T, Cheng B, Jiao R, Zhang X, Zhang D, Cheng X, Ling N, Ye Y. Characterization of a novel high-efficiency cracking Burkholderia gladiolus phage vB_BglM_WTB and its application in black fungus. Int J Food Microbiol 2024; 414:110615. [PMID: 38325260 DOI: 10.1016/j.ijfoodmicro.2024.110615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/22/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Burkholderia gladiolus (B. gladiolus) is foodborne pathogenic bacteria producing bongkrekic acid (BA), which causes food poisoning and has a mortality rate of up to 40 % or more. However, no drugs have been reported in the literature for the prevention and treatment of this infection. In this study, a phage was identified to control B. gladiolus. The novel phage vB_BglM_WTB (WTB), which lyse B. gladiolus with high efficiency, was isolated from sewage of Huaihe Road Throttle Well Sewage Treatment Plant in Hefei. Transmission electron microscopy showed that WTB had an icosahedral head (69 ± 2 nm) and a long retractable tail (108 ± 2 nm). Its optimal temperature and pH ranges to control B. gladiolus were 25 °C -65 °C and 3-11 respectively. The phage WTB was identified as a linear double-stranded DNA phage of 68, 541 bp with 60.04 % G + C content, with a long latent period of 60 min. Phylogenetic analysis and comparative genetic analysis indicated that phage WTB has low identity (<50 %) with other phages, with the highest similarity to Burkholderia phage Maja (25.7 %), which showed that it does not belong to any previous genera recognized by the International Committee on Taxonomy of Viruses (ICTV) and was a candidate for a new genus within the Caudoviricetes. We have submitted a new proposal to ICTV to create a new genus, Bglawtbvirus. No transfer RNA (tRNA), virulence associated and antibiotic resistance genes were detected in phage WTB. Experimental results indicated that WTB at 4 °C and 25 °C had excellent inhibition activity against B. gladiolus in the black fungus, with an inhibition efficiency of over 99 %. The amount of B. gladiolus in the black fungus was reduced to a minimum of 89 CFU/mL when treated by WTB at 25 °C for 2 h. The inhibition rate remained at 99.97 % even after 12 h. The findings showed that the phage WTB could be applied as a food-cleaning agent for enhancing food safety and contributed to our understanding of phage biology and diversity.
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Affiliation(s)
- Ting Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Bin Cheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Rui Jiao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiyan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Diwei Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Xiangyu Cheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
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Yao G, Le T, Korn AM, Peterson HN, Liu M, Gonzalez CF, Gill JJ. Phage Milagro: a platform for engineering a broad host range virulent phage for Burkholderia. J Virol 2023; 97:e0085023. [PMID: 37943040 PMCID: PMC10688314 DOI: 10.1128/jvi.00850-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/21/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Burkholderia infections are a significant concern in people with CF and other immunocompromising disorders, and are difficult to treat with conventional antibiotics due to their inherent drug resistance. Bacteriophages, or bacterial viruses, are now seen as a potential alternative therapy for these infections, but most of the naturally occurring phages are temperate and have narrow host ranges, which limit their utility as therapeutics. Here we describe the temperate Burkholderia phage Milagro and our efforts to engineer this phage into a potential therapeutic by expanding the phage host range and selecting for phage mutants that are strictly virulent. This approach may be used to generate new therapeutic agents for treating intractable infections in CF patients.
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Affiliation(s)
- Guichun Yao
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Tram Le
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Abby M. Korn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Hannah N. Peterson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Carlos F. Gonzalez
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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Stanton CR, Batinovic S, Petrovski S. Burkholderia contaminans Bacteriophage CSP3 Requires O-Antigen Polysaccharides for Infection. Microbiol Spectr 2023; 11:e0533222. [PMID: 37199610 PMCID: PMC10269572 DOI: 10.1128/spectrum.05332-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/20/2023] [Indexed: 05/19/2023] Open
Abstract
The Burkholderia cepacia complex is a group of opportunistic pathogens that cause both severe acute and chronic respiratory infections. Due to their large genomes containing multiple intrinsic and acquired antimicrobial resistance mechanisms, treatment is often difficult and prolonged. One alternative to traditional antibiotics for treatment of bacterial infections is bacteriophages. Therefore, the characterization of bacteriophages infective for the Burkholderia cepacia complex is critical to determine their suitability for any future use. Here, we describe the isolation and characterization of novel phage, CSP3, infective against a clinical isolate of Burkholderia contaminans. CSP3 is a new member of the Lessievirus genus that targets various Burkholderia cepacia complex organisms. Single nucleotide polymorphism (SNP) analysis of CSP3-resistant B. contaminans showed that mutations to the O-antigen ligase gene, waaL, consequently inhibited CSP3 infection. This mutant phenotype is predicted to result in the loss of cell surface O-antigen, contrary to a related phage that requires the inner core of the lipopolysaccharide for infection. Additionally, liquid infection assays showed that CSP3 provides suppression of B. contaminans growth for up to 14 h. Despite the inclusion of genes that are typical of the phage lysogenic life cycle, we saw no evidence of CSP3's ability to lysogenize. Continuation of phage isolation and characterization is crucial in developing large and diverse phage banks for global usage in cases of antibiotic-resistant bacterial infections. IMPORTANCE Amid the global antibiotic resistance crisis, novel antimicrobials are needed to treat problematic bacterial infections, including those from the Burkholderia cepacia complex. One such alternative is the use of bacteriophages; however, a lot is still unknown about their biology. Bacteriophage characterization studies are of high importance for building phage banks, as future work in developing treatments such as phage cocktails should require well-characterized phages. Here, we report the isolation and characterization of a novel Burkholderia contaminans phage that requires the O-antigen for infection, a distinct phenotype seen among other related phages. Our findings presented in this article expand on the ever-evolving phage biology field, uncovering unique phage-host relationships and mechanisms of infection.
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Affiliation(s)
- Cassandra R. Stanton
- Department of Microbiology, Anatomy, Physiology & Pharmacology, La Trobe University, Bundoora, Australia
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology & Pharmacology, La Trobe University, Bundoora, Australia
- Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology & Pharmacology, La Trobe University, Bundoora, Australia
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4
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Characterization and complete genome sequence analysis of the novel phage RPZH3 infecting Ralstonia solanacearum. Arch Virol 2023; 168:105. [PMID: 36899129 DOI: 10.1007/s00705-023-05737-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023]
Abstract
A novel lytic Ralstonia phage, RPZH3, was isolated from the soil of a tobacco field via a double agar overlay plaque assay. The phage has an icosahedral head 75 ± 5 nm in diameter with a short tail about 15 ± 5 nm in length. It was able to infect 18 out of 30 tested strains of R. solanacearum isolated from tobacco, sweet potato, tomato, pepper, and eggplant. The latent period of the phage was 80 min, and the burst period was 60 min with a burst size of about 27 pfu/cell. The phage was stable at pH 4-12 at 28°C, and it was also stable at temperatures from 45°C to 60°C at pH 7.0. The complete genome of phage RPZH3 consists of 65,958 bp, with a GC content of 64.93%. The genome contains 93 open reading frames (ORFs) and encodes a tRNA for cysteine. Nucleotide sequence alignment and phylogenetic analysis indicated that RPZH3 is a new member of the genus Gervaisevirus belonging to the class Caudoviricetes.
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Davis CM, Ruest MK, Cole JH, Dennis JJ. The Isolation and Characterization of a Broad Host Range Bcep22-like Podovirus JC1. Viruses 2022; 14:v14050938. [PMID: 35632679 PMCID: PMC9144972 DOI: 10.3390/v14050938] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
Bacteriophage JC1 is a Podoviridae phage with a C1 morphotype, isolated on host strain Burkholderia cenocepacia Van1. Phage JC1 is capable of infecting an expansive range of Burkholderia cepacia complex (Bcc) species. The JC1 genome exhibits significant similarity and synteny to Bcep22-like phages and to many Ralstonia phages. The genome of JC1 was determined to be 61,182 bp in length with a 65.4% G + C content and is predicted to encode 76 proteins and 1 tRNA gene. Unlike the other Lessieviruses, JC1 encodes a putative helicase gene in its replication module, and it is in a unique organization not found in previously analyzed phages. The JC1 genome also harbours 3 interesting moron genes, that encode a carbon storage regulator (CsrA), an N-acetyltransferase, and a phosphoadenosine phosphosulfate (PAPS) reductase. JC1 can stably lysogenize its host Van1 and integrates into the 5′ end of the gene rimO. This is the first account of stable integration identified for Bcep22-like phages. JC1 has a higher global virulence index at 37 °C than at 30 °C (0.8 and 0.21, respectively); however, infection efficiency and lysogen stability are not affected by a change in temperature, and no observable temperature-sensitive switch between lytic and lysogenic lifestyle appears to exist. Although JC1 can stably lysogenize its host, it possesses some desirable characteristics for use in phage therapy. Phage JC1 has a broad host range and requires the inner core of the bacterial LPS for infection. Bacteria that mutate to evade infection by JC1 may develop a fitness disadvantage as seen in previously characterized LPS mutants lacking inner core.
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Gonzales MF, Piya DK, Koehler B, Zhang K, Yu Z, Zeng L, Gill JJ. New Insights into the Structure and Assembly of Bacteriophage P1. Viruses 2022; 14:v14040678. [PMID: 35458408 PMCID: PMC9024508 DOI: 10.3390/v14040678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophage P1 is the premier transducing phage of E. coli. Despite its prominence in advancing E. coli genetics, modern molecular techniques have not been applied to thoroughly understand P1 structure. Here, we report the proteome of the P1 virion as determined by liquid chromatography tandem mass-spectrometry. Additionally, a library of single-gene knockouts identified the following five previously unknown essential genes: pmgA, pmgB, pmgC, pmgG, and pmgR. In addition, proteolytic processing of the major capsid protein is a known feature of P1 morphogenesis, and we identified the processing site by N-terminal sequencing to be between E120 and S121, producing a 448-residue, 49.3 kDa mature peptide. Furthermore, the P1 defense against restriction (Dar) system consists of six known proteins that are incorporated into the virion during morphogenesis. The largest of these, DarB, is a 250 kDa protein that is believed to translocate into the cell during infection. DarB deletions indicated the presence of an N-terminal packaging signal, and the N-terminal 30 residues of DarB are shown to be sufficient for directing a heterologous reporter protein to the capsid. Taken together, the data expand on essential structural P1 proteins as well as introduces P1 as a nanomachine for cellular delivery.
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Affiliation(s)
- Miguel F. Gonzales
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Interdisciplinary Program in Genetics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| | - Denish K. Piya
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Brian Koehler
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Kailun Zhang
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Zihao Yu
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Lanying Zeng
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA;
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA; (M.F.G.); (D.K.P.); (K.Z.); (Z.Y.); (L.Z.)
- Interdisciplinary Program in Genetics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA
- Correspondence: ; Tel.: +1-979-458-6368
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Enwuru NV, Gill JJ, Anttonen KP, Enwuru CA, Young R, Coker AO, Cirillo JD. Isolation and characterization of novel phage (Podoviridae ɸParuNE1) and its efficacy against multi-drug-resistant Pseudomonas aeruginosa planktonic cells and biofilm. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00137-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
Bacterial pathogen (Pseudomonas aeruginosa) could form biofilm that conveys multi-drug resistance. Bacteriophage as an alternative to antibacterial resistance is useful against biofilm complications. This study evaluated antibacterial and biofilm removal activities of lytic phage, specific against multi-drug-resistant clinical P. aeruginosa.
Results
The phage showed a wide range of pH (5–10) and heat (7–44 °C) stability. Electron microscopy showed ɸPauNE1 phage head (60 nm in diameter) and non-contractile tail (12 nm in length by 8 nm in width); hence, the family Podoviridae and the order Caudovirales. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed structured protein of 55 kDa and double-stranded DNA of 45 kb. The phage was species specific and had broad host range activity. It inhibited bacterial growth at multiplicity of infection (MOI) 1–0.000001 pfu/ml. Inhibition was maximal at both low (1 × 105) and high (1 × 109) bacterial CFU/ml. Biofilm removal test showed that the phage removed more than 60% cell biomass within CFU/ml of 1.5 × 108, 6.0 × 108 and l.0 × 109.
Conclusion
Phage (ɸPauNE1) was unique and had broad host range activity. The phage exhibited strong bacteriolytic activity against biofilm forming multi-drug-resistant strains. It had no lytic effect on the heterogeneous strains and so a promising bioagent.
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Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins. Viruses 2021; 13:v13081504. [PMID: 34452369 PMCID: PMC8402733 DOI: 10.3390/v13081504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Tailed double-stranded DNA bacteriophages inject some proteins with their dsDNA during infection. Phage P22 injects about 12, 12, and 30 molecules of the proteins encoded by genes 7, 16 and 20, respectively. After their ejection from the virion, they assemble into a trans-periplasmic conduit through which the DNA passes to enter the cytoplasm. The location of these proteins in the virion before injection is not well understood, although we recently showed they reside near the portal protein barrel in DNA-filled heads. In this report we show that when these proteins are missing from the virion, a longer than normal DNA molecule is encapsidated by the P22 headful DNA packaging machinery. Thus, the ejection proteins occupy positions within the virion that can be occupied by packaged DNA when they are absent.
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Lauman P, Dennis JJ. Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex. Viruses 2021; 13:1331. [PMID: 34372537 PMCID: PMC8310193 DOI: 10.3390/v13071331] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/29/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy-the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy.
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Affiliation(s)
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
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10
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Xie Y, Thompson T, O'Leary C, Crosby S, Nguyen QX, Liu M, Gill JJ. Differential Bacteriophage Efficacy in Controlling Salmonella in Cattle Hide and Soil Models. Front Microbiol 2021; 12:657524. [PMID: 34262535 PMCID: PMC8273493 DOI: 10.3389/fmicb.2021.657524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/04/2021] [Indexed: 01/18/2023] Open
Abstract
Asymptomatic Salmonella carriage in beef cattle is a food safety concern and the beef feedlot environment and cattle hides are reservoirs of this pathogen. Bacteriophages present an attractive non-antibiotic strategy for control of Salmonella in beef. In this study, four diverse and genetically unrelated Salmonella phages, Sergei, Season12, Sw2, and Munch, were characterized and tested alone and in combination for their ability to control Salmonella in cattle hide and soil systems, which are relevant models for Salmonella control in beef production. Phage Sergei is a member of the genus Sashavirus, phage Season12 was identified as a member of the Chivirus genus, Sw2 was identified as a member of the T5-like Epseptimavirus genus, and Munch was found to be a novel “jumbo” myovirus. Observed pathogen reductions in the model systems ranged from 0.50 to 1.75 log10 CFU/cm2 in hides and from 0.53 to 1.38 log10 CFU/g in soil, with phages Sergei and Sw2 producing greater reductions (∼1 log10 CFU/cm2 or CFU/g) than Season12 and Munch. These findings are in accordance with previous observations of phage virulence, suggesting the simple ability of a phage to form plaques on a bacterial strain is not a strong indicator of antimicrobial activity, but performance in liquid culture assays provides a better predictor. The antimicrobial efficacies of phage treatments were found to be phage-specific across model systems, implying that a phage capable of achieving bacterial reduction in one model is more likely to perform well in another. Phage combinations did not produce significantly greater efficacy than single phages even after 24 h in the soil model, and phage-insensitive colonies were not isolated from treated samples, suggesting that the emergence of phage resistance was not a major factor limiting efficacy in this system.
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Affiliation(s)
- Yicheng Xie
- Department of Animal Science, Texas A&M University, College Station, TX, United States.,Center for Phage Technology, Texas A&M University, College Station, TX, United States
| | - Tyler Thompson
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Chandler O'Leary
- Center for Phage Technology, Texas A&M University, College Station, TX, United States.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Stephen Crosby
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Quang X Nguyen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Mei Liu
- Center for Phage Technology, Texas A&M University, College Station, TX, United States
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX, United States.,Center for Phage Technology, Texas A&M University, College Station, TX, United States
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11
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Trotereau A, Boyer C, Bornard I, Pécheur MJB, Schouler C, Torres-Barceló C. High genomic diversity of novel phages infecting the plant pathogen Ralstonia solanacearum, isolated in Mauritius and Reunion islands. Sci Rep 2021; 11:5382. [PMID: 33686106 PMCID: PMC7940629 DOI: 10.1038/s41598-021-84305-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/11/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is among the most important plant diseases worldwide, severely affecting a high number of crops and ornamental plants in tropical regions. Only a limited number of phages infecting R. solanacearum have been isolated over the years, despite the importance of this bacterium and the associated plant disease. The antibacterial effect or morphological traits of these R. solanacearum viruses have been well studied, but not their genomic features, which need deeper consideration. This study reports the full genome of 23 new phages infecting RSSC isolated from agricultural samples collected in Mauritius and Reunion islands, particularly affected by this plant bacterial pathogen and considered biodiversity hotspots in the Southwest Indian Ocean. The complete genomic information and phylogenetic classification is provided, revealing high genetic diversity between them and weak similarities with previous related phages. The results support our proposal of 13 new species and seven new genera of R. solanacearum phages. Our findings highlight the wide prevalence of phages of RSSC in infected agricultural settings and the underlying genetic diversity. Discoveries of this kind lead more insight into the diversity of phages in general and to optimizing their use as biocontrol agents of bacterial diseases of plants in agriculture.
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Affiliation(s)
| | - Claudine Boyer
- Plant Populations and Bio-aggressors in Tropical Ecosystems, Saint Pierre, Reunion, France
| | | | | | | | - Clara Torres-Barceló
- Plant Populations and Bio-aggressors in Tropical Ecosystems, Saint Pierre, Reunion, France. .,Plant Pathology, INRAE, 84140, Montfavet, France.
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12
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Petrzik K, Lukavský J, Koloniuk I. Novel Virus on Filamentous Arthronema africanum Cyanobacterium. MICROBIAL ECOLOGY 2021; 81:454-459. [PMID: 32901386 DOI: 10.1007/s00248-020-01599-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Widely distributed in water environments and in soil, cyanobacteria are hosts of lysogenic or lytic bacterioviruses. A novel, probably lysogenic virus (phage) for which the name Arthronema africanum virus TR020 (Aa-TR020) is proposed, has been isolated from filamentous freshwater cyanobacterium Arthronema africanum. The virus formed turbid plaques on plate culture of A. africanum strain 1980/01 but not on other Arthronema strain and other bacterial species. The genome of Aa-TR020 is linear molecule of dsDNA, 44,805 bp in length with 216 bp long terminal repeats and with G + C content of 46%. Fifty-five genes organized on plus and minus strands were predicted there. The genome size, gene arrangement, and selected protein sequences showed relatedness to Phormidium virus Pf-WMP3 and other viruses known to infect cyanobacteria and classified in the family Podoviridae.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| | - Jaromír Lukavský
- Centre for Phycology, Institute of Botany, Czech Academy of Sciences, Dukelská 135, Třeboň, Czech Republic
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic
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Sobrero PM, Valverde C. Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas. Front Mol Biosci 2020; 7:127. [PMID: 32754614 PMCID: PMC7366521 DOI: 10.3389/fmolb.2020.00127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).
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Affiliation(s)
- Patricio Martín Sobrero
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
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14
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Abstract
The T7-like podophage Pagan infects Xanthomonas sp. strain ATCC PTA-13101, which was isolated from rice. The 44-kbp Pagan genome contains direct terminal repeats and contains 59 genes, 27 of which have a predicted function. Pagan is most closely related to Xanthomonas phage phi Xc10 and Xylella phage Prado. The T7-like podophage Pagan infects Xanthomonas sp. strain ATCC PTA-13101, which was isolated from rice. The 44-kbp Pagan genome contains direct terminal repeats and contains 59 genes, 27 of which have a predicted function. Pagan is most closely related to Xanthomonas phage phi Xc10 and Xylella phage Prado.
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Abstract
Serratia marcescens is an opportunistic human pathogen with multiple resistance mechanisms that infects hospitalized patients. Here, we report the full genome sequence of S. marcescens podophage Parlo. Parlo is most similar to Erwinia phage PEp14 and encodes a 3,764-residue protein assumed to be a homolog of DarB, an antirestriction protein.
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16
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Characterization and complete genome sequence analysis of phage GP4, a novel lytic Bcep22-like podovirus. Arch Virol 2019; 164:2339-2343. [DOI: 10.1007/s00705-019-04309-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/06/2019] [Indexed: 11/30/2022]
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17
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Thompson DW, Casjens SR, Sharma R, Grose JH. Genomic comparison of 60 completely sequenced bacteriophages that infect Erwinia and/or Pantoea bacteria. Virology 2019; 535:59-73. [PMID: 31276862 DOI: 10.1016/j.virol.2019.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
Erwinia and Pantoea are closely related bacterial plant pathogens in the Gram negative Enterobacteriales order. Sixty tailed bacteriophages capable of infecting these pathogens have been completely sequenced by investigators around the world and are in the current databases, 30 of which were sequenced by our lab. These 60 were compared to 991 other Enterobacteriales bacteriophage genomes and found to be, on average, just over twice the overall average length. These Erwinia and Pantoea phages comprise 20 clusters based on nucleotide and protein sequences. Five clusters contain only phages that infect the Erwinia and Pantoea genera, the other 15 clusters are closely related to bacteriophages that infect other Enterobacteriales; however, within these clusters the Erwinia and Pantoea phages tend to be distinct, suggesting ecological niche may play a diversification role. The failure of many of their encoded proteins to have predicted functions highlights the need for further study of these phages.
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Affiliation(s)
- Daniel W Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, UT, 84112, USA; School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA.
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18
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Attai H, Brown PJB. Isolation and Characterization T4- and T7-Like Phages that Infect the Bacterial Plant Pathogen Agrobacterium tumefaciens. Viruses 2019; 11:v11060528. [PMID: 31181591 PMCID: PMC6630229 DOI: 10.3390/v11060528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 01/21/2023] Open
Abstract
In the rhizosphere, bacteria-phage interactions are likely to have important impacts on the ecology of microbial communities and microbe-plant interactions. To better understand the dynamics of Agrobacteria-phage interactions, we have isolated diverse bacteriophages which infect the bacterial plant pathogen, Agrobacterium tumefaciens. Here, we complete the genomic characterization of Agrobacterium tumefaciens phages Atu_ph04 and Atu_ph08. Atu_ph04-a T4-like phage belonging to the Myoviridae family-was isolated from waste water and has a 143,349 bp genome that encodes 223 predicted open reading frames (ORFs). Based on phylogenetic analysis and whole-genome alignments, Atu_ph04 is a member of a newly described T4 superfamily that contains other Rhizobiales-infecting phages. Atu_ph08, a member of the Podoviridae T7-like family, was isolated from waste water, has a 59,034 bp genome, and encodes 75 ORFs. Based on phylogenetic analysis and whole-genome alignments, Atu_ph08 may form a new T7 superfamily which includes Sinorhizobium phage PCB5 and Ochrobactrum phage POI1126. Atu_ph08 is predicted to have lysogenic activity, as we found evidence of an integrase and several transcriptional repressors with similarity to proteins in transducing phage P22. Together, this data suggests that Agrobacterium phages are diverse in morphology, genomic content, and lifestyle.
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Affiliation(s)
- Hedieh Attai
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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19
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Addy HS, Ahmad AA, Huang Q. Molecular and Biological Characterization of Ralstonia Phage RsoM1USA, a New Species of P2virus, Isolated in the United States. Front Microbiol 2019; 10:267. [PMID: 30837978 PMCID: PMC6389784 DOI: 10.3389/fmicb.2019.00267] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
The first Ralstonia-infecting bacteriophage from soil of the United States, designated RsoM1USA, was isolated from a tomato field in Florida. Electron microscopy revealed that phage RsoM1USA is member of the genus P2virus in the family Myoviridae with an icosahedral head of about 66 nm in diameter, a contractile tail of about 152 nm in length, and a long “neck.” Phage RsoM1USA infected 12 of the 30 tested R. solanacearum species complex strains collected worldwide in each of the three Ralstonia species: R. solanacearum, R. pseudosolanacearum, and R. syzygii. The phage completed its infection cycle 180 min post infection with a burst size of about 56 particles per cell. Phage RsoM1USA has a genome of 39,309 nucleotides containing 58 open reading frames (ORFs) and is closely related to Ralstonia phage RSA1 of the species Ralstonia virus RSA1. The genomic organization of phage RsoM1USA is also similar to that of phage RSA1, but their integrases share no sequence homology. In addition, we determined that the integration of phage RsoM1USA into its susceptible R. solanacearum strain K60 is mediated by the 3′ 45-base portion of the threonine tRNA (TGT), not arginine tRNA (CCG) as reported for phage RSA1, confirming that the two phages use different mechanism for integration. Our proteomic analysis of the purified virions supported the annotation of the main structural proteins. Infection of a susceptible R. solanacearum strain RUN302 by phage RsoM1USA resulted in significantly reduced growth of the infected bacterium in vitro, but not virulence in tomato plants, as compared to its uninfected RUN302 strain. Due to its differences from phage RSA1, phage RsoM1USA should be considered the type member of a new species with a proposed species name of Ralstonia virus RsoM1USA.
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Affiliation(s)
- Hardian Susilo Addy
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States.,Department of Plant Protection, Faculty of Agriculture, University of Jember, Jember, Indonesia
| | - Abdelmonim Ali Ahmad
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States.,Department of Plant Pathology, Faculty of Agriculture, Minia University, El-minia, Egypt
| | - Qi Huang
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, United States
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20
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Xiong Z, Wang Y, Dong Y, Zhang Q, Xu X. Cyanophage A-1(L) Adsorbs to Lipopolysaccharides of Anabaena sp. Strain PCC 7120 via the Tail Protein Lipopolysaccharide-Interacting Protein (ORF36). J Bacteriol 2019; 201:e00516-18. [PMID: 30420453 PMCID: PMC6349090 DOI: 10.1128/jb.00516-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Ecological functions of cyanophages in aquatic environments depend on their interactions with cyanobacterial hosts. The first step of phage-host interaction involves adsorption to the cell surface. We report that adsorption of a cyanophage, A-1(L), to the outer membrane of Anabaena sp. strain PCC 7120 is based on the binding of a tail protein, ORF36, to the O antigen of lipopolysaccharides (LPS). Removal of O antigen by gene inactivation abolished infection by A-1(L); consistently, preincubation of the cyanophage with extracted Anabaena LPS partially blocked infection. In contrast, inactivation of major outer membrane protein genes in Anabaena or addition of Synechocystis LPS showed no effect on infection. ORF35 and ORF36 are two predicted tail proteins of A-1(L). Antibodies against either ORF35 or ORF36 strongly inhibited infection. Enzyme-linked immunosorbent assay showed a specific interaction between ORF36 and the LPS of Anabaena sp. strain PCC 7120. These findings indicate that ORF35 and ORF36 are probably both required for adsorption of A-1(L) to the cell surface, but ORF36 specifically binds to the O antigen of LPS.IMPORTANCE Cyanophages play an important role in regulating the dynamics of cyanobacterial communities in aquatic environments. Hitherto, the mechanisms for cyanophage infection have been barely investigated. In this study, the first cyanophage tail protein that binds to the receptor (LPS) on cell surface was identified and shown to be essential for the A-1(L) infection of Anabaena sp. strain PCC 7120. The protein-LPS interaction may represent an important route for adsorption of cyanophages to their hosts.
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Affiliation(s)
- Zhenzhen Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yali Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yanling Dong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xudong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
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21
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da Silva Xavier A, da Silva FP, Vidigal PMP, Lima TTM, de Souza FO, Alfenas-Zerbini P. Genomic and biological characterization of a new member of the genus Phikmvvirus infecting phytopathogenic Ralstonia bacteria. Arch Virol 2018; 163:3275-3290. [DOI: 10.1007/s00705-018-4006-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
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22
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Hernandez-Morales AC, Lessor LL, Wood TL, Migl D, Mijalis EM, Cahill J, Russell WK, Young RF, Gill JJ. Genomic and Biochemical Characterization of Acinetobacter Podophage Petty Reveals a Novel Lysis Mechanism and Tail-Associated Depolymerase Activity. J Virol 2018; 92:e01064-17. [PMID: 29298884 PMCID: PMC5827379 DOI: 10.1128/jvi.01064-17] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/06/2017] [Indexed: 01/08/2023] Open
Abstract
The increased prevalence of drug-resistant, nosocomial Acinetobacter infections, particularly from pathogenic members of the Acinetobacter calcoaceticus-baumannii complex, necessitates the exploration of novel treatments such as phage therapy. In the present study, we characterized phage Petty, a novel podophage that infects multidrug-resistant Acinetobacter nosocomialis and Acinetobacter baumannii Genome analysis reveals that phage Petty is a 40,431-bp ϕKMV-like phage, with a coding density of 92.2% and a G+C content of 42.3%. Interestingly, the lysis cassette encodes a class I holin and a single-subunit endolysin, but it lacks canonical spanins to disrupt the outer membrane. Analysis of other ϕKMV-like genomes revealed that spaninless lysis cassettes are a feature of phages infecting Acinetobacter within this subfamily of bacteriophages. The observed halo surrounding Petty's large clear plaques indicated the presence of a phage-encoded depolymerase capable of degrading capsular exopolysaccharides (EPS). The product of gene 39, a putative tail fiber, was hypothesized to possess depolymerase activity based on weak homology to previously reported phage tail fibers. The 101.4-kDa protein gene product 39 (gp39) was cloned and expressed, and its activity against Acinetobacter EPS in solution was determined. The enzyme degraded purified EPS from its host strain A. nosocomialis AU0783, reducing its viscosity, and generated reducing ends in solution, indicative of hydrolase activity. Given that the accessibility to cells within a biofilm is enhanced by degradation of EPS, phages with depolymerases may have enhanced diagnostic and therapeutic potential against drug-resistant Acinetobacter strains.IMPORTANCE Bacteriophage therapy is being revisited as a treatment for difficult-to-treat infections. This is especially true for Acinetobacter infections, which are notorious for being resistant to antimicrobials. Thus, sufficient data need to be generated with regard to phages with therapeutic potential, if they are to be successfully employed clinically. In this report, we describe the isolation and characterization of phage Petty, a novel lytic podophage, and its depolymerase. To our knowledge, it is the first phage reported to be able to infect both A. baumannii and A. nosocomialis The lytic phage has potential as an alternative therapeutic agent, and the depolymerase could be used for modulating EPS both during infections and in biofilms on medical equipment, as well as for capsular typing. We also highlight the lack of predicted canonical spanins in the phage genome and confirm that, unlike the rounding of lambda lysogens lacking functional spanin genes, A. nosocomialis cells infected with phage Petty lyse by bursting. This suggests that phages like Petty employ a different mechanism to disrupt the outer membrane of Acinetobacter hosts during lysis.
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Affiliation(s)
- A C Hernandez-Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - L L Lessor
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - T L Wood
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - D Migl
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - E M Mijalis
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - J Cahill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - W K Russell
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - R F Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - J J Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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23
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Roux D, Schaefers M, Clark BS, Weatherholt M, Renaud D, Scott D, LiPuma JJ, Priebe G, Gerard C, Yoder-Himes DR. A putative lateral flagella of the cystic fibrosis pathogen Burkholderia dolosa regulates swimming motility and host cytokine production. PLoS One 2018; 13:e0189810. [PMID: 29346379 PMCID: PMC5773237 DOI: 10.1371/journal.pone.0189810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023] Open
Abstract
Burkholderia dolosa caused an outbreak in the cystic fibrosis clinic at Boston Children's Hospital and was associated with high mortality in these patients. This species is part of a larger complex of opportunistic pathogens known as the Burkholderia cepacia complex (Bcc). Compared to other species in the Bcc, B. dolosa is highly transmissible; thus understanding its virulence mechanisms is important for preventing future outbreaks. The genome of one of the outbreak strains, AU0158, revealed a homolog of the lafA gene encoding a putative lateral flagellin, which, in other non-Bcc species, is used for movement on solid surfaces, attachment to host cells, or movement inside host cells. Here, we analyzed the conservation of the lafA gene and protein sequences, which are distinct from those of the polar flagella, and found lafA homologs to be present in numerous β-proteobacteria but notably absent from most other Bcc species. A lafA deletion mutant in B. dolosa showed a greater swimming motility than wild-type due to an increase in the number of polar flagella, but did not appear to contribute to biofilm formation, host cell invasion, or murine lung colonization or persistence over time. However, the lafA gene was important for cytokine production in human peripheral blood mononuclear cells, suggesting it may have a role in recognition by the human immune response.
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Affiliation(s)
- Damien Roux
- INSERM, IAME, UMR 1137, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
- AP-HP, Louis Mourier Hospital, Intensive Care Unit, Colombes, France
| | - Matthew Schaefers
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bradley S. Clark
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Molly Weatherholt
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Diane Renaud
- Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - David Scott
- Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - John J. LiPuma
- Division of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gregory Priebe
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Craig Gerard
- Division of Respiratory Diseases, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Deborah R. Yoder-Himes
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail:
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Pratama AA, van Elsas JD. A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437. Sci Rep 2017; 7:9156. [PMID: 28831124 PMCID: PMC5567305 DOI: 10.1038/s41598-017-09317-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/20/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages constitute key gene transfer agents in many bacteria. Specifically, they may confer gene mobility to Paraburkholderia spp. that dwells in soil and the mycosphere. In this study, we first screened mycosphere and bulk soils for phages able to produce plaques, however found these to be below detection. Then, prophage identification methods were applied to the genome sequences of the mycosphere-derived Paraburkholderia terrae strains BS001, BS007, BS110 and BS437, next to P. phytofirmans strains BS455, BIFAS53, J1U5 and PsJN. These analyses revealed all bacterial genomes to contain considerable amounts [up to 13.3%] of prophage-like sequences. One sequence predicted to encode a complete phage was found in the genome of P. terrae BS437. Using the inducing agent mitomycin C, we produced high-titered phage suspensions. These indeed encompassed the progeny of the identified prophage (denoted ɸ437), as evidenced using phage major capsid gene molecular detection. We obtained the full sequence of phage ɸ437, which, remarkably, had undergone a reshuffling of two large gene blocks. One predicted moron gene was found, and it is currently analyzed to understand the extent of its ecological significance for the host.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands.
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25
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Jäckel C, Hertwig S, Scholz HC, Nöckler K, Reetz J, Hammerl JA. Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages. Front Microbiol 2017; 8:1207. [PMID: 28713341 PMCID: PMC5492332 DOI: 10.3389/fmicb.2017.01207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/14/2017] [Indexed: 11/13/2022] Open
Abstract
Ochrobactrum and Brucella are closely related bacteria that populate different habitats and differ in their pathogenic properties. Only little is known about mobile genetic elements in these genera which might be important for survival and virulence. Previous studies on Brucella lysogeny indicated that active phages are rare in this genus. To gain insight into the presence and nature of prophages in Ochrobactrum, temperate phages were isolated from various species and characterized in detail. In silico analyses disclosed numerous prophages in published Ochrobactrum genomes. Induction experiments showed that Ochrobactrum prophages can be induced by various stress factors and that some strains released phage particles even under non-induced conditions. Sixty percent of lysates prepared from 125 strains revealed lytic activity. The host range and DNA similarities of 19 phages belonging to the families Myoviridae, Siphoviridae, or Podoviridae were determined suggesting that they are highly diverse. Some phages showed relationship to the temperate Brucella inopinata phage BiPB01. The genomic sequences of the myovirus POA1180 (41,655 bp) and podovirus POI1126 (60,065 bp) were analyzed. Phage POA1180 is very similar to a prophage recently identified in a Brucella strain isolated from an exotic frog. The POA1180 genome contains genes which may confer resistance to chromate and the ability to take up sulfate. Phage POI1126 is related to podoviruses of Sinorhizobium meliloti (PCB5), Erwinia pyrifoliae (Pep14), and Burkholderia cenocepacia (BcepIL02) and almost identical to an unnamed plasmid of the Ochrobactrum intermedium strain LMG 3301. Further experiments revealed that the POI1126 prophage indeed replicates as an extrachromosomal element. The data demonstrate for the first time that active prophages are common in Ochrobactrum and suggest that atypical brucellae also may be a reservoir for temperate phages.
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Affiliation(s)
- Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Holger C Scholz
- German Center for Infection Research, Bundeswehr Institute of MicrobiologyMunich, Germany
| | - Karsten Nöckler
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jochen Reetz
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jens A Hammerl
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
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26
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Piya D, Vara L, Russell WK, Young R, Gill JJ. The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis. Mol Microbiol 2017; 105:399-412. [PMID: 28509398 DOI: 10.1111/mmi.13705] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2017] [Indexed: 01/16/2023]
Abstract
Bacterial Type I restriction-modification (R-M) systems present a major barrier to foreign DNA entering the bacterial cell. The temperate phage P1 packages several proteins into the virion that protect the phage DNA from host restriction. Isogenic P1 deletion mutants were used to reconstitute the previously described restriction phenotypes associated with darA and darB. While P1ΔdarA and P1ΔdarB produced the expected phenotypes, deletions of adjacent genes hdf and ddrA also produced darA-like phenotypes and deletion of ulx produced a darB-like phenotype, implicating several new proteins of previously unknown function in the P1 dar antirestriction system. Interestingly, disruption of ddrB decreased P1's sensitivity to EcoB and EcoK restriction. Proteomic analysis of purified virions suggests that packaging of antirestriction components into P1 virions follows a distinct pathway that begins with the incorporation of DarA and Hdf and concludes with DarB and Ulx. Electron microscopy analysis showed that hdf and darA mutants also produce abnormally high proportions of virions with aberrant small heads, which suggests Hdf and DarA play a role in capsid morphogenesis. The P1 antirestriction system is more complex than previously realized and is comprised of multiple proteins including DdrA, DdrB, Hdf, and Ulx in addition to DarA and DarB.
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Affiliation(s)
- Denish Piya
- Center for Phage Technology, Texas A-M University, College Station, TX, 77843, USA.,Departments of Biochemistry & Biophysics, Texas A-M University, College Station, TX, 77843, USA
| | - Leonardo Vara
- Departments of Biology, Texas A-M University, College Station, TX, 77843, USA
| | - William K Russell
- Departments of Chemistry, Texas A-M University, College Station, TX, 77843, USA
| | - Ry Young
- Center for Phage Technology, Texas A-M University, College Station, TX, 77843, USA.,Departments of Biochemistry & Biophysics, Texas A-M University, College Station, TX, 77843, USA
| | - Jason J Gill
- Center for Phage Technology, Texas A-M University, College Station, TX, 77843, USA.,Departments of Animal Science, Texas A&M University, College Station, TX, 77843, USA
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Xu Y, Buss EA, Boucias DG. Impacts of Antibiotic and Bacteriophage Treatments on the Gut-Symbiont-Associated Blissus insularis (Hemiptera: Blissidae). INSECTS 2016; 7:insects7040061. [PMID: 27827869 PMCID: PMC5198209 DOI: 10.3390/insects7040061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/16/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022]
Abstract
The Southern chinch bug, Blissus insularis, possesses specialized midgut crypts that harbor dense populations of the exocellular symbiont Burkholderia. Oral administration of antibiotics suppressed the gut symbionts in B. insularis and negatively impacted insect host fitness, as reflected by retarded development, smaller body size, and higher susceptibility to an insecticide, bifenthrin. Considering that the antibiotics probably had non-lethal but toxic effects on host fitness, attempts were conducted to reduce gut symbionts using bacteriophage treatment. Soil-lytic phages active against the cultures of specific Burkholderia ribotypes were successfully isolated using a soil enrichment protocol. Characterization of the BiBurk16MC_R phage determined its specificity to the Bi16MC_R_vitro ribotype and placed it within the family Podoviridae. Oral administration of phages to fifth-instar B. insularis, inoculated with Bi16MC_R_vitro as neonates had no deleterious effects on host fitness. However, the ingested phages failed to impact the crypt-associated Burkholderia. The observed inactivity of the phage was likely due to the blockage of the connection between the anterior and posterior midgut regions. These findings suggest that the initial colonization by Burkholderia programs the ontogeny of the midgut, providing a sheltered residence protected from microbial antagonists.
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Affiliation(s)
- Yao Xu
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA.
| | - Eileen A Buss
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA.
| | - Drion G Boucias
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA.
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Abstract
Bacteriophage play many varied roles in microbial ecology and evolution. This chapter collates a vast body of knowledge and expertise on Yersinia pestis phages, including the history of their isolation and classical methods for their isolation and identification. The genomic diversity of Y. pestis phage and bacteriophage islands in the Y. pestis genome are also discussed because all phage research represents a branch of genetics. In addition, our knowledge of the receptors that are recognized by Y. pestis phage, advances in phage therapy for Y. pestis infections, the application of phage in the detection of Y. pestis, and clustered regularly interspaced short palindromic repeats (CRISPRs) sequences of Y. pestis from prophage DNA are all reviewed here.
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Jachiet PA, Colson P, Lopez P, Bapteste E. Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network. Genome Biol Evol 2014; 6:2195-205. [PMID: 25104113 PMCID: PMC4202312 DOI: 10.1093/gbe/evu168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
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Affiliation(s)
- Pierre-Alain Jachiet
- UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France
| | - Philippe Colson
- URMITE UMR CNRS 6236 IRD 198, Facultés de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Philippe Lopez
- UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France
| | - Eric Bapteste
- UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France
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Worley-Morse TO, Zhang L, Gunsch CK. The long-term effects of phage concentration on the inhibition of planktonic bacterial cultures. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2014; 16:81-87. [PMID: 24301469 DOI: 10.1039/c3em00427a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Since the early 1920s there has been an interest in using bacteriophages (phages) for the control of bacterial pathogens. While there are many factors that have limited the success of phage bio-control, one particular problem is the variability of outcomes between phages and bacteria. Specifically, there is a significant need for a better understanding of how initial phage concentrations affect long-term bacterial inhibition. In work reported herein three phages were isolated for Escherichia coli K12, Pseudomonas aeruginosa PAO1, as well as Bacillus cereus and bio-control experiments were performed with phage concentrations ranging from 10(5) to 10(8) plaque forming units per mL over the course of 72 h. For four of the nine phages isolated there was a linear relationship between inhibition and phage concentration, suggesting the effect of phage concentration is important at longer time scales. For three of the isolated phages, phage concentrations had no effect on bacterial inhibition suggesting that even at the lowest concentration the method of action was saturated and lower concentrations might still be effective. Additionally, a cocktail was created and was compared to the previously isolated phages. There was no statistical difference between the cocktail and the best performing phage highlighting the importance of selecting the appropriate phages for treatment. These results suggest that, for certain phages, there is a strong relationship between phage concentration and long-term bacterial growth inhibition and the initial phage concentration is an important indicator of the long-term outcome.
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Affiliation(s)
- Thomas O Worley-Morse
- Department of Civil and Environmental Engineering, Duke University, Box 90287, Durham, NC 27708, USA.
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Hoe S, Semler DD, Goudie AD, Lynch KH, Matinkhoo S, Finlay WH, Dennis JJ, Vehring R. Respirable Bacteriophages for the Treatment of Bacterial Lung Infections. J Aerosol Med Pulm Drug Deliv 2013; 26:317-35. [DOI: 10.1089/jamp.2012.1001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Susan Hoe
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
| | - Diana D. Semler
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Amanda D. Goudie
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Karlene H. Lynch
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Sadaf Matinkhoo
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
| | - Warren H. Finlay
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Reinhard Vehring
- Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada
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Characterization of novel virulent broad-host-range phages of Xylella fastidiosa and Xanthomonas. J Bacteriol 2013; 196:459-71. [PMID: 24214944 DOI: 10.1128/jb.01080-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The xylem-limited bacterium Xylella fastidiosa is the causal agent of several plant diseases, most notably Pierce's disease of grape and citrus variegated chlorosis. We report the isolation and characterization of the first virulent phages for X. fastidiosa, siphophages Sano and Salvo and podophages Prado and Paz, with a host range that includes Xanthomonas spp. Phages propagated on homologous hosts had observed adsorption rate constants of ~4 × 10(-12) ml cell(-1) min(-1) for X. fastidiosa strain Temecula 1 and ~5 × 10(-10) to 7 × 10(-10) ml cell(-1) min(-1) for Xanthomonas strain EC-12. Sano and Salvo exhibit >80% nucleotide identity to each other in aligned regions and are syntenic to phage BcepNazgul. We propose that phage BcepNazgul is the founding member of a novel phage type, to which Sano and Salvo belong. The lysis genes of the Nazgul-like phage type include a gene that encodes an outer membrane lipoprotein endolysin and also spanin gene families that provide insight into the evolution of the lysis pathway for phages of Gram-negative hosts. Prado and Paz, although exhibiting no significant DNA homology to each other, are new members of the phiKMV-like phage type, based on the position of the single-subunit RNA polymerase gene. The four phages are type IV pilus dependent for infection of both X. fastidiosa and Xanthomonas. The phages may be useful as agents for an effective and environmentally responsible strategy for the control of diseases caused by X. fastidiosa.
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Lynch KH, Abdu AH, Schobert M, Dennis JJ. Genomic characterization of JG068, a novel virulent podovirus active against Burkholderia cenocepacia. BMC Genomics 2013; 14:574. [PMID: 23978260 PMCID: PMC3765740 DOI: 10.1186/1471-2164-14-574] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/09/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND As is true for many other antibiotic-resistant Gram-negative pathogens, members of the Burkholderia cepacia complex (BCC) are currently being assessed for their susceptibility to phage therapy as an antimicrobial treatment. The objective of this study was to perform genomic and limited functional characterization of the novel BCC phage JG068 (vB_BceP_JG068). RESULTS JG068 is a podovirus that forms large, clear plaques on Burkholderia cenocepacia K56-2. Host range analysis indicates that this phage can infect environmental, clinical, and epidemic isolates of Burkholderia multivorans, B. cenocepacia, Burkholderia stabilis, and Burkholderia dolosa, likely through interaction with the host lipopolysaccharide as a receptor. The JG068 chromosome is 41,604 base pairs (bp) in length and is flanked by 216 bp short direct terminal repeats. Gene expression originates from both host and phage promoters and is in the forward direction for all 49 open reading frames. The genome sequence shows similarity to Ralstonia phage ϕRSB1, Caulobacter phage Cd1, and uncharacterized genetic loci of blood disease bacterium R229 and Burkholderia pseudomallei 1710b. CoreGenesUniqueGenes analysis indicates that JG068 belongs to the Autographivirinae subfamily and ϕKMV-like phages genus. Modules within the genome encode proteins involved in DNA-binding, morphogenesis, and lysis, but none associated with pathogenicity or lysogeny. Similar to the signal-arrest-release (SAR) endolysin of ϕKMV, inducible expression of the JG068 SAR endolysin causes lysis of Escherichia coli that is dependent on the presence of an N-terminal signal sequence. In an in vivo assay using the Galleria mellonella infection model, treatment of B. cenocepacia K56-2-infected larvae with JG068 results in a significant increase in larval survival. CONCLUSIONS As JG068 has a broad host range, does not encode virulence factors, is obligately lytic, and has activity against an epidemic B. cenocepacia strain in vivo, this phage is a highly promising candidate for BCC phage therapy development.
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Affiliation(s)
- Karlene H Lynch
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
| | - Ashraf H Abdu
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
| | - Max Schobert
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jonathan J Dennis
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
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Gill JJ, Berry JD, Russell WK, Lessor L, Escobar-Garcia DA, Hernandez D, Kane A, Keene J, Maddox M, Martin R, Mohan S, Thorn AM, Russell DH, Young R. The Caulobacter crescentus phage phiCbK: genomics of a canonical phage. BMC Genomics 2012; 13:542. [PMID: 23050599 PMCID: PMC3556154 DOI: 10.1186/1471-2164-13-542] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/01/2012] [Indexed: 11/30/2022] Open
Abstract
Background The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives. Results Five novel phiCbK-like C. crescentus bacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of the C. crescentus cell cycle regulator GcrA, which may allow the phage to alter the host cell’s replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level. Conclusions Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions in C. crescentus.
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Affiliation(s)
- Jason J Gill
- Center for Phage Technology, 2128 TAMU, Texas A&M University, College Station, Texas, TX 77843, USA
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Lynch KH, Stothard P, Dennis JJ. Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages. BMC Genomics 2012; 13:223. [PMID: 22676492 PMCID: PMC3483164 DOI: 10.1186/1471-2164-13-223] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 05/15/2012] [Indexed: 11/17/2022] Open
Abstract
Background Genomic analysis of bacteriophages infecting the Burkholderia cepacia complex (BCC) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. The objective of this study was to characterize KL1 (vB_BceS_KL1) and AH2 (vB_BceS_AH2), two novel Burkholderia cenocepacia-specific siphoviruses isolated from environmental samples. Results KL1 and AH2 exhibit several unique phenotypic similarities: they infect the same B. cenocepacia strains, they require prolonged incubation at 30°C for the formation of plaques at low titres, and they do not form plaques at similar titres following incubation at 37°C. However, despite these similarities, we have determined using whole-genome pyrosequencing that these phages show minimal relatedness to one another. The KL1 genome is 42,832 base pairs (bp) in length and is most closely related to Pseudomonas phage 73 (PA73). In contrast, the AH2 genome is 58,065 bp in length and is most closely related to Burkholderia phage BcepNazgul. Using both BLASTP and HHpred analysis, we have identified and analyzed the putative virion morphogenesis, lysis, DNA binding, and MazG proteins of these two phages. Notably, MazG homologs identified in cyanophages have been predicted to facilitate infection of stationary phase cells and may contribute to the unique plaque phenotype of KL1 and AH2. Conclusions The nearly indistinguishable phenotypes but distinct genomes of KL1 and AH2 provide further evidence of both vast diversity and convergent evolution in the BCC-specific phage population.
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Affiliation(s)
- Karlene H Lynch
- 6-008 Centennial Centre for Interdisciplinary Science, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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Lynch KH, Dennis JJ. Cangene Gold Medal Award Lecture — Genomic analysis and modification ofBurkholderia cepaciacomplex bacteriophages1This article is based on a presentation by Dr. Karlene Lynch at the 61st Annual Meeting of the Canadian Society of Microbiologists in St. John’s, Newfoundland and Labrador, on 21 June 2011. Dr. Lynch was the recipient of the 2011 Cangene Gold Medal as the Canadian Graduate Student Microbiologist of the Year, an annual award sponsored by Cangene Corporation intended to recognize excellence in graduate research. Can J Microbiol 2012; 58:221-35. [DOI: 10.1139/w11-135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of 17 Gram-negative predominantly environmental bacterial species that cause potentially fatal opportunistic infections in cystic fibrosis (CF) patients. Although its prevalence in these individuals is lower than that of Staphylococcus aureus and Pseudomonas aeruginosa , the Bcc remains a serious problem in the CF community because of the pathogenicity, transmissibility, and inherent antibiotic resistance of these organisms. An alternative treatment for Bcc infections that is currently being developed is phage therapy, the clinical use of viruses that infect bacteria. To assess the suitability of individual phage isolates for therapeutic use, the complete genome sequences of a panel of Bcc‐specific phages were determined and analyzed. These sequences encode a broad range of proteins with a gradient of relatedness to phage and bacterial gene products from Burkholderia and other genera. The majority of these phages were found not to encode virulence factors, and despite their predominantly temperate nature, a proof-of-principle experiment has shown that they may be modified to a lytic form. Both the genomic characterization and subsequent engineering of Bcc‐specific phages are fundamental to the development of an effective phage therapy strategy for these bacteria.
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Affiliation(s)
- Karlene H. Lynch
- 6-008 Centennial Centre for Interdisciplinary Science, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jonathan J. Dennis
- 6-008 Centennial Centre for Interdisciplinary Science, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Semler DD, Lynch KH, Dennis JJ. The promise of bacteriophage therapy for Burkholderia cepacia complex respiratory infections. Front Cell Infect Microbiol 2012; 1:27. [PMID: 22919592 PMCID: PMC3417384 DOI: 10.3389/fcimb.2011.00027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 12/31/2011] [Indexed: 11/13/2022] Open
Abstract
In recent times, increased attention has been given to evaluating the efficacy of phage therapy, especially in scenarios where the bacterial infectious agent of interest is highly antibiotic resistant. In this regard, phage therapy is especially applicable to infections caused by the Burkholderia cepacia complex (BCC) since members of the BCC are antibiotic pan-resistant. Current studies in BCC phage therapy are unique from many other avenues of phage therapy research in that the investigation is not only comprised of phage isolation, in vitro phage characterization and assessment of in vivo infection model efficacy, but also adapting aerosol drug delivery techniques to aerosol phage formulation delivery and storage.
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Affiliation(s)
- Diana D. Semler
- Department of Biological Sciences, Centennial Centre for Interdisciplinary Science, University of AlbertaEdmonton, AB, Canada
| | - Karlene H. Lynch
- Department of Biological Sciences, Centennial Centre for Interdisciplinary Science, University of AlbertaEdmonton, AB, Canada
| | - Jonathan J. Dennis
- Department of Biological Sciences, Centennial Centre for Interdisciplinary Science, University of AlbertaEdmonton, AB, Canada
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Abstract
Bcep22-like phages are a recently described group of podoviruses that infect strains of Burkholderia cenocepacia. We have isolated and characterized a novel member of this group named DC1. This podovirus shows many genomic similarities to BcepIL02 and Bcep22, but it infects strains belonging to multiple Burkholderia cepacia complex (BCC) species.
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