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The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy. Viruses 2021; 13:v13040656. [PMID: 33920240 PMCID: PMC8069663 DOI: 10.3390/v13040656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.
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A Novel Vibriophage vB_VcaS_HC Containing Lysogeny-Related Gene Has Strong Lytic Ability against Pathogenic Bacteria. Virol Sin 2020; 36:281-290. [PMID: 32767211 DOI: 10.1007/s12250-020-00271-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
To avoid the negative effects of antibiotics, using phage to prevent animal disease becomes a promising method in aquaculture. Here, a lytic phage provisionally named vB_VcaS_HC that can infect the pathogen (i.e., Vibrio campbellii 18) of prawn was isolated. The phage has an isometric head and a non-contractile tail. During phage infection, the induced host mortality in 5.5 h reached ca. 96%, with a latent period of 1.5 h and a burst size of 172 PFU/cell. It has an 81,566 bp circular dsDNA genome containing 121 open reading frames (ORFs), and ca. 71% of the ORFs are functionally unknown. Comparative genomic and phylogenetic analysis revealed that it is a novel phage belonging to Delepquintavirus, Siphoviridae, Caudovirales. In the phage genome, besides the ordinary genes related to structure assembly and DNA metabolism, there are 10 auxiliary metabolic genes. For the first time, the pyruvate phosphate dikinase (PPDK) gene was found in phages whose product is a key rate-limiting enzyme involving Embden-Meyerhof-Parnas (EMP) reaction. Interestingly, although the phage has a strong bactericidal activity and contains a potential lysogeny related gene, i.e., the recombinase (RecA) gene, we did not find the phage turned into a lysogenic state. Meanwhile, the phage genome does not contain any bacterial virulence gene or antimicrobial resistance gene. This study represents the first comprehensive characterization of a lytic V. campbellii phage and indicates that it is a promising candidate for the treatment of V. campbellii infections.
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Zhang XH, He X, Austin B. Vibrio harveyi: a serious pathogen of fish and invertebrates in mariculture. MARINE LIFE SCIENCE & TECHNOLOGY 2020; 2:231-245. [PMID: 32419972 PMCID: PMC7223180 DOI: 10.1007/s42995-020-00037-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/26/2020] [Indexed: 05/12/2023]
Abstract
Vibrio harveyi, which belongs to family Vibrionaceae of class Gammaproteobacteria, includes the species V. carchariae and V. trachuri as its junior synonyms. The organism is a well-recognized and serious bacterial pathogen of marine fish and invertebrates, including penaeid shrimp, in aquaculture. Diseased fish may exhibit a range of lesions, including eye lesions/blindness, gastro-enteritis, muscle necrosis, skin ulcers, and tail rot disease. In shrimp, V. harveyi is regarded as the etiological agent of luminous vibriosis in which affected animals glow in the dark. There is a second condition of shrimp known as Bolitas negricans where the digestive tract is filled with spheres of sloughed-off tissue. It is recognized that the pathogenicity mechanisms of V. harveyi may be different in fish and penaeid shrimp. In shrimp, the pathogenicity mechanisms involved the endotoxin lipopolysaccharide, and extracellular proteases, and interaction with bacteriophages. In fish, the pathogenicity mechanisms involved extracellular hemolysin (encoded by duplicate hemolysin genes), which was identified as a phospholipase B and could inactivate fish cells by apoptosis, via the caspase activation pathway. V. harveyi may enter the so-called viable but nonculturable (VBNC) state, and resuscitation of the VBNC cells may be an important reason for vibriosis outbreaks in aquaculture. Disease control measures center on dietary supplements (including probiotics), nonspecific immunostimulants, and vaccines and to a lesser extent antibiotics and other antimicrobial compounds.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100 China
| | - Xinxin He
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA Scotland, UK
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vB_LspM-01: a novel myovirus displaying pseudolysogeny in Lysinibacillus sphaericus C3-41. Appl Microbiol Biotechnol 2018; 102:10691-10702. [PMID: 30362075 DOI: 10.1007/s00253-018-9424-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Lysinibacillus sphaericus has great application potential not only in the biocontrol of mosquitoes but also in the bioremediation of toxic metals. Phages contribute to the genetic diversity and niche adaptation of bacteria, playing essential roles in their life cycle, but may also cause economic damage for industrially important bacteria through phage contamination during fermentation. In this study, the L. sphaericus phage vB_LspM-01, which belongs to the Myoviridae family, was isolated and characterized. Results showed that vB_LspM-01 could specifically infect most tested L. sphaericus isolates but was not active against isolates belonging to other species. Furthermore, phage-born endolysin exhibited a broader antimicrobial spectrum than the host range of the phage. The vB_LspM-01 genome had no obvious similarity with that of its host, and ca. 22.6% of putative ORFs could not get a match with the public databases. Phylogenic analysis based on the putative terminase large subunit showed high similarity with the phages identified with pac-type headful packaging. The vB_LspM-01 encoding genes were only detected in a tiny percentage of L. sphaericus C3-41 individual cells in the wild population, whereas they showed much higher frequency in the resistant population grown within the plaques; however, the phage genes could not be stably inherited during host cell division. Additionally, the vB_LspM-01 encoding genes were only detected in the host population during the logarithmic growth phase. The mitomycin C induction helped the propagation and lysogeny-lysis switch of vB_LspM-01. The study demonstrated that vB_LspM-01 can be present in a pseudolysogenic state in L. sphaericus C3-41 populations.
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Yatip P, Nitin Chandra Teja D, Flegel TW, Soowannayan C. Extract from the fermented soybean product Natto inhibits Vibrio biofilm formation and reduces shrimp mortality from Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2018; 72:348-355. [PMID: 29127029 DOI: 10.1016/j.fsi.2017.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/28/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Many bacteria, including Vibrio pathogens of shrimp, need to colonize and/or form biofilms in hosts or the environment to cause disease. Thus, one possible control strategy for shrimp Vibriosis is biofilm inhibition. With this objective, an extract from the Japanese fermented soybean product, Natto was tested with the luminescent shrimp pathogen Vibrio harveyi (VH) for its ability to inhibit or degrade biofilm and to interfere with cell growth in broth. Natto is a traditional fermentation product of Bacillus subtilis var Natto (BSN1). Using 96 well microtiter plates coated with 0.4% chitosan, we found that biofilm formation by VH was inhibited, while growth in parallel broth cultures was not. When an extract from Natto prepared using BSN1 was mixed with feed for the whiteleg shrimp Penaeus vannamei before immersion challenge with V. harveyi at 106 cfu/ml, survival was significantly higher (p≤0.05) than for control shrimp given feed without these additives. Further work done to test whether d-amino acids were involved in biofilm formation as previously reported for B. subtilis, Staphylococus aureus and Pseudomonas aeruginosa gave negative results. In conclusion, we discovered that Natto extract can inhibit Vibrio biofilm formation and that it or BSN1 alone added to shrimp feed can significantly reduce shrimp mortality in immersion challenges with pathogenic VH. This shows some promise for possible application against Vibriosis in shrimp since Natto is generally regarded as safe (GRAS) for human consumption.
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Affiliation(s)
- Pattanan Yatip
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX SHRIMP), Mahidol University, Bangkok, 10400, Thailand
| | - D Nitin Chandra Teja
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX SHRIMP), Mahidol University, Bangkok, 10400, Thailand
| | - Timothy W Flegel
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX SHRIMP), Mahidol University, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Nueng, Klong Luang, Pathumtani, Thailand
| | - Chumporn Soowannayan
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX SHRIMP), Mahidol University, Bangkok, 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Nueng, Klong Luang, Pathumtani, Thailand.
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Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. Sci Rep 2017; 7:41394. [PMID: 28145490 PMCID: PMC5286417 DOI: 10.1038/srep41394] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 01/09/2023] Open
Abstract
The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.
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Uhlich GA, Chen CY, Cottrell BJ, Hofmann CS, Yan X, Nguyen L. Stx1prophage excision inEscherichia colistrain PA20 confers strong curli and biofilm formation by restoring nativemlrA. FEMS Microbiol Lett 2016; 363:fnw123. [DOI: 10.1093/femsle/fnw123] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 01/01/2023] Open
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Roach DR, Sjaarda DR, Sjaarda CP, Ayala CJ, Howcroft B, Castle AJ, Svircev AM. Absence of lysogeny in wild populations of Erwinia amylovora and Pantoea agglomerans. Microb Biotechnol 2015; 8:510-8. [PMID: 25678125 PMCID: PMC4408183 DOI: 10.1111/1751-7915.12253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 12/03/2022] Open
Abstract
Lytic bacteriophages are in development as biological control agents for the prevention of fire blight disease caused by Erwinia amylovora. Temperate phages should be excluded as biologicals since lysogeny produces the dual risks of host resistance to phage attack and the transduction of virulence determinants between bacteria. The extent of lysogeny was estimated in wild populations of E. amylovora and Pantoea agglomerans with real-time polymerase chain reaction primers developed to detect E. amylovora phages belonging to the Myoviridae and Podoviridae families. Pantoea agglomerans, an orchard epiphyte, is easily infected by Erwinia spp. phages, and it serves as a carrier in the development of the phage-mediated biological control agent. Screening of 161 E. amylovora isolates from 16 distinct geographical areas in North America, Europe, North Africa and New Zealand and 82 P. agglomerans isolates from southern Ontario, Canada showed that none possessed prophage. Unstable phage resistant clones or lysogens were produced under laboratory conditions. Additionally, a stable lysogen was recovered from infection of bacterial isolate Ea110R with Podoviridae phage ΦEa35-20. These laboratory observations suggested that while lysogeny is possible in E. amylovora, it is rare or absent in natural populations, and there is a minimal risk associated with lysogenic conversion and transduction by Erwinia spp. phages.
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Affiliation(s)
- Dwayne R Roach
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - David R Sjaarda
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Calvin P Sjaarda
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Carlos Juarez Ayala
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Brittany Howcroft
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
| | - Alan J Castle
- Department of Biological Science, Brock University500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
| | - Antonet M Svircev
- Agriculture and Agri-Food Canada4902 Victoria Ave. North, P.O. Box 6000, Vineland Station, ON, L0R 2E0, Canada
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Complete genome sequence analysis of two Pseudomonas plecoglossicida phages, potential therapeutic agents. Appl Environ Microbiol 2014; 81:874-81. [PMID: 25416766 DOI: 10.1128/aem.03038-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas plecoglossicida is a lethal pathogen of ayu (Plecoglossus altivelis) in Japan and is responsible for substantial economic costs to ayu culture. Previously, we demonstrated the efficacy of phage therapy against P. plecoglossicida infection using two lytic phages (PPpW-3 and PPpW-4) (S. C. Park, I. Shimamura, M. Fukunaga, K. Mori, and T. Nakai, Appl Environ Microbiol 66:1416-1422, 2000, http://dx.doi.org/10.1128/AEM.66.4.1416-1422.2000; S. C. Park and T. Nakai, Dis Aquat Org 53:33-39, 2003, http://dx.doi.org/10.3354/dao053033). In the present study, the complete genome sequences of these therapeutic P. plecoglossicida phages were determined and analyzed for deleterious factors as therapeutic agents. The genome of PPpW-3 (myovirus) consisted of 43,564 bp with a GC content of 61.1% and 66 predicted open reading frames (ORFs). Approximately half of the genes were similar to the genes of the Escherichia coli phage vB_EcoM_ECO1230-10 (myovirus). The genome of PPpW-4 (podovirus) consisted of 41,386 bp with a GC content of 56.8% and 50 predicted ORFs. More than 70% of the genes were similar to the genes of Pseudomonas fluorescens phage ϕIBB-PF7A and Pseudomonas putida phage ϕ15 (podoviruses). The whole-genome analysis revealed that no known virulence genes were present in PPpW-3 and PPpW-4. An integrase gene was found in PPpW-3, but other factors used for lysogeny were not confirmed. The PCR detection of phage genes in phage-resistant variants provided no evidence of lysogenic activity in PPpW-3 and PPpW-4. We conclude that these two lytic phages qualify as therapeutic agents.
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Friedman CS, Wight N, Crosson LM, Vanblaricom GR, Lafferty KD. Reduced disease in black abalone following mass mortality: phage therapy and natural selection. Front Microbiol 2014; 5:78. [PMID: 24672512 PMCID: PMC3957727 DOI: 10.3389/fmicb.2014.00078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/12/2014] [Indexed: 11/13/2022] Open
Abstract
Black abalone, Haliotis cracherodii, populations along the NE Pacific ocean have declined due to the rickettsial disease withering syndrome (WS). Natural recovery on San Nicolas Island (SNI) of Southern California suggested the development of resistance in island populations. Experimental challenges in one treatment demonstrated that progeny of disease-selected black abalone from SNI survived better than did those from naïve black abalone from Carmel Point in mainland coastal central California. Unexpectedly, the presence of a newly observed bacteriophage infecting the WS rickettsia (WS-RLO) had strong effects on the survival of infected abalone. Specifically, presence of phage-infected RLO (RLOv) reduced the host response to infection, RLO infection loads, and associated mortality. These data suggest that the black abalone: WS-RLO relationship is evolving through dual host mechanisms of resistance to RLO infection in the digestive gland via tolerance to infection in the primary target tissue (the post-esophagus) coupled with reduced pathogenicity of the WS-RLO by phage infection, which effectively reduces the infection load in the primary target tissue by half. Sea surface temperature patterns off southern California, associated with a recent hiatus in global-scale ocean warming, do not appear to be a sufficient explanation for survival patterns in SNI black abalone. These data highlight the potential for natural recovery of abalone populations over time and that further understanding of mechanisms governing host–parasite relationships will better enable us to manage declining populations.
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Affiliation(s)
- Carolyn S Friedman
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Nathan Wight
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Lisa M Crosson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Glenn R Vanblaricom
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA ; Washington Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Washington Seattle, WA, USA
| | - Kevin D Lafferty
- Western Ecological Research Center, U.S. Geological Survey, c/o Marine Science Institute, University of California at Santa Barbara Santa Barbara, CA, USA
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Denyes JM, Krell PJ, Manderville RA, Ackermann HW, She YM, Kropinski AM. The genome and proteome of Serratia bacteriophage η which forms unstable lysogens. Virol J 2014; 11:6. [PMID: 24433577 PMCID: PMC3918226 DOI: 10.1186/1743-422x-11-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/10/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Serratia marcescens phage η is a temperate unclassified member of the Siphoviridae which had been reported as containing hypermodified guanine residues. METHODS The DNA was characterized by enzymatic digestion followed by HPLC analysis of the nucleoside composition, and by DNA sequencing and proteomic analysis. Its ability to form stable lysogens and integrate was also investigated. RESULTS Enzymatic digestion and HPLC analysis revealed phage η DNA did not contain modified bases. The genome sequence of this virus, determined using pyrosequencing, is 42,724 nucleotides in length with a mol% GC of 49.9 and is circularly permuted. Sixty-nine putative CDSs were identified of which 19 encode novel proteins. While seven close genetic relatives were identified, they shared sequence similarity with only genes 40 to 69 of the phage η genome, while gp1 to gp39 shared no conserved relationship. The structural proteome, determined by SDS-PAGE and mass spectrometry, revealed seven unique proteins. This phage forms very unstable lysogens with its host S. marcescens.
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Affiliation(s)
- Jenna M Denyes
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Current address: ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Peter J Krell
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Hans-Wolfgang Ackermann
- Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Laval University, Quebec, QC G1X 4C6, Canada
| | - Yi-Min She
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, China
| | - Andrew M Kropinski
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, Ontario N1G 3W4, Canada
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Serendipitous isolation of non-Vibrio bacterial strains carrying the cholera toxin gene from environmental waters in indonesia. Int J Microbiol 2013; 2013:406078. [PMID: 24368914 PMCID: PMC3866716 DOI: 10.1155/2013/406078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 11/17/2022] Open
Abstract
We initially attempted to isolate a Vibrio cholerae O1 El Tor biotype that carries a novel variant of the cholera toxin gene (ctxAB) from environmental waters of Indonesia, where the seventh cholera pandemic by V. cholerae O1 El Tor biotype began. Nested PCR targeting the gene revealed that a total of eight strains were found to carry ctxAB. However, sequencing of the 16S rRNA genes of these isolates showed they were not V. cholerae but were either Klebsiella, Enterobacter, Pantoea, or Aeromonas. Subsequent nested PCR assays targeting all genes known to be encoded on the CTX phage (i.e., zot, ace, orfU, cep, rstB, rstA, and rstR) showed that one isolate belonged to the Enterobacter genus carried all the genes tested, while the other isolates lacked either 2, 3, or 5 of the genes. This evidence suggests that phages with ctxAB are genetically diverse and can infect not only V. cholerae and V. mimicus but also other species and genera in the form of a pseudolysogen.
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Abstract
Pseudolysogeny can be defined as the stage of stalled development of a bacteriophage in a host cell without either multiplication of the phage genome (as in lytic development) or its replication synchronized with the cell cycle and stable maintenance in the cell line (as in lysogenization), which proceeds with no viral genome degradation, thus allowing the subsequent restart of virus development. This phenomenon is usually caused by unfavorable growth conditions for the host cell (such as starvation) and is terminated with initiation of either true lysogenization or lytic growth when growth conditions improve. Pseudolysogeny has been known for tens of years; however, its role has often been underestimated. Currently, it is being considered more often as an important aspect of phage-host interactions. The reason for this is mostly an increased interest in phage-host interactions in the natural environment. Pseudolysogeny seems to play an important role in phage survival, as bacteria in a natural environment are starved or their growth is very slow. This phenomenon can be an important aspect of phage-dependent bacterial mortality and may influence the virulence of some bacterial strains.
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Affiliation(s)
- Marcin Łoś
- Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
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Krylov V, Shaburova O, Krylov S, Pleteneva E. A genetic approach to the development of new therapeutic phages to fight pseudomonas aeruginosa in wound infections. Viruses 2012; 5:15-53. [PMID: 23344559 PMCID: PMC3564109 DOI: 10.3390/v5010015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 12/03/2012] [Accepted: 12/12/2012] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is a frequent participant in wound infections. Emergence of multiple antibiotic resistant strains has created significant problems in the treatment of infected wounds. Phage therapy (PT) has been proposed as a possible alternative approach. Infected wounds are the perfect place for PT applications, since the basic condition for PT is ensured; namely, the direct contact of bacteria and their viruses. Plenty of virulent ("lytic") and temperate ("lysogenic") bacteriophages are known in P. aeruginosa. However, the number of virulent phage species acceptable for PT and their mutability are limited. Besides, there are different deviations in the behavior of virulent (and temperate) phages from their expected canonical models of development. We consider some examples of non-canonical phage-bacterium interactions and the possibility of their use in PT. In addition, some optimal approaches to the development of phage therapy will be discussed from the point of view of a biologist, considering the danger of phage-assisted horizontal gene transfer (HGT), and from the point of view of a surgeon who has accepted the Hippocrates Oath to cure patients by all possible means. It is also time now to discuss the possible approaches in international cooperation for the development of PT. We think it would be advantageous to make phage therapy a kind of personalized medicine.
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Affiliation(s)
- Victor Krylov
- Laboratory for Bacteriophages Genetics. Mechnikov Research Institute of Vaccines and Sera, 5a Maliy Kazenniy per., Moscow, Russia.
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Baudoux AC, Hendrix RW, Lander GC, Bailly X, Podell S, Paillard C, Johnson JE, Potter CS, Carragher B, Azam F. Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ Microbiol 2012; 14:2071-86. [PMID: 22225728 PMCID: PMC3338904 DOI: 10.1111/j.1462-2920.2011.02685.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.
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Affiliation(s)
- A-C Baudoux
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA.
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16
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Nigro OD, Culley AI, Steward GF. Complete genome sequence of bacteriophage VvAW1, which infects Vibrio vulnificus. Stand Genomic Sci 2012; 6:415-26. [PMID: 23408718 PMCID: PMC3558961 DOI: 10.4056/sigs.2846206] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Investigating the bacteriophages of vibrios has led to significant insights into the evolution and pathogenicity of their host strains. This report presents the first complete genome sequence of a bacteriophage that infects the deadly human pathogen Vibrio vulnificus. The phage was isolated from the surface waters of the Ala Wai Canal, which is part of an urban watershed in eastern Honolulu, Hawaii, USA. The phage particle is icosahedral, with a diameter of 35-40 nm, and a small non-contractile tail. The genome was sequenced in its entirety, rendering a 38 kb sequence located on a single, linear, circularly permuted chromosome. Here, we present the annotation and genomic features of the bacteriophage, VvAW1.
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Affiliation(s)
- Olivia D Nigro
- University of Hawaii Department of Oceanography Center for Microbial Oceanography: Research and Education Honolulu, HI
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17
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Complete genome sequence of virulence-enhancing Siphophage VHS1 from Vibrio harveyi. Appl Environ Microbiol 2012; 78:2790-6. [PMID: 22307287 DOI: 10.1128/aem.05929-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio harveyi siphophage 1 (VHS1) is a tailed phage with an icosahedral head of approximately 66 nm in diameter and an unornamented, flexible tail of approximately 153 nm in length. When Vibrio harveyi 1114GL is lysogenized with VHS1, its virulence for the black tiger shrimp (Penaeus monodon) increases by more than 100 times, and this coincides with production of a toxin(s) associated with shrimp hemocyte agglutination. Curiously, the lysogen does not show increased virulence for the whiteleg shrimp (Penaeus [Litopenaeus] vannamei). Here we present and annotate the complete, circular genome of VHS1 (81,509 kbp; GenBank accession number JF713456). By software analysis, the genome contains 125 putative open reading frames (ORFs), all of which appear to be located on the same DNA strand, similar to the case for many other bacteriophages. Most of the putative ORFs show no significant homology to known sequences in GenBank. Notable exceptions are ORFs for a putative DNA polymerase and putative phage structural proteins, including a portal protein, a phage tail tape measure protein, and a phage head protein. The last protein was identified as a component of the species-specific toxin mixture described above as being associated with agglutination of hemocytes from P. monodon.
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18
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Pasharawipas T. Inducible viral receptor, A possible concept to induce viral protection in primitive immune animals. Virol J 2011; 8:326. [PMID: 21711515 PMCID: PMC3148565 DOI: 10.1186/1743-422x-8-326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 06/28/2011] [Indexed: 11/10/2022] Open
Abstract
A pseudolysogen (PL) is derived from the lysogenic Vibrio harveyi (VH) which is infected with the VHS1 (Vibrio harveyi Siphoviridae-like 1) bacteriophage. The lysogenic Vibrio harveyi undergoes an unequivalent division of the extra-chromosomal VHS1 phage genome and its VH host chromosome and produces a true lysogen (TL) and pseudolysogen (PL). The PL is tolerant to super-infection of VHS1, as is of the true lysogen (TL), but the PL does not contain the VHS1 phage genome while the TL does. However, the PL can become susceptible to VHS1 phage infection if the physiological state of the PL is changed. It is postulated that this is due to a phage receptor molecule which can be inducible to an on-and-off regulation influence by an alternating condition of the bacterial host cell. This characteristic of the PL leads to speculate that this phenomenon can also occur in high organisms with low immunity such as shrimp. This article proposes a hypothesis that the viral receptor molecule on the target cell can play a crucial role in which the invertebrate aquaculture animals can become tolerant to viral infection. A possible mechanism may be that the target cell disrupts the viral receptor molecule to prevent super infection. This concept can explain a mechanism for the prevention of viral infection in invertebrate animals which do not have acquired immunity in response to pathogens. It can guide us to develop a mechanism of immunity to viral infection in low-evolved-immune animals. Also, it can be an additional mechanism that exists in high immune organism, as in human for the prevention of viral infection
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Affiliation(s)
- Tirasak Pasharawipas
- Microbiology Unit, Department of Medical Science, Faculty of Science, Rangsit University, Pahonyothin Rd., Pathumthani, Thailand.
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19
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Savijoki K, Lietzén N, Kankainen M, Alatossava T, Koskenniemi K, Varmanen P, Nyman TA. Comparative Proteome Cataloging of Lactobacillus rhamnosus Strains GG and Lc705. J Proteome Res 2011; 10:3460-73. [DOI: 10.1021/pr2000896] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kirsi Savijoki
- Institute of Biotechnology, University of Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Niina Lietzén
- Institute of Biotechnology, University of Helsinki, Finland
| | | | - Tapani Alatossava
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | | | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Tuula A. Nyman
- Institute of Biotechnology, University of Helsinki, Finland
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20
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Pasharawip T, Manopviset J, Flegel T. Phage Treatment of Vibrio harveyi: A General Concept of Protection against Bacterial Infection. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/jm.2011.560.567] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Ruwandeepika H, Defoirdt T, Bhowmick P, Shekar M, Bossier P, Karunasagar I. Presence of typical and atypical virulence genes in vibrio isolates belonging to the Harveyi clade. J Appl Microbiol 2010; 109:888-99. [DOI: 10.1111/j.1365-2672.2010.04715.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Pleteneva EA, Krylov SV, Shaburova OV, Bourkal’tseva MV, Miroshnikov KA, Krylov VN. Pseudolysogeny of Pseudomonas aeruginosa bacteria infected with φKZ-like bacteriophages. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410010047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Spears PA, Suyemoto MM, Palermo AM, Horton JR, Hamrick TS, Havell EA, Orndorff PE. A Listeria monocytogenes mutant defective in bacteriophage attachment is attenuated in orally inoculated mice and impaired in enterocyte intracellular growth. Infect Immun 2008; 76:4046-54. [PMID: 18559424 PMCID: PMC2519439 DOI: 10.1128/iai.00283-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/09/2008] [Accepted: 06/09/2008] [Indexed: 11/20/2022] Open
Abstract
A Listeria monocytogenes bacteriophage was used to identify a phage-resistant Tn917 insertion mutant of the mouse-virulent listerial strain F6214-1. The mutant was attenuated when it was inoculated orally into female A/J mice and failed to replicate efficiently in cultured mouse enterocytes. Phage binding studies indicated that the mutant had a cell surface alteration that precluded phage attachment. All phenotypes associated with the mutation could be complemented in trans by a single open reading frame (ORF) that corresponded to the ORF interrupted by the Tn917 insertion. The complementation effected was, in all cases, at a level indistinguishable from that of the parent. The Tn917 insertion interrupted a gene that is predicted to encode a group 2 glycosyl transferase (provisionally designated glcV). A similar glcV gene is present in Listeria welshimeri and Listeria innocua and in some serotypes of L. monocytogenes. We speculate that the loss of the glcV product results in a defective phage receptor and that this alteration coincidentally influences a feature of the normal host-pathogen interaction required for virulence. Interestingly, the glcV lesion, while preventing phage attachment, did not alter the mutant's ability to bind to cultured mouse enterocyte monolayers. Rather, the mutation appeared to alter a subsequent step in intracellular replication measured by a reduction in plaque-forming efficiency and plaque size. In vivo, the mutant was undetectable in the liver and spleen 48 h after oral inoculation. The mutation is significant in part because it is one of the few that produce attenuation when the mutant is delivered orally.
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Affiliation(s)
- Patricia A Spears
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27606, USA
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24
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Rico R, Tapia-Paniagua S, Martínez-Manzanares E, Balebona M, Moriñigo M. Characterization ofVibrio harveyistrains recovered from diseased farmed Senegalese sole (Solea senegalensis). J Appl Microbiol 2008; 105:752-60. [DOI: 10.1111/j.1365-2672.2008.03786.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Prestel E, Salamitou S, DuBow MS. An examination of the bacteriophages and bacteria of the Namib desert. J Microbiol 2008; 46:364-72. [PMID: 18758725 DOI: 10.1007/s12275-008-0007-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 06/13/2008] [Indexed: 10/21/2022]
Abstract
Bacteria and their viruses (called bacteriophages, or phages), have been found in virtually every ecological niche on Earth. Arid regions, including their most extreme form called deserts, represent the single largest ecosystem type on the Earth's terrestrial surface. The Namib desert is believed to be the oldest (80 million years) desert. We report here an initial analysis of bacteriophages isolated from the Namib desert using a combination of electron microscopy and genomic approaches. The virus-like particles observed by electron microscopy revealed 20 seemingly different phage-like morphologies and sizes belonging to the Myoviridae and Siphoviridae families of tailed phages. Pulsed-field gel electrophoresis revealed a majority of phage genomes of 55-65 kb in length, with genomes of approximately 200, 300, and 350 kb also observable. Sample sequencing of cloned phage DNA fragments revealed that approximately 50% appeared to be of bacterial origin. Of the remaining DNA sequences, approximately 50% displayed no significant match to any sequence in the databases. The majority of the 16S rDNA sequences amplified from DNA extracted from the sand displayed considerable (94-98%) homology to members of the Firmicutes, and in particular to members of the genus Bacillus, though members of the Bacteroidetes, Planctomycetes, Chloroflexi, and delta-Proteobacteria groups were also observed.
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Affiliation(s)
- Eric Prestel
- Laboratoire de Génomique et Biodiversité Microbienne des Biofilms, Université Paris-Sud 11, Institut de Génétique et Microbiologie, CNRS UMR 8621, Bâtiment 409, 91405 Orsay, France
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26
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The cycle for a Siphoviridae-like phage (VHS1) of Vibrio harveyi is dependent on the physiological state of the host. Virus Res 2008; 135:332-5. [PMID: 18448184 DOI: 10.1016/j.virusres.2008.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 03/10/2008] [Accepted: 03/14/2008] [Indexed: 11/22/2022]
Abstract
In a previous report, we isolated Vibrio harveyi (VH) 1114 together with its bacteriophage, VHS1, from a black tiger shrimp-rearing pond. The VHS1 has its lysogenic relationship to the VH1114 host as either true lysogen (TL) or pseudolysogen (PL). The characters of TL are based on the extrachromosomal existence of the VHS1 phage genome in the VH host which also simultaneously produces the VHS1 phage particles and is resistant to super-infection. The original VH1114 host exhibits a clear plaque after infection with VHS1 phage. The PL, on the other hand, exhibits a turbid plaque and does not possess the phage genome but shows toleration to the phage infection. Maintaining the PL in artificial seawater (ASW) for 1h causes the PL to be sensitive to VHS1 infection and results in clear plaques as in the original clone. A chloramphenical-added-ASW treated pseudolysogen clone (PLC), however, prevented VHS1 infection. It is postulated that the infection of VHS1 phage is regulated with a phage binding receptor which supposed to be inducible.
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Abstract
Vibrio harveyi, which now includes Vibrio carchariae as a junior synonym, is a serious pathogen of marine fish and invertebrates, particularly penaeid shrimp. In fish, the diseases include vasculitis, gastro-enteritis and eye lesions. With shrimp, the pathogen is associated with luminous vibriosis and Bolitas negricans. Yet, the pathogenicity mechanisms are imprecisely understood, with likely mechanisms involving the ability to attach and form biofilms, quorum sensing, various extracellular products including proteases and haemolysins, lipopolysaccharide, and interaction with bacteriophage and bacteriocin-like substances.
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Affiliation(s)
- B Austin
- School of Life Sciences, John Muir Building, Heriot-Watt University, Riccarton, Edinburgh, UK.
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