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Chen F, Wang D, Lu T, Li S. Identification of a novel type II-C Cas9 from the fish pathogen Flavobacterium psychrophilum. Front Microbiol 2023; 14:1181303. [PMID: 37396349 PMCID: PMC10309648 DOI: 10.3389/fmicb.2023.1181303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Flavobacterium psychrophilum is the causative agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish worldwide. As an important fish pathogen, F. psychrophilum is frequently exposed to multiple invading genetic elements in natural environments. Endonuclease Cas9 provides bacteria with adaptive interference against invading genetic elements. Previous studies revealed that several F. psychrophilum strains harbored a type II-C Cas9 called Fp1Cas9, but little is known about the potential role of this endonuclease against invading genetic elements. In this work, we identified a gene encoding a novel type II-C Cas9 called Fp2Cas9 from F. psychrophilum strain CN46. Through bacterial RNA sequencing, we demonstrated active transcription of both Fp2Cas9 and pre-crRNAs in strain CN46. Bioinformatics analysis further revealed that the transcription of Fp2Cas9 and pre-crRNAs was driven by a newly integrated promoter sequence and a promoter element embedded within each CRISPR repeat, respectively. To formally demonstrate that Fp2Cas9 and associated crRNAs yielded functional interference in strain CN46, a plasmid interference assay was performed, resulting in adaptive immunity to target DNA sequences in Flavobacterium bacteriophages. Phylogenetic analysis demonstrated that Fp2Cas9 was present only in several F. psychrophilum isolates. Phylogenetic analysis revealed that this novel endonuclease was probably acquired through horizontal gene transfer from the CRISPR-Cas9 system in an unidentified Flavobacterium species. Comparative genomics analysis further showed that the Fp2Cas9 was integrated into the type II-C CRISPR-Cas locus in strain CN38 instead of the original Fp1Cas9. Taken together, our results shed light on the origin and evolution of Fp2Cas9 gene and demonstrated that this novel endonuclease provided adaptive interference against bacteriophage infections.
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Affiliation(s)
- Fuguang Chen
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Di Wang
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Tongyan Lu
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Shaowu Li
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
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2
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Jørgensen J, Sundell K, Castillo D, Dramshøj LS, Jørgensen NB, Madsen SB, Landor L, Wiklund T, Donati VL, Madsen L, Dalsgaard I, Middelboe M. Reversible mutations in gliding motility and virulence genes: A flexible and efficient phage defence mechanism in Flavobacterium psychrophilum. Environ Microbiol 2022; 24:4915-4930. [PMID: 35837851 DOI: 10.1111/1462-2920.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 01/07/2023]
Abstract
Flavobacteria are among the most important pathogens in freshwater salmonid aquaculture worldwide. Due to concerns regarding development of antibiotic resistance, phage therapy has been proposed as a solution to decrease pathogen load. However, application of phages is challenged by the development of phage resistance, and knowledge of the mechanisms and implications of phage resistance is therefore required. To study this, 27 phage-resistant isolates of F. psychrophilum were genome sequenced and characterized to identify genetic modifications and evaluate changes in phenotypic traits, including virulence against rainbow trout. Phage-resistant isolates showed reduction or loss of gliding motility, proteolytic activity, and adhesion to surfaces, and most isolates were completely non-virulent against rainbow trout fry. Genomic analysis revealed that most phage-resistant isolates had mutations in genes associated with gliding motility and virulence. Reversal of these mutations in a sub-set of isolates led to regained motility, proteolytic activity, virulence and phage susceptibility. Although costly, the fast generation of phage resistance driven by single, reversible mutations likely represents a flexible and efficient phage defence mechanism in F. psychrophilum. The results further suggest that phage administration in aquaculture systems to prevent F. psychrophilum outbreaks selects for non-virulent phage-resistant phenotypes.
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Affiliation(s)
| | - Krister Sundell
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Daniel Castillo
- Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Liv S Dramshøj
- Department of Biology, University of Copenhagen, Helsingør, Denmark
| | | | - Susie B Madsen
- Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lotta Landor
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Valentina L Donati
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Madsen
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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3
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Donati VL, Madsen L, Middelboe M, Strube ML, Dalsgaard I. The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies. Front Microbiol 2022; 13:771296. [PMID: 35620089 PMCID: PMC9128845 DOI: 10.3389/fmicb.2022.771296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/07/2022] [Indexed: 01/15/2023] Open
Abstract
In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.
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Affiliation(s)
- Valentina Laura Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
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Castledine M, Sierocinski P, Inglis M, Kay S, Hayward A, Buckling A, Padfield D. Greater Phage Genotypic Diversity Constrains Arms-Race Coevolution. Front Cell Infect Microbiol 2022; 12:834406. [PMID: 35310856 PMCID: PMC8931298 DOI: 10.3389/fcimb.2022.834406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Antagonistic coevolution between hosts and parasites, the reciprocal evolution of host resistance and parasite infectivity, has important implications in ecology and evolution. The dynamics of coevolution—notably whether host or parasite has an evolutionary advantage—is greatly affected by the relative amount of genetic variation in host resistance and parasite infectivity traits. While studies have manipulated genetic diversity during coevolution, such as by increasing mutation rates, it is unclear how starting genetic diversity affects host–parasite coevolution. Here, we (co)evolved the bacterium Pseudomonas fluorescens SBW25 and two bacteriophage genotypes of its lytic phage SBW25ɸ2 in isolation (one phage genotype) and together (two phage genotypes). Bacterial populations rapidly evolved phage resistance, and phage reciprocally increased their infectivity in response. When phage populations were evolved with bacteria in isolation, bacterial resistance and phage infectivity increased through time, indicative of arms-race coevolution. In contrast, when both phage genotypes were together, bacteria did not increase their resistance in response to increasing phage infectivity. This was likely due to bacteria being unable to evolve resistance to both phage via the same mutations. These results suggest that increasing initial parasite genotypic diversity can give parasites an evolutionary advantage that arrests long-term coevolution. This study has important implications for the applied use of phage in phage therapy and in understanding host–parasite dynamics in broader ecological and evolutionary theory.
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Castillo D, Højsting AR, Roosvall A, Smyrlis G, Jørgensen J, Middelboe M. In Vitro Evolution of Specific Phages Infecting the Fish Pathogen Flavobacterium psychrophilum. PHAGE 2022; 3:28-37. [PMID: 37025924 PMCID: PMC10071593 DOI: 10.1089/phage.2022.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background Flavobacterium psychrophilum is the causative agent of the bacterial cold-water disease and rainbow trout fry syndrome. Owing to the issues associated with increasing use of antibiotics to control the diseases, phage therapy has been proposed as an alternative method to control Flavobacterium infection within the industry. Materials and Methods We explored two simple and fast in vitro strategies for the isolation of evolved F. psychrophilum phages, using three well-characterized phages FpV4, FpV9, and FPSV-S20. Results During in vitro serial transfer experiments, 12 evolved phages were selected 72-96 h after phage exposure in the first or second week. Phenotype analysis showed improvement of host range and efficiency of plating and adsorption constants. Comparative genomic analysis of the evolved phages identified 13 independent point mutations causing amino acid changes mostly in hypothetical proteins. Conclusions These results confirmed the reliability and effectivity of two strategies to isolate evolved F. psychrophilum phages, which may be used to expand phage-host range and target phage-resistant pathogens in phage therapy applications against Flavobacterium infections.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
- Instituto de Investigación Interdisciplinar en Ciencias Biomédicas SEK (I3CBSEK), Universidad SEK, Santiago, Chile
| | | | - Andrea Roosvall
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Giorgos Smyrlis
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Johanna Jørgensen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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6
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Comparative Genomic Analyses of Flavobacterium psychrophilum Isolates Reveals New Putative Genetic Determinants of Virulence Traits. Microorganisms 2021; 9:microorganisms9081658. [PMID: 34442736 PMCID: PMC8400371 DOI: 10.3390/microorganisms9081658] [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: 06/02/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022] Open
Abstract
The fish pathogen Flavobacterium psychrophilum is currently one of the main pathogenic bacteria hampering the productivity of salmonid farming worldwide. Although putative virulence determinants have been identified, the genetic basis for variation in virulence of F. psychrophilum is not fully understood. In this study, we analyzed whole-genome sequences of a collection of 25 F. psychrophilum isolates from Baltic Sea countries and compared genomic information with a previous determination of their virulence in juvenile rainbow trout. The results revealed a conserved population of F. psychrophilum that were consistently present across the Baltic Sea countries, with no clear association between genomic repertoire, phylogenomic, or gene distribution and virulence traits. However, analysis of the entire genome of four F. psychrophilum isolates by hybrid assembly provided an unprecedented resolution for discriminating even highly related isolates. The results showed that isolates with different virulence phenotypes harbored genetic variances on a number of consecutive leucine-rich repeat (LRR) proteins, repetitive motifs in gliding motility-associated protein, and the insertion of transposable elements into intergenic and genic regions. Thus, these findings provide novel insights into the genetic variation of these elements and their putative role in the modulation of F. psychrophilum virulence.
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7
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Daniel C, Johanna J, Krister S, Lone M, Inger D, Tom W, Mathias M. Genome-informed approach to identify genetic determinants of Flavobacterium psychrophilum phage susceptibility. Environ Microbiol 2021; 23:4185-4199. [PMID: 33989443 DOI: 10.1111/1462-2920.15593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/08/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022]
Abstract
The fish pathogen Flavobacterium psychrophilum infects farmed salmonids worldwide, and application of bacteriophages has been suggested for controlling disease outbreaks in aquaculture. Successful application of phages requires detailed knowledge about the variability in phage susceptibility of the host communities. In this study, we analysed the genetic diversity of F. psychrophilum hosts and phages from the Baltic Sea area to identify genetic determinants of phage-host interaction patterns. A host range analysis of 103 phages tested against 177 F. psychrophilum strains (18 231 phage-host interactions) identified nine phage clusters, infecting from 10% to 91% of the strain collection. The core genome-based comparison of 35 F. psychrophilum isolates revealed an extremely low overall genomic diversity (>99.5% similarity). However, a small subset of 16 ORFs, including genes involved in the type IX secretion system (T9SS), gliding motility and hypothetical cell-surface related proteins, exhibited a highly elevated genetic diversity. These specific genetic variations were linked to variability in phage infection patterns obtained from experimental studies, indicating that these genes are key determinants of phage susceptibility. These findings provide novel insights on the molecular mechanisms determining phage susceptibility in F. psychrophilum and emphasizes the importance of phages as drivers of core genomic diversity in this pathogen.
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Affiliation(s)
- Castillo Daniel
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.,Instituto de Investigación Interdisciplinar en Ciencias Biomédicas SEK (I3CBSEK), Universidad SEK, Santiago, Chile
| | - Jørgensen Johanna
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Sundell Krister
- Laboratory of Aquatic Pathobiology, Marine and Environmental Biology, Åbo Akademi University, Turku, Finland
| | - Madsen Lone
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dalsgaard Inger
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Wiklund Tom
- Laboratory of Aquatic Pathobiology, Marine and Environmental Biology, Åbo Akademi University, Turku, Finland
| | - Middelboe Mathias
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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8
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Donati VL, Dalsgaard I, Sundell K, Castillo D, Er-Rafik M, Clark J, Wiklund T, Middelboe M, Madsen L. Phage-Mediated Control of Flavobacterium psychrophilum in Aquaculture: In vivo Experiments to Compare Delivery Methods. Front Microbiol 2021; 12:628309. [PMID: 33763046 PMCID: PMC7983945 DOI: 10.3389/fmicb.2021.628309] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
Phage-based approaches have gained increasing interest as sustainable alternative strategies to antibiotic treatment or as prophylactic measures against disease outbreaks in aquaculture. The potential of three methods (oral, bath, and injection) for delivering a two-component phage mixture to rainbow trout fry for controlling Flavobacterium psychrophilum infections and reduce fish mortality was investigated using bacteriophages FpV4 and FPSV-D22. For the oral administration experiment, bacteriophages were applied on feed pellets by spraying (1.6 × 108 PFU g-1) or by irreversible immobilization (8.3 × 107 PFU g-1), using the corona discharge technology (Fixed Phage Ltd.). The fish showed normal growth for every group and no mortality was observed prior to infection as well as in control groups during the infection. Constant detection of phages in the intestine (∼103 PFU mg-1) and more sporadic occurrence in kidney, spleen, and brain was observed. When fish were exposed to F. psychrophilum, no significant effect on fish survival, nor a direct impact on the number of phages in the sampled organs, were detected. Similarly, no significant increase in fish survival was detected when phages were delivered by bath (1st and 2nd bath: ∼106 PFU ml-1; 3rd bath: ∼105 PFU ml-1). However, when phages FpV4 and FPSV-D22 (1.7 × 108 PFU fish-1) were administered by intraperitoneal injection 3 days after the bacterial challenge, the final percent survival observed in the group injected with bacteriophages FpV4 and FPSV-D22 (80.0%) was significantly higher than in the control group (56.7%). The work demonstrates the delivery of phages to fish organs by oral administration, but also suggests that higher phage dosages than the tested ones may be needed on feed pellets to offer fish an adequate protection against F. psychrophilum infections.
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Affiliation(s)
- Valentina Laura Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Krister Sundell
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Mériem Er-Rafik
- National Centre for Nano Fabrication and Characterization, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
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9
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Castillo D, Rørbo N, Jørgensen J, Lange J, Tan D, Kalatzis PG, Svenningsen SL, Middelboe M. Phage defense mechanisms and their genomic and phenotypic implications in the fish pathogen Vibrio anguillarum. FEMS Microbiol Ecol 2020; 95:5281231. [PMID: 30624625 DOI: 10.1093/femsec/fiz004] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/08/2019] [Indexed: 01/21/2023] Open
Abstract
Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species. Although phage therapy has been proposed as an alternative treatment, the defense mechanisms against phage infection in V. anguillarum and their impact on host function are not fully understood. Here, we examined phage defense strategies in four V. anguillarum strains during exposure to the broad-host-range bacteriophage KVP40. Whole-genome sequences of phage-resistant V. anguillarum isolates showed mutations causing premature stop codons, frameshifts and amino acid changes in the OmpK phage receptor. Moreover, certain phage-resistant variants recovered susceptibility to phage infection following re-culturing, suggesting alternative protection mechanisms, such as formation of biofilm, receptor downregulation and phage inactivation by proteases. Also, the lack of phage production by some strains despite strong phage control suggested an abortive infection mechanism was in play. In addition, examination of the virulence properties and extracellular enzyme secretion of the phage-resistant variants suggested that phage resistance was associated with reduced virulence in V. anguillarum. Altogether, the results identified a variety of phage resistance mechanisms in V. anguillarum including both mutational and non-mutational defenses and demonstrated a significant fitness loss associated with mutational changes, which may explain the selection for alternative defense mechanisms.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Nanna Rørbo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Jóhanna Jørgensen
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Janina Lange
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark.,Zoological Institute, Christian-Albrechts-University, Am botanischen Garten 1-9, G-24116 Kiel, Germany
| | - Demeng Tan
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark.,Section for Biomolecular Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Panos G Kalatzis
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Sine Lo Svenningsen
- Section for Biomolecular Science, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
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10
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Large Phenotypic and Genetic Diversity of Prophages Induced from the Fish Pathogen Vibrio anguillarum. Viruses 2019; 11:v11110983. [PMID: 31653117 PMCID: PMC6893619 DOI: 10.3390/v11110983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023] Open
Abstract
Vibrio anguillarum is a marine pathogenic bacterium that causes vibriosis in fish and shellfish. Although prophage-like sequences have been predicted in V. anguillarum strains, many are not characterized, and it is not known if they retain the functional capacity to form infectious particles that can infect and lysogenize other bacterial hosts. In this study, the genome sequences of 28 V. anguillarum strains revealed 55 different prophage-related elements. Chemical and spontaneous induction allowed a collection of 42 phage isolates, which were classified in seven different groups according to a multiplex PCR assay. One shared prophage sequence, p41 (group III), was present in 17 V. anguillarum strains, suggesting that this specific element is very dynamically exchanged among V. anguillarum populations. Interestingly, the host range of genetically identical phages was highly dependent on the strains used for proliferation, indicating that phenotypic properties of phages were partly regulated by the host. Finally, experimental evidence displayed that the induced phage ɸVa_90-11-287_p41 was able to lysogenize V. anguillarum strain Ba35, and subsequently spontaneously become released from the lysogenized cells, demonstrating an efficient transfer of the phage among V. anguillarum strains. Altogether, the results showed large genetic and functional diversity and broad distribution of prophages in V. anguillarum, and demonstrated the potential of prophages as drivers of evolution in V. anguillarum strains.
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11
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Bacteriophage Interactions with Marine Pathogenic Vibrios: Implications for Phage Therapy. Antibiotics (Basel) 2018; 7:antibiotics7010015. [PMID: 29495270 PMCID: PMC5872126 DOI: 10.3390/antibiotics7010015] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/27/2022] Open
Abstract
A global distribution in marine, brackish, and freshwater ecosystems, in combination with high abundances and biomass, make vibrios key players in aquatic environments, as well as important pathogens for humans and marine animals. Incidents of Vibrio-associated diseases (vibriosis) in marine aquaculture are being increasingly reported on a global scale, due to the fast growth of the industry over the past few decades years. The administration of antibiotics has been the most commonly applied therapy used to control vibriosis outbreaks, giving rise to concerns about development and spreading of antibiotic-resistant bacteria in the environment. Hence, the idea of using lytic bacteriophages as therapeutic agents against bacterial diseases has been revived during the last years. Bacteriophage therapy constitutes a promising alternative not only for treatment, but also for prevention of vibriosis in aquaculture. However, several scientific and technological challenges still need further investigation before reliable, reproducible treatments with commercial potential are available for the aquaculture industry. The potential and the challenges of phage-based alternatives to antibiotic treatment of vibriosis are addressed in this review.
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12
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Xiang Y, Wang S, Li J, Wei Y, Zhang Q, Lin L, Ji X. Isolation and characterization of two lytic cold-active bacteriophages infecting Pseudomonas fluorescens from the Napahai plateau wetland. Can J Microbiol 2017; 64:183-190. [PMID: 29253355 DOI: 10.1139/cjm-2017-0572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As the "kidneys of the Earth", wetlands play important roles as biodiversity reservoirs, in water purification, and in flood control. In this study, 2 lytic cold-active bacteriophages, named VW-6S and VW-6B, infecting Pseudomonas fluorescens W-6 cells from the Napahai plateau wetland in China were isolated and characterized. Electron microscopy showed that both VW-6S and VW-6B had an icosahedral head (66.7 and 61.1 nm, respectively) and a long tail (8.3 nm width × 233.3 nm length and 11.1 nm width × 166.7 nm length, respectively). The bacteriophages VW-6S and VW-6B were classified as Siphoviridae and had an approximate genome size of 30-40 kb. The latent and burst periods of VW-6S were 60 and 30 min, whereas those of VW-6B were 30 and 30 min, respectively. The optimal pH values for the bacteriophages VW-6S and VW-6B were 8.0 and 10.0, respectively, and their activity decreased rapidly at temperatures higher than 60 °C. These cold-active bacteriophages provide good materials for further study of cold-adaptation mechanisms and interaction with the host P. fluorescens.
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Affiliation(s)
- Yingying Xiang
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.,b Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming 650031, China
| | - Shuang Wang
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jiankai Li
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yunlin Wei
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Qi Zhang
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Lianbing Lin
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiuling Ji
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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13
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Genetic hurdles limit the arms race between Prochlorococcus and the T7-like podoviruses infecting them. ISME JOURNAL 2017; 11:1836-1851. [PMID: 28440802 PMCID: PMC5520035 DOI: 10.1038/ismej.2017.47] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/31/2017] [Accepted: 02/28/2017] [Indexed: 01/21/2023]
Abstract
Phages and hosts coexist in nature with a high degree of population diversity. This is often explained through coevolutionary models, such as the arms race or density-dependent fluctuating selection, which differ in assumptions regarding the emergence of phage mutants that overcome host resistance. Previously, resistance in the abundant marine cyanobacterium, Prochlorococcus, was found to occur frequently. However, little is known about the ability of phages to overcome this resistance. Here we report that, in some cases, T7-like cyanophage mutants emerge to infect resistant Prochlorococcus strains. These resistance-breaking phages retained the ability to infect the wild-type host. However, fitness of the mutant phages differed on the two hosts. Furthermore, in one case, resistance-breaking was accompanied by costs of decreased fitness on the wild-type host and decreased adsorption specificity, relative to the wild-type phage. In two other cases, fitness on the wild-type host increased. Whole-genome sequencing revealed mutations in probable tail-related genes. These were highly diverse in isolates and natural populations of T7-like cyanophages, suggesting that antagonistic coevolution enhances phage genome diversity. Intriguingly, most interactions did not yield resistance-breaking phages. Thus, resistance mutations raise genetic barriers to continuous arms race cycles and are indicative of an inherent asymmetry in coevolutionary capacity, with hosts having the advantage. Nevertheless, phages coexist with hosts, which we propose relies on combined, parallel action of a limited arms race, fluctuating selection and passive host-switching within diverse communities. Together, these processes generate a constantly changing network of interactions, enabling stable coexistence between hosts and phages in nature.
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14
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Emerging Interaction Patterns in the Emiliania huxleyi-EhV System. Viruses 2017; 9:v9030061. [PMID: 28327527 PMCID: PMC5371816 DOI: 10.3390/v9030061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 01/25/2023] Open
Abstract
Viruses are thought to be fundamental in driving microbial diversity in the oceanic planktonic realm. That role and associated emerging infection patterns remain particularly elusive for eukaryotic phytoplankton and their viruses. Here we used a vast number of strains from the model system Emiliania huxleyi/Emiliania huxleyi Virus to quantify parameters such as growth rate (µ), resistance (R), and viral production (Vp) capacities. Algal and viral abundances were monitored by flow cytometry during 72-h incubation experiments. The results pointed out higher viral production capacity in generalist EhV strains, and the virus-host infection network showed a strong co-evolution pattern between E. huxleyi and EhV populations. The existence of a trade-off between resistance and growth capacities was not confirmed.
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15
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Castillo D, Middelboe M. Genomic diversity of bacteriophages infecting the fish pathogenFlavobacterium psychrophilum. FEMS Microbiol Lett 2016; 363:fnw272. [DOI: 10.1093/femsle/fnw272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/05/2016] [Accepted: 11/29/2016] [Indexed: 01/21/2023] Open
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16
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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17
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Hanson CA, Marston MF, Martiny JBH. Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates. Front Microbiol 2016; 7:983. [PMID: 27446023 PMCID: PMC4919323 DOI: 10.3389/fmicb.2016.00983] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/07/2016] [Indexed: 11/13/2022] Open
Abstract
Despite the important role of phages in marine systems, little is understood about how their diversity is distributed in space. Biogeographic patterns of marine phages may be difficult to detect due to their vast genetic diversity, which may not be accurately represented by conserved marker genes. To investigate the spatial biogeographic structure of marine phages, we isolated over 400 cyanophages on Synechococcus host strain WH7803 at three coastal locations in the United States (Rhode Island, Washington, and southern California). Approximately 90% of the cyanophage isolates were myoviruses, while the other 10% were podoviruses. The diversity of isolates was further characterized in two ways: (i) taxonomically, using conserved marker genes and (ii) phenotypically, by testing isolates for their ability to infect a suite of hosts, or their "host range." Because host range is a highly variable trait even among closely related isolates, we hypothesized that host range phenotypes of cyanophage isolates would vary more strongly among locations than would taxonomic composition. Instead, we found evidence for strong biogeographic variation both in taxonomic composition and host range phenotypes, with little taxonomic overlap among the three coastal regions. For both taxonomic composition and host range phenotypes, cyanophage communities from California and Rhode Island were the most dissimilar, while Washington communities exhibited similarity to each of the other two locations. These results suggest that selection imposed by spatial variation in host dynamics influence the biogeographic distribution of cyanophages.
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Affiliation(s)
- China A Hanson
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonUK; Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CAUSA
| | - Marcia F Marston
- Department of Biology and Marine Biology, Roger Williams University, Bristol, RI USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA USA
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18
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Christiansen RH, Madsen L, Dalsgaard I, Castillo D, Kalatzis PG, Middelboe M. Effect of Bacteriophages on the Growth of Flavobacterium psychrophilum and Development of Phage-Resistant Strains. MICROBIAL ECOLOGY 2016; 71:845-859. [PMID: 26898695 DOI: 10.1007/s00248-016-0737-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
The controlling effect of single and multiple phages on the density of Flavobacterium psychrophilum at different initial multiplicity of infection (MOI) was assessed in batch cultures to explore the potential for phage-based treatment of this important fish pathogen. A high initial phage concentration (MOI = 0.3-4) was crucial for efficient viral lysis, resulting in a 10(4)-10(5)-fold reduction of phage-sensitive cells (both single phages and phage cocktails), which was maintained throughout the incubation (>10 days). Following cell lysis, regrowth of phage-resistant strains was examined and resistant strains were isolated for further characterization. The application of a mathematical model allowed simulation of phage-host interactions and resistance development, confirming indications from strain isolations that phage-sensitive strains dominated the regrowing population (>99.8%) at low MOI and phage-resistant strains (>87.8%) dominated at high MOI. A cross-infectivity test covering 68 isolated strains and 22 phages resulted in 23 different host susceptibility patterns, with 20 of the isolates being resistant to all the applied phages. Eleven isolated strains with different susceptibility patterns had lower growth rates (0.093 to 0.31 h(-1)) than the host strain (0.33 h(-1)), while 10 of 14 examined strains had lost the ability to take up specific substrates as shown by BIOLOG profiles. Despite increased selection for phage resistance at high MOI, the results emphasize that high initial MOI is essential for fast and effective control of F. psychrophilum infection and suggest that the small populations of resistant clones had reduced competitive abilities relative to the sensitive ancestral strain.
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Affiliation(s)
- Rói Hammershaimb Christiansen
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000, Helsingør, Denmark
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark
| | - Lone Madsen
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark
| | - Inger Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark
| | - Daniel Castillo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000, Helsingør, Denmark
| | - Panos G Kalatzis
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000, Helsingør, Denmark
- Hellenic Centre for Marine Research, Institute of Aquaculture, Heraklion, 71003, Crete, Greece
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000, Helsingør, Denmark.
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19
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Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Espejo R, Middelboe M. Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum. PLoS One 2016; 11:e0152515. [PMID: 27071075 PMCID: PMC4829187 DOI: 10.1371/journal.pone.0152515] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
Flavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259–93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Rói Hammershaimb Christiansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Inger Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Lone Madsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Romilio Espejo
- Centro Nacional de Genómica y Bioinformática and Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Macul, Santiago, Chile
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- * E-mail:
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20
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Convergent evolution toward an improved growth rate and a reduced resistance range in Prochlorococcus strains resistant to phage. Proc Natl Acad Sci U S A 2015; 112:E2191-200. [PMID: 25922520 DOI: 10.1073/pnas.1420347112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prochlorococcus is an abundant marine cyanobacterium that grows rapidly in the environment and contributes significantly to global primary production. This cyanobacterium coexists with many cyanophages in the oceans, likely aided by resistance to numerous co-occurring phages. Spontaneous resistance occurs frequently in Prochlorococcus and is often accompanied by a pleiotropic fitness cost manifested as either a reduced growth rate or enhanced infection by other phages. Here, we assessed the fate of a number of phage-resistant Prochlorococcus strains, focusing on those with a high fitness cost. We found that phage-resistant strains continued evolving toward an improved growth rate and a narrower resistance range, resulting in lineages with phenotypes intermediate between those of ancestral susceptible wild-type and initial resistant substrains. Changes in growth rate and resistance range often occurred in independent events, leading to a decoupling of the selection pressures acting on these phenotypes. These changes were largely the result of additional, compensatory mutations in noncore genes located in genomic islands, although genetic reversions were also observed. Additionally, a mutator strain was identified. The similarity of the evolutionary pathway followed by multiple independent resistant cultures and clones suggests they undergo a predictable evolutionary pathway. This process serves to increase both genetic diversity and infection permutations in Prochlorococcus populations, further augmenting the complexity of the interaction network between Prochlorococcus and its phages in nature. Last, our findings provide an explanation for the apparent paradox of a multitude of resistant Prochlorococcus cells in nature that are growing close to their maximal intrinsic growth rates.
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21
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Khan Mirzaei M, Nilsson AS. Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS One 2015; 10:e0118557. [PMID: 25761060 PMCID: PMC4356574 DOI: 10.1371/journal.pone.0118557] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
Phage therapy, treating bacterial infections with bacteriophages, could be a future alternative to antibiotic treatment of bacterial infections. There are, however, several problems to be solved, mainly associated to the biology of phages, the interaction between phages and their bacterial hosts, but also to the vast variation of pathogenic bacteria which implies that large numbers of different phages are going to be needed. All of these phages must under present regulation of medical products undergo extensive clinical testing before they can be applied. It will consequently be of great economic importance that effective and versatile phages are selected and collected into phage libraries, i.e., the selection must be carried out in a way that it results in highly virulent phages with broad host ranges. We have isolated phages using the Escherichia coli reference (ECOR) collection and compared two methods, spot testing and efficiency of plating (EOP), which are frequently used to identify phages suitable for phage therapy. The analyses of the differences between the two methods show that spot tests often overestimate both the overall virulence and the host range and that the results are not correlated to the results of EOP assays. The conclusion is that single dilution spot tests cannot be used for identification and selection of phages to a phage library and should be replaced by EOP assays. The difference between the two methods can be caused by many factors. We have analysed if the differences and lack of correlation could be caused by lysis from without, bacteriocins in the phage lysate, or by the presence of prophages harbouring genes coding for phage resistance systems in the genomes of the bacteria in the ECOR collection.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail:
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22
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Castillo D, Christiansen RH, Dalsgaard I, Madsen L, Middelboe M. Bacteriophage resistance mechanisms in the fish pathogen Flavobacterium psychrophilum: linking genomic mutations to changes in bacterial virulence factors. Appl Environ Microbiol 2015; 81:1157-67. [PMID: 25480749 PMCID: PMC4292493 DOI: 10.1128/aem.03699-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/26/2014] [Indexed: 01/21/2023] Open
Abstract
Flavobacterium psychrophilum is an important fish pathogen in salmonid aquaculture worldwide. Due to increased antibiotic resistance, pathogen control using bacteriophages has been explored as a possible alternative treatment. However, the effective use of bacteriophages in pathogen control requires overcoming the selection for phage resistance in the bacterial populations. Here, we analyzed resistance mechanisms in F. psychrophilum after phage exposure using whole-genome sequencing of the ancestral phage-sensitive strain 950106-1/1 and six phage-resistant isolates. The phage-resistant strains had all obtained unique insertions and/or deletions and point mutations distributed among intergenic and genic regions. Mutations in genes related to cell surface properties, gliding motility, and biosynthesis of lipopolysaccharides and cell wall were found. The observed links between phage resistance and the genetic modifications were supported by direct measurements of bacteriophage adsorption rates, biofilm formation, and secretion of extracellular enzymes, which were all impaired in the resistant strains, probably due to superficial structural changes. The clustered regularly interspaced short palindromic repeat (CRISPR) region was unaffected in the resistant isolates and thus did not play a role as a resistance mechanism for F. psychrophilum under the current conditions. All together, the results suggest that resistance in F. psychrophilum was driven by spontaneous mutations, which were associated with a number of derived effects on the physiological properties of the pathogen, including reduced virulence under in vitro conditions. Consequently, phage-driven physiological changes associated with resistance may have implications for the impact of the pathogen in aquaculture, and these effects of phage resistance on host properties are therefore important for the ongoing exploration of phage-based control of F. psychrophilum.
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Affiliation(s)
- Daniel Castillo
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Rói Hammershaimb Christiansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Inger Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Lone Madsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
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23
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Ji X, Yu H, Zhang Q, Lin L, Wei Y. Isolation and characterization of a novel lytic cold-active bacteriophage VNPH-1 from the Napahai wetland in China. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-1018-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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