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Thunes NC, Evenhuis JP, Lipscomb RS, Pérez-Pascual D, Stevick RJ, Birkett C, Ghigo JM, McBride MJ. Gliding motility proteins GldJ and SprB contribute to Flavobacterium columnare virulence. J Bacteriol 2024; 206:e0006824. [PMID: 38517170 PMCID: PMC11025331 DOI: 10.1128/jb.00068-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Flavobacterium columnare causes columnaris disease in fish. Columnaris disease is incompletely understood, and adequate control measures are lacking. The type IX secretion system (T9SS) is required for F. columnare gliding motility and virulence. The T9SS and gliding motility machineries share some, but not all, components. GldN (required for gliding and for secretion) and PorV (involved in secretion but not required for gliding) are both needed for virulence, implicating T9SS-mediated secretion in virulence. The role of motility in virulence is uncertain. We constructed and analyzed sprB, sprF, and gldJ mutants that were defective for motility but that maintained T9SS function to understand the role of motility in virulence. Wild-type cells moved rapidly and formed spreading colonies. In contrast, sprB and sprF deletion mutants were partially defective in gliding and formed nonspreading colonies. Both mutants exhibited reduced virulence in rainbow trout fry. A gldJ deletion mutant was nonmotile, secretion deficient, and avirulent in rainbow trout fry. To separate the roles of GldJ in secretion and in motility, we generated gldJ truncation mutants that produce nearly full-length GldJ. Mutant gldJ563, which produces GldJ truncated at amino acid 563, was defective for gliding but was competent for secretion as measured by extracellular proteolytic activity. This mutant displayed reduced virulence in rainbow trout fry, suggesting that motility contributes to virulence. Fish that survived exposure to the sprB deletion mutant or the gldJ563 mutant exhibited partial resistance to later challenge with wild-type cells. The results aid our understanding of columnaris disease and may suggest control strategies.IMPORTANCEFlavobacterium columnare causes columnaris disease in many species of freshwater fish in the wild and in aquaculture systems. Fish mortalities resulting from columnaris disease are a major problem for aquaculture. F. columnare virulence is incompletely understood, and control measures are inadequate. Gliding motility and protein secretion have been suggested to contribute to columnaris disease, but evidence directly linking motility to disease was lacking. We isolated and analyzed mutants that were competent for secretion but defective for motility. Some of these mutants exhibited decreased virulence. Fish that had been exposed to these mutants were partially protected from later exposure to the wild type. The results contribute to our understanding of columnaris disease and may aid development of control strategies.
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Affiliation(s)
- Nicole C. Thunes
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jason P. Evenhuis
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, West Virginia, USA
| | - Ryan S. Lipscomb
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, West Virginia, USA
| | - David Pérez-Pascual
- Institut Pasteur, Université Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Rebecca J. Stevick
- Institut Pasteur, Université Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Clayton Birkett
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, West Virginia, USA
| | - Jean-Marc Ghigo
- Institut Pasteur, Université Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Mark J. McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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2
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de Freitas Almeida GM, Hoikkala V, Ravantti J, Rantanen N, Sundberg LR. Mucin induces CRISPR-Cas defense in an opportunistic pathogen. Nat Commun 2022; 13:3653. [PMID: 35752617 PMCID: PMC9233685 DOI: 10.1038/s41467-022-31330-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/14/2022] [Indexed: 01/21/2023] Open
Abstract
Parasitism by bacteriophages has led to the evolution of a variety of defense mechanisms in their host bacteria. However, it is unclear what factors lead to specific defenses being deployed upon phage infection. To explore this question, we co-evolved the bacterial fish pathogen Flavobacterium columnare and its virulent phage V156 in presence and absence of a eukaryotic host signal (mucin) for sixteen weeks. The presence of mucin leads to a dramatic increase in CRISPR spacer acquisition, especially in low nutrient conditions where over 60% of colonies obtain at least one new spacer. Additionally, we show that the presence of a competitor bacterium further increases CRISPR spacer acquisition in F. columnare. These results suggest that ecological factors are important in determining defense strategies against phages, and that the phage-bacterium interactions on mucosal surfaces may select for the diversification of bacterial immune systems.
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Affiliation(s)
- Gabriel Magno de Freitas Almeida
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland
- Faculty of Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ville Hoikkala
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland
| | - Janne Ravantti
- University of Helsinki, Molecular and Integrative Biosciences Research Programme, Helsinki, Finland
| | - Noora Rantanen
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland.
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3
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de Freitas Almeida GM, Hoikkala V, Ravantti J, Rantanen N, Sundberg LR. Mucin induces CRISPR-Cas defense in an opportunistic pathogen. Nat Commun 2022; 13:3653. [PMID: 35752617 DOI: 10.1101/2021.08.10.455787v1.abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/14/2022] [Indexed: 05/27/2023] Open
Abstract
Parasitism by bacteriophages has led to the evolution of a variety of defense mechanisms in their host bacteria. However, it is unclear what factors lead to specific defenses being deployed upon phage infection. To explore this question, we co-evolved the bacterial fish pathogen Flavobacterium columnare and its virulent phage V156 in presence and absence of a eukaryotic host signal (mucin) for sixteen weeks. The presence of mucin leads to a dramatic increase in CRISPR spacer acquisition, especially in low nutrient conditions where over 60% of colonies obtain at least one new spacer. Additionally, we show that the presence of a competitor bacterium further increases CRISPR spacer acquisition in F. columnare. These results suggest that ecological factors are important in determining defense strategies against phages, and that the phage-bacterium interactions on mucosal surfaces may select for the diversification of bacterial immune systems.
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Affiliation(s)
- Gabriel Magno de Freitas Almeida
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland
- Faculty of Biosciences, Fisheries and Economics, Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ville Hoikkala
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland
| | - Janne Ravantti
- University of Helsinki, Molecular and Integrative Biosciences Research Programme, Helsinki, Finland
| | - Noora Rantanen
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, Jyväskylä, Finland.
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4
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Pulkkinen K, Ketola T, Laakso J, Mappes J, Sundberg L. Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen. Evol Appl 2022; 15:417-428. [PMID: 35386393 PMCID: PMC8965373 DOI: 10.1111/eva.13355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/05/2022] Open
Abstract
Phenotypic variation is suggested to facilitate the persistence of environmentally growing pathogens under environmental change. Here, we hypothesized that the intensive farming environment induces higher phenotypic variation in microbial pathogens than natural environment, because of high stochasticity for growth and stronger survival selection compared to the natural environment. We tested the hypothesis with an opportunistic fish pathogen Flavobacterium columnare isolated either from fish farms or from natural waters. We measured growth parameters of two morphotypes from all isolates in different resource concentrations and two temperatures relevant for the occurrence of disease epidemics at farms and tested their virulence using a zebrafish (Danio rerio) infection model. According to our hypothesis, isolates originating from the fish farms had higher phenotypic variation in growth between the morphotypes than the isolates from natural waters. The difference was more pronounced in higher resource concentrations and the higher temperature, suggesting that phenotypic variation is driven by the exploitation of increased outside-host resources at farms. Phenotypic variation of virulence was not observed based on isolate origin but only based on morphotype. However, when in contact with the larger fish, the less virulent morphotype of some of the isolates also had high virulence. As the less virulent morphotype also had higher growth rate in outside-host resources, the results suggest that both morphotypes can contribute to F. columnare epidemics at fish farms, especially with current prospects of warming temperatures. Our results suggest that higher phenotypic variation per se does not lead to higher virulence, but that environmental conditions at fish farms could select isolates with high phenotypic variation in bacterial population and hence affect evolution in F. columnare at fish farms. Our results highlight the multifaceted effects of human-induced environmental alterations in shaping epidemiology and evolution in microbial pathogens.
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Affiliation(s)
- Katja Pulkkinen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Tarmo Ketola
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Jouni Laakso
- Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of HelsinkiHelsinkiFinland
| | - Johanna Mappes
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of HelsinkiHelsinkiFinland
| | - Lotta‐Riina Sundberg
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
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5
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Laanto E, Mäkelä K, Hoikkala V, Ravantti JJ, Sundberg LR. Adapting a Phage to Combat Phage Resistance. Antibiotics (Basel) 2020; 9:E291. [PMID: 32486059 PMCID: PMC7345892 DOI: 10.3390/antibiotics9060291] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 01/24/2023] Open
Abstract
Phage therapy is becoming a widely recognized alternative for fighting pathogenic bacteria due to increasing antibiotic resistance problems. However, one of the common concerns related to the use of phages is the evolution of bacterial resistance against the phages, putatively disabling the treatment. Experimental adaptation of the phage (phage training) to infect a resistant host has been used to combat this problem. Yet, there is very little information on the trade-offs of phage infectivity and host range. Here we co-cultured a myophage FCV-1 with its host, the fish pathogen Flavobacterium columnare, in lake water and monitored the interaction for a one-month period. Phage resistance was detected within one day of co-culture in the majority of the bacterial isolates (16 out of the 18 co-evolved clones). The primary phage resistance mechanism suggests defense via surface modifications, as the phage numbers rose in the first two days of the experiment and remained stable thereafter. However, one bacterial isolate had acquired a spacer in its CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas locus, indicating that also CRISPR-Cas defense was employed in the phage-host interactions. After a week of co-culture, a phage isolate was obtained that was able to infect 18 out of the 32 otherwise resistant clones isolated during the experiment. Phage genome sequencing revealed several mutations in two open reading frames (ORFs) likely to be involved in the regained infectivity of the evolved phage. Their location in the genome suggests that they encode tail genes. Characterization of this evolved phage, however, showed a direct cost for the ability to infect several otherwise resistant clones-adsorption was significantly lower than in the ancestral phage. This work describes a method for adapting the phage to overcome phage resistance in a fish pathogenic system.
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Affiliation(s)
- Elina Laanto
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme, University of Helsinki, 00014 Helsinki, Finland;
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (K.M.); (V.H.); (L.R.S.)
| | - Kati Mäkelä
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (K.M.); (V.H.); (L.R.S.)
| | - Ville Hoikkala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (K.M.); (V.H.); (L.R.S.)
| | - Janne J. Ravantti
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme, University of Helsinki, 00014 Helsinki, Finland;
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (K.M.); (V.H.); (L.R.S.)
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6
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Mwega E, Colquhoun DJ, Tuntufye H, Mdegela R, Mutoloki S, Evensen Ø, Wasteson Y. Isolation and Characterization of Flavobacteriaceae from Farmed and Wild Nile Tilapia in Tanzania. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:23-30. [PMID: 30291645 DOI: 10.1002/aah.10048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
The present study was conducted to explore the occurrence of Flavobacteriaceae in wild Nile Tilapia Oreochromis niloticus (n = 108) collected from Lake Victoria and farmed Nile Tilapia (n = 187) collected from 12 ponds in the Morogoro region of Tanzania. The size of the ponds surveyed ranged from 130 to 150 m2 . Pond parameters and fish morphometric data were recorded during sampling. In total, 67 Flavobacterium-like isolates (n = 44 from farmed fish; n = 23 from wild fish) were identified on the basis of colony morphology and biochemical tests. Sequences from the 16S ribosomal RNA (rRNA) gene revealed that all 67 isolates belonged to the genera Flavobacterium and Chryseobacterium. Based on 16S rRNA nucleotide identity, 26 isolates showed high similarity with C. indologenes (99-100% identity), 16 showed similarity to C. joostei (98-99.9%), and 17 were similar to diverse species of Chryseobacterium (97-99%). Three isolates were similar to F. aquatile and three were similar to F. indicum, with 99-100% nucleotide identity in both cases, and two isolates were similar to F. oryzae (99-100% identity). The findings obtained in this study provide a baseline for future studies and contribute to an understanding of the threats presented by the aquatic Flavobacteriaceae reservoir toward the development of healthy fish farming in Tanzania. Such knowledge is vital for the development of a sustainable aquaculture industry in Tanzania that will contribute to increased food security.
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Affiliation(s)
- Elisa Mwega
- College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Post Office Box 3019, Morogoro, Tanzania
| | - Duncan J Colquhoun
- Norwegian Veterinary Institute, Post Office Box 750, Sentrum, N-0106, Oslo, Norway
| | - Huruma Tuntufye
- College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Post Office Box 3019, Morogoro, Tanzania
| | - Robinson Mdegela
- College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Post Office Box 3019, Morogoro, Tanzania
| | - Stephen Mutoloki
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Post Office Box 369, Sentrum, N-0102, Oslo, Norway
| | - Øystein Evensen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Post Office Box 369, Sentrum, N-0102, Oslo, Norway
| | - Yngvild Wasteson
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Post Office Box 369, Sentrum, N-0102, Oslo, Norway
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7
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Ashrafi R, Bruneaux M, Sundberg L, Pulkkinen K, Valkonen J, Ketola T. Broad thermal tolerance is negatively correlated with virulence in an opportunistic bacterial pathogen. Evol Appl 2018; 11:1700-1714. [PMID: 30344637 PMCID: PMC6183471 DOI: 10.1111/eva.12673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 05/31/2018] [Accepted: 06/22/2018] [Indexed: 01/10/2023] Open
Abstract
Predicting the effects of global increase in temperatures on disease virulence is challenging, especially for environmental opportunistic bacteria, because pathogen fitness may be differentially affected by temperature within and outside host environment. So far, there is very little empirical evidence on the connections between optimal temperature range and virulence in environmentally growing pathogens. Here, we explored whether the virulence of an environmentally growing opportunistic fish pathogen, Flavobacterium columnare, is malleable to evolutionary changes via correlated selection on thermal tolerance. To this end, we experimentally quantified the thermal performance curves (TPCs) for maximum biomass yield of 49 F. columnare isolates from eight different geographic locations in Finland over ten years (2003-2012). We also characterized virulence profiles of these strains in a zebra fish (Danio rerio) infection model. We show that virulence among the strains increased over the years, but thermal generalism, and in particular tolerance to higher temperatures, was negatively associated with virulence. Our data suggest that temperature has a strong effect on the pathogen genetic diversity and therefore presumably also on disease dynamics. However, the observed increase in frequency and severity of F. columnare epidemics over the last decade cannot be directly linked to bacterial evolution due to increased mean temperature, but is most likely associated with factors related to increased length of growing season, or other time-dependent change in environment. Our study demonstrates that complex interactions between the host, the pathogen and the environment influence disease virulence of an environmentally growing opportunistic pathogen.
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Affiliation(s)
- Roghaieh Ashrafi
- Department of Biological and Environmental Science (and Nanoscience Center)Centre of Excellence in Biological InteractionsUniversity of JyväskyläJyväskyläFinland
| | - Matthieu Bruneaux
- Department of Biological and Environmental Science (and Nanoscience Center)Centre of Excellence in Biological InteractionsUniversity of JyväskyläJyväskyläFinland
| | - Lotta‐Riina Sundberg
- Department of Biological and Environmental Science (and Nanoscience Center)Centre of Excellence in Biological InteractionsUniversity of JyväskyläJyväskyläFinland
| | - Katja Pulkkinen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Janne Valkonen
- Department of Biological and Environmental Science (and Nanoscience Center)Centre of Excellence in Biological InteractionsUniversity of JyväskyläJyväskyläFinland
| | - Tarmo Ketola
- Department of Biological and Environmental Science (and Nanoscience Center)Centre of Excellence in Biological InteractionsUniversity of JyväskyläJyväskyläFinland
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Hamza F, Satpute S, Banpurkar A, Kumar AR, Zinjarde S. Biosurfactant from a marine bacterium disrupts biofilms of pathogenic bacteria in a tropical aquaculture system. FEMS Microbiol Ecol 2018; 93:4566513. [PMID: 29087455 DOI: 10.1093/femsec/fix140] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/25/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial infections are major constraints in aquaculture farming. These pathogens often adapt to the biofilm mode of growth and resist antibiotic treatments. We have used a non-toxic glycolipid biosurfactant (BS-SLSZ2) derived from a marine epizootic bacterium Staphylococcus lentus to treat aquaculture associated infections in an eco-friendly manner. We found that BS-SLSZ2 contained threose, a four-carbon sugar as the glycone component, and hexadecanoic and octadecanoic acids as the aglycone components. The critical micelle concentration of the purified glycolipid was 18 mg mL-1. This biosurfactant displayed anti-adhesive activity and inhibited biofilm formation by preventing initial attachment of cells onto surfaces. The biosurfactant (at a concentration of 20 μg) was able to inhibit Vibrio harveyi and Pseudomonas aeruginosa biofilms by 80.33 ± 2.16 and 82 ± 2.03%, respectively. At this concentration, it was also able to disrupt mature biofilms of V. harveyi (78.7 ± 1.93%) and P. aeruginosa (81.7 ± 0.59%). The biosurfactant was non-toxic towards Artemia salina. In vivo challenge experiments showed that the glycolipid was effective in protecting A. salina nauplii against V. harveyi and P. aeruginosa infections. This study highlights the significance of marine natural products in providing alternative biofilm controlling agents and decreasing the usage of antibiotics in aquaculture settings.
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Affiliation(s)
- Faseela Hamza
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Surekha Satpute
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Arun Banpurkar
- Department of Physics, Savitribai Phule Pune University, Pune, 411007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
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9
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Long-term genomic coevolution of host-parasite interaction in the natural environment. Nat Commun 2017; 8:111. [PMID: 28740072 PMCID: PMC5524643 DOI: 10.1038/s41467-017-00158-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Antagonistic coevolution of parasite infectivity and host resistance may alter the biological functionality of species, yet these dynamics in nature are still poorly understood. Here we show the molecular details of a long-term phage-bacterium arms race in the environment. Bacteria (Flavobacterium columnare) are generally resistant to phages from the past and susceptible to phages isolated in years after bacterial isolation. Bacterial resistance selects for increased phage infectivity and host range, which is also associated with expansion of phage genome size. We identified two CRISPR loci in the bacterial host: a type II-C locus and a type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appear in the variable ends of both loci over time. The spacers mostly target the terminal end of the phage genomes, which also exhibit the most variation across time, resulting in arms-race-like changes in the protospacers of the coevolving phage population.Arms races between phage and bacteria are well known from lab experiments, but insight from field systems is limited. Here, the authors show changes in the resistance and CRISPR loci of bacteria and the infectivity, host range and genome size of phage over multiple years in an aquaculture environment.
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10
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Dong HT, Senapin S, LaFrentz B, Rodkhum C. Virulence assay of rhizoid and non-rhizoid morphotypes of Flavobacterium columnare in red tilapia, Oreochromis sp., fry. JOURNAL OF FISH DISEASES 2016; 39:649-655. [PMID: 25953003 DOI: 10.1111/jfd.12385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/07/2015] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Numerous isolates of Flavobacterium columnare were previously recovered from red tilapia, Oreochromis sp., exhibiting columnaris-like disease in Thai farms, and the phenotypic and genetic characteristics were described. The objective of this study was to determine the virulence of two morphotypes (rhizoid and non-rhizoid colonies) of F. columnare and to determine their ability to adhere to and persist in red tilapia fry. The results showed that the typical rhizoid isolate (CUVET1214) was a highly virulent isolate and caused 100% mortality within 24 h following bath challenge of red tilapia with three different doses. The non-rhizoid isolate (CUVET1201) was avirulent to red tilapia fry. Both morphotypes adhered to and persisted in tilapia similarly at 0.5 and 6 h post-challenge as determined by whole fish bacterial loads. At 24 and 48 h post-challenge, fry challenged with the rhizoid morphotype exhibited significantly higher bacterial loads than the non-rhizoid morphotype. The results suggested that an inability of the non-rhizoid morphotype to persist in tilapia fry may explain lack of virulence.
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Affiliation(s)
- H T Dong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - S Senapin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Mahidol University, Bangkok, Thailand
| | - B LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service, Auburn, AL, USA
| | - C Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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11
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Dong HT, LaFrentz B, Pirarat N, Rodkhum C. Phenotypic characterization and genetic diversity of Flavobacterium columnare isolated from red tilapia, Oreochromis sp., in Thailand. JOURNAL OF FISH DISEASES 2015; 38:901-913. [PMID: 25287048 DOI: 10.1111/jfd.12304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/08/2014] [Accepted: 07/26/2014] [Indexed: 06/03/2023]
Abstract
Flavobacterium columnare is the aetiological agent of columnaris disease and severely affects various freshwater aquaculture fish species worldwide. The objectives of this study were to determine the phenotypic characteristics and genetic variability among F. columnare isolates isolated from red tilapia in Thailand. Forty-four F. columnare isolates were recovered from diseased fish in different geographical locations. The isolates exhibited homologous phenotypic characteristics but exhibited genetic diversity. One isolate was assigned to genomovar I, and the remainder were assigned to genomovar II, indicating the coexistence of these genomovars but predominance of genomovar II. Phylogenetic analysis of the 16S-23S ISR sequences revealed that a subset of the Thai isolates (n = 25) contained a smaller intergenic spacer region (ISR) (523-537 bp) and formed a unique ISR phylogenetic group. Phylogenetic analysis of the 16S rRNA gene supported the unique cluster of Thai isolates. This is the first description of the phenotypic and molecular characteristics of F. columnare isolated from red tilapia in Thailand as well as five isolates of F. columnare derived from other fish species including Nile tilapia, koi carp and striped catfish.
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Affiliation(s)
- H T Dong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - B LaFrentz
- United States Department of Agriculture-Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, AL, USA
| | - N Pirarat
- Department of Veterinary Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - C Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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12
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Laanto E, Bamford JKH, Ravantti JJ, Sundberg LR. The use of phage FCL-2 as an alternative to chemotherapy against columnaris disease in aquaculture. Front Microbiol 2015; 6:829. [PMID: 26347722 PMCID: PMC4541368 DOI: 10.3389/fmicb.2015.00829] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/28/2015] [Indexed: 01/21/2023] Open
Abstract
Flavobacterium columnare, the causative agent of columnaris disease in fish, causes millions of dollars of losses in the US channel catfish industry alone, not to mention aquaculture industry worldwide. Novel methods are needed for the control and treatment of bacterial diseases in aquaculture to replace traditionally used chemotherapies. A potential solution could be the use of phages, i.e., bacterial viruses, host-specific and self-enriching particles that can be can easily distributed via water flow. We examined the efficacy of phages to combat columnaris disease. A previously isolated phage, FCL-2, infecting F. columnare, was characterized by sequencing. The 47 142 bp genome of the phage had G + C content of 30.2%, and the closest similarities regarding the structural proteins were found in Cellulophaga phage phiSM. Under controlled experimental conditions, two host fish species, rainbow trout (Oncorhynchus mykiss) and zebrafish (Danio rerio), were used to study the success of phage therapy to prevent F. columnare infections. The survival of both fish species was significantly higher in the presence of the phage. Hundred percent of the zebrafish and 50% of the rainbow trout survived in the phage treatment (survival without phage 0 and 8.3%, respectively). Most importantly, the rainbow trout population was rescued from infection by a single addition of the phage into the water in a flow-through fish tank system. Thus, F. columnare could be used as a model system to test the benefits and risks of phage therapy on a larger scale.
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Affiliation(s)
- Elina Laanto
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of JyvaskylaJyvaskyla, Finland
| | - Jaana K. H. Bamford
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of JyvaskylaJyvaskyla, Finland
| | - Janne J. Ravantti
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of JyvaskylaJyvaskyla, Finland
- Department of Biosciences and Institute of Biotechnology, University of HelsinkiHelsinki, Finland
| | - Lotta-Riina Sundberg
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of JyvaskylaJyvaskyla, Finland
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Buyuk F, Sahin M, Cooper C, Celebi O, Saglam AG, Baillie L, Celik E, Akca D, Otlu S. The effect of prolonged storage on the virulence of isolates of Bacillus anthracis obtained from environmental and animal sources in the Kars Region of Turkey. FEMS Microbiol Lett 2015; 362:fnv102. [PMID: 26109359 DOI: 10.1093/femsle/fnv102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/13/2022] Open
Abstract
The stability of the plasmid-mediated virulence factors of Bacillus anthracis, a tripartite toxin located on pXO1 and an antiphagocytic capsule encoded by genes located on pXO2, following long-term storage was investigated. A collection of 159 isolates of B. anthracis were collected from the Kars region of Turkey between 2000 and 2013 and stored at -20°C in Brucella broth supplemented with 20% glycerine. A total of 142 isolates were recovered of which one failed to express a capsule upon primary culture. A further 35 isolates yielded a mixture of mucoid and non-mucoid colonies; the majority of which had lost the pXO2 plasmid as determined by PCR analysis. Results would suggest that pXO2 is more unstable than pXO1 and that this instability increases with the length of storage. It is possible that the pXO2-deficient isolates of B. anthracis described here could be developed into a vaccine to treat at risk animals in the Kars region as many animal vaccines are based upon pXO2 deficiency.
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Affiliation(s)
- Fatih Buyuk
- Faculty of Veterinary Medicine, Department of Microbiology, University of Kafkas, Kars, Turkey
| | - Mitat Sahin
- Faculty of Veterinary Medicine, Department of Microbiology, University of Kafkas, Kars, Turkey
| | - Callum Cooper
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, UK
| | - Ozgur Celebi
- Faculty of Veterinary Medicine, Department of Microbiology, University of Kafkas, Kars, Turkey
| | - Aliye Gulmez Saglam
- Faculty of Veterinary Medicine, Department of Microbiology, University of Kafkas, Kars, Turkey
| | - Les Baillie
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, UK
| | - Elif Celik
- Faculty of Veterinary Medicine, Department of Microbiology, University of Kafkas, Kars, Turkey
| | - Dogan Akca
- Kars Health School, University of Kafkas, Kars, Turkey
| | - Salih Otlu
- Faculty of Veterinary Medicine, Department of Microbiology, University of Kafkas, Kars, Turkey
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