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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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Evseev P, Gutnik D, Shneider M, Miroshnikov K. Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of Duplodnaviria Viruses. Biomolecules 2023; 13:biom13010110. [PMID: 36671495 PMCID: PMC9855967 DOI: 10.3390/biom13010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm Duplodnaviria, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified Duplodnaviria families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal Duplodnaviria groups, and problems relating to the taxonomic classification of Duplodnaviria have been discussed.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Daria Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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3
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Puri P, Sharma JG, Singh R. Biotherapeutic microbial supplementation for ameliorating fish health: developing trends in probiotics, prebiotics, and synbiotics use in finfish aquaculture. Anim Health Res Rev 2022; 23:113-135. [PMID: 36597760 DOI: 10.1017/s1466252321000165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nutrition demands in aquaculture can be realized through quality aquafeeds as compounded diets that contribute to the growth and health of aquaculture species. Functional additives in feed, notably probiotics, prebiotics, and their admixture synbiotics, have been recently recognized for their biotherapeutic role as immunostimulants capable of conferring disease resistance, stress tolerance, and gastrointestinal health; counteracting the negative effects of anti-nutrients, pathogenic prevalence, and antimicrobials in finfish aquaculture. Formulated diets based on probiotics, prebiotics, and as a supplemental combination for synbiotics can significantly influence fish gut microbiomes, establishing the modalities of microbial dynamics to maximize host-associated benefits. These microbial functional-feed supplements are acclaimed to be biocompatible, biodegradable, and safe for dietary consumption as well as the environment. In fed fish aquaculture, prebiotic appended probiotic diet 'synbiotic' has propounded larger attention for its additional health and nutritional benefits. Synbiotic, prebiotic, and probiotic usage as functional feeds for finfish aquaculture thus provides promising prospects. Developing trends in their intended application are reviewed here forth.
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Affiliation(s)
- Parul Puri
- Department of Biotechnology, Delhi Technological University, Delhi, India
- Department of Zoology, Sri Aurobindo College, University of Delhi, Delhi, India
| | - Jai Gopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Ram Singh
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
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4
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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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5
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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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Runtuvuori‐Salmela A, Kunttu HMT, Laanto E, Almeida GMF, Mäkelä K, Middelboe M, Sundberg L. Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control. Environ Microbiol 2022; 24:2404-2420. [PMID: 35049114 PMCID: PMC9304149 DOI: 10.1111/1462-2920.15901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Intensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage-based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 phages against F. columnare from Finland and Sweden in 2017. Bacterial isolates were virulent on rainbow trout (Oncorhynchus mykiss) and fell into four previously described genetic groups A, C, E and G, with genetic groups C and E being the most virulent. Phage host range studied against a collection of 227 bacterial isolates (from 2013 to 2017) demonstrated modular infection patterns based on host genetic group. Phages infected contemporary and previously isolated bacterial hosts, but bacteria isolated most recently were generally resistant to previously isolated phages. Despite large differences in geographical origin, isolation year or host range of the phages, whole-genome sequencing of 56 phages showed high level of genetic similarity to previously isolated F. columnare phages (Ficleduovirus, Myoviridae). Altogether, this phage collection demonstrates a potential for use in phage therapy.
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Affiliation(s)
- Anniina Runtuvuori‐Salmela
- Department of Biological and Environmental Science and Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
| | - Heidi M. T. Kunttu
- Department of Biological and Environmental Science and Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
| | - Elina Laanto
- Department of Biological and Environmental Science and Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
- Faculty of Biological and Environmental SciencesMolecular and Integrative Biosciences Research Programme, University of HelsinkiHelsinkiFinland
| | - Gabriel M. F. Almeida
- Department of Biological and Environmental Science and Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
- Faculty of Biosciences, Fisheries and Economics, Norwegian College of Fishery ScienceUiT The Arctic University of NorwayTromsøNorway
| | - Kati Mäkelä
- Department of Biological and Environmental Science and Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
| | - Mathias Middelboe
- Department of Biology, Marine Biological SectionUniversity of CopenhagenHelsingørDenmark
| | - Lotta‐Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience CenterUniversity of JyväskyläJyväskyläFinland
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7
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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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8
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Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022; 38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 12/16/2022] Open
Abstract
The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.
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Affiliation(s)
- Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Renate A A A Ruigrok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Rinse K Weersma
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
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9
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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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10
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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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11
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Donati VL, Dalsgaard I, Runtuvuori-Salmela A, Kunttu H, Jørgensen J, Castillo D, Sundberg LR, Middelboe M, Madsen L. Interactions between Rainbow Trout Eyed Eggs and Flavobacterium spp. Using a Bath Challenge Model: Preliminary Evaluation of Bacteriophages as Pathogen Control Agents. Microorganisms 2021; 9:971. [PMID: 33946270 PMCID: PMC8146780 DOI: 10.3390/microorganisms9050971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
The microbial community surrounding fish eyed eggs can harbor pathogenic bacteria. In this study we focused on rainbow trout (Oncorhynchus mykiss) eyed eggs and the potential of bacteriophages against the pathogenic bacteria Flavobacterium psychrophilum and F. columnare. An infection bath method was first established, and the effects of singular phages on fish eggs was assessed (survival of eyed eggs, interaction of phages with eyed eggs). Subsequently, bacteria-challenged eyed eggs were exposed to phages to evaluate their effects in controlling the bacterial population. Culture-based methods were used to enumerate the number of bacteria and/or phages associated with eyed eggs and in the surrounding environment. The results of the study showed that, with our infection model, it was possible to re-isolate F. psychrophilum associated with eyed eggs after the infection procedure, without affecting the survival of the eggs in the short term. However, this was not possible for F. columnare, as this bacterium grows at higher temperatures than the ones recommended for incubation of rainbow trout eyed eggs. Bacteriophages do not appear to negatively affect the survival of rainbow trout eyed eggs and they do not seem to strongly adhere to the surface of eyed eggs either. Finally, the results demonstrated a strong potential for short term (24 h) phage control of F. psychrophilum. However, further studies are needed to explore if phage control can be maintained for a longer period and to further elucidate the mechanisms of interactions between Flavobacteria and their phages in association with fish eggs.
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Affiliation(s)
- Valentina L. Donati
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (I.D.); (L.M.)
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (I.D.); (L.M.)
| | - Anniina Runtuvuori-Salmela
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland; (A.R.-S.); (H.K.); (L.-R.S.)
| | - Heidi Kunttu
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland; (A.R.-S.); (H.K.); (L.-R.S.)
| | - Johanna Jørgensen
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark; (J.J.); (D.C.); (M.M.)
| | - Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark; (J.J.); (D.C.); (M.M.)
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland; (A.R.-S.); (H.K.); (L.-R.S.)
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark; (J.J.); (D.C.); (M.M.)
| | - Lone Madsen
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (I.D.); (L.M.)
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12
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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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13
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Laanto E, Ravantti JJ, Sundberg LR. Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen. Microorganisms 2020; 8:E1919. [PMID: 33276599 PMCID: PMC7761591 DOI: 10.3390/microorganisms8121919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022] Open
Abstract
The role of prophages in the evolution, diversification, or virulence of the fish pathogen Flavobacterium columnare has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the F. columnare type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of F. columnare Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between F. columnare strains and the fF4 phage, and another putative prophage in the F. columnare strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen F. columnare ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese F. columnare strains. Second, CRISPR analysis revealed four F. columnare strains that contain unique spacers targeting different regions of the putative prophage p49512 in the F. columnare strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the F. columnare prophages and different host strains.
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Affiliation(s)
- Elina Laanto
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Janne J. Ravantti
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland;
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14
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Sundell K, Landor L, Castillo D, Middelboe M, Wiklund T. Bacteriophages as Biocontrol Agents for Flavobacterium psychrophilum Biofilms and Rainbow Trout Infections. ACTA ACUST UNITED AC 2020; 1:198-204. [PMID: 33409498 PMCID: PMC7774876 DOI: 10.1089/phage.2020.0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Bacteriophages (phages) have been proposed as an alternative to antibiotics and surface disinfectants for treatment of Flavobacterium psychrophilum biofilms and fish infections in aquaculture settings. The aim of the study was to estimate the minimal phage:host ratio (PHR) required for the control of in vitro biofilm formation and mortalities caused by F. psychrophilum in experimentally infected fish. Materials and Methods: F. psychrophilum cells in different stages of biofilm formation were exposed to the lytic phage FPSV-D22 at different PHRs. Results: Our results show that an initial PHR of 0.01 is sufficient for more than an 80% inhibition of attachment and colonization, and disruption of maturated F. psychrophilum biofilms, whereas greater ratios resulted in almost complete interruption of the different biofilm stages. Interestingly, a similar response was observed in a phage therapy trial with live rainbow trout (Oncorhynchus mykiss), where treatment of F. psychrophilum-infected fish by injection of serial bacteriophage doses resulted in significantly (***p ≤ 0.001) higher survival already at a PHR of 0.02. Conclusions: These results indicate that phages have the potential to be effective for control and treatment of F. psychrophilum infections in fish farms even when applied in concentrations lower than previously expected.
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Affiliation(s)
- Krister Sundell
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Lotta Landor
- 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
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
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15
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Tominaga K, Morimoto D, Nishimura Y, Ogata H, Yoshida T. In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes. Front Microbiol 2020; 11:738. [PMID: 32411107 PMCID: PMC7198788 DOI: 10.3389/fmicb.2020.00738] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
Bacteroidetes is one of the most abundant heterotrophic bacterial taxa in the ocean and play crucial roles in recycling phytoplankton-derived organic matter. Viruses of Bacteroidetes are also expected to have an important role in the regulation of host communities. However, knowledge on marine Bacteroidetes viruses is biased toward cultured viruses from a few species, mainly fish pathogens or Bacteroidetes not abundant in marine environments. In this study, we investigated the recently reported 1,811 marine viral genomes to identify putative Bacteroidetes viruses using various in silico host prediction techniques. Notably, we used microbial metagenome-assembled genomes (MAGs) to augment the marine Bacteroidetes reference genomic data. The examined viral genomes and MAGs were derived from simultaneously collected samples. Using nucleotide sequence similarity-based host prediction methods, we detected 31 putative Bacteroidetes viral genomes. The MAG-based method substantially enhanced the predictions (26 viruses) when compared with the method that is solely based on the reference genomes from NCBI RefSeq (7 viruses). Previously unrecognized genus-level groups of Bacteroidetes viruses were detected only by the MAG-based method. We also developed a host prediction method based on the proportion of Bacteroidetes homologs in viral genomes, which detected 321 putative Bacteroidetes virus genomes including 81 that were newly recognized as Bacteroidetes virus genomes. The majority of putative Bacteroidetes viruses were detected based on the proportion of Bacteroidetes homologs in both RefSeq and MAGs; however, some were detected in only one of the two datasets. Putative Bacteroidetes virus lineages included not only relatives of known viruses but also those phylogenetically distant from the cultured viruses, such as marine Far-T4 like viruses known to be widespread in aquatic environments. Our MAG and protein homology-based host prediction approaches enhanced the existing knowledge on the diversity of Bacteroidetes viruses and their potential interaction with their hosts in marine environments.
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Affiliation(s)
- Kento Tominaga
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Daichi Morimoto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Hiroyuki Ogata
- Chemical Life Science, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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16
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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages. Viruses 2020; 12:v12020158. [PMID: 32019073 PMCID: PMC7077304 DOI: 10.3390/v12020158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 02/06/2023] Open
Abstract
Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage–host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria—LMO6, LMO9, LMO8—and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage–host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.
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17
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Almeida GMF, Laanto E, Ashrafi R, Sundberg LR. Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria. mBio 2019; 10:e01984-19. [PMID: 31744913 PMCID: PMC6867891 DOI: 10.1128/mbio.01984-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/17/2019] [Indexed: 11/20/2022] Open
Abstract
Metazoans were proposed to host bacteriophages on their mucosal surfaces in a symbiotic relationship, where phages provide an external immunity against bacterial infections and the metazoans provide phages a medium for interacting with bacteria. However, scarce empirical evidence and model systems have left the phage-mucus interaction poorly understood. Here, we show that phages bind both to porcine mucus and to rainbow trout (Oncorhynchus mykiss) primary mucus, persist up to 7 days in the mucosa, and provide protection against Flavobacterium columnare Also, exposure to mucus changes the bacterial phenotype by increasing bacterial virulence and susceptibility to phage infections. This trade-off in bacterial virulence reveals ecological benefit of maintaining phages in the metazoan mucosal surfaces. Tests using other phage-bacterium pairs suggest that phage binding to mucus may be widespread in the biosphere, indicating its importance for disease, ecology, and evolution. This phenomenon may have significant potential to be exploited in preventive phage therapy.IMPORTANCE The mucosal surfaces of animals are habitat for microbes, including viruses. Bacteriophages-viruses that infect bacteria-were shown to be able to bind to mucus. This may result in a symbiotic relationship in which phages find bacterial hosts to infect, protecting the mucus-producing animal from bacterial infections in the process. Here, we studied phage binding on mucus and the effect of mucin on phage-bacterium interactions. The significance of our research is in showing that phage adhesion to mucus results in preventive protection against bacterial infections, which will serve as basis for the development of prophylactic phage therapy approaches. Besides, we also reveal that exposure to mucus upregulates bacterial virulence and that this is exploited by phages for infection, adding one additional layer to the metazoan-bacterium-phage biological interactions and ecology. This phenomenon might be widespread in the biosphere and thus crucial for understanding mucosal diseases, their outcome and treatment.
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Affiliation(s)
- Gabriel M F Almeida
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
- Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Elina Laanto
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
- Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
- Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science, University of Jyvaskyla, Jyvaskyla, Finland
- Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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18
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Sundell K, Landor L, Nicolas P, Jørgensen J, Castillo D, Middelboe M, Dalsgaard I, Donati VL, Madsen L, Wiklund T. Phenotypic and Genetic Predictors of Pathogenicity and Virulence in Flavobacterium psychrophilum. Front Microbiol 2019; 10:1711. [PMID: 31396199 PMCID: PMC6668605 DOI: 10.3389/fmicb.2019.01711] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/11/2019] [Indexed: 02/05/2023] Open
Abstract
Flavobacterium psychrophilum causes bacterial cold-water disease (BCWD) in farmed rainbow trout (Oncorhynchus mykiss), with the multilocus sequence typing (MLST) clonal complex (CC) CC-ST10 accounting for the majority of outbreaks globally. The development of alternative strategies to antibiotic treatment of BCWD using bacteriophage-based control of F. psychrophilum, or virulence factors as targets for therapy, requires knowledge of the phage-sensitivity of outbreak strains and of universal traits contributing to their pathogenicity. To examine the association between virulence and both genetic (MLST sequence type (ST) and PCR-serotype) and phenotypic characteristics (adherence, antibiotic resistance, colony spreading motility, hemolytic and proteolytic activity), the median lethal dose (LD50) of 26 geographically disparate F. psychrophilum isolates was determined in rainbow trout. Furthermore, the in vitro sensitivity of the isolates against five bacteriophages was determined by the efficiency of plating (EOP). The tested F. psychrophilum isolates were mainly represented by CC-ST10 genotypes (22 out of 26) and showed up to 3-log differences in LD50 (8.9 × 103 to 3.1 × 106 CFU). No association between MLST ST and virulence was found because of a high variation in LD50 within STs. All identified serotypes (0, 1, and 2) were pathogenic, but ten most virulent isolates belonged to serotype 1 or 2. Isolates of high (LD50 < 105 CFU), moderate (LD50 = 105–106 CFU), and weak (LD50 > 106 CFU) virulence were similar in phenotypic characteristics in vitro. However, the only non-virulent CC-ST10 isolate was deficient in spreading motility and proteolytic activity, indicating that the characteristics are required for pathogenicity in F. psychrophilum. Univariate correlation studies found only non-significant associations between LD50 and the measured phenotypic characteristics, and the multivariable analysis did neither reveal any significant predictors of virulence. The majority of isolates (16 out of 26) were sensitive to at least four bacteriophages, with up to a 6-log variation in the EOP. Most CC-ST10 isolates (16 out of 22) were sensitive to the examined phages, including 5 out of the 7 most virulent isolates represented by prevalent and antibiotic-resistant STs. Our findings suggest that control of BCWD using lytic phages or interventions targeting shared characteristics of pathogenic F. psychrophilum strains should be further explored.
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Affiliation(s)
- Krister Sundell
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Lotta Landor
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Pierre Nicolas
- Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jóhanna Jørgensen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Daniel Castillo
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Inger Dalsgaard
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kongens Lyngby, Denmark
| | - 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
| | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
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19
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Complete Genome Sequence of an Aquaculture-Associated Phage, FL-1, Infecting Flavobacterium spp. GENOME ANNOUNCEMENTS 2017; 5:5/23/e00014-17. [PMID: 28596384 PMCID: PMC5465603 DOI: 10.1128/genomea.00014-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
FL-1, a myophage of Flavobacterium, was found to have a 53-kb genome with 87 putative coding sequences.
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