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Han R, Hong Y, Xu R, Guo W, Zhang M, Lu Z, Han Q, Mo Z, Dan X, Li Y. Genomic evidence of genetic diversity and functional evolution in Flavobacterium columnare. Front Microbiol 2023; 14:1240471. [PMID: 37840739 PMCID: PMC10568018 DOI: 10.3389/fmicb.2023.1240471] [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: 06/21/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish. Columnaris disease can cause heavy economic losses in aquaculture. In this study, whole-genome sequencing was used to characterize this pathogen. F. columnare isolate AH-01 had a circular chromosome and plasmid that encoded a total of 3,022 genes. Isolate GX-01 only had a circular chromosome and encoded 2,965 genes. Genomic islands, prophage regions, and CRISPR/Cas systems were identified in both genomes. Both genomes presented evidence of gene variation and horizontal transfer, both of which are the essential components of genetic diversity, genome plasticity, and functional evolution. Single-gene phylogeny and comparative genome analyses were performed to investigate the variation and evolution of this pathogen. Genetic analysis of 16S rRNA and housekeeping gene sequences significantly clustered 55 F. columnare isolates into four clades. The intragroup identity of the 16S rRNA gene exceeded 99%, while the intergroup identity was below the species delineation threshold. We discovered significant translocation, inversion, and rearrangement events that influenced local synteny within each group. Notably, the observed alignments varied considerably among all the studied groups. The core genomes of all strains with available sequences comprised 747 genes, corresponding to approximately 25% of the genome. Core genome multilocus sequence typing, genome-wide orthology and phylogenetic analyses, and average nucleotide identity suggested that the currently existing F. columnare was an assemblage of several distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. The present investigation provided genomic evidence of gene variation and horizontal transfer, which were the basis of genetic diversity, genome plasticity, and functional evolution. The findings supported a proposed new taxonomic perspective on F. columnare.
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Affiliation(s)
- Rui Han
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
| | - Yuhao Hong
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Ruilong Xu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wenjie Guo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Mingshu Zhang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Zijun Lu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qing Han
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zequan Mo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
| | - Xueming Dan
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
| | - Yanwei Li
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
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Kim M, Cha IT, Lee KE, Li M, Park SJ. Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium. Microbiol Spectr 2023; 11:e0100323. [PMID: 37594286 PMCID: PMC10655711 DOI: 10.1128/spectrum.01003-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, Jeju, South Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, South Korea
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Fraslin C, Robledo D, Kause A, Houston RD. Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss). Genet Sel Evol 2023; 55:59. [PMID: 37580697 PMCID: PMC10424455 DOI: 10.1186/s12711-023-00832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that affects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of the host resistance. However, genomic selection is expensive partly because of the cost of genotyping large numbers of animals using high-density single nucleotide polymorphism (SNP) arrays. The objective of this study was to assess the efficiency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2874 challenged fish and 469 fish from the parental generation (n = 81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD panels was assessed for 10 panels of different densities, which were created in silico using two sampling methods, random and equally spaced. All LD panels were also imputed to the full 28K HD panel using the parental generation as the reference population, and genomic predictions were re-evaluated. The potential of prioritizing SNPs that are associated with resistance to F. columnare was also tested for the six lower-density panels. RESULTS The accuracies of both imputation and genomic predictions were similar with random and equally-spaced sampling of SNPs. Using LD panels of at least 3000 SNPs or lower-density panels (as low as 300 SNPs) combined with imputation resulted in accuracies that were comparable to those of the 28K HD panel and were 11% higher than the pedigree-based predictions. CONCLUSIONS Compared to using the commercial HD panel, LD panels combined with imputation may provide a more affordable approach to genomic prediction of breeding values, which supports a more widespread adoption of genomic selection in aquaculture breeding programmes.
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Affiliation(s)
- Clémence Fraslin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Antti Kause
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Ross D Houston
- Benchmark Genetics, Edinburgh Technopole, 1 Pioneer Building, Penicuik, EH26 0GB, UK
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Kaimal S, Farmer BD, Renukdas NN, Abdelrahman HA, Kelly AM. Evaluating Stress-Mediated Microbial Pathogenesis in Golden Shiners, Notemigonus crysoleucas. Front Physiol 2022; 13:886480. [PMID: 35634142 PMCID: PMC9132093 DOI: 10.3389/fphys.2022.886480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022] Open
Abstract
Flavobacterium covae (columnaris) is a microbial pathogen of the Golden Shiner (Notemigonus crysoleucas), a principal bait species. We investigated the effects of density and water temperature on the survival of fish subjected to a columnaris challenge and whether flow cytometry (FCM) could be a fast and reliable method to distinguish and enumerate F. covae populations from water and fish in experimental tanks. Juvenile Golden Shiners averaging 2.62 (±0.78 S.D.) g (negative for F. covae) were used in simultaneous trials at 22°C and 28°C in two ultra-low flow-through systems: each consisting of four treatments and five replicates per treatment. Treatments were fish stocked at either 600 fish/m3 or 2,400 fish/m3 and either challenged with F. covae or not; survival was observed for 48 h after challenge. Samples of water and fish tissue were obtained for FCM enumerations and validation by qPCR. No significant differences in survival were recorded between density treatments; however, high temperature and columnaris challenge treatments showed significantly higher mortality. Bacterial enumeration (number/mL) by FCM highly correlated with bacterial counts r = 0.81 (p = 0.001) in the water samples. Higher water temperatures may have increased columnaris infections and mortality in Golden Shiners. Flow cytometry is a reliable method of enumerating F. covae from experimental tank water samples.
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Affiliation(s)
- Sindhu Kaimal
- Department of Aquaculture and Fisheries, The University of Arkansas at Pine Bluff, Pine Bluff, AR, United States
| | - Bradley D. Farmer
- United States Department of Agriculture, Agriculture Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, United States
| | - Nilima N. Renukdas
- Department of Aquaculture and Fisheries, The University of Arkansas at Pine Bluff, Pine Bluff, AR, United States
| | - Hisham A. Abdelrahman
- Department of Veterinary Hygiene and Management, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- Alabama Fish Farming Center, Auburn University, Greensboro, AL, United States
| | - Anita M. Kelly
- Department of Aquaculture and Fisheries, The University of Arkansas at Pine Bluff, Pine Bluff, AR, United States
- *Correspondence: Anita M. Kelly,
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Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
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Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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LaFrentz BR, Králová S, Burbick CR, Alexander TL, Phillips CW, Griffin MJ, Waldbieser GC, García JC, de Alexandre Sebastião F, Soto E, Loch TP, Liles MR, Snekvik KR. The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare. Syst Appl Microbiol 2021; 45:126293. [PMID: 35026686 DOI: 10.1016/j.syapm.2021.126293] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023]
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36T), F. davisii sp. nov. (90-106T), and F. oreochromis sp. nov. (Costa Rica 04-02-TNT) are proposed to represent genetic groups 2, 3, and 4, respectively.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States.
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Conner W Phillips
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS, United States
| | - Geoffrey C Waldbieser
- Warmwater Aquaculture Research Unit, USDA-ARS, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, United States
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States
| | | | - Esteban Soto
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
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Rahmatelahi H, El-Matbouli M, Menanteau-Ledouble S. Delivering the pain: an overview of the type III secretion system with special consideration for aquatic pathogens. Vet Res 2021; 52:146. [PMID: 34924019 PMCID: PMC8684695 DOI: 10.1186/s13567-021-01015-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
Gram-negative bacteria are known to subvert eukaryotic cell physiological mechanisms using a wide array of virulence factors, among which the type three-secretion system (T3SS) is often one of the most important. The T3SS constitutes a needle-like apparatus that the bacterium uses to inject a diverse set of effector proteins directly into the cytoplasm of the host cells where they can hamper the host cellular machinery for a variety of purposes. While the structure of the T3SS is somewhat conserved and well described, effector proteins are much more diverse and specific for each pathogen. The T3SS can remodel the cytoskeleton integrity to promote intracellular invasion, as well as silence specific eukaryotic cell signals, notably to hinder or elude the immune response and cause apoptosis. This is also the case in aquatic bacterial pathogens where the T3SS can often play a central role in the establishment of disease, although it remains understudied in several species of important fish pathogens, notably in Yersinia ruckeri. In the present review, we summarise what is known of the T3SS, with a special focus on aquatic pathogens and suggest some possible avenues for research including the potential to target the T3SS for the development of new anti-virulence drugs.
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Affiliation(s)
- Hadis Rahmatelahi
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria.
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Ø, Denmark.
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Type IX secretion system effectors and virulence of the model Flavobacterium columnare strain MS-FC-4. Appl Environ Microbiol 2021; 88:e0170521. [PMID: 34818105 DOI: 10.1128/aem.01705-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flavobacterium columnare causes columnaris disease in wild and cultured freshwater fish and is a major problem for sustainable aquaculture worldwide. The F. columnare type IX secretion system (T9SS) secretes many proteins and is required for virulence. The T9SS component GldN is required for secretion and for gliding motility over surfaces. Genetic manipulation of F. columnare is inefficient, which has impeded identification of secreted proteins that are critical for virulence. Here we identified a virulent wild-type F. columnare strain (MS-FC-4) that is highly amenable to genetic manipulation. This facilitated isolation and characterization of two deletion mutants lacking core components of the T9SS. Deletion of gldN disrupted protein secretion and gliding motility and eliminated virulence in zebrafish and rainbow trout. Deletion of porV disrupted secretion and virulence but not motility. Both mutants exhibited decreased extracellular proteolytic, hemolytic, and chondroitin sulfate lyase activities. They also exhibited decreased biofilm formation and decreased attachment to fish fins and to other surfaces. Using genomic and proteomic approaches, we identified proteins secreted by the T9SS. We deleted ten genes encoding secreted proteins and characterized the virulence of mutants lacking individual or multiple secreted proteins. A mutant lacking two genes encoding predicted peptidases exhibited reduced virulence in rainbow trout, and mutants lacking a predicted cytolysin showed reduced virulence in zebrafish and rainbow trout. The results establish F. columnare strain MS-FC-4 as a genetically amenable model to identify virulence factors. This may aid development of measures to control columnaris disease and impact fish health and sustainable aquaculture. IMPORTANCE: Flavobacterium columnare causes columnaris disease in wild and aquaculture-reared freshwater fish and is a major problem for aquaculture. Little is known regarding the virulence factors involved in this disease and control measures are inadequate. The type IX secretion system (T9SS) secretes many proteins and is required for virulence, but the secreted virulence factors are not known. We identified a strain of F. columnare (MS-FC-4) that is well suited for genetic manipulation. The components of the T9SS and the proteins secreted by this system were identified. Deletion of core T9SS genes eliminated virulence. Genes encoding ten secreted proteins were deleted. Deletion of two peptidase-encoding genes resulted in decreased virulence in rainbow trout, and deletion of a cytolysin-encoding gene resulted in decreased virulence in rainbow trout and zebrafish. Secreted peptidases and cytolysins are likely virulence factors and are targets for the development of control measures.
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Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont. Arch Microbiol 2021; 203:5783-5792. [PMID: 34515811 DOI: 10.1007/s00203-021-02566-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022]
Abstract
During a study aiming at isolation and genomic characterization of non-pathogenic fish symbionts, strain F-328T was isolated from skin mucus of healthy-seeming rainbow trout (Oncorhynchus mykiss) and subjected to polyphasic characterization, including a comprehensive genome analysis. Strain F-328T was Gram stain negative, none-gliding, strictly aerobic, and rod shaped. The 16S rRNA gene sequence of strain F-328T exhibited the highest level of identity (98.9%) with F. turcicum F-339T. The major fatty acids were iso-C15:0, C15:1 ω6c, and summed feature 3 (C16:1 ω7c, C16:1 ω6c). The polar lipid profile consisted mainly of phosphatidylethanolamine and aminolipids, while the predominant menaquinone was MK-6. The DNA G + C content and genome size of the strain were 35.3% and 3.4 Mb, respectively. Strain F-328T shows 93.8% average nucleotide identity and 53% digital DNA-DNA hybridization identity with the closest type strain F. turcicum F-339T. In addition, strain F-328T was found to carry antimicrobial resistance genes, which confer resistance to several antimicrobials, including aminoglycoside, macrolides, and streptogramin. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain F-328T should be classified as a novel species of the genus Flavobacterium for which the name Flavobacterium erciyesense sp. nov. is proposed, with F-328T as the type strain (= JCM 34201T = KCTC 82261T).
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Kunttu HMT, Runtuvuori-Salmela A, Sundell K, Wiklund T, Middelboe M, Landor L, Ashrafi R, Hoikkala V, Sundberg LR. Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and the Type IX Secretion System. Appl Environ Microbiol 2021; 87:e0081221. [PMID: 34106011 PMCID: PMC8315173 DOI: 10.1128/aem.00812-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/30/2021] [Indexed: 02/08/2023] Open
Abstract
Increasing problems with antibiotic resistance have directed interest toward phage therapy in the aquaculture industry. However, phage resistance evolving in target bacteria is considered a challenge. To investigate how phage resistance influences the fish pathogen Flavobacterium columnare, two wild-type bacterial isolates, FCO-F2 and FCO-F9, were exposed to phages (FCO-F2 to FCOV-F2, FCOV-F5, and FCOV-F25, and FCO-F9 to FCL-2, FCOV-F13, and FCOV-F45), and resulting phenotypic and genetic changes in bacteria were analyzed. Bacterial viability first decreased in the exposure cultures but started to increase after 1 to 2 days, along with a change in colony morphology from original rhizoid to rough, leading to 98% prevalence of the rough morphotype. Twenty-four isolates (including four isolates from no-phage treatments) were further characterized for phage resistance, antibiotic susceptibility, motility, adhesion, and biofilm formation, protease activity, whole-genome sequencing, and virulence in rainbow trout fry. The rough isolates arising in phage exposure were phage resistant with low virulence, whereas rhizoid isolates maintained phage susceptibility and high virulence. Gliding motility and protease activity were also related to the phage susceptibility. Observed mutations in phage-resistant isolates were mostly located in genes encoding the type IX secretion system, a component of the Bacteroidetes gliding motility machinery. However, not all phage-resistant isolates had mutations, indicating that phage resistance in F. columnare is a multifactorial process, including both genetic mutations and changes in gene expression. Phage resistance may not, however, be a challenge for development of phage therapy against F. columnare infections since phage resistance is associated with decreases in bacterial virulence. IMPORTANCE Phage resistance of infectious bacteria is a common phenomenon posing challenges for the development of phage therapy. Along with a growing world population and the need for increased food production, constantly intensifying animal farming has to face increasing problems of infectious diseases. Columnaris disease, caused by Flavobacterium columnare, is a worldwide threat for salmonid fry and juvenile farming. Without antibiotic treatments, infections can lead to 100% mortality in a fish stock. Phage therapy of columnaris disease would reduce the development of antibiotic-resistant bacteria and antibiotic loads by the aquaculture industry, but phage-resistant bacterial isolates may become a risk. However, phenotypic and genetic characterization of phage-resistant F. columnare isolates in this study revealed that they are less virulent than phage-susceptible isolates and thus not a challenge for phage therapy against columnaris disease. This is valuable information for the fish farming industry globally when considering phage-based prevention and curing methods for F. columnare infections.
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Affiliation(s)
- Heidi M. T. Kunttu
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Anniina Runtuvuori-Salmela
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Krister Sundell
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Mathias Middelboe
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Lotta Landor
- Laboratory of Aquatic Pathobiology, Åbo Akademi University, Turku, Finland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Ville Hoikkala
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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Sato K, Naya M, Hatano Y, Kasahata N, Kondo Y, Sato M, Takebe K, Naito M, Sato C. Biofilm Spreading by the Adhesin-Dependent Gliding Motility of Flavobacterium johnsoniae: 2. Role of Filamentous Extracellular Network and Cell-to-Cell Connections at the Biofilm Surface. Int J Mol Sci 2021; 22:ijms22136911. [PMID: 34199128 PMCID: PMC8269157 DOI: 10.3390/ijms22136911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022] Open
Abstract
Flavobacterium johnsoniae forms a thin spreading colony on nutrient-poor agar using gliding motility. As reported in the first paper, WT cells in the colony were sparsely embedded in self-produced extracellular polymeric matrix (EPM), while sprB cells were densely packed in immature biofilm with less matrix. The colony surface is critical for antibiotic resistance and cell survival. We have now developed the Grid Stamp-Peel method whereby the colony surface is attached to a TEM grid for negative-staining microscopy. The images showed that the top of the spreading convex WT colonies was covered by EPM with few interspersed cells. Cells exposed near the colony edge made head-to-tail and/or side-to-side contact and sometimes connected via thin filaments. Nonspreading sprB and gldG and gldK colonies had a more uniform upper surface covered by different EPMs including vesicles and filaments. The EPM of sprB, gldG, and WT colonies contained filaments ~2 nm and ~5 nm in diameter; gldK colonies did not include the latter. Every cell near the edge of WT colonies had one or two dark spots, while cells inside WT colonies and cells in SprB-, GldG-, or GldK-deficient colonies did not. Together, our results suggest that the colony surface structure depends on the capability to expand biofilm.
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Affiliation(s)
- Keiko Sato
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan;
- Correspondence: (K.S.); (C.S.); Tel.: +81-95-819-7649 (K.S.); +81-29-861-5562 (C.S.)
| | - Masami Naya
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (N.K.); (M.S.)
| | - Yuri Hatano
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (N.K.); (M.S.)
| | - Naoki Kasahata
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (N.K.); (M.S.)
| | - Yoshio Kondo
- Department of Pediatric Dentistry, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan;
| | - Mari Sato
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (N.K.); (M.S.)
| | - Katsuki Takebe
- Oral and Maxillofacial Surgery II, Graduate School of Dentistry, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Mariko Naito
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan;
| | - Chikara Sato
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan; (M.N.); (Y.H.); (N.K.); (M.S.)
- Correspondence: (K.S.); (C.S.); Tel.: +81-95-819-7649 (K.S.); +81-29-861-5562 (C.S.)
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12
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Mühle E, Abry C, Leclerc P, Goly GM, Criscuolo A, Busse HJ, Kämpfer P, Bernardet JF, Clermont D, Chesneau O. Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s. Int J Syst Evol Microbiol 2020; 71. [PMID: 33253083 DOI: 10.1099/ijsem.0.004576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome sequence analysis of two strains collected in Canada at the end of the 1970s and deposited in 1998 at the Collection de l'Institut Pasteur has led to the taxonomic description of a novel fish-associated species in the genus Flavobacterium. Both strains, CIP 105534T and CIP 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically in a temperature range from 5 to 30 °C with optimal growth at 25 °C on trypticase soy or Reasoner's 2A agar but they did not grow on marine agar. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH (shown as summed feature 3), C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 0. The major polyamine was sym-homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 and unidentified aminophospholipid APL1 were major polar lipids. A yellow pigment spot was visible after chromatographic analysis. The predominant respiratory quinone was MK-6. The G+C content of the two genomes was 34 mol% and their size was around 5.8 Mb. Comparison of the 16S rRNA gene sequences with those of the closely related type strains showed high levels of relatedness with Flavobacterium collinsii and Flavobacterium pectinovorum. All average nucleotide identity (ANI) and digital DNA-DNA hybridization values estimated against publicly available Flavobacterium genome assemblies were lower than 90 and 30 %, respectively. Phylogenetic, phenotypic and chemotaxonomic data indicated that the two strains represent a novel species of the genus Flavobacterium, for which the name Flavobacterium bizetiae sp. nov. is proposed. The type strain is CIP 105534T (=LMG 1342T). The unique ability of F. bizetiae to use melibiose as a sole source of carbon could provide a simple phenotypic test to discriminate F. bizetiae from its closest relatives.
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Affiliation(s)
- Estelle Mühle
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Chloé Abry
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Priscilla Leclerc
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Gogoa-Marthe Goly
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du docteur Roux, 75015 Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, 1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, Heinrich-Buff-Ring 26 (IFZ), 35392 Giessen, Germany
| | - Jean-François Bernardet
- Unité de Virologie et Immunologie Moléculaires, Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE), 4 avenue Jean Jaurès, 78350 Jouy-en-Josas, France
| | - Dominique Clermont
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Département de Microbiologie, Institut Pasteur, 28 rue du docteur Roux, 75015 Paris, France
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13
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Kayansamruaj P, Areechon N, Unajak S. Development of fish vaccine in Southeast Asia: A challenge for the sustainability of SE Asia aquaculture. FISH & SHELLFISH IMMUNOLOGY 2020; 103:73-87. [PMID: 32335313 DOI: 10.1016/j.fsi.2020.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/23/2020] [Accepted: 04/15/2020] [Indexed: 05/08/2023]
Abstract
Southeast (SE) Asia plays an important role in global food security as this region has been regarded as one of the major producers of aquaculture product and, to date, freshwater fish accounted for one-third of the total aquaculture in SE Asia. The intensification of freshwater farming corresponding to increase of consumer demands has inevitably led to the emergence and re-emergence of diseases causing tremendous economic loss in the region. Nile tilapia (Oreochromis niloticus) and striped catfish (Pangasianodon hypophthalmus), the major freshwater fish species of SE Asia, have been reported susceptible to several bacterial pathogens, e.g. Streptococcus agalactiae, Edwardsiella ictalurid and Flavobacterium columnare. Since only a limited number of vaccines being registered and marketed, these pathogenic organisms still represent a severe threat to aquaculture industry in SE Asia. However, there is profound advancement in the understanding of disease epidemiology, pathogenic mechanisms, teleost mucosal immunity and vaccine delivery system over the last few years. This review aimed to summarize those recent findings which hopefully can provide novel insight into the future development of suitable vaccine and vaccination regime against bacterial infection in SE Asia region.
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Affiliation(s)
- Pattanapon Kayansamruaj
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.
| | - Nontawith Areechon
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, 10900, Chatuchak, Bangkok, Thailand.
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14
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Gibbs GD, Griffin MJ, Mauel MJ, Lawrence ML. Validation of a quantitative PCR assay for the detection of 2 Flavobacterium columnare genomovars. J Vet Diagn Invest 2020; 32:356-362. [PMID: 32310022 DOI: 10.1177/1040638720915760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in a variety of fish hosts. Using modifications to previously established protocols, a quantitative PCR (qPCR) assay was validated for the detection of 2 predominant F. columnare genomovars. The oligonucleotide primer and probe combination was designed to amplify a 203-bp region of the chondroitin AC lyase gene (GenBank AY912281) of F. columnare. There were no significant differences in amplification between genomovars. Comparable quantities of genomic DNA from 10 F. columnare strains, 5 representatives of each genomovar, produced similar results. Serial dilutions of purified PCR product demonstrated the limit of sensitivity for the assay was ~ 10 copies per reaction. The presence of gill and spleen tissue did not significantly affect the sensitivity of the assay. Comparably, bacterial DNA detected from the liver and kidney was less sensitive than pure bacterial DNA. However, detection from these tissues was within one order of magnitude of other tissues, indicating this reduction may have minimal analytic significance. This validated assay was used to approximate the minimum infectious dose for F. columnare isolate 94-081 in channel catfish and assess bacterial loads in gill and kidney tissues 48 h post-infection.
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Affiliation(s)
- Gordon D Gibbs
- Fish Health Services, Oregon Department of Fish and Wildlife, Department of Microbiology, Oregon State University, Corvallis, OR (Gibbs).,Thad Cochran National Warmwater Aquaculture Center (Griffin), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS.,Department of Basic Sciences (Mauel, Lawrence), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS
| | - Matthew J Griffin
- Fish Health Services, Oregon Department of Fish and Wildlife, Department of Microbiology, Oregon State University, Corvallis, OR (Gibbs).,Thad Cochran National Warmwater Aquaculture Center (Griffin), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS.,Department of Basic Sciences (Mauel, Lawrence), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS
| | - Michael J Mauel
- Fish Health Services, Oregon Department of Fish and Wildlife, Department of Microbiology, Oregon State University, Corvallis, OR (Gibbs).,Thad Cochran National Warmwater Aquaculture Center (Griffin), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS.,Department of Basic Sciences (Mauel, Lawrence), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS
| | - Mark L Lawrence
- Fish Health Services, Oregon Department of Fish and Wildlife, Department of Microbiology, Oregon State University, Corvallis, OR (Gibbs).,Thad Cochran National Warmwater Aquaculture Center (Griffin), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS.,Department of Basic Sciences (Mauel, Lawrence), College of Veterinary Medicine, Mississippi State University, Mississippi State, MS
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15
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Kumru S, Tekedar HC, Blom J, Lawrence ML, Karsi A. Genomic diversity in flavobacterial pathogens of aquatic origin. Microb Pathog 2020; 142:104053. [PMID: 32058022 DOI: 10.1016/j.micpath.2020.104053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
Flavobacterium species are considered important fish pathogens in wild and cultured fish throughout the world. They can cause acute, subacute, and chronic infections, which are mainly characterized by gill damage, skin lesions, and deep necrotic ulcerations. Primarily, three Flavobacterium species, F. branchiophilum, F. columnare, and F. psychrophilum, have been reported to cause substantial losses to freshwater fish. In this study, we evaluated genomes of 86 Flavobacterium species isolated from aquatic hosts (mainly fish) to identify their unique and shared genome features. Our results showed that F. columnare genomes cluster into four different genetic groups. In silico secretion system analysis identified that all genomes carry type I (T1SS) and type IX (T9SS) secretion systems, but the number of type I secretion system genes shows diversity between species. F. branchiophilum, F. araucananum, F. chilense, F. spartansii, and F. tructae genomes have full type VI secretion system (T6SS). F. columnare, F. hydatis, and F. plurextorum carry partial T6SS with some of the T6SS genes missing. F. columnare, F. araucananum, F. chilense, F. spartansii, F. araucananum, F. tructae, Flavobacterium sp., F. crassostreae, F. succinicans, F. hydatis, and F. plurextorum carry most of the type IV secretion system genes (T4SS). F. columnare genetic groups 1 and 2, Flavobacterium sp., and F. crassostreae encode the least number of antibiotic resistance elements. F. hydatis, F. chilense, and F. plurextorum encode the greatest number of antibiotic resistance genes. Additionally, F. spartansii, F. araucananum, and chilense encode the greatest number of virulence genes while Flavobacterium sp. and F. crassostreae encode the least number of virulence genes. In conclusion, comparative genomics of Flavobacterium species of aquatic origin will help our understanding of Flavobacterium pathogenesis.
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Affiliation(s)
- Salih Kumru
- Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Hasan C Tekedar
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States.
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16
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LaFrentz BR, García JC, Shelley JP. Multiplex PCR for genotyping Flavobacterium columnare. JOURNAL OF FISH DISEASES 2019; 42:1531-1542. [PMID: 31469439 DOI: 10.1111/jfd.13068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Recent research has identified four distinct genetic groups among isolates of Flavobacterium columnare through multilocus phylogenetic analyses; however, there are no quick methods to determine the genotype of an isolate. The objective of this research was to develop a multiplex PCR to rapidly genotype F. columnare to genetic group. Comparative bacterial genomics was used to identify regions in the genomes unique to each genetic group, and primers were designed to specifically amplify different sized amplicons for each genetic group. The optimized assay was demonstrated to be specific for each genetic group and F. columnare, and no specific amplicons were generated using gDNA from a panel of other Flavobacterium spp. and bacterial fish pathogens. The analytical sensitivity of the assay ranged from 209 to 883 genome equivalents depending on the genetic group. The multiplex PCR was evaluated by genotyping a panel of 22 unknown F. columnare isolates and performing DNA sequencing of the dnaK gene in parallel. The results demonstrated 100% accordance between multiplex PCR results and assignment to genetic group via phylogenetic analysis. The multiplex PCR provides a useful tool for assigning an unknown isolate to genetic group and may be used to determine which genetic groups of F. columnare are circulating and most predominant in different aquaculture industries.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - John P Shelley
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
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17
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Declercq AM, Cai W, Naranjo E, Thongda W, Eeckhaut V, Bauwens E, Arias C, De La Fuente L, Beck BH, Lange MD, Peatman E, Haesebrouck F, Aerts J, Decostere A. Evidence that the stress hormone cortisol regulates biofilm formation differently among Flavobacterium columnare isolates. Vet Res 2019; 50:24. [PMID: 30971289 PMCID: PMC6458827 DOI: 10.1186/s13567-019-0641-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/24/2019] [Indexed: 12/19/2022] Open
Abstract
The impact of cortisol on Flavobacterium columnare biofilm formation was explored. Firstly, the dynamics of biofilm formation by one highly (HV) and one low virulent (LV) F. columnare isolate with and without the stress hormone cortisol under microfluidic flow conditions was characterized. This to confirm that F. columnare cells could form biofilm under cortisol supplementation, and to compare the temporal and structural differences between different treatment groups. One trial revealed that in both isolates cell aggregates resembling biofilms occurred within 7-h post-inoculation. Consequently, cell clusters were sloughed away, followed by a rebuilding of bacterial cell aggregates, suggestive for a high spreading capacity. While the HV isolate revealed cell aggregates formed upstream at all time-points, for the LV isolate this was only seen upon cortisol supplementation. Secondly, the transcriptional effect of genes (gldK, gldL, gldM, gldN, sprA, sprE, sprT, and porV) belonging to the Type IX secretion system involved in gliding motility was investigated in planktonic and biofilm cells of a HV and LV isolate to which no, a low (LD) or high (HD) dose of cortisol was added. Significantly lower expression of gliding genes gldK, gldL, gldM and gldN, and of protein secretion regulator porV was seen in the LV isolate planktonic cells supplemented with a HD-cortisol. The LV isolate biofilm cells treated with the HD-cortisol showed a significant upregulation of sprT, encoding mobile surface adhesion important in bacterial colonization. This is the first evidence for the co-regulatory effect of cortisol on biofilm formation and F. columnare gliding gene expression.
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Affiliation(s)
- Annelies Maria Declercq
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, 9000, Belgium. .,Stress Physiology Research Group, Faculty of Pharmaceutical Sciences, Ghent University, Ostend, 8400, Belgium.
| | - Wenlong Cai
- School of Fisheries, Aquaculture, and Aquatic Sciences, Aquatic Microbiology Laboratory, Auburn University, Auburn, AL, 36849, USA
| | - Eber Naranjo
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture, and Aquatic Sciences, Aquatic Genetics and Genomics, Auburn University, Auburn, AL, 36849, USA
| | - Venessa Eeckhaut
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, 9000, Belgium
| | - Eva Bauwens
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, 9000, Belgium
| | - Covadonga Arias
- School of Fisheries, Aquaculture, and Aquatic Sciences, Aquatic Microbiology Laboratory, Auburn University, Auburn, AL, 36849, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin H Beck
- United States Department of Agriculture, Agricultural Research Service, Aquatic Animal Health Research Unit, Auburn, AL, 36849, USA
| | - Miles D Lange
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, 72160, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture, and Aquatic Sciences, Aquatic Genetics and Genomics, Auburn University, Auburn, AL, 36849, USA
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, 9000, Belgium
| | - Johan Aerts
- Stress Physiology Research Group, Faculty of Pharmaceutical Sciences, Ghent University, Ostend, 8400, Belgium.,Stress Physiology Research Group, Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Ostend, 8400, Belgium
| | - Annemie Decostere
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, 9000, Belgium
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18
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Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH-97028 (=CIP 109753). GENOME ANNOUNCEMENTS 2018; 6:6/14/e00222-18. [PMID: 29622616 PMCID: PMC5887026 DOI: 10.1128/genomea.00222-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Flavobacterium columnare strain PH-97028 (=CIP 109753) is a genomovar III reference strain that was isolated from a diseased Ayu fish in Japan. We report here the analysis of the first available genomovar III sequence of this species to aid in identification, epidemiological tracking, and virulence studies.
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19
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LaFrentz BR, García JC, Waldbieser GC, Evenhuis JP, Loch TP, Liles MR, Wong FS, Chang SF. Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations. Front Microbiol 2018; 9:452. [PMID: 29593693 PMCID: PMC5859164 DOI: 10.3389/fmicb.2018.00452] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/27/2018] [Indexed: 12/04/2022] Open
Abstract
Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, whereby six established genomovars have been described to date. However, little has been done to quantify or characterize this diversity further in a systematic fashion. The objective of this research was to perform phylogenetic analyses of 16S rRNA and housekeeping gene sequences to decipher the genetic diversity of F. columnare. Fifty isolates and/or genomes of F. columnare, originating from diverse years, geographic locations, fish hosts, and representative of the six genomovars were analyzed in this study. A multilocus phylogenetic analysis (MLPA) of the 16S rRNA and six housekeeping genes supported four distinct F. columnare genetic groups. There were associations between genomovar and genetic group, but these relationships were imperfect indicating that genomovar assignment does not accurately reflect F. columnare genetic diversity. To expand the dataset, an additional 90 16S rRNA gene sequences were retrieved from GenBank and a phylogenetic analysis of this larger dataset also supported the establishment of four genetic groups. Examination of isolate historical data indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from specific fish species or families. It is proposed that F. columnare isolates be assigned to the four genetic groups defined in this study rather than genomovar in order to facilitate a standard nomenclature across the scientific community. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries may allow for the development of improved targeted control and treatment measures for columnaris disease.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service, Auburn, AL, United States
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service, Auburn, AL, United States
| | - Geoffrey C Waldbieser
- Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, United States Department of Agriculture - Agricultural Research Service, Stoneville, MS, United States
| | - Jason P Evenhuis
- National Center for Cool and Cold Water Aquaculture, United States Department of Agriculture - Agricultural Research Service, Kearneysville, WV, United States
| | - Thomas P Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Fong S Wong
- MSD Animal Health Innovation Pte. Ltd., Singapore, Singapore
| | - Siow F Chang
- MSD Animal Health Innovation Pte. Ltd., Singapore, Singapore
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20
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21
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Duchaud E, Rochat T, Habib C, Barbier P, Loux V, Guérin C, Dalsgaard I, Madsen L, Nilsen H, Sundell K, Wiklund T, Strepparava N, Wahli T, Caburlotto G, Manfrin A, Wiens GD, Fujiwara-Nagata E, Avendaño-Herrera R, Bernardet JF, Nicolas P. Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum. Front Microbiol 2018; 9:138. [PMID: 29467746 PMCID: PMC5808330 DOI: 10.3389/fmicb.2018.00138] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/22/2018] [Indexed: 12/04/2022] Open
Abstract
Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless “open” according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.
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Affiliation(s)
- Eric Duchaud
- Unité de Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Tatiana Rochat
- Unité de Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Christophe Habib
- Unité de Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France.,Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Paul Barbier
- Unité de Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Valentin Loux
- Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cyprien Guérin
- Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Inger Dalsgaard
- Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lone Madsen
- Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hanne Nilsen
- Department of Aquatic Animal health, Norwegian Veterinary Institute, Bergen, Norway
| | - Krister Sundell
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Nicole Strepparava
- Laboratory of Applied Microbiology, Department for Environment Constructions and Design, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Thomas Wahli
- Centre for Fish and Wildlife Health (FIWI), University of Bern, Bern, Switzerland
| | - Greta Caburlotto
- Department of Fish Pathology, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Amedeo Manfrin
- Department of Fish Pathology, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | | | - Ruben Avendaño-Herrera
- Departamento Facultad de Ciencias Biológicas, Universidad Andres Bello, Universidad Andres BelloViña del Mar, Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Jean-François Bernardet
- Unité de Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - 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
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Chen S, Blom J, Loch TP, Faisal M, Walker ED. The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation. Front Microbiol 2017; 8:2339. [PMID: 29250046 PMCID: PMC5714932 DOI: 10.3389/fmicb.2017.02339] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/29/2023] Open
Abstract
Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16T. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of F. spartansii T16T and were conserved in most of the analyzed pathogenic Flavobacterium. F. spartansii was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into F. spartansii virulence in vivo, a transposon-based random mutagenesis strategy was attempted in F. spartansii T16T using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis.
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Affiliation(s)
- Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
| | - Thomas P Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Mohamed Faisal
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States.,Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Edward D Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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