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Thunes NC, Evenhuis JP, Lipscomb RS, Pérez-Pascual D, Stevick RJ, Birkett C, Ghigo JM, McBride MJ. Gliding motility proteins GldJ and SprB contribute to Flavobacterium columnare virulence. J Bacteriol 2024; 206:e0006824. [PMID: 38517170 PMCID: PMC11025331 DOI: 10.1128/jb.00068-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Flavobacterium columnare causes columnaris disease in fish. Columnaris disease is incompletely understood, and adequate control measures are lacking. The type IX secretion system (T9SS) is required for F. columnare gliding motility and virulence. The T9SS and gliding motility machineries share some, but not all, components. GldN (required for gliding and for secretion) and PorV (involved in secretion but not required for gliding) are both needed for virulence, implicating T9SS-mediated secretion in virulence. The role of motility in virulence is uncertain. We constructed and analyzed sprB, sprF, and gldJ mutants that were defective for motility but that maintained T9SS function to understand the role of motility in virulence. Wild-type cells moved rapidly and formed spreading colonies. In contrast, sprB and sprF deletion mutants were partially defective in gliding and formed nonspreading colonies. Both mutants exhibited reduced virulence in rainbow trout fry. A gldJ deletion mutant was nonmotile, secretion deficient, and avirulent in rainbow trout fry. To separate the roles of GldJ in secretion and in motility, we generated gldJ truncation mutants that produce nearly full-length GldJ. Mutant gldJ563, which produces GldJ truncated at amino acid 563, was defective for gliding but was competent for secretion as measured by extracellular proteolytic activity. This mutant displayed reduced virulence in rainbow trout fry, suggesting that motility contributes to virulence. Fish that survived exposure to the sprB deletion mutant or the gldJ563 mutant exhibited partial resistance to later challenge with wild-type cells. The results aid our understanding of columnaris disease and may suggest control strategies.IMPORTANCEFlavobacterium columnare causes columnaris disease in many species of freshwater fish in the wild and in aquaculture systems. Fish mortalities resulting from columnaris disease are a major problem for aquaculture. F. columnare virulence is incompletely understood, and control measures are inadequate. Gliding motility and protein secretion have been suggested to contribute to columnaris disease, but evidence directly linking motility to disease was lacking. We isolated and analyzed mutants that were competent for secretion but defective for motility. Some of these mutants exhibited decreased virulence. Fish that had been exposed to these mutants were partially protected from later exposure to the wild type. The results contribute to our understanding of columnaris disease and may aid development of control strategies.
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Affiliation(s)
- Nicole C. Thunes
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jason P. Evenhuis
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, West Virginia, USA
| | - Ryan S. Lipscomb
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, West Virginia, USA
| | - David Pérez-Pascual
- Institut Pasteur, Université Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Rebecca J. Stevick
- Institut Pasteur, Université Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Clayton Birkett
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, West Virginia, USA
| | - Jean-Marc Ghigo
- Institut Pasteur, Université Paris-Cité, CNRS UMR 6047, Genetics of Biofilms Laboratory, Paris, France
| | - Mark J. McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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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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Tuttle JT, Bruce TJ, Butts IAE, Roy LA, Abdelrahman HA, Beck BH, Kelly AM. Investigating the Ability of Edwardsiella ictaluri and Flavobacterium covae to Persist within Commercial Catfish Pond Sediments under Laboratory Conditions. Pathogens 2023; 12:871. [PMID: 37513718 PMCID: PMC10385248 DOI: 10.3390/pathogens12070871] [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: 04/11/2023] [Revised: 05/26/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Two prevalent bacterial diseases in catfish aquaculture are enteric septicemia of catfish and columnaris disease caused by Edwardsiella ictaluri and Flavobacterium covae, respectively. Chronic and recurring outbreaks of these bacterial pathogens result in significant economic losses for producers annually. Determining if these pathogens can persist within sediments of commercial ponds is paramount. Experimental persistence trials (PT) were conducted to evaluate the persistence of E. ictaluri and F. covae in pond sediments. Twelve test chambers containing 120 g of sterilized sediment from four commercial catfish ponds were inoculated with either E. ictaluri (S97-773) or F. covae (ALG-00-530) and filled with 8 L of disinfected water. At 1, 2, 4-, 6-, 8-, and 15-days post-inoculation, 1 g of sediment was removed, and colony-forming units (CFU) were enumerated on selective media using 6 × 6 drop plate methods. E. ictaluri population peaked on Day 3 at 6.4 ± 0.5 log10 CFU g-1. Correlation analysis revealed no correlation between the sediment physicochemical parameters and E. ictaluri log10 CFU g-1. However, no viable F. covae colonies were recovered after two PT attempts. Future studies to improve understanding of E. ictaluri pathogenesis and persistence, and potential F. covae persistence in pond bottom sediments are needed.
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Affiliation(s)
- James T Tuttle
- Alabama Fish Farming Center, Greensboro, AL 36744, USA
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Timothy J Bruce
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ian A E Butts
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Luke A Roy
- Alabama Fish Farming Center, Greensboro, AL 36744, USA
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Hisham A Abdelrahman
- Alabama Fish Farming Center, Greensboro, AL 36744, USA
- Department of Veterinary Hygiene and Management, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Benjamin H Beck
- Aquatic Animal Health Research Unit, US Department of Agriculture, Agricultural Research Service, Auburn, AL 36832, USA
| | - Anita M Kelly
- Alabama Fish Farming Center, Greensboro, AL 36744, USA
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
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Lima A, Carolina Barbosa Caetano A, Hurtado Castillo R, Gonçalves Dos Santos R, Lucas Neres Rodrigues D, de Jesus Sousa T, Kato RB, Vinicius Canário Viana M, Cybelle Pinto Gomide A, Figueira Aburjaile F, Tiwari S, Jaiswal A, Gala-García A, Seyffert N, Luiz de Paula Castro T, Brenig B, Matiuzzi da Costa M, Maria Seles Dorneles E, Le Loir Y, Azevedo V. Comparative genomic analysis of ovine and other host associated isolates of Staphylococcus aureus exhibit the important role of mobile genetic elements and virulence factors in host adaptation. Gene 2023; 855:147131. [PMID: 36539044 DOI: 10.1016/j.gene.2022.147131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Staphylococcus aureus is the main etiological agent of mastitis in small ruminants worldwide. This disease has a difficult cure and possible relapse, leading to significant economic losses in production, milk quality and livestock. This study performed comparative genomic analyses between 73 S. aureus genomes from different hosts (human, bovine, pig and others). This work isolated and sequenced 12 of these genomes from ovine. This study contributes to the knowledge of genomic specialization and the role of specific genes in establishing infection in ovine mastitis-associated S. aureus. The genomes of S. aureus isolated from sheep maintained a higher representation when grouped with clonal complexes 130 and 133. The genomes showed high genetic similarity, the species pan-genome consisting of 4200 genes (central = 2008, accessory = 1559 and unique = 634). Among these, 277 unique genes were related to the genomes isolated from sheep, with 39.6 % as hypothetical proteins, 6.4 % as phages, 6.4 % as toxins, 2.9 % as transporters, and 44.7 % as related to other proteins. Furthermore, at the pathogen level, they showed 80 genes associated with virulence factors and 19 with antibiotic resistance shared in almost all isolates. Although S. aureus isolated from ovine showed susceptibility to antimicrobials in vitro, ten genes were predicted to be associated with antibiotic inactivation and efflux pump, suggesting resistance to gentamicin and penicillin. This work may contribute to identifying genes acquired by horizontal transfer and their role in host adaptation, virulence, bacterial resistance, and characterization of strains affecting ovine.
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Affiliation(s)
- Alessandra Lima
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Raquel Hurtado Castillo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Diego Lucas Neres Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Anne Cybelle Pinto Gomide
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flavia Figueira Aburjaile
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Programa de Pós-graduação em Imunologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil.; Programa de Pós-graduação em Microbiologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Arun Jaiswal
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alfonso Gala-García
- Faculdade de Odontologia, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Núbia Seyffert
- Programa de Pós-graduação em Imunologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Thiago Luiz de Paula Castro
- Programa de Pós-graduação em Imunologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany
| | - Mateus Matiuzzi da Costa
- Laboratório de Microbiologia e Imunologia Animal, Campus Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), Petrolina, Pernambuco, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Yves Le Loir
- Institut National de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Paris, France
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Siderophores Produced by the Fish Pathogen Flavobacterium columnare Strain MS-FC-4 Are Not Essential for Its Virulence. Appl Environ Microbiol 2022; 88:e0094822. [PMID: 35969053 PMCID: PMC9469716 DOI: 10.1128/aem.00948-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Flavobacterium columnare causes columnaris disease in wild and aquaculture-reared freshwater fish. F. columnare virulence mechanisms are not well understood, and current methods to control columnaris disease are inadequate. Iron acquisition from the host is important for the pathogenicity and virulence of many bacterial pathogens. F. columnare iron acquisition has not been studied in detail. We identified genes predicted to function in siderophore production for ferric iron uptake. Genes predicted to encode the proteins needed for siderophore synthesis, export, uptake, and regulation were deleted from F. columnare strain MS-FC-4. The mutants were examined for defects in siderophore production, for growth defects in iron-limited conditions, and for virulence against zebrafish and rainbow trout. Mutants lacking all siderophore activity were obtained. These mutants displayed growth defects when cultured under iron-limited conditions, but they retained virulence against zebrafish and rainbow trout similar to that exhibited by the wild type, indicating that the F. columnare MS-FC-4 siderophores are not required for virulence under the conditions tested. IMPORTANCE Columnaris disease, which is caused by Flavobacterium columnare, is a major problem for freshwater aquaculture. Little is known regarding F. columnare virulence factors, and control measures are limited. Iron acquisition mechanisms such as siderophores are important for virulence of other pathogens. We identified F. columnare siderophore biosynthesis, export, and uptake genes. Deletion of these genes eliminated siderophore production and resulted in growth defects under iron-limited conditions but did not alter virulence in rainbow trout or zebrafish. The results indicate that the F. columnare strain MS-FC-4 siderophores are not critical virulence factors under the conditions tested but may be important for survival under iron-limited conditions in natural aquatic environments or aquaculture systems.
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Pereira WA, Mendonça CMN, Urquiza AV, Marteinsson VÞ, LeBlanc JG, Cotter PD, Villalobos EF, Romero J, Oliveira RPS. Use of Probiotic Bacteria and Bacteriocins as an Alternative to Antibiotics in Aquaculture. Microorganisms 2022; 10:microorganisms10091705. [PMID: 36144306 PMCID: PMC9503917 DOI: 10.3390/microorganisms10091705] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
In addition to their use in human medicine, antimicrobials are also used in food animals and aquaculture, and their use can be categorized as therapeutic against bacterial infections. The use of antimicrobials in aquaculture may involve a broad environmental application that affects a wide variety of bacteria, promoting the spread of bacterial resistance genes. Probiotics and bacteriocins, antimicrobial peptides produced by some types of lactic acid bacteria (LAB), have been successfully tested in aquatic animals as alternatives to control bacterial infections. Supplementation might have beneficial impacts on the intestinal microbiota, immune response, development, and/or weight gain, without the issues associated with antibiotic use. Thus, probiotics and bacteriocins represent feasible alternatives to antibiotics. Here, we provide an update with respect to the relevance of aquaculture in the animal protein production sector, as well as the present and future challenges generated by outbreaks and antimicrobial resistance, while highlighting the potential role of probiotics and bacteriocins to address these challenges. In addition, we conducted data analysis using a simple linear regression model to determine whether a linear relationship exists between probiotic dose added to feed and three variables of interest selected, including specific growth rate, feed conversion ratio, and lysozyme activity.
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Affiliation(s)
- Wellison Amorim Pereira
- Microbial Biomolecules Laboratory, Faculty of Pharmaceutical Sciences, São Paulo University, Rua do Lago 250, Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Carlos Miguel N. Mendonça
- Microbial Biomolecules Laboratory, Faculty of Pharmaceutical Sciences, São Paulo University, Rua do Lago 250, Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | | | | | - Jean Guy LeBlanc
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucuman T4000, Argentina
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland, T12 K8AF Cork, Ireland
| | - Elías Figueroa Villalobos
- Nucleus of Research in Food Production, Faculty of Natural Resources, Catholic University of Temuco, Temuco 4780000, Chile
- Correspondence:
| | - Jaime Romero
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutricion y Tecnologia de los Alimentos (INTA), Universidad de Chile, El Libano 5524, Santiago 783090, Chile
| | - Ricardo P. S. Oliveira
- Microbial Biomolecules Laboratory, Faculty of Pharmaceutical Sciences, São Paulo University, Rua do Lago 250, Cidade Universitária, São Paulo 05508-000, SP, Brazil
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8
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Wang N, Yin Y, Xia C, Li Y, Liu J, Li Y. Zn-Enriched Bacillus cereus Alleviates Cd Toxicity in Mirror Carp (Cyprinus carpio): Intestinal Microbiota, Bioaccumulation, and Oxidative Stress. Biol Trace Elem Res 2022; 200:812-821. [PMID: 33740179 DOI: 10.1007/s12011-021-02657-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/25/2021] [Indexed: 11/28/2022]
Abstract
Cadmium (Cd) poisoning in humans and fish represents a significant global problem. Bacillus cereus (B. cereus) is a widely used probiotic in aquaculture. The objective of this study was to evaluate the potential of B. cereus in ameliorating Cd-induced toxicity in mirror carp. The biosorption rate of Zn for the B. cereus in 85.99% was significantly more than five strains. All fishes were exposed for 30 days to dietary ZnCl2 (30mg/kg), waterborne Cd (1 mg/L), and/or dietary Zn-enriched B. cereus (Zn 30mg/kg and 107cfu/g B. cereus). At 15 and 30 days, the fishes were sampled, and bioaccumulation, antioxidant activity, and intestinal microbiota were measured. Waterborne Cd exposure caused marked alterations in the composition of the microbiota. Dietary supplementation with Zn-enriched B. cereus can reduce the changes in the composition of intestinal microbiota in Cd exposure and decrease the pathogenic bacteria of Flavobacterium and Pseudomonas in Zn-enriched B. cereus groups. The results obtained indicate that Zn-enriched B. cereus can provide a significant protective effect on the toxicity of cadmium by inhibiting alterations in the levels of bioaccumulation and antioxidant enzyme including superoxide dismutase (SOD), catalase (CAT), total antioxidant (T-AOC), and malonaldehyde (MDA). Our results suggest that administration of Zn-enriched B. cereus has the potential to combat Cd toxicity in mirror carp.
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Affiliation(s)
- Nan Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- Ministry of Education Laboratory of Animal Production and Quality Security, Jilin Agricultural University, Changchun, 130118, China
| | - Yuwei Yin
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- HongShi Farm of Henan Province, Zhoukou, 466263, China
| | - Changge Xia
- Xinlicheng Reservoir Management Bureau, Changchun, Jilin Province, 130119, People's Republic of China
| | - Yueru Li
- Laboratory of Ginseng and Antler Products Quality and Safety Risk Assessment, Ministry of Agriculture, Changchun, 130118, China
| | - Jia Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
- Ministry of Education Laboratory of Animal Production and Quality Security, Jilin Agricultural University, Changchun, 130118, China
| | - Yuehong Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
- Ministry of Education Laboratory of Animal Production and Quality Security, Jilin Agricultural University, Changchun, 130118, China.
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9
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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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11
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Duman M, Ay H, Altun S, Sahin N, Saticioglu IB. Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout. Int J Syst Evol Microbiol 2021; 71. [PMID: 34296991 DOI: 10.1099/ijsem.0.004903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented isolates, F-60T and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60T and F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain of Flavobacterium crassostreae LPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on blast (ANIb) values for strains F-60T and F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623T while those values for F. crassostreae LPB0076T were obtained as 21.4-21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60T as the type strain (=JCM 34196T=KCTC 82256T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
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12
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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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13
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Sebastião FD, Shahin K, Heckman TI, LaFrentz BR, Griffin MJ, Loch TP, Mukkatira K, Veek T, Richey C, Adkison M, Holt RA, Soto E. Genetic characterization of Flavobacterium columnare isolates from the Pacific Northwest, USA. DISEASES OF AQUATIC ORGANISMS 2021; 144:151-158. [PMID: 33955853 DOI: 10.3354/dao03588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Flavobacterium columnare is the causative agent of columnaris disease. Previous work has demonstrated a high degree of genetic variability among F. columnare isolates, identifying 4 genetic groups (GGs) with some host associations. Herein, a total of 49 F. columnare isolates were characterized, the majority of which were collected from 15 different locations throughout the US Pacific Northwest. Most isolates were collected from 2015-2018 and originated from disease outbreaks in salmonid hatcheries and rearing ponds, sturgeon hatcheries and ornamental fish. Other isolates were part of collections recovered from 1980-2018. Initial identification was confirmed by F. columnare species-specific qPCR. Study isolates were further characterized using a multiplex PCR that differentiates between the 4 currently recognized F. columnare GGs. Multiplex PCR results were supported by repetitive sequence-mediated PCR fingerprinting and gyrB sequence analysis. F. columnare GG1 was the most prevalent (83.7%, n = 41/49), represented by isolates from salmonids (n = 32), white sturgeon (n = 2), channel catfish (n = 1), ornamental goldfish (n = 1), koi (n = 3), wild sunfish (n = 1) and 1 unknown host. Six isolates (12.2%, n = 6/49) were identified as GG3, which were cultured from rainbow trout (n = 3) and steelhead trout (n = 3). Two isolates were identified as GG2 (4.1%, n = 2/49) and were from ornamental fish. No GG4 isolates were cultured in this study. The biological significance of this genetic variability remains unclear, but this variation could have significant implications for fish health management. The results from this study provide baseline data for future work developing strategies to ameliorate columnaris-related losses in the US Pacific Northwest.
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Affiliation(s)
- Fernanda de Sebastião
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, California 95616, USA
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14
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Kitiyodom S, Trullàs C, Rodkhum C, Thompson KD, Katagiri T, Temisak S, Namdee K, Yata T, Pirarat N. Modulation of the mucosal immune response of red tilapia (Oreochromis sp.) against columnaris disease using a biomimetic-mucoadhesive nanovaccine. FISH & SHELLFISH IMMUNOLOGY 2021; 112:81-91. [PMID: 33675991 DOI: 10.1016/j.fsi.2021.02.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Columnaris, a highly contagious bacterial disease caused by Flavobacterium columnare, is recognized as one of the most important infectious diseases in farmed tilapia, especially during the fry and fingerling stages of production. The disease is associated with characteristic lesions in the mucosa of affected fish, particularly their skin and gills. Vaccines delivered via the mucosa are therefore of great interest to scientists developing vaccines for this disease. In the present study, we characterized field isolates of F. columnare obtained from clinical columnaris outbreaks in red tilapia to select an isolate to use as a candidate for our vaccine study. This included characterizing its colony morphology, genotype and virulence status. The isolate was incorporated into a mucoadhesive polymer chitosan-complexed nanovaccine (CS-NE), the efficacy of which was determined by experimentally infecting red tilapia that had been vaccinated with the nanoparticles by immersion. The experimental infection was performed 30-days post-vaccination (dpv), which resulted in 89% of the unvaccinated control fish dying, while the relative percentage survival (RPS) of the CS-NE vaccinated group was 78%. Histology of the mucosal associated lymphoid tissue (MALT) showed a significantly higher presence of leucocytes and a greater antigen uptake by the mucosal epithelium in CS-NE vaccinated fish compared to control fish and whole cell vaccinated fish, respectively, and there was statistically significant up-regulation of IgT, IgM, TNF α, IL1-β and MHC-1 genes in the gill of the CS-NE vaccinated group. Overall, the results of our study confirmed that the CS-NE particles achieved better adsorption onto the mucosal surfaces of the fish, elicited great vaccine efficacy and modulated the MALT immune response better than the conventional whole cell-killed vaccine, demonstrating the feasibility of the mucoadhesive nano-immersion vaccine as an effective delivery system for the induction of a mucosal immune response against columnaris disease in tilapia.
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Affiliation(s)
- Sirikorn Kitiyodom
- Wildlife Exotic Aquatic Animal Pathology-Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Clara Trullàs
- Wildlife Exotic Aquatic Animal Pathology-Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Channarong Rodkhum
- Department of Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kim D Thompson
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
| | - Takayuki Katagiri
- Laboratory of Fish Health Management, Course of Aquatic Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Sasithon Temisak
- Bio Analysis Group, Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani, 12120, Thailand
| | - Katawut Namdee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Teerapong Yata
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Nopadon Pirarat
- Wildlife Exotic Aquatic Animal Pathology-Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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15
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Zhang XT, Yu YY, Xu HY, Huang ZY, Liu X, Cao JF, Meng KF, Wu ZB, Han GK, Zhan MT, Ding LG, Kong WG, Li N, Takizawa F, Sunyer JO, Xu Z. Prevailing Role of Mucosal Igs and B Cells in Teleost Skin Immune Responses to Bacterial Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:1088-1101. [PMID: 33495235 PMCID: PMC11152320 DOI: 10.4049/jimmunol.2001097] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
Abstract
The skin of vertebrates is the outermost organ of the body and serves as the first line of defense against external aggressions. In contrast to mammalian skin, that of teleost fish lacks keratinization and has evolved to operate as a mucosal surface containing a skin-associated lymphoid tissue (SALT). Thus far, IgT representing the prevalent Ig in SALT have only been reported upon infection with a parasite. However, very little is known about the types of B cells and Igs responding to bacterial infection in the teleost skin mucosa, as well as the inductive or effector role of the SALT in such responses. To address these questions, in this study, we analyzed the immune response of trout skin upon infection with one of the most widespread fish skin bacterial pathogens, Flavobacterium columnare This pathogen induced strong skin innate immune and inflammatory responses at the initial phases of infection. More critically, we found that the skin mucus of fish having survived the infection contained significant IgT- but not IgM- or IgD-specific titers against the bacteria. Moreover, we demonstrate the local proliferation and production of IgT+ B cells and specific IgT titers, respectively, within the SALT upon bacterial infection. Thus, our findings represent the first demonstration that IgT is the main Ig isotype induced by the skin mucosa upon bacterial infection and that, because of the large surface of the skin, its SALT probably represents a prominent IgT-inductive site in fish.
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Affiliation(s)
- Xiao-Ting Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yong-Yao Yu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hao-Yue Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhen-Yu Huang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xia Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jia-Feng Cao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Kai-Feng Meng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zheng-Ben Wu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Guang-Kun Han
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Meng-Ting Zhan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Li-Guo Ding
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Wei-Guang Kong
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Nan Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Fumio Takizawa
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui 917-0003, Japan
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104; and
| | - Zhen Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, Hubei, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, Shandong, China
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16
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Declercq AM, Tilleman L, Gansemans Y, De Witte C, Haesebrouck F, Van Nieuwerburgh F, Smet A, Decostere A. Comparative genomics of Flavobacterium columnare unveils novel insights in virulence and antimicrobial resistance mechanisms. Vet Res 2021; 52:18. [PMID: 33579339 PMCID: PMC7881675 DOI: 10.1186/s13567-021-00899-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/18/2021] [Indexed: 11/28/2022] Open
Abstract
This study reports the comparative analyses of four Flavobacterium columnare isolates that have different virulence and antimicrobial resistance patterns. The main research goal was to reveal new insights into possible virulence genes by comparing the genomes of bacterial isolates that could induce tissue damage and mortality versus the genome of a non-virulent isolate. The results indicated that only the genomes of the virulent isolates possessed unique genes encoding amongst others a methyl-accepting chemotaxis protein possibly involved in the initial colonization of tissue, and several VgrG proteins engaged in interbacterial competition. Furthermore, comparisons of genes unique for the genomes of the highly virulent (HV) carp and trout isolates versus the, respectively, low and non-virulent carp and trout isolates were performed. An important part of the identified unique virulence genes of the HV-trout isolate was located in one particular gene region identified as a genomic island. This region contained araC and nodT genes, both linked to pathogenic and multidrug-resistance, and a luxR-gene, functional in bacterial cell-to-cell communication. Furthermore, the genome of the HV-trout isolate possessed unique sugar-transferases possibly important in bacterial adhesion. The second research goal was to obtain insights into the genetic basis of acquired antimicrobial resistance. Several point-mutations were discovered in gyrase-genes of an isolate showing phenotypic resistance towards first and second-generation quinolones, which were absent in isolates susceptible to quinolones. Tetracycline-resistance gene tetA was found in an isolate displaying acquired phenotypic resistance towards oxytetracycline. Although not localized on a prophage, several flanking genes were indicative of the gene’s mobile character.
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Affiliation(s)
- Annelies Maria Declercq
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium. .,Flanders Marine Institute, Wandelaarkaai 7, 8400, Ostend, Belgium. .,Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Annemieke Smet
- Laboratory Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Annemie Decostere
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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17
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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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18
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Kerddee P, Dong HT, Chokmangmeepisarn P, Rodkhum C, Srisapoome P, Areechon N, Del-Pozo J, Kayansamruaj P. Simultaneous detection of scale drop disease virus and Flavobacterium columnare from diseased freshwater-reared barramundi Lates calcarifer. DISEASES OF AQUATIC ORGANISMS 2020; 140:119-128. [PMID: 32759470 DOI: 10.3354/dao03500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Freshwater farming of barramundi Lates calcarifer in Thailand is a growing sector in aquaculture, but mortalities due to infectious diseases are still a major threat to this industry. In 2018, an episode of severe mortality in juvenile barramundi was noted in a freshwater earth pond site. Fish presented with severe gill necrosis, as well as severe cutaneous hemorrhages, scale loss, and discoloration at the base of dorsal fin (saddleback lesions). Histopathology revealed extensive necrosis of skeletal muscle and gill filaments, as well as basophilic inclusion bodies and megalocytosis in muscle, gill, liver, and kidney. Scale drop disease virus (SDDV) infection was subsequently confirmed by virus-specific semi-nested PCR. Further, DNA sequences of the viral major capsid protein (MCP) and ATPase genes had a respective homology of 99.85 and 99.92% with sequences of SDDV infecting barramundi in saltwater culture. Gill necrosis and saddleback lesions are not typical lesions associated with scale drop syndrome. Their presence was explained by Flavobacterium columnare isolation from the gill, followed by positive F. columnare-specific PCR. To our knowledge, this is the first report of SDDV-associated mortality in freshwater-farmed barramundi. Furthermore, this mortality presented as a concurrent infection with SDDV and F. columnare, with typical lesions of both infections.
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Affiliation(s)
- Pattarawit Kerddee
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
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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: 27] [Impact Index Per Article: 6.8] [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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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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21
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Lange MD, Farmer BD, Abernathy J. Vertebrate mucus stimulates biofilm development and upregulates iron acquisition genes in Flavobacterium columnare. JOURNAL OF FISH DISEASES 2020; 43:101-110. [PMID: 31709555 DOI: 10.1111/jfd.13103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
Columnaris disease is responsible for substantial losses throughout the production of many freshwater fish species. One of the ways in which the bacterium Flavobacterium columnare is so effective in initiating disease is through the formation of biofilms on fish skin and gills. To further explore the interaction between host factors and bacterial cells, we assayed the ability of vertebrate mucus to enhance F. columnare biofilm development. Different concentrations of catfish, tilapia and pig mucus (5-60 µg/ml) increased biofilm growth at varying degrees among F. columnare isolates. Our data suggest that vertebrate mucus acts as a signalling molecule for the development of F. columnare biofilms; however, there are clear disparities in how individual isolates respond to different mucus fractions to stimulate biofilms. The expression of iron acquisition genes among two genomovar II isolates showed that ferroxidase, TonB receptor and the siderophore synthetase gene were all significantly upregulated among F. columnare biofilms. Interestingly, the siderophore acetyltransferase gene was only shown to be significantly upregulated in one of the genomovar II isolates. This work provides insight into our understanding of the interaction between F. columnare and vertebrate mucus, which likely contributes to the growth of planktonic cells and the transition into biofilms.
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Affiliation(s)
- Miles D Lange
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, USA
| | - Bradley D Farmer
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, USA
| | - Jason Abernathy
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, AR, USA
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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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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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Bhattacharya M, Malick RC, Mondal N, Patra P, Pal BB, Patra BC, Kumar Das B. Computational characterization of epitopic region within the outer membrane protein candidate in Flavobacterium columnare for vaccine development. J Biomol Struct Dyn 2019; 38:450-459. [PMID: 30744535 DOI: 10.1080/07391102.2019.1580222] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gram-negative bacteria is the main causative agents for columnaris disease outbreak to finfishes. The outer membrane proteins (OMPs) candidate of Flavobacterium columnare bacterial cell served a critical component for cellular invasion targeted to the eukaryotic cell and survival inside the macrophages. Therefore, OMPs considered as the supreme element for the development of promising vaccine against F. columnare. Implies advanced in silico approaches, the predicted 3-D model of targeted OMPs were characterized by the Swiss model server and validated through Procheck programs and Protein Structure Analysis (ProSA) web server. The protein sequences having B-cell binding sites were preferred from sequence alignment; afterwards the B cell epitopes prediction was prepared using the BCPred and amino acid pairs (AAP) prediction algorithms modules of BCPreds. Consequently, the selected antigenic amino acids sequences (B-cell epitopic regions) were analyzed for T-cell epitopes determination (MHC I and MHC II alleles binding sequence) performing the ProPred 1 and ProPred server respectively. The epitopes (9 mer: IKKYEPAPV, YGPNYKWKF and YRGLNVGTS) within the OMPs binds to both of the MHC classes (MHC I and MHC II) and covered highest number of MHC alleles are characterized. OMPs of F. columnare being conserved across serotypes and highly immunogenic for their exposed epitopes on the cell surface as a potent candidate focus to vaccine development for combating the disease problems in commercial aquaculture. The portrayed epitopes might be beneficial for practical designing of abundant peptide-based vaccine development against the columnaris through boosting up the advantageous immune responses.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manojit Bhattacharya
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Ramesh Chandra Malick
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India.,bMicrobiology Division, Regional Medical Research Centre, (ICMR), Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Niladri Mondal
- cCentre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, India
| | - Prasanta Patra
- Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, India
| | - Bibhuti Bhusan Pal
- Microbiology Division, Regional Medical Research Centre, (ICMR), Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Bidhan Chandra Patra
- Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
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25
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Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:9319345. [PMID: 30410420 PMCID: PMC6206559 DOI: 10.1155/2018/9319345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/22/2018] [Indexed: 11/18/2022]
Abstract
Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.
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26
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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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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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Shukla S, Shukla SK, Sharma R. Species identification of aquatic mycobacterium isolates by sequencing and PCR-RFLP of the 16S–23S rDNA internal transcribed spacer (ITS) region. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2017.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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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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The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium columnare. Appl Environ Microbiol 2017; 83:AEM.01769-17. [PMID: 28939608 DOI: 10.1128/aem.01769-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 09/18/2017] [Indexed: 01/21/2023] Open
Abstract
Flavobacterium columnare, a member of the phylum Bacteroidetes, causes columnaris disease in wild and aquaculture-reared freshwater fish. The mechanisms responsible for columnaris disease are not known. Many members of the phylum Bacteroidetes use type IX secretion systems (T9SSs) to secrete enzymes, adhesins, and proteins involved in gliding motility. The F. columnare genome has all of the genes needed to encode a T9SS. gldN, which encodes a core component of the T9SS, was deleted in wild-type strains of F. columnare The F. columnare ΔgldN mutants were deficient in the secretion of several extracellular proteins and lacked gliding motility. The ΔgldN mutants exhibited reduced virulence in zebrafish, channel catfish, and rainbow trout, and complementation restored virulence. PorV is required for the secretion of a subset of proteins targeted to the T9SS. An F. columnare ΔporV mutant retained gliding motility but exhibited reduced virulence. Cell-free spent media from exponentially growing cultures of wild-type and complemented strains caused rapid mortality, but spent media from ΔgldN and ΔporV mutants did not, suggesting that soluble toxins are secreted by the T9SS.IMPORTANCE Columnaris disease, caused by F. columnare, is a major problem for freshwater aquaculture. Little is known regarding the virulence factors produced by F. columnare, and control measures are limited. Analysis of targeted gene deletion mutants revealed the importance of the type IX protein secretion system (T9SS) and of secreted toxins in F. columnare virulence. T9SSs are common in members of the phylum Bacteroidetes and likely contribute to the virulence of other animal and human pathogens.
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