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Xue M, Huang X, Xue J, He R, Liang G, Liang H, Liu J, Wen C. Comparative Genomic Analysis of Seven Vibrio alginolyticus Strains Isolated From Shrimp Larviculture Water With Emphasis on Chitin Utilization. Front Microbiol 2022; 13:925747. [PMID: 35966654 PMCID: PMC9364117 DOI: 10.3389/fmicb.2022.925747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
The opportunistic pathogen Vibrio alginolyticus is gaining attention because of its disease-causing risks to aquatic animals and humans. In this study, seven Vibrio strains isolated from different shrimp hatcheries in Southeast China were subjected to genome sequencing and subsequent comparative analysis to explore their intricate relationships with shrimp aquaculture. The seven isolates had an average nucleotide identity of ≥ 98.3% with other known V. alginolyticus strains. The species V. alginolyticus had an open pan-genome, with the addition of ≥ 161 novel genes following each new genome for seven isolates and 14 publicly available V. alginolyticus strains. The percentages of core genes of the seven strains were up to 83.1–87.5%, indicating highly conserved functions, such as chitin utilization. Further, a total of 14 core genes involved in the chitin degradation pathway were detected on the seven genomes with a single copy, 12 of which had undergone significant purifying selection (dN/dS < 1). Moreover, the seven strains could utilize chitin as the sole carbon-nitrogen source. In contrast, mobile genetic elements (MGEs) were identified in seven strains, including plasmids, prophages, and genomic islands, which mainly encoded accessory genes annotated as hypothetical proteins. The infection experiment showed that four of the seven strains might be pathogenic because the survival rates of Litopenaeus vannamei postlarvae were significantly reduced (P < 0.05) when compared to the control. However, no obvious correlation was noted between the number of putative virulence factors and toxic effects of the seven strains. Collectively, the persistence of V. alginolyticus in various aquatic environments may be attributed to its high genomic plasticity via the acquisition of novel genes by various MGEs. In view of the strong capability of chitin utilization by diverse vibrios, the timely removal of massive chitin-rich materials thoroughly in shrimp culture systems may be a key strategy to inhibit proliferation of vibrios and subsequent infection of shrimp. In addition, transcontinental transfer of potentially pathogenic V. alginolyticus strains should receive great attention to avoid vibriosis.
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Wang D, Loor A, Bels LD, Stappen GV, den Broeck WV, Nevejan N. Dynamic Immune Response to Vibriosis in Pacific Oyster Crassostrea gigas Larvae during the Infection Process as Supported by Accurate Positioning of GFP-Tagged Vibrio Strains. Microorganisms 2021; 9:microorganisms9071523. [PMID: 34361958 PMCID: PMC8303456 DOI: 10.3390/microorganisms9071523] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022] Open
Abstract
As the immune system is not fully developed during the larval stage, hatchery culture of bivalve larvae is characterized by frequent mass mortality caused by bacterial pathogens, especially Vibrio spp. However, the knowledge is limited to the pathogenesis of vibriosis in oyster larvae, while the immune response to pathogenic microorganisms in this early life stage is still far from being fully elucidated. In this study, we combined green fluorescent protein (GFP)-tagging, histological and transcriptomic analyses to clarify the pathogenesis of experimental vibriosis and the mechanisms used by the host Pacific oyster Crassostrea gigas larvae to resist infection. The Vibrio strains first colonized the digestive system and rapidly proliferated, while only the transcription level of IκB kinase (IKK) and nuclear factor κB (NF-κB) associated with signaling transduction were up-regulated in oyster at 18 h post challenge (hpc). The mRNA levels for integrin β-1, peroxinectin, and heat shock protein 70 (HSP70), which are associated with phagocytosis, cell adhesion, and cytoprotection, were not upregulated until 30 hpc when the necrosis already happened in the larval digestive system. This suggested that the immunity in the early stages of C. gigas is not strong enough to prevent vibriosis and future research may focus on the strengthening of the gastrointestinal immune ability to defend vibriosis in bivalve larvae.
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Affiliation(s)
- Dongdong Wang
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (A.L.); (G.V.S.); (N.N.)
- Correspondence: or
| | - Alfredo Loor
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (A.L.); (G.V.S.); (N.N.)
| | - Lobke De Bels
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (L.D.B.); (W.V.d.B.)
| | - Gilbert Van Stappen
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (A.L.); (G.V.S.); (N.N.)
| | - Wim Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (L.D.B.); (W.V.d.B.)
| | - Nancy Nevejan
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (A.L.); (G.V.S.); (N.N.)
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Papadopoulou A, Garvey K, Hill T, Ramirez-Paredes JG, Monaghan SJ, Baily JL, Davie A, Katsiadaki I, Verner-Jeffreys D, Wallis T, Migaud H, Adams A. Novel atypical Aeromonas salmonicida bath challenge model for juvenile ballan wrasse (Labrus bergylta, Ascanius). J Fish Dis 2021; 44:823-835. [PMID: 33277726 DOI: 10.1111/jfd.13312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Atypical Aeromonas salmonicida (aAs) is currently one of the most routinely recovered bacterial pathogens isolated during disease outbreaks in farmed cleaner fish, ballan wrasse (Labrus bergylta, Ascanius). Vibrionaceae family bacteria have also been isolated from ballan wrasse in Scotland. This study determined the infectivity, pathogenicity and virulence of aAs and Vibrionaceae isolates in juvenile farmed ballan wrasse (n = 50; approx. 2 g) using a bath challenge, and fish were monitored for a period of 16 days. Atypical As caused significant mortalities in contrast to Vibrionaceae isolates. Notably, differential virulence was observed between two aAs vapA type V strains at similar challenge doses. Diseased fish exhibited a systemic infection where aAs was detected in all analysed tissues (liver, spleen and kidney) by PCR and qPCR. Macroscopically, moribund and survivor fish exhibited hepatomegaly and splenomegaly. In moribund and surviving fish, histopathology showed granulomatous hepatitis with eosinophilic granular cells surrounding bacterial colonies and endocarditis along with splenic histiocytosis. This is the first report of a successful aAs bath challenge model for juvenile ballan wrasse which provides an important tool for future studies on vaccine efficacy and immunocompetence.
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Affiliation(s)
- Athina Papadopoulou
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Kathryn Garvey
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Tom Hill
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | - Jose G Ramirez-Paredes
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Ridgeway Biologicals Ltd. a Ceva Santé Animale company, Compton, UK
| | - Sean J Monaghan
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Johanna L Baily
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Andrew Davie
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Ioanna Katsiadaki
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| | | | - Timothy Wallis
- Ridgeway Biologicals Ltd. a Ceva Santé Animale company, Compton, UK
| | - Herve Migaud
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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Guardiola-Avila I, Sánchez-Busó L, Acedo-Félix E, Gomez-Gil B, Zúñiga-Cabrera M, González-Candelas F, Noriega-Orozco L. Core and Accessory Genome Analysis of Vibrio mimicus. Microorganisms 2021; 9:microorganisms9010191. [PMID: 33477474 PMCID: PMC7831076 DOI: 10.3390/microorganisms9010191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 01/21/2023] Open
Abstract
Vibrio mimicus is an emerging pathogen, mainly associated with contaminated seafood consumption. However, little is known about its evolution, biodiversity, and pathogenic potential. This study analyzes the pan-, core, and accessory genomes of nine V. mimicus strains. The core genome yielded 2424 genes in chromosome I (ChI) and 822 genes in chromosome II (ChII), with an accessory genome comprising an average of 10.9% of the whole genome for ChI and 29% for ChII. Core genome phylogenetic trees were obtained, and V. mimicus ATCC-33654 strain was the closest to the outgroup in both chromosomes. Additionally, a phylogenetic study of eight conserved genes (ftsZ, gapA, gyrB, topA, rpoA, recA, mreB, and pyrH), including Vibrio cholerae, Vibrio parilis, Vibrio metoecus, and Vibrio caribbenthicus, clearly showed clade differentiation. The main virulence genes found in ChI corresponded with type I secretion proteins, extracellular components, flagellar proteins, and potential regulators, while, in ChII, the main categories were type-I secretion proteins, chemotaxis proteins, and antibiotic resistance proteins. The accessory genome was characterized by the presence of mobile elements and toxin encoding genes in both chromosomes. Based on the genome atlas, it was possible to characterize differential regions between strains. The pan-genome of V. mimicus encompassed 3539 genes for ChI and 2355 genes for ChII. These results give us an insight into the virulence and gene content of V. mimicus, as well as constitute the first approach to its diversity.
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Affiliation(s)
- Iliana Guardiola-Avila
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico; (I.G.-A.); (E.A.-F.)
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), 46020 Valencia, Spain;
| | - Evelia Acedo-Félix
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico; (I.G.-A.); (E.A.-F.)
| | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD) Mazatlán, Unit for Aquaculture and Environmental Management, Mazatlan, Sinaloa 82112, Mexico;
| | - Manuel Zúñiga-Cabrera
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSSIC), 46980 Paterna, Spain;
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de Valencia, I2SysBio, CIBERESP, 46980 Valencia, Spain;
| | - Lorena Noriega-Orozco
- Guaymas Unit, Centro de Investigación en Alimentación y Desarrollo (CIAD), Guaymas, Sonora 85480, Mexico
- Correspondence: ; Tel.: +52-662-289-2400
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Hansen MJ, Kudirkiene E, Dalsgaard I. Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity. PeerJ 2020; 8:e10451. [PMID: 33344086 PMCID: PMC7719292 DOI: 10.7717/peerj.10451] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A genomes is most likely the reason why vaccines provide good protection from some strains, but not from others. Hopefully, the new genomic data and knowledge provided in this study might help develop an optimized vaccine against V. anguillarum in the future to reduce the use of antibiotics, minimize economic losses and improve the welfare of the fish.
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Affiliation(s)
- Mie Johanne Hansen
- National Institute of Aquatic Resources Technical University of Denmark, Kongens Lyngby, Denmark
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Inger Dalsgaard
- National Institute of Aquatic Resources Technical University of Denmark, Kongens Lyngby, Denmark
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6
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Vasquez I, Cao T, Chakraborty S, Gnanagobal H, O’Brien N, Monk J, Boyce D, Westcott JD, Santander J. Comparative Genomics Analysis of Vibrio anguillarum Isolated from Lumpfish ( Cyclopterus lumpus) in Newfoundland Reveal Novel Chromosomal Organizations. Microorganisms 2020; 8:E1666. [PMID: 33121102 PMCID: PMC7716436 DOI: 10.3390/microorganisms8111666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/31/2022] Open
Abstract
Vibrio anguillarum is a Gram-negative marine pathogen causative agent of vibriosis in a wide range of hosts, including invertebrates and teleosts. Lumpfish (Cyclopterus lumpus), a native fish of the North Atlantic Ocean, is utilized as cleaner fish to control sea lice (Lepeophtheirus salmonis) infestations in the Atlantic salmon (Salmo salar) aquaculture industry. V. anguillarum is one of the most frequent bacterial pathogens affecting lumpfish. Here, we described the phenotype and genomic characteristics of V. anguillarum strain J360 isolated from infected cultured lumpfish in Newfoundland, Canada. Koch's postulates determined in naïve lumpfish showed lethal acute vibriosis in lumpfish. The V. anguillarum J360 genome was shown to be composed of two chromosomes and two plasmids with a total genome size of 4.56 Mb with 44.85% G + C content. Phylogenetic and comparative analyses showed that V. anguillarum J360 is closely related to V. anguillarum strain VIB43, isolated in Scotland, with a 99.8% genome identity. Differences in the genomic organization were identified and associated with insertion sequence elements (ISs). Additionally, V. anguillarum J360 does not possess a pJM1-like plasmid, typically present in virulent isolates from the Pacific Ocean, suggesting that acquisition of this extrachromosomal element and the virulence of V. anguillarum J360 or other Atlantic isolates could increase.
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Affiliation(s)
- Ignacio Vasquez
- Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University, Logy Bay, NL A1C 5S7, Canada; (I.V.); (T.C.); (S.C.); (H.G.)
| | - Trung Cao
- Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University, Logy Bay, NL A1C 5S7, Canada; (I.V.); (T.C.); (S.C.); (H.G.)
| | - Setu Chakraborty
- Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University, Logy Bay, NL A1C 5S7, Canada; (I.V.); (T.C.); (S.C.); (H.G.)
| | - Hajarooba Gnanagobal
- Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University, Logy Bay, NL A1C 5S7, Canada; (I.V.); (T.C.); (S.C.); (H.G.)
| | - Nicole O’Brien
- Department of Fisheries and Land Resources, Aquatic Animal Health Division, Government of Newfoundland and Labrador, St. John’s, NL A1E 3Y5, Canada;
| | - Jennifer Monk
- Dr. Joe Brown Aquatic Research Building (JBARB), Department of Ocean Sciences, Memorial University of Newfoundland, Logy Bay, NL A1C 5S7, Canada; (J.M.); (D.B.)
| | - Danny Boyce
- Dr. Joe Brown Aquatic Research Building (JBARB), Department of Ocean Sciences, Memorial University of Newfoundland, Logy Bay, NL A1C 5S7, Canada; (J.M.); (D.B.)
| | - Jillian D. Westcott
- Fisheries and Marine Institute, Memorial University of Newfoundland, St. John’s, NL A1C 5R3, Canada;
| | - Javier Santander
- Microbial Pathogenesis and Vaccinology Laboratory, Department of Ocean Sciences, Memorial University, Logy Bay, NL A1C 5S7, Canada; (I.V.); (T.C.); (S.C.); (H.G.)
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7
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Coyle NM, Bartie KL, Bayliss SC, Bekaert M, Adams A, McMillan S, Verner-Jeffreys DW, Desbois AP, Feil EJ. A Hopeful Sea-Monster: A Very Large Homologous Recombination Event Impacting the Core Genome of the Marine Pathogen Vibrio anguillarum. Front Microbiol 2020; 11:1430. [PMID: 32695083 PMCID: PMC7336808 DOI: 10.3389/fmicb.2020.01430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Vibrio anguillarum is the causative agent of vibriosis in many species important to aquaculture. We generated whole genome sequence (WGS) data on a diverse collection of 64 V. anguillarum strains, which we supplemented with 41 publicly available genomes to produce a combined dataset of 105 strains. These WGS data resolved six major lineages (L1-L6), and the additional use of multilocus sequence analysis (MLSA) clarified the association of L1 with serotype O1 and Salmonidae hosts (salmon/trout), and L2 with serotypes O2a/O2b/O2c and Gadidae hosts (cod). Our analysis also revealed a large-scale homologous replacement of 526-kb of core genome in an L2 strain from a con-specific donor. Although the strains affected by this recombination event are exclusively associated with Gadidae, we find no clear genetic evidence that it has played a causal role in host specialism. Whilst it is established that Vibrio species freely recombine, to our knowledge this is the first report of a contiguous recombinational replacement of this magnitude in any Vibrio genome. We also note a smaller accessory region of high single nucleotide polymorphism (SNP) density and gene content variation that contains lipopolysaccharide biosynthesis genes which may play a role in determining serotype.
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Affiliation(s)
- Nicola M Coyle
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Kerry L Bartie
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Stuart McMillan
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | | | - Andrew P Desbois
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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8
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Akter T, Lindegaard M, Pedersen K, Strube ML, Ronco T, Dalsgaard I. Sequence Analysis of Plasmids in Vibrio anguillarum from Different Fish and Locations. J Aquat Anim Health 2020; 32:21-27. [PMID: 31986229 DOI: 10.1002/aah.10093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
The genetic diversity of Vibrio anguillarum pJM1-like plasmids was investigated. Plasmids were isolated from 18 V. anguillarum serovar O1 strains collected from different geographic locations and fish species. The plasmids were sequenced and compared with the complete sequence of the published virulence plasmid pJM1. All 18 strains contained pJM1-like plasmids with approximately 65 kbp and all plasmids encoded the virulence genes responsible for the anguibactin iron sequestering system. The plasmids were highly conserved but minor differences were observed in some genes. A single nucleotide polymorphisms (SNPs) analysis showed 0-11 nucleotide variations between each of the 18 plasmids and the pJM1 plasmid. Compared with the sequence of pJM1, nonsynonymous SNPs were identified in fatC, angR, angL, pJM1_p19, and angE. In particular, a mutation found in 15 out of 18 sequenced plasmids in angR has previously been linked to hyperproduction of anguibactin and was found in all the European isolates. However, overall the pJM1-like plasmids isolated from V. anguillarum serovar O1 exhibited a high degree of conservation regardless of their geographical origin or fish species.
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Affiliation(s)
- Tasmina Akter
- National Veterinary Institute, Technical University of Denmark, Anker Engelunds Vej 1, DK-2800, Kongens Lyngby, Denmark
| | - Mikkel Lindegaard
- National Veterinary Institute, Technical University of Denmark, Anker Engelunds Vej 1, DK-2800, Kongens Lyngby, Denmark
| | - Karl Pedersen
- National Veterinary Institute, Technical University of Denmark, Anker Engelunds Vej 1, DK-2800, Kongens Lyngby, Denmark
| | - Mikael L Strube
- National Veterinary Institute, Technical University of Denmark, Anker Engelunds Vej 1, DK-2800, Kongens Lyngby, Denmark
| | - Troels Ronco
- National Veterinary Institute, Technical University of Denmark, Anker Engelunds Vej 1, DK-2800, Kongens Lyngby, Denmark
| | - Inger Dalsgaard
- National Veterinary Institute, Technical University of Denmark, Anker Engelunds Vej 1, DK-2800, Kongens Lyngby, Denmark
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9
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Holm KO, Bækkedal C, Söderberg JJ, Haugen P. Complete Genome Sequences of Seven Vibrio anguillarum Strains as Derived from PacBio Sequencing. Genome Biol Evol 2018; 10:1127-1131. [PMID: 29635365 PMCID: PMC5905569 DOI: 10.1093/gbe/evy074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Abstract
We report here the complete genome sequences of seven Vibrio anguillarum strains isolated from multiple geographic locations, thus increasing the total number of genomes of finished quality to 11. The genomes were de novo assembled from long-sequence PacBio reads. Including draft genomes, a total of 44 V. anguillarum genomes are currently available in the genome databases. They represent an important resource in the study of, for example, genetic variations and for identifying virulence determinants. In this article, we present the genomes and basic genome comparisons of the 11 complete genomes, including a BRIG analysis, and pan genome calculation. We also describe some structural features of superintegrons on chromosome 2 s, and associated insertion sequence (IS) elements, including 18 new ISs (ISVa3 - ISVa20), both of importance in the complement of V. anguillarum genomes.
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Affiliation(s)
- Kåre Olav Holm
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT?-?The Arctic University of Norway, Tromsø, Norway
| | - Cecilie Bækkedal
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT?-?The Arctic University of Norway, Tromsø, Norway
| | - Jenny Johansson Söderberg
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT?-?The Arctic University of Norway, Tromsø, Norway
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT?-?The Arctic University of Norway, Tromsø, Norway
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Vadstein O, Attramadal KJK, Bakke I, Forberg T, Olsen Y, Verdegem M, Giatsis C, Skjermo J, Aasen IM, Gatesoupe FJ, Dierckens K, Sorgeloos P, Bossier P. Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture. Front Microbiol 2018; 9:1820. [PMID: 30210457 PMCID: PMC6119882 DOI: 10.3389/fmicb.2018.01820] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/19/2018] [Indexed: 12/24/2022] Open
Abstract
The availability of high-quality juveniles is a bottleneck in the farming of many marine fish species. Detrimental larvae-microbe interactions are a main reason for poor viability and quality in larval rearing. In this review, we explore the microbial community of fish larvae from an ecological and eco-physiological perspective, with the aim to develop the knowledge basis for microbial management. The larvae are exposed to a huge number of microbes from external and internal sources in intensive aquaculture, but their relative importance depend on the rearing technology used (especially flow-through vs. recirculating systems) and the retention time of the water in the fish tanks. Generally, focus has been on microbes entering the system, but microbes from growth within the system is normally a substantial part of the microbes encountered by larvae. Culture independent methods have revealed an unexpected high richness of bacterial species associated with larvae, with 100-250 operational taxonomic units associated with one individual. The microbiota of larvae changes rapidly until metamorphosis, most likely due to changes in the selection pressure in the digestive tract caused by changes in host-microbe and microbe-microbe interactions. Even though the microbiota of larvae is distinctly different from the microbiota of the water and the live food, the microbiota of the water strongly affects the microbiota of the larvae. We are in the early phase of understanding larvae-microbe interactions in vivo, but some studies with other animals than fish emphasize that we so far have underestimated the complexity of these interactions. We present examples demonstrating the diversity of these interactions. A large variety of microbial management methods exist, focusing on non-selective reduction of microbes, selective enhancement of microbes, and on improvement of the resistance of larvae against microbes. However, relatively few methods have been studied extensively. We believe that there is a lot to gain by increasing the diversity of approaches for microbial management. As many microbial management methods are perturbations of the microbial community, we argue that ecological theory is needed to foresee and test for longer term consequences in microbe-microbe and microbe-larvae interactions. We finally make some recommendations for future research and development.
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Affiliation(s)
- Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kari J. K. Attramadal
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biology, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingrid Bakke
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Torunn Forberg
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Yngvar Olsen
- Department of Biology, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Marc Verdegem
- Aquaculture and Fisheries Group, Wageningen University, Wageningen, Netherlands
| | - Cristos Giatsis
- Aquaculture and Fisheries Group, Wageningen University, Wageningen, Netherlands
| | - Jorunn Skjermo
- Department of Environment and New Resources, SINTEF Ocean, Trondheim, Norway
| | - Inga M. Aasen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | | | - Kristof Dierckens
- Faculty of Bioscience Engineering, Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Patrick Sorgeloos
- Faculty of Bioscience Engineering, Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
| | - Peter Bossier
- Faculty of Bioscience Engineering, Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium
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Balado M, Lages MA, Fuentes-Monteverde JC, Martínez-Matamoros D, Rodríguez J, Jiménez C, Lemos ML. The Siderophore Piscibactin Is a Relevant Virulence Factor for Vibrio anguillarum Favored at Low Temperatures. Front Microbiol 2018; 9:1766. [PMID: 30116232 PMCID: PMC6083037 DOI: 10.3389/fmicb.2018.01766] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/16/2018] [Indexed: 11/13/2022] Open
Abstract
Vibrio anguillarum causes vibriosis, a hemorrhagic septicaemia that affects many cultured marine fish species worldwide. Two catechol siderophores, vanchrobactin and anguibactin, were previously identified in this bacterium. While vanchrobactin is a chromosomally encoded system widespread in all pathogenic and environmental strains, anguibactin is a plasmid-encoded system restricted to serotype O1 strains. In this work, we have characterized, from a serotype O2 strain producing vanchrobactin, a novel genomic island containing a cluster of genes that would encode the synthesis of piscibactin, a siderophore firstly described in the fish pathogen Photobacterium damselae subsp. piscicida. The chemical characterization of this siderophore confirmed that some strains of V. anguillarum produce piscibactin. An in silico analysis of the available genomes showed that this genomic island is present in many of the highly pathogenic V. anguillarum strains lacking the anguibactin system. The construction of single and double biosynthetic mutants for vanchrobactin and piscibactin allowed us to study the contribution of each siderophore to iron uptake, cell fitness, and virulence. Although both siderophores are simultaneously produced, piscibactin constitute a key virulence factor to infect fish, while vanchrobactin seems to have a secondary role in virulence. In addition, a transcriptional analysis of the gene cluster encoding piscibactin in V. anguillarum showed that synthesis of this siderophore is favored at low temperatures, being the transcriptional activity of the biosynthetic genes three-times higher at 18°C than at 25°C. We also show that iron levels and temperature contribute to balance the synthesis of both siderophores.
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Affiliation(s)
- Miguel Balado
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta A Lages
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan C Fuentes-Monteverde
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), Universidade da Coruña, A Coruña, Spain
| | - Diana Martínez-Matamoros
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), Universidade da Coruña, A Coruña, Spain
| | - Jaime Rodríguez
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), Universidade da Coruña, A Coruña, Spain
| | - Carlos Jiménez
- Department of Chemistry, Faculty of Sciences and Center for Advanced Scientific Research (CICA), Universidade da Coruña, A Coruña, Spain
| | - Manuel L Lemos
- Department of Microbiology and Parasitology, Institute of Aquaculture, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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12
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Castillo D, Alvise PD, Xu R, Zhang F, Middelboe M, Gram L. Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits. mSystems 2017; 2:e00001-17. [PMID: 28293680 DOI: 10.1128/mSystems.00001-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 01/30/2023] Open
Abstract
Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.
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13
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Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A, Feil EJ. The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. Front Microbiol 2017; 8:121. [PMID: 28217117 PMCID: PMC5290457 DOI: 10.3389/fmicb.2017.00121] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/17/2017] [Indexed: 01/23/2023] Open
Abstract
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.
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Affiliation(s)
- Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| | | | - Kerry L Bartie
- Institute of Aquaculture, University of Stirling Stirling, UK
| | - David M Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondon, UK; The Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusCambridge, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling Stirling, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
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