1
|
Riborg A, Gulla S, Fiskebeck EZ, Ryder D, Verner-Jeffreys DW, Colquhoun DJ, Welch TJ. Pan-genome survey of the fish pathogen Yersinia ruckeri links accessory- and amplified genes to virulence. PLoS One 2023; 18:e0285257. [PMID: 37167256 PMCID: PMC10174560 DOI: 10.1371/journal.pone.0285257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/18/2023] [Indexed: 05/13/2023] Open
Abstract
While both virulent and putatively avirulent Yersinia ruckeri strains exist in aquaculture environments, the relationship between the distribution of virulence-associated factors and de facto pathogenicity in fish remains poorly understood. Pan-genome analysis of 18 complete genomes, representing established virulent and putatively avirulent lineages of Y. ruckeri, revealed the presence of a number of accessory genetic determinants. Further investigation of 68 draft genome assemblies revealed that the distribution of certain putative virulence factors correlated well with virulence and host-specificity. The inverse-autotransporter invasin locus yrIlm was, however, the only gene present in all virulent strains, while absent in lineages regarded as avirulent. Strains known to be associated with significant mortalities in salmonid aquaculture display a combination of serotype O1-LPS and yrIlm, with the well-documented highly virulent lineages, represented by MLVA clonal complexes 1 and 2, displaying duplication of the yrIlm locus. Duplication of the yrIlm locus was further found to have evolved over time in clonal complex 1, where some modern, highly virulent isolates display up to three copies.
Collapse
Affiliation(s)
- Andreas Riborg
- Norwegian Veterinary Institute, Ås, Norway
- Vaxxinova Norway AS, Bergen, Norway
| | | | | | - David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - David W Verner-Jeffreys
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, United Kingdom
| | - Duncan J Colquhoun
- Norwegian Veterinary Institute, Ås, Norway
- University of Bergen, Bergen, Norway
| | - Timothy J Welch
- National Centre for Cool and Coldwater Aquaculture, USDA-ARS, Leetown, WV, United States of America
| |
Collapse
|
2
|
Wrobel A, Leo JC, Linke D. Overcoming Fish Defences: The Virulence Factors of Yersinia ruckeri. Genes (Basel) 2019; 10:E700. [PMID: 31514317 PMCID: PMC6770984 DOI: 10.3390/genes10090700] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease, a bacterial infection of marine and freshwater fish. The disease mainly affects salmonids, and outbreaks have significant economic impact on fish farms all over the world. Vaccination routines are in place against the major serotypes of Y. ruckeri but are not effective in all cases. Despite the economic importance of enteric redmouth disease, a detailed molecular understanding of the disease is lacking. A considerable number of mostly omics-based studies have been performed in recent years to identify genes related to Y. ruckeri virulence. This review summarizes the knowledge on Y. ruckeri virulence factors. Understanding the molecular pathogenicity of Y. ruckeri will aid in developing more efficient vaccines and antimicrobial compounds directed against enteric redmouth disease.
Collapse
Affiliation(s)
- Agnieszka Wrobel
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Jack C Leo
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK.
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| |
Collapse
|
3
|
Furmanczyk EM, Lipinski L, Dziembowski A, Sobczak A. Genomic and Functional Characterization of Environmental Strains of SDS-Degrading Pseudomonas spp., Providing a Source of New Sulfatases. Front Microbiol 2018; 9:1795. [PMID: 30174655 PMCID: PMC6107682 DOI: 10.3389/fmicb.2018.01795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/17/2018] [Indexed: 01/09/2023] Open
Abstract
Biochemical, physiological and genomic comparisons of two Pseudomonas strains, assigned previously to the Pseudomonas jessenii subgroup, which are efficient SDS-degraders were carried out. A GO enrichment analysis showed that the genomes of SDS-degraders encode more genes connected with bacterial cell wall biosynthesis and alkanesulfonate monooxygenase activity than their closest relatives from the P. jessenii subgroup. A transcriptomic analysis of the most promising strain exposed to detergent suggests that although SDS can be later utilized as a carbon source, in early stages it influences cell envelope integrity, causing a global stress response followed by cell wall modification and induction of repair mechanisms. Genomes of the analyzed strains from P. jessenii group encode multiple putative sulfatases and their enzymatic activity was experimentally verified, which led to the identification of three novel enzymes exhibiting activity toward SDS. Two of the novel alkylsulfatases showed their highest activity at pH 8.0 and the temperature of 60°C or 70°C. One of the enzymes retained its activity even after 1 h of incubation at 60°C. Ions like K+ and Mg2+ enhanced enzymatic activity of both proteins, whereas Cu2+ or EDTA had inhibitory effects.
Collapse
Affiliation(s)
- Ewa M Furmanczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| |
Collapse
|
4
|
Guijarro JA, García-Torrico AI, Cascales D, Méndez J. The Infection Process of Yersinia ruckeri: Reviewing the Pieces of the Jigsaw Puzzle. Front Cell Infect Microbiol 2018; 8:218. [PMID: 29998086 PMCID: PMC6028603 DOI: 10.3389/fcimb.2018.00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
Finding the keys to understanding the infectious process of Yersinia ruckeri was not a priority for many years due to the prompt development of an effective biotype 1 vaccine which was used mainly in Europe and USA. However, the gradual emergence of outbreaks in vaccinated fish, which have been reported since 2003, has awakened interest in the mechanism of virulence in this pathogen. Thus, during the last two decades, a large number of studies have considerably enriched our knowledge of many aspects of the pathogen and its interaction with the host. By means of both conventional and a variety of novel strategies, such as cell GFP tagging, bioluminescence imaging and optical projection tomography, it has been possible to determine three putative Y. ruckeri infection routes, the main point of entry for the bacterium being the gill lamellae. Moreover, a wide range of potential virulence factors have been highlighted by specific gene mutagenesis strategies or genome-wide transposon/plasmid insertion-based screening approaches, such us in vivo expression technology (IVET) and signature tagged mutagenesis (STM). Finally, recent proteomic and whole genomic analyses have allowed many of the genes and systems that are potentially implicated in the organism's pathogenicity and its adaptation to the host environmental conditions to be elucidated. Altogether, these studies contribute to a better understanding of the infectious process of Y. ruckeri in fish, which is crucial for the development of more effective strategies for preventing or treating enteric redmouth disease (ERM).
Collapse
Affiliation(s)
- José A Guijarro
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | - Ana I García-Torrico
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | - Desirée Cascales
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | - Jessica Méndez
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Instituto de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| |
Collapse
|
5
|
Kumar G, Menanteau-Ledouble S, Saleh M, El-Matbouli M. Yersinia ruckeri, the causative agent of enteric redmouth disease in fish. Vet Res 2015; 46:103. [PMID: 26404907 PMCID: PMC4581093 DOI: 10.1186/s13567-015-0238-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/11/2015] [Indexed: 11/30/2022] Open
Abstract
Enteric redmouth disease (ERM) is a serious septicemic bacterial disease of salmonid fish species. It is caused by Yersinia ruckeri, a Gram-negative rod-shaped enterobacterium. It has a wide host range, broad geographical distribution, and causes significant economic losses in the fish aquaculture industry. The disease gets its name from the subcutaneous hemorrhages, it can cause at the corners of the mouth and in gums and tongue. Other clinical signs include exophthalmia, darkening of the skin, splenomegaly and inflammation of the lower intestine with accumulation of thick yellow fluid. The bacterium enters the fish via the secondary gill lamellae and from there it spreads to the blood and internal organs. Y. ruckeri can be detected by conventional biochemical, serological and molecular methods. Its genome is 3.7 Mb with 3406–3530 coding sequences. Several important virulence factors of Y. ruckeri have been discovered, including haemolyin YhlA and metalloprotease Yrp1. Both non-specific and specific immune responses of fish during the course of Y. ruckeri infection have been well characterized. Several methods of vaccination have been developed for controlling both biotype 1 and biotype 2 Y. ruckeri strains in fish. This review summarizes the current state of knowledge regarding enteric redmouth disease and Y. ruckeri: diagnosis, genome, virulence factors, interaction with the host immune responses, and the development of vaccines against this pathogen.
Collapse
Affiliation(s)
- Gokhlesh Kumar
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
| | - Mona Saleh
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
| |
Collapse
|