Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry

Bayliss, Sion C.; Verner–Jeffreys, David W.; Ryder, David; Suárez, Rudy; Ramírez, Roxana Olvera; Romero, Jaime; Pascoe, Ben; Sheppard, S K; Godoy, Marcos; Feil, Edward J.

doi:10.1099/mgen.0.000201

Cited by 13 publications

(25 citation statements)

References 23 publications

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“…For instance, rainbow trout and Atlantic salmon are comparatively resistant to BKD [8,9] while two subfamilies of Salmonidae: Thymallinae, and Coregoninae are considered to be particularly sensitive [10]. BKD is a chronic, slow developing infection and has a significant impact on fish populations, both wild and farmed [11]. Mortality occurs mostly in 6 to 12 month-old juvenile salmon and pre-spawning adults [12].…”

Section: Introductionmentioning

confidence: 99%

Renibacterium salmoninarum and Mycobacterium spp.: two bacterial pathogens present at low levels in wild brown trout (Salmo trutta fario) populations in Austrian rivers

et al. 2020

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Background: Renibacterium salmoninarum and Mycobacterium sp. are important bacterial pathogens of fish. R. salmoninarum is the causative agent of bacterial kidney disease, a Gram-positive bacterium mostly known for causing chronic infections in salmonid fish, while multiple species belonging to the Mycobacterium genus have been associated with mycobacteriosis in fish as well as in human. The objective of this study was to determine the prevalence of these two bacterial pathogens in populations of wild brown trout (Salmo trutta fario) in four rivers (Kamp, Wulka, Traun and Ybbs) in Austria. Results: A total of 457 kidney samples were examined for both bacterial agents using nested and conventional PCR as well as bacterial cultivation on KDM-2, histological examination and immunohistochemistry. Molecular evidence showed an estimated prevalence level of 0.94% for R. salmoninarum in 2017 while the bacterium could not be detected in 2018 and histology showed signs consistent with a low-level chronic inflammation in the kidney of infected fish. Similarly, no fish were found positive for Mycobacterium in 2017 but in 2018, the prevalence was found to be 37.03% in the Kamp river (4.08% across all rivers). The sequencing data confirmed that these fish carried Mycobacterium sp. although the precise species of Mycobacterium could not be ascertained. Conclusions: This survey constitutes the first insight into the prevalence rate of R. salmoninarum and Mycobacterium sp. in wild brown trout (Salmo trutta fario) populations in Austria. Both of these pathogens were only detected in the summer months (June and July), which might suggest that the stress linked to increased water temperature could act as stressor factor and contribute to the outbreak of these diseases. The age of the fish might also play a role, especially in the case of Mycobacterium sp. as all the infected fish were in their first summer (June).

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Section: Introductionmentioning

confidence: 99%

Renibacterium salmoninarum and Mycobacterium spp.: two bacterial pathogens present at low levels in wild brown trout (Salmo trutta fario) populations in Austrian rivers

et al. 2020

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“…These authors were able to identify four groups corresponding to the multiple introductions of this bacterium from different countries over the course of the years. This study demonstrated the importance of fish transfer in the international spread of the bacterium [ 1 ].…”

Section: Historical Background and Classificationmentioning

confidence: 87%

“…Similarly, Bayliss et al [ 1 ] applied whole genome sequencing (WGS) to construct a phylogenetic tree for 42 R. salmoninarum isolates identified in Chile between 2012 and 2016. These authors were able to identify four groups corresponding to the multiple introductions of this bacterium from different countries over the course of the years.…”

Section: Historical Background and Classificationmentioning

confidence: 99%

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Renibacterium salmoninarum—The Causative Agent of Bacterial Kidney Disease in Salmonid Fish

2020

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Renibacterium salmoninarum is one of the oldest known bacterial pathogens of fish. This Gram-positive bacterium is the causative agent of bacterial kidney disease, a chronic infection that is mostly known to infect salmonid fish at low temperatures. Externally, infected fish can display exophthalmia as well as blebs on the skin and ulcerations alongside haemorrhages at the base of the fins and alongside the lateral line. Internally, the kidney, heart, spleen and liver can show signs of swelling. Granulomas can be seen on various internal organs, as can haemorrhages, and the organs can be covered with a false membrane. Ascites can also accumulate in the abdominal cavity. The bacterium is generally cultivated on specialized media such as kidney disease medium-1 (KDM-1), KDM-2 and selective kidney disease medium (SKDM), and a diagnostic is performed using molecular tools such as PCRs or real-time quantitative PCRs (RT-qPCRs). Several virulence mechanisms have been identified in R. salmoninarum, in particular the protein p57 that is known to play a role in both agglutination and immunosuppression of the host’s defense mechanisms. Control of the disease is difficult; the presence of asymptomatic carriers complicates the eradication of the disease, as does the ability of the bacterium to gain entrance inside the eggs. Bacterin-killed vaccines have proven to be of doubtful efficacy in controlling the disease, and even more recent application of a virulent environmental relative of R. salmoninarum is of limited efficacy. Treatment by antibiotics such as erythromycin, azithromycin and enrofloxacin can be effective but it is slow and requires prolonged treatment. Moreover, antibiotic-resistant strains have been reported. Despite being known for a long time, there is still much to be discovered about R. salmoninarum, notably regarding its virulence mechanisms and its vaccine potential. Consequently, these gaps in knowledge continue to hinder control of this bacterial disease in aquaculture settings.

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“…In fact, using less water surface, Chile competes to Norway in salmon production [12]. As consequence, Chilean aquaculture has faced several sanitary problems, related with outbreaks of viruses such as infectious pancreatic necrosis virus (IPNV) [13] and infectious salmon anemia virus (ISAV) [14]; bacterial pathogens such as Piscirickettsia salmonis [15], Flavobacterium psychrophilum [16], and Renibacterium salmoninarum [17]; and parasites such as Caligus rogercresseyi [15]. Diseases caused by viruses are one of the great challenges of Chilean salmon farming industry; the first virus being identified in Chile was IPNV, which is highly persistent and causes severe mortality.…”

Section: Microbiological Threats Facing Chilean Aquaculturementioning

confidence: 99%

Application of Metagenomics to Chilean Aquaculture

Tello¹,

Valdés²,

Vargas³

et al. 2020

Metagenomics - Basics, Methods and Applications

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Aquaculture is a rapidly expanding food production sector, facing the challenge of growth both increasing its efficiency and reducing its negative impact on the environment. Metagenomics is an emerging tool in aquaculture that helps to understand the complex host (fish-shellfish)-microbiota-pathogen-environment relationship underlying disease outbreaks, monitoring the dynamics of microbial diversity in farmed animals subject to different environmental conditions or perturbations. As Chile takes an important share of world aquaculture market, this chapter reviews the actual and potential applications of metagenomics to support a sustainable expansion and diversification of Chilean aquaculture. The focus is on (i) the role and function of the gut microbiota in the proper immunostimulation and disease control and (ii) the role of metagenomics in monitoring environmental microbial biodiversity and dynamics in relation to disease persistence and ecosystem stability. We conclude that despite the importance of the aquaculture sector in Chile, the application of metagenomics to deal with disease control and ecosystem preservation is still an emerging field of study. Understanding host (fish-shellfish)microbiota-pathogen-environment diversity of interactions in a more holistic view, i.e., the holobiome approach, could be key to develop rational strategies to improve productivity by increasing resistance to diseases and reducing the use of antibiotics and their negative environmental impact.

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Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry

Cited by 13 publications

References 23 publications

Renibacterium salmoninarum and Mycobacterium spp.: two bacterial pathogens present at low levels in wild brown trout (Salmo trutta fario) populations in Austrian rivers

Renibacterium salmoninarum and Mycobacterium spp.: two bacterial pathogens present at low levels in wild brown trout (Salmo trutta fario) populations in Austrian rivers

Renibacterium salmoninarum—The Causative Agent of Bacterial Kidney Disease in Salmonid Fish

Application of Metagenomics to Chilean Aquaculture

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