Recovery of Renibacterium salmoninarum from naturally infected salmonine stocks in Michigan using a modified culture protocol

Detection of Nucleic Acids of the Fish Pathogen Yersinia ruckeri from Planktonic and Biofilm Samples with a CRISPR/Cas13a-Based Assay

Yersinia ruckeri is the cause of hemorrhagic septicemia, known as enteric redmouth disease, in salmonid fish species. This bacterial pathogen can form biofilms on abiotic surfaces of aquaculture settings or even on the surfaces of the fish themselves, contributing to their persistence in the aquatic environment. Detection methods for this and other fish pathogens can be time-consuming and lack specificity and sensitivity, limiting timely monitoring, the treatment of microbial infections, and effective control of their transmission in aquaculture settings. Rapid and sensitive detection methods for nucleic acids can be crucial for an appropriate surveillance of bacterial pathogens, and the CRISPR/Cas-based assays have emerged as a good alternative since it has been proven to be a useful tool for the rapid, specific, and sensitive detection of viruses and some bacteria. In this study, we explored the capability of the CRISPR/Cas13a system (SHERLOCK) to specifically detect both DNA and RNA (gene transcripts) from planktonic and biofilm samples of the bacterial fish pathogen Y. ruckeri. The assay was designed to detect the gyrA gene and the small noncoding RNAs (sRNAs) MicA and RprA from planktonic cultures and biofilm samples prepared in marine broth. The specific crRNA designed for these gene targets included a 28 nt specific gene sequence, and a scaffold sequence necessary for Cas13-binding. For all the assays, the nucleic acids obtained from samples were previously subjected to isothermal amplification with the recombinase polymerase amplification (RPA) method and the subsequent T7 transcription of the RPA amplicons. Finally, the detection of nucleic acids of Y. ruckeri was by means of a reporter signal released by the Cas13a collateral RNA cleavage triggered upon target recognition, measured by fluorescence- or lateral-flow-based readouts. This CRISPR/Cas13a-based assay was able to specifically detect both DNA and sRNAs from the Y. ruckeri samples, and the sensitivity was comparable to that obtained with qPCR analysis, highlighting the potential applicability of this CRISPR/Cas13a-based assay for fish pathogen surveillance.

ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES

Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon (Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum, is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20-40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.

Comparison of injection and immersion challenges of Renibacterium salmoninarum strains in Rainbow Trout

OBJECTIVE

Renibacterium salmoninarum is a pathogenic gram-positive bacterium and is the causative agent of bacterial kidney disease (BKD), a malady that mainly impacts salmonid species. Experimental challenges were conducted to assess the virulence and challenge route for select R. salmoninarum strains (CK-90 and ATCC 33739) in Rainbow Trout Oncorhynchus mykiss.

METHODS

The CK-90 strain was intracoelomically injected (100 μL) at a high dose containing 4.80 × 10⁶  CFU/g of fish (optical density at 525 nm [OD₅₂₅ ] = 1.779) and a low dose containing 6.86 × 10⁵  CFU/g of fish (OD₅₂₅  = 1.077); alternatively, fish were immersed in a solution containing 4.5 × 10⁷  CFU/mL of fish (OD₅₂₅  = 0.886). The ATCC 33739 strain (originating from Brook Trout Salvelinus fontinalis) was also included and intracoelomically injected at 3.58 × 10⁵  CFU/g of fish (OD₅₂₅  = 1.431) to discern differences in virulence between the strains.

RESULT

Clinical signs of BKD manifested at approximately 10 d postchallenge, and mortalities began at 19 days postchallenge. To confirm infection and quantify R. salmoninarum antigen load, an enzyme-linked immunosorbent assay (ELISA) was conducted using kidney tissue collected after the challenge. Rainbow Trout that were challenged with CK-90 by injection (both high- and low-dose groups) exhibited significantly higher mortality than fish that were injected with ATCC 33739 or those that were exposed to CK-90 via immersion challenge. The R. salmoninarum p57 (57-kDa protein) antigen was confirmed via ELISA. Antigen load for fish injected with CK-90 (high dose: OD₄₀₅  = 0.71; low dose: OD₄₀₅  = 0.66) was significantly higher than that for fish injected with ATCC 33739 (OD₄₀₅  = 0.34). The CK-90 strain (both high and low doses) was more virulent than ATCC 33739, which caused no mortalities over the 28-days trial. Although there were no mortalities among ATCC 33739 fish, the ELISA confirmed that the R. salmoninarum antigen infiltrated kidney tissue in those fish.

CONCLUSION

The immersion challenge methodology for R. salmoninarum CK-90 was ineffective for inducing mortalities at the examined dose.

Antimicrobial Susceptibility Profiles of Bacteria Commonly Isolated from Farmed Salmonids in Atlantic Canada (2000–2021)

Bacterial infection and antimicrobial resistance are important constraints in the production and sustainability of farmed salmonids. This retrospective study aimed to describe the frequency of bacterial isolates and antimicrobial resistance profiles in salmonid aquaculture in Atlantic Canada. Bacterial isolates and antimicrobial susceptibility testing (AST) results assessed by disk diffusion testing were summarized for 18,776 Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) samples from 2291 unique cases submitted to the Atlantic Veterinary College, Aquatic Diagnostic Services Bacteriology Laboratory from 2000 to 2021. Kidney was the most commonly submitted tissue (60.29%, n = 11,320), and these specimens were mostly submitted as swabs (63.68%, n = 11,957). The most prevalent pathogens detected in these cases were Yersinia ruckeri type 1 (5.54%, n = 127), Renibacterium salmoninarum (2.10%, n = 48), Aeromonas salmonicida (atypical) (1.66%, n = 38), and Pseudomonas fluorescens (1.22%, n = 28). Most bacterial isolates tested (n = 918) showed resistance to florfenicol, oxytetracycline, ormetoprim-sulfadimethoxine, and trimethoprim-sulfamethoxazole, but not to enrofloxacin. This report provides baseline data for antimicrobial surveillance programs that investigate emerging antimicrobial resistance trends in salmonid aquaculture in Atlantic Canada.

Evidence for the existence of extracellular vesicles in Renibacterium salmoninarum and related cytotoxic effects on SHK-1 cells

Extracellular vesicles (EVs) in bacteria have been implicated in invasive and, through enzymes, infective processes. One Gram-positive bacterium lacking any EV research, despite having commercial impacts on the aquaculture industry, is Renibacterium salmoninarum. We addressed this gap in knowledge by utilizing scanning electron microscopy to provide the first reported evidence for the production of EVs by R. salmoninarum strain H-2. Dispersive light scattering detected that the EVs were heterogeneous in size, and the protein compositions were similar to the bacterial membrane and contained the virulent protein factors p22 and p57. The EVs additionally had a concentrated negative charge compared with R. salmoninarum H-2, as determined by Z potential. Finally, these particles seemed to play a role in host invasion in vitro in the salmon head kidney cell line, as demonstrated by the occurrence of a cytotoxic effect within the first 48 hr post-infection. Higher EV concentrations (i.e. 52.6 µg/ml) were more toxic than R. salmoninarum H-2. This information serves as a foundation to develop and test possible uses for R. salmoninarum EVs in salmon aquaculture, inspiring future advances against bacterial kidney disease.

HIGH PREVALENCE OF CIRCULATING ANTIBODIES TO RENIBACTERIUM SALMONINARUM IN SPAWNING ONCORHYNCHUS SPP. FROM LAKE MICHIGAN, USA

Bacterial kidney disease, caused by Renibacterium salmoninarum, threatens salmonids worldwide. Following devastating mortality episodes in Oncorhynchus spp. in Lake Michigan, US, in the 1980s and infection rates >90%, pathogen prevalence has steadily declined to <5% over three decades in the three state-managed stocks. In this study, we sought to determine if the declining infection rates were associated with heightened circulating antibodies in state-managed Oncorhynchus spp. residing in the Lake Michigan watershed. A single-dilution, indirect enzyme-linked immunosorbent assay (ELISA) was modified to detect circulating antibodies against R. salmoninarum. Baseline values were delineated from naive chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (Oncorhynchus mykiss). The assay was first used to assess primary antibody production over a 4-wk period in chinook salmon experimentally infected with R. salmoninarum. Mean antibody response was detected as early as 2 wk postinfection and continued to increase to the end of the observation period. The modified ELISA was then used to detect antibodies in serum samples collected from feral adult chinook salmon, coho salmon (Oncorhynchus kisutch), and steelhead trout (O. mykiss) returning to spawn at Lake Michigan weirs in 2009 and 2013. Results demonstrated that about 80% of feral Oncorhynchus spp. had measurable titers of circulating antibodies to R. salmoninarum. The relative ease and reasonable costs of this modified ELISA makes it a valuable serosurveillance tool for assessing the humoral immune status of feral salmonid populations.

Proposed protocol for performing MIC testing to determine the antimicrobial susceptibility of Renibacterium salmoninarum in Chilean salmon farms

Surveillance of antibiotic resistance is of paramount importance for animal welfare and production. Despite aquaculture being a main source of animal protein, studies on antibiotic susceptibility in fish pathogens are scarce. Renibacterium salmoninarum, the aetiological agent of bacterial kidney disease (BKD), is one of the most common bacterial pathogens affecting salmon farming. In this work, we present an analysis of susceptibility patterns using determinations of minimum inhibitory concentration (MIC) for 65 field isolates, which were collected over seven years (2013-2019) from Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch) farms across southern Chile. The MIC protocol described by the Clinical Laboratory Standards Institute (CLSI) was used, but with microdilution instead of macrodilution and eight instead of four days of incubation. Two laboratories independently conducted analyses to provide data on the epidemiological cut-off values for R. salmoninarum to florfenicol, oxytetracycline and erythromycin. By using two calculation methods, our results provide evidence for an evolving subpopulation of non-wild-type isolates for the macrolide erythromycin, which is consistent with the respective treatment frequencies prescribed against BKD. Contrasting with what was expected, R. salmoninarum isolates were most susceptible to florfenicol and oxytetracycline, both of which are widely used antibiotics currently used in the Chilean salmon industry. The presented findings can serve as a reference for national or international antibiotic surveillance programmes, for both MIC interpretation and to identify emerging resistance to the conventional drugs used in BKD management. Finally, our results indicate that an 8-day incubation period for establishing MIC values of R. salmoninarum should be considered in a future revision of the CLSI guidelines.

Effects of Hatchery Rearing Density, Handling, and Nutrition on Renibacterium salmoninarum Infection Prevalence in Juvenile Chinook Salmon

Bacterial kidney disease, caused by Renibacterium salmoninarum (RS), is a chronic and often fatal disease of salmonid species, and can be particularly harmful to hatchery-reared Chinook Salmon Oncorhynchus tshawytscha. A considerable amount of research has focused on the prevention of vertical and horizontal transmission; however, a comparatively little amount has investigated factors that increase the prevalence of RS infection in captive environments. We evaluated the effects of three common hatchery conditions (handling, nutrition level, and rearing density) on RS infection prevalence. Fish were sampled at 30-d and 60-d postexposure to RS. Of 577 juveniles examined, 65 (11.27%) had anterior kidneys infected with RS. Using a logistic mixed model analysis, we found effects of nutrition level (P = 0.018), handling (P = 0.010), and sampling period (P = 0.003) on the prevalence of RS. The interactions of nutrition and handling (P = 0.008) and nutrition and time (P < 0.001) were also significant. When fed a standard-nutrition diet, proportionately fewer fish were infected with RS when not handled (7.16% versus 0.04%; P = 0.003). Fish in the standard-nutrition group also had a lower prevalence of RS during the second sampling period (4.08% versus 0.08%, respectively; P < 0.001). When not handled, rearing with standard nutrition (11.50% versus 0.04%; P = 0.004) resulted in a reduction in prevalence of RS infection. Additionally, nonhandled fish had a much lower prevalence of RS infection during the second sampling period (2.66% versus 0.21%; P = 0.009). While density did not affect the prevalence of RS infection (P = 0.145), fish reared at a higher density had lower RS infection when not handled (16.48% versus 0.84%, P = 0.004). For fish at a higher density, the RS prevalence was lower during the second sampling period (10.57% versus 1.40%; P = 0.002). Our results suggest that hatchery managers can reduce RS infection prevalence by maintaining an adequate nutritional regime as recommended by the manufacturer. Additionally, the prevalence of RS may be reduced if managers decrease handling of hatchery-reared Chinook Salmon if exposed to RS.

Resurgence of Salmonid Herpesvirus-3 Infection (Epizootic Epitheliotropic Disease) in Hatchery-Propagated Lake Trout in Michigan

Over the past century, populations of Lake Trout Salvelinus namaycush have declined throughout the Great Lakes basin due to overfishing, habitat destruction, introduction of invasive species, and associated recruitment issues from high thiaminase, as well as emerging infectious diseases. To combat these declines, state and federal fishery management agencies undertook substantial stock enhancement efforts, including more stringent regulation of sport and commercial catch limits and increasing hatchery propagation of Lake Trout stocked into Great Lakes basin waterways. One state fish hatchery involved in these rehabilitation efforts experienced mass mortality events in 2012 and 2017. In 2012, following a period of abnormally heavy rain, hatchery staff observed abnormal behavior followed by increased mortalities in two strains of Lake Trout fingerlings, reaching upwards of 20% mortality and totaling a loss of approximately 100,000 fish. In 2017, following another heavy-rain season, 6-8% of 2-year-old Lake Trout experienced morbidity and mortality similar to that observed in 2012. During the 2012 event, Brook Trout Salvelinus fontinalis and splake (Lake Trout × Brook Trout hybrid) reared in flow-through systems receiving water from diseased Lake Trout remained clinically unaffected. Molecular analyses revealed all lots of affected Lake Trout were infected with the salmonid herpesvirus-3 (epizootic epitheliotropic disease virus [EEDV]), a disease that caused complete depopulation of this hatchery in the late 1980s and until 2012 was never again detected in this hatchery or in Michigan. Further sampling detected EEDV in apparently healthy 5-year-old Lake Trout and in wild Mottled Sculpin Cottus bairdii collected in the hatchery source water. The ability of the virus to replicate in tissues of infected fish was verified by exposing naïve Lake Trout to the filtered tissue homogenates of infected fish resulting in similar disease signs. Despite the virus going undetected for many years, these two EEDV episodes clearly demonstrate the continued presence of this deadly herpesvirus in the Great Lakes basin.

Detection accuracy of Renibacterium salmoninarum in Chinook salmon, Oncorhynchus tshawytscha (Walbaum) from non-lethally collected samples: Effects of exposure route and disease severity

Bacterial kidney disease (BKD), caused by Renibacterium salmoninarum, threatens salmonid populations throughout the Northern hemisphere. Many fishery regulatory authorities require ongoing disease monitoring in hatcheries and spawning runs prior to gamete collection to prevent BKD outbreaks and spread. According to diagnostic protocols of the American Fisheries Society-Fish Health Section, monitoring for R. salmoninarum generally consists of lethal sampling of visceral organs from fish. However, non-lethal sampling would be preferable, especially for valuable broodstock or endangered species. In this study, non-lethal sampling methods were evaluated for their ability to detect R. salmoninarum in Chinook salmon (Oncorhynchus tshawytscha) that were experimentally infected via two different routes (e.g., intraperitoneal injection and waterborne immersion) to mimic acute and chronic disease courses. Non-lethal (e.g., blood, mucus, and a urine/feces mixture) and lethal (e.g., kidney and spleen homogenate) samples were collected from challenged and mock-challenged Chinook salmon and the presence of R. salmoninarum was assessed by culture on modified kidney disease medium, nested polymerase chain reaction (nPCR), and semi-quantitative enzyme-linked immunosorbent assay (ELISA). Sensitivity, specificity, and accuracy of lethal and non-lethal samples in detecting R. salmoninarum were calculated using receiver operating characteristic (ROC) analyses. For ROC analyses, true disease status was evaluated under two different assumptions: 1) that lethal samples represented the true disease status and 2) that all experimentally challenged fish were truly infected. We found that sensitivity and specificity of non-lethal samples depended upon time of sampling after experimental infection, sample type, and R. salmoninarum exposure route. Uro-fecal samples had the greatest potential as non-lethal samples compared to mucus and blood. In terms of future monitoring, combining lethal samples tested by ELISA assay with uro-fecal samples tested by nPCR could be the best strategy for detecting R. salmoninarum prevalence in a population as it reduces the overall number of fish required for sampling.

Bacterial infections of Chinook salmon, Oncorhynchus tshawytscha (Walbaum), returning to gamete collecting weirs in Michigan

Herein, we describe the prevalence of bacterial infections in Chinook salmon, Oncorhynchus tshawytscha (Walbaum), returning to spawn in two tributaries within the Lake Michigan watershed. Ten bacterial genera, including Renibacterium, Aeromonas, Carnobacterium, Serratia, Proteus, Pseudomonas, Hafnia, Salmonella, Shewanella and Morganella, were detected in the kidneys of Chinook salmon (n = 480) using culture, serological and molecular analyses. Among these, Aeromonas salmonicida was detected at a prevalence of ∼15%. Analyses revealed significant interactions between location/time of collection and gender for these infections, whereby overall infection prevalence increased greatly later in the spawning run and was significantly higher in females. Renibacterium salmoninarum was detected in fish kidneys at an overall prevalence of >25%. Logistic regression analyses revealed that R. salmoninarum prevalence differed significantly by location/time of collection and gender, with a higher likelihood of infection later in the spawning season and in females vs. males. Chi-square analyses quantifying non-independence of infection by multiple pathogens revealed a significant association between R. salmoninarum and motile aeromonad infections. Additionally, greater numbers of fish were found to be co-infected by multiple bacterial species than would be expected by chance alone. The findings of this study suggest a potential synergism between bacteria infecting spawning Chinook salmon.