Development and validation of main spectral profile for rapid identification of Yersinia ruckeri isolated from Atlantic salmon using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows rapid and reliable identification of microorganisms. The accuracy of bacterial identification using MALDI-TOF MS depends on main spectral profiles (MSPs) provided in a quality-assured commercial reference library, which requires ongoing improvement. This study aimed to develop and validate an in-house MALDI-TOF MS MSP to rapidly identify Yersinia ruckeri isolated from Atlantic salmon (Salmo salar). The novel MSP was prepared using an isolate of Y. ruckeri recovered from Atlantic salmon and confirmed by 16S rRNA gene sequencing. Subsequently, a validation set which comprises 29 isolates of Y. ruckeri were examined from three fishes: Atlantic salmon (Salmo salar) (n = 26), American eel (Anguilla rostrata) (n = 1), and Atlantic cod (Gadus morhua) (n = 2). These isolates were randomly selected from the Atlantic Veterinary College, Aquatic Diagnostic Services Bacteriology Laboratory's culture collection to validate the novel MSP. Analytical sensitivity of MALDI-TOF MS using the novel MSP to identify the validation set was 86.2%. Repeatability was assessed by acquiring spectra from 30 different spots of a randomly-selected isolate of Y. ruckeri, and analyzed spectra from each spot were compared against the novel MSP. The coefficient of variation was 3.3%. The novel MSP clustered with Bruker MSPs (n = 3) of Y. ruckeri in the reference library and did not falsely identify any closely related bacteria to Y. ruckeri. This study reports the development of a novel MSP of high analytical sensitivity and specificity for rapid identification of Y. ruckeri using MALDI-TOF MS.

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.

Unpacking factors influencing antimicrobial use in global aquaculture and their implication for management: a review from a systems perspective.

Global seafood provides almost 20% of all animal protein in diets, and aquaculture is, despite weakening trends, the fastest growing food sector worldwide. Recent increases in production have largely been achieved through intensification of existing farming systems, resulting in higher risks of disease outbreaks. This has led to increased use of antimicrobials (AMs) and consequent antimicrobial resistance (AMR) in many farming sectors, which may compromise the treatment of bacterial infections in the aquaculture species itself and increase the risks of AMR in humans through zoonotic diseases or through the transfer of AMR genes to human bacteria. Multiple stakeholders have, as a result, criticized the aquaculture industry, resulting in consequent regulations in some countries. AM use in aquaculture differs from that in livestock farming due to aquaculture's greater diversity of species and farming systems, alternative means of AM application, and less consolidated farming practices in many regions. This, together with less research on AM use in aquaculture in general, suggests that large data gaps persist with regards to its overall use, breakdowns by species and system, and how AMs become distributed in, and impact on, the overall social-ecological systems in which they are embedded. This paper identifies the main factors (and challenges) behind application rates, which enables discussion of mitigation pathways. From a set of identified key mechanisms for AM usage, six proximate factors are identified: vulnerability to bacterial disease, AM access, disease diagnostic capacity, AMR, target markets and food safety regulations, and certification. Building upon these can enable local governments to reduce AM use through farmer training, spatial planning, assistance with disease identification, and stricter regulations. National governments and international organizations could, in turn, assist with disease-free juveniles and vaccines, enforce rigid monitoring of the quantity and quality of AMs used by farmers and the AM residues in the farmed species and in the environment, and promote measures to reduce potential human health risks associated with AMR.

Correction: Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast.

[This corrects the article DOI: 10.1371/journal.pone.0141475.].

Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast.

Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

Infectious diseases affect marine fisheries and aquaculture economics.

Seafood is a growing part of the economy, but its economic value is diminished by marine diseases. Infectious diseases are common in the ocean, and here we tabulate 67 examples that can reduce commercial species' growth and survivorship or decrease seafood quality. These impacts seem most problematic in the stressful and crowded conditions of aquaculture, which increasingly dominates seafood production as wild fishery production plateaus. For instance, marine diseases of farmed oysters, shrimp, abalone, and various fishes, particularly Atlantic salmon, cost billions of dollars each year. In comparison, it is often difficult to accurately estimate disease impacts on wild populations, especially those of pelagic and subtidal species. Farmed species often receive infectious diseases from wild species and can, in turn, export infectious agents to wild species. However, the impact of disease export on wild fisheries is controversial because there are few quantitative data demonstrating that wild species near farms suffer more from infectious diseases than those in other areas. The movement of exotic infectious agents to new areas continues to be the greatest concern.

Trends in antimicrobial use in Marine Harvest Canada farmed salmon production in British Columbia (2003-2011).

Marine Havest Canada has significantly reduced its antimicrobial usage in salmon farming over the last 8 years. Change has come about largely through improvements in production, health management, and livestock selection. However, antimicrobial treatments are still required for stomatitis and bacterial kidney disease. Lack of efficacious vaccines and the limited number of licensed antimicrobials available to the industry continue to be of concern.

Tendances de l'utilisation des antimicrobiens dans la production de saumons d'élevage de Marine Harvest Canada en Colombie-Britannique (2003­2011). Marine Havest Canada a significativement réduit son utilisation d'antimicrobiens dans l'élevage du saumon au cours des 8 dernières années. Le changement s'est produit surtout à l'aide d'améliorations au niveau de la production, de la gestion de la santé et de la sélection des poissons d'élevage. Cependant, les traitements antimicrobiens sont toujours requis pour la stomatite et la maladie rénale bactérienne. L'absence de vaccins efficaces et le nombre limité d'antimicrobiens homologués disponibles dans l'industrie continuent de susciter des préoccupations.(Traduit par Isabelle Vallières).

Relationship of farm salmon, sea lice, and wild salmon populations.

Increased farm salmon production has heightened concerns about the association between disease on farm and wild fish. The controversy is particularly evident in the Broughton Archipelago of Western Canada, where a high prevalence of sea lice (ectoparasitic copepods) was first reported on juvenile wild pink salmon (Oncorhynchus gorbuscha) in 2001. Exposure to sea lice from farmed Atlantic salmon (Salmo salar) was thought to be the cause of the 97% population decline before these fish returned to spawn in 2002, although no diagnostic investigation was done to rule out other causes of mortality. To address the concern that sea lice from fish farms would cause population extinction of wild salmon, we analyzed 10-20 y of fish farm data and 60 y of pink salmon data. We show that the number of pink salmon returning to spawn in the fall predicts the number of female sea lice on farm fish the next spring, which, in turn, accounts for 98% of the annual variability in the prevalence of sea lice on outmigrating wild juvenile salmon. However, productivity of wild salmon is not negatively associated with either farm lice numbers or farm fish production, and all published field and laboratory data support the conclusion that something other than sea lice caused the population decline in 2002. We conclude that separating farm salmon from wild salmon--proposed through coordinated fallowing or closed containment--will not increase wild salmon productivity and that medical analysis can improve our understanding of complex issues related to aquaculture sustainability.

Recent salmon declines: a result of lost feeding opportunities due to bad timing?

As the timing of spring productivity blooms in near-shore areas advances due to warming trends in global climate, the selection pressures on out-migrating salmon smolts are shifting. Species and stocks that leave natal streams earlier may be favoured over later-migrating fish. The low post-release survival of hatchery fish during recent years may be in part due to static release times that do not take the timing of plankton blooms into account. This study examined the effects of release time on the migratory behaviour and survival of wild and hatchery-reared coho salmon (Oncorhynchus kisutch) using acoustic and coded-wire telemetry. Plankton monitoring and near-shore seining were also conducted to determine which habitat and food sources were favoured. Acoustic tags (n = 140) and coded-wire tags (n = 266,692) were implanted into coho salmon smolts at the Seymour and Quinsam Rivers, in British Columbia, Canada. Differences between wild and hatchery fish, and early and late releases were examined during the entire lifecycle. Physiological sampling was also carried out on 30 fish from each release group. The smolt-to-adult survival of coho salmon released during periods of high marine productivity was 1.5- to 3-fold greater than those released both before and after, and the fish's degree of smoltification affected their downstream migration time and duration of stay in the estuary. Therefore, hatchery managers should consider having smolts fully developed and ready for release during the peak of the near-shore plankton blooms. Monitoring chlorophyll a levels and water temperature early in the spring could provide a forecast of the timing of these blooms, giving hatcheries time to adjust their release schedule.

Evaluation of a reverse transcriptase polymerase chain reaction test and virus isolation on field samples collected for the diagnosis of infectious hematopoietic necrosis virus in cultured Atlantic salmon in British Columbia.

Infectious hematopoietic necrosis virus (IHNV) has been found to cause disease in cultured salmon of the Pacific Northwest region of North America. Diagnosis of IHNV by virus isolation (VI) can take over 2 weeks. Recently, a rapid reverse transcriptase (RT) polymerase chain reaction (PCR) test on fish tissues has been used for diagnosis. Test performances of the VI and RT PCR assays were compared using samples collected in the field. The effect of different storage conditions (tissue frozen with or without RNAlater [Ambion, Inc., Austin, Texas] versus fresh tissue) on the diagnostic tests was also evaluated. Based on the limited number of samples tested, the operating characteristics of RT PCR were very similar to those of VI; therefore, this method is likely suitable for testing field samples for IHNV. The ability of the tests to identify a positive fish ranged from 74% to 89%. Freezing samples at -80 degrees C before testing did not negatively affect the performance of RT PCR or VI. However, due to reduced test performance, RNAlater frozen storage is not recommended without further investigation.