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Abstract Monitoring mortality is an essential strategy for fish health management. Commercial marine finfish sites in British Columbia, Canada, are required to report mortality events (MEs) to Fisheries and Oceans Canada (DFO), which makes these data publicly available. This study aimed to analyze the spatial and temporal patterns of ME composition and total MEs. Between June 2011 and June 2022, 561 MEs were reported. The annual incidence ranged from 1.36 (95% CI: 0.55–2.81) MEs per 100 active site-months in 2013 to 17.98 (95% CI: 13.26–23.84) MEs per 100 active site-months in 2022, with a broadly increasing trend over the period under consideration. The primary causes of MEs were low levels of dissolved oxygen, fish health treatments, and harmful algal blooms (HABs). Both HABs and low dissolved oxygen followed similar patterns, increasing from 2014, peaking in 2019, and declining thereafter. Treatment-related MEs were first reported in 2017 and saw a sharp increase in subsequent years, becoming the leading cause of MEs by 2020. Nearly all treatment-related MEs were linked to sea lice treatments, highlighting the urgent need for adaptive strategies to mitigate these impacts. Sites on the west coast of Vancouver Island demonstrated a higher risk of reporting MEs compared to Mainland sites, likely due to their higher levels of exposure to fluctuating oceanographic conditions. Long-term climate change and persistent periods of warming events, such as marine heat waves, are warming the oceans, altering water parameters, and likely increasing the occurrence and severity of HABs and low dissolved oxygen-related MEs. Further studies are needed to quantify the effects of ocean warming on salmon aquaculture and the resulting increase in fish mortalities.

Abstract Aim This study aimed to summarize the frequency and the antimicrobial susceptibility profiles of the Salmonella serotypes identified from the specimens of companion animals, livestock, avian, wildlife and exotic species within Atlantic Canada. Materials and Methods The retrospective electronic laboratory data of microbiological analyses of a selected subset of samples from 03 January 2012 to 29 December 2021 submitted from various animal species were retrieved. The frequency of Salmonella serotypes identified, and their antimicrobial susceptibility results obtained using the disk diffusion or broth method were analysed. The test results were interpreted according to the Clinical and Laboratory Standards Institute standard. The Salmonella serotypes were identified by slide agglutination (Kauffman–White‐Le‐Minor Scheme) and/or the Whole Genome Sequencing for the Salmonella in silico Serovar Typing Resource–based identification. Results Of the cases included in this study, 4.6% (n = 154) had at least one Salmonella isolate, corresponding to 55 different serovars. Salmonella isolation was highest from exotic animal species (n = 40, 1.20%), followed by porcine (n = 26, 0.78%), and canine (n = 23, 0.69%). Salmonella subsp. enterica serovar Typhimurium was predominant among exotic mammals, porcine and caprine samples, whereas S. Enteritidis was mostly identified in bovine and canine samples. S. Typhimurium of porcine origin was frequently resistant (>70.0%) to ampicillin. In contrast, S. Typhimurium isolates from porcine and caprine samples were susceptible (>70.0%) to florfenicol. S. Oranienburg from equine samples was susceptible to chloramphenicol, but frequently resistant (>90.0%) to azithromycin. In avian samples, S. Copenhagen was susceptible (>90.0%) to florfenicol, whereas Muenchen was frequently resistant (>90.0%) to florfenicol. S. subsp. diarizonae serovar IIIb:61:k:1,5 of ovine origin was resistant (50.0% isolates) to sulfadimethoxine. No significant changes were observed in the antibiotic resistance profiles across the study years. Conclusions This report provides data for surveillance studies, distribution of Salmonella serotypes and their antimicrobial resistance among veterinary specimens of Atlantic Canada.

Host-microbe dynamics are of increasing interest in marine research due to their role in host health and productivity. Changes in the shell microbiome of American lobsters have been associated with epizootic shell disease, a syndrome that is spreading northwards across the eastern U.S. and Canadian Atlantic coast. This study analyzed differences in alpha and beta diversity, as well as differentially abundant taxa, in the shell-associated bacterial community of apparently healthy lobsters from four lobster fishing areas (LFAs) in Atlantic Canada. Over 180 lobsters from New Brunswick, Nova Scotia and Prince Edward Island (PEI) were sampled during seven sampling events over four sampling months. The bacterial community was identified using novel PacBio long-read sequencing, while alpha and beta diversity parameters were analyzed using linear regression models and weighted UniFrac distances. The bacterial richness, diversity and evenness differed by sampling location, sampling month, and molt stage, but not by lobster sex or size, nor sampling depth. Similarly, based on LFA, sampling month, year and lobster molt stage, the shell microbiome differed in microbial community composition with up to 34 out of 162 taxa differing significantly in abundance between sampling groups. This large-scale microbial survey suggests that the shell microbial diversity of apparently healthy lobsters is influenced by spatial and temporal factors such as geographic location, as well as the length of time the carapace is exposed to the surrounding seawater.

Dissolved oxygen (DO), an important water-quality parameter required to support aquatic life, is a critical factor for determining the general biological health of the aquatic ecosystem, and the concentration of DO is a critical factor in determining salmon growth and welfare. This study used longitudinal DO concentration, recorded hourly from 21 aquaculture sites, each with loggers in three separate cages, in four areas in British Columbia, Canada, between 2015 and 2017. The measurements were evaluated based on the recommended DO concentrations for protection of salmonids from hypoxia. Using a two-stage time-series analysis, we described variations in DO concentrations measured over the study period and their associations with environmental factors. Based on the water quality criteria for DO concentration, 42.3, 56.5, and 1.2% of the hourly DO data from the overall 21 aquaculture sites were classified as ‘optimal’, ‘sub-optimal’, and ‘stressed’, respectively. The frequency of hypoxic episodes differed substantially among seasons, aquaculture sites and even among cages within sites. The effects of environmental variables on DO concentration had markedly different patterns depending on the season. Significant associations with DO concentrations were observed for temperatures in the summer and winter months, and both wind direction and remotely-sensed estimated absorption from phytoplankton [aph(443)] in the winter months. The time-series regression model results showed overall (year-round) associations of temperature, wind speed, and aph(443) with DO concentrations. Describing DO measurements at these aquaculture sites provided an understanding of how much they deviated from the recommended DO concentrations, as well as provide baseline information for future water resource planning, including continued and improved water quality monitoring in aquaculture areas.

The shell microbial community of lobsters—a key factor in the development of epizootic shell disease (ESD)—is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.

Measurement(s) Lobster sex • Lobster size • Lobster moult stage • °Brix value of hemolymph • Lobster shell hardness Technology Type(s) Eye • Vernier Caliper • Microscopic assessemnt of pleopods • Refractometer • Physical assessment of lobster carapace Factor Type(s) Year • Month • Lobster fishing area (LFA) • Location • Sampling event • Water depth Sample Characteristic - Organism Homarus americanus Sample Characteristic - Environment marine water body Sample Characteristic - Location Northwest Atlantic Ocean coastal waters of Canada

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.

Abstract Background Hepatitis E virus (HEV) is a zoonotic disease and has been reported around the world. The main objective of this study was to evaluate the sero-prevalence and phylogenetic analysis of HEV in Vietnam. Pig blood and fecal pooled samples were collected to assess the prevalence of HEV. We assessed the true prevalence (TP) of HEV from apparent prevalence (AP) by taking into account the sensitivity and specificity of diagnostic tests using a Bayesian approach. For phylogenetic analysis, the data compared with worldwide HEV reference strains including all eight genotypes (G1-G8) which were identified in previous study. Results A total of 475 sera and 250 fecal pooled samples were collected at slaughterhouses and pig farms from five provinces, in Viet Nam. Overall, the sero-AP of HEV was 58.53% (95% confidence interval: 53.95–62.70) while the sero-TP was slightly higher (65.43, 95% credible interval: 47.19–84.70). In terms of pooled samples, overall, the RNA-AP was 6.80% (95% confidence interval: 4.01–10.66). One strain in Hanoi, two strains in Dak Lak, seven strains in An Giang, four strains in Son La and two strains in Nghe An were isolated. The phylogenetic tree demonstrated that 19 Vietnamese strains were clustered into HEV 3 and 4. Conclusions This study provided evidence that HEV is circulating in domestic pigs in Vietnam. From a public health perspective, it is very important to raise public awareness for high-risk groups (e.g. slaughterhouse workers, pig traders, farmers and market sellers) who have more opportunities to come in contact with pig and contaminated meats.

Accurate monitoring of sea lice levels on salmon farms is critical to the efficient management of louse infestation, as decisions around whether and when to apply treatment depend on an estimation of abundance. However, as with all sampling, the estimated abundance of salmon lice through sampling salmon cannot perfectly represent the abundance on a given farm. While suggestions to improve the accuracy of lice abundance estimates have previously been made, the significance of the accuracy of such estimation has been poorly understood. Understanding the extent of error or bias in sample estimates can facilitate an assessment as to how influential this “imperfect” information will likely be on management decisions, and support methods to mitigate negative outcomes associated with such imperfect estimates. Here, we built a model of a hypothetical Atlantic salmon farm using ordinary differential equations and simulated salmon lice (Lepeophtheirus salmonis) abundance over an entire production cycle, during which salmon were periodically sampled using Monte Carlo approaches that adopted a variety of sample sizes, treatment thresholds, and sampling intervals. The model could thus track two instances of salmon lice abundance: true abundance (based on the underlying model) and monitored abundance (based on the values that could be estimated under different simulated sampling protocols). Treatments, which depend on monitored abundance, could be characterized as early, timely, or late, as a result of over-estimation, appropriate estimation, and under-estimation, respectively. To achieve timely treatment, it is important to delay treatments until true abundance equals some treatment threshold and to execute treatment as soon as this threshold is reached. Adopting larger sample sizes increased the frequency of timely treatments, largely by reducing the incidence of early treatments due to less variance in the monitored abundance. Changes in sampling interval and treatment threshold also influenced the accuracy of abundance estimates and thus the frequency of timely treatments. This study has implications for the manner in which fish should be sampled on salmon farms to ensure accurate salmon lice abundance estimates and consequently the effective application treatment.

Porcine Reproductive and Respiratory Syndrome (PRRS) is a viral swine disease that causes reproductive failure in breeding sows and respiratory distress in growing pigs. The main objectives were to simulate the transmission patterns of PRRS in Uganda using North American Animal Disease Spread Model (NAADSM) and to evaluate the potential effect of prevention and control options such as vaccination and movement control. The median number of infectious farms at the end of 52 weeks for the baseline scenario was 735 (36.75% of the 2,000 farms). The best effects of vaccination were observed in scenarios 60% farm coverage and 80% farm coverage, which resulted in 82 and 98.2% reduction in the median number of infectious farms at the end of the simulation, respectively. Vaccination of all medium and large farms only (33% of the farms) resulted in a 71.2% decrease in the median number of infectious farms at the end of 52 weeks. Movement control (MC) results showed that the median number of infectious farms at the end of 52 weeks decreased by 21.6, 52.3, 79.4, and 92.4% for scenarios MC 20, MC 40, MC 60, and MC 80%, respectively. This study provides new insights to the government of Uganda on how PRRS can be controlled. The large and medium farms need to be prioritized for vaccination, which would be a feasible and effective way to limit the spread of PRRS in Uganda. Scavenging pigs should be confined at all times, whether in the presence or absence of any disease outbreaks.

Tenacibaculosis remains a major health issue for a number of important aquaculture species globally. On the west coast of Canada, yellow mouth (YM) disease is responsible for significant economic loss to the Atlantic salmon industry. While Tenacibaculum maritimum is considered to be the primary agent of clinical YM, the impact of YM on the resident microbial community and their influence on the oral cavity is poorly understood. Using a 16s rRNA amplicon sequencing analysis, the present study demonstrates a significant dysbiosis and a reduction in diversity of the microbial community in the YM affected Atlantic salmon. The microbial community of YM affected fish was dominated by two amplicon sequence variants (ASVs) of T. maritimum, although other less abundant ASVs were also found. Interestingly clinically unaffected (healthy) and YM surviving fish also had a high relative abundance of T. maritimum, suggesting that the presence of T. maritimum is not solely responsible for YM. A statistically significant association was observed between the abundance of T. maritimum and increased abundance of Vibrio spp. within fish displaying clinical signs of YM. Findings from our study provide further evidence that YM is a complex multifactorial disease, characterized by a profound dysbiosis of the microbial community which is dominated by distinct ASVs of T. maritimum. Opportunistic taxa, including Vibrio spp., may also play a role in clinical disease progression.

The American lobster (Homarus americanus) fishery is an economically important commercial activity in Prince Edward Island (PEI), Canada. This fishery requires substantial amounts of bait, resulting in an emerging conservation challenge. To address this issue, an alternative lobster bait, manufactured using fresh and process pelagic fish, and dehydrated fish, corresponding to 75% less fresh pelagic fish than traditional bait has been developed by Bait Masters Inc. The performance of the alternative bait compared to that of the traditional bait was evaluated in a field study. This field trial was conducted in eight lobster fishing bays around PEI, during the 2019 lobster fishing seasons. Bait effectiveness was assessed based on catch-per-unit-effort (total lobsters and number of legal-sized lobsters caught per trap), and the ability to produce a catch. An average of five lobsters per trap were caught for both alternative and traditional baits. The results showed that both lobster bait types performed equally well in all PEI lobster fishing areas studied. This indicates that the alternative bait is a viable replacement for traditional bait, allowing the lobster fishery industry to address the bait-species shortage and ongoing conservation challenge.

Infectious diseases are likely contributing to large-scale declines in chinook salmon stocks in the Pacific Northwest, but the specific agents and diseases involved, and the prevalences in migratory salmon, are mostly unknown. We applied a high-throughput microfluidics platform to screen for 45 infectious agents in 556 out-migrating juvenile chinook salmon, collected from freshwater (FW) and saltwater (SW) locations in the Cowichan River system on Vancouver Island, Canada, during 2014. Nineteen agents (5 bacterial, 2 viral, and 12 parasitic) were detected, with prevalences ranging from 0.2% to 57.6%. Co-infections between Candidatus Branchiomonas cysticola Toenshoff, Kvellestad, Mitchell, Steinum, Falk, Colquhoun & Horn, 2012, Paranucleospora theridion Nylund, Nylund, Watanabe, Arnesen & Kalrsbakk, 2010, and gill chlamydia, all associated with gill disease, were observed in SW samples. We detected agents known to cause large-scale mortalities in Pacific salmon (Ceratonova shasta (Noble, 1950), Parvicapsula minibicornis Kent, Whitaker & Dawe, 1977), and agents only recently reported in Pacific salmon in BC (Ca. B. cysticola, P. theridion, Facilispora margolisi Jones, Prosperi-Porta & Kim, 2012 and Parvicapsula pseudobranchicola Karlsbakk, Saether, Hostlund, Fjellsoy & Nylund, 2002). Wild and hatchery fish were most divergent in agent profiles in FW, with higher agent diversity in wild fish. Differences in prevalence largely dissipated once they converged in the marine environment, although hatchery fish may be infected by a greater diversity of agents sooner after ocean entry by virtue of their more rapid migration from nearshore to offshore environments.

Soft-shelled lobsters pose economic challenges to the lobster industry due to low meat yields and survivability during holding and transportation. Our objectives were to describe spatio-temporal patterns of soft-shelled lobsters in southwestern Nova Scotia, and identify environmental and lobster-related factors associated with shell quality. We analyzed data obtained from a broad-scale, intensive monitoring project and remotely sensed water temperatures. Mixed-effect logistic regression and linear regression methods analyzed more than 130 000 samples collected between 2004 and 2014. The annual overall prevalence of soft-shelled lobsters ranged from 9% to 38% and varied significantly among fishing areas. Shell quality was influenced by sex and size, and in the 2 months before the fishing season, lower water temperatures (4–6 weeks prior to sampling) were associated with reduced prevalence of soft-shells. High annual variability of soft-shell prevalence, that water temperature alone could not explain, suggests that adjusting fishing seasons, arbitrarily, in two fishing areas will not improve the overall shell quality of landed lobsters. Further research is needed to evaluate the effects of long-term temperature and ecosystem changes on lobster health in eastern Canada.

Sea surface temperature (SST) and salinity (SSS) are essential variables at the ocean and atmosphere interface when considering risk factors for disease in farmed and wild fish stocks. Ecological research has witnessed a recent trend in use of digital and satellite technologies, including remote-sensing tools. We explored spatial coverage of remotely-sensed SST and SSS data and compared them with in situ measurements of water temperatures and salinity, which led to suggested adjustments to the remotely-sensed data for its use in aquaculture research. The in situ data were from farms and wild surveillance sites in coastal British Columbia, Canada, from 2003 to 2016. Concurrent SST and SSS values were extracted from remotely-sensed products and compared with 20,513 and 20,038 in situ records for water temperature and salinity, respectively, from 232 different sites. Among nine SST products evaluated, the UKMO OSTIA SST (UK Meteorological Office) had the highest retrieval, and highest concordance correlation coefficient (0.86), highest index of agreement (0.93), fewest missing values, and smallest mean and SD values for bias, when compared to in situ measurements. A mixed linear regression model with UKMO OSTIA SST as the predictor for in situ measurements estimated an adjustment coefficient of 0.89°C for UKMO OSTIA SST. None of the three SSS products evaluated provided appropriate corresponding values for in situ sites, suggesting that spatial coverage for the study area is currently lacking. This study demonstrates that, among SST products, UKMO OSTIA SST is currently best suited for aquaculture studies in coastal BC. The near real-time availability of these data with the estimated adjustment would allow their use in forecast models, surveillance of pathogens, and the creation of risk maps.

African swine fever virus is highly contagious, and mortality rates reach up to 100% depending on the host, virus dose, and the transmission routes. The main objective of this study was to develop a network-based simulation model for the farm-level transmission of ASF virus to evaluate the impact of changes in farm connectivity on ASF spread in Vietnam. A hypothetical population of 1,000 pig farms was created and used for the network-based simulation, where each farm represented a node, and the connection between farms represented an edge. The three scenarios modelled in this way (baseline, low, and high) evaluated the impact of connectivity on disease transmission. The median number of infected farms was higher as the connectivity increased (low: 659, baseline: 968 and high: 993). In addition, we evaluated the impact of the culling strategy on the number of infected farms. A total of four scenarios were simulated depending on the timing of culling after a farm was infected. We found that the timing of culling at 16, 12, 8, and 6 weeks had resulted in a reduction of the number of median infected farms by 81.92%, 91.63%, 100%, and 100%, respectively. Finally, our evaluation of the implication of stability of ties between farms indicated that if the farms were to have the same trading partners for at least six months could significantly reduce the median number of infected farms to two (95th percentile: 413) than in the basic model. Our study showed that pig movements among farms had a significant influence on the transmission dynamics of ASF virus. In addition, we found that the either timing of culling, reduction in the number of trading partners each farm had, or decreased mean contact rate during the outbreaks were essential to prevent or stop further outbreaks.

BackgroundLeptospirosis is an important zoonotic disease with a global distribution, affecting a wide range of mammalian animals and humans. Japanese encephalitis (JE) virus is the major vector-borne zoonotic disease in the Asia-Pacific region. The main objective of this study was to evaluate the seroprevalence of serovar-specific Leptospira and JE in swine from 10 provinces in Vietnam.MethodsSamples were initially collected for swine influenza surveillance from March to April 2017 at large-scale farms (with at least 50 sows and/or 250 fattening pigs) with pigs that tested positive for influenza in the previous surveillance period (2015-16).FindingsA total of 2,000 sera samples were analyzed from 10 provinces. Overall, the seroprevalence of leptospirosis was 21.05% (95% CI: 19.28-22.90) using a cut-off titer of ≥ 1:100. The apparent prevalence of JE was 73.45% (95% CI: 71.46-75.37) while the true prevalence was slightly higher (74.46%, 95% credible interval: 73.73-86.41). We found a relatively high presence of leptospirosis and JE in pigs kept on large farms. Prevalence was comparable with other studies suggesting opportunistic testing of samples collected for other surveillance purposes can be a valuable tool to better understand and prevent the potential transmission of these zoonotic diseases from pigs to people in Vietnam.ConclusionOur study provides evidence to veterinarians and animal health professionals for evidence-based practice such as diagnosis, vaccination and zoonotic control. Further investigation into the possible role of different domestic animals, wildlife species or environmental factors is needed to identify the potential risk factors and transmission routes in Vietnam.

Background: Cellular deterioration occurs with blood sample aging, impacting white blood cell (WBC) identification and differential accuracy. This may be exacerbated in samples from patients experiencing inflammation. Previously, bovine serum albumin (BSA) has been shown to improve cellular preservation of blood and other samples, but the effect on cell preservation in canine blood has not been assessed., Objectives: We aimed to determine the effects of BSA on neutrophil nuclear area when added to potassium ethylene diamine tetra-acetic acid (K 3 -EDTA)-anticoagulated canine blood prior to blood smear preparation. We evaluated the impact of inflammatory leukograms, sample storage temperatures (4° and 20°C), and time on outcomes., Materials and Methods: Canine K 3 -EDTA-anticoagulated blood samples stored at 4° and 20°C were used from unique patients, 10 with and 10 without inflammatory leukograms. Blood smears were prepared from aliquots with or without the addition of 22% BSA at 0, 4, 8, 24, 48, and 72 h. The nuclear area was measured for 25 randomly selected neutrophils per slide using Fiji software. Mixed-effect linear regression modeling was performed (significance: P < 0.05)., Results: Nuclear area increased over time with and without added BSA. Both sample storage temperatures and the presence or absence of an inflammatory leukogram significantly impacted neutrophil nuclear area. Samples with added BSA had slightly higher predicted nuclear areas than those without BSA, but this difference was not statistically significant., Conclusions: BSA did not significantly impact neutrophil nuclear area and did not improve neutrophil preservation in canine blood samples., (© 2023 American Society for Veterinary Clinical Pathology.)

Introduction: The knowledge of animal movements is key to formulating strategic animal disease control policies and carrying out targeted surveillance. This study describes the characteristics of district-level cattle, small ruminant, and pig trade networks in the Cattle Corridor of Uganda between 2019 and 2021., Methodology: The data for the study was extracted from 7,043 animal movement permits (AMPs) obtained from the Ministry of Agriculture, Animal Industry and Fisheries (MAAIF) of Uganda. Most of the data was on cattle (87.2%), followed by small ruminants (11.2%) and pigs (1.6%). Two types of networks representing animal shipments between districts were created for each species based on monthly (n = 30) and seasonal (n = 10) temporal windows. Measures of centrality and cohesiveness were computed for all the temporal windows and our analysis identified the most central districts in the networks., Results: The median in-degree for monthly networks ranged from 0-3 for cattle, 0-1 for small ruminants and 0-1 for pigs. The highest median out-degrees for cattle, small ruminant and pig monthly networks were observed in Lira, Oyam and Butambala districts, respectively. Unlike the pig networks, the cattle and small ruminant networks were found to be of small-world and free-scale topologies., Discussion: The cattle and small ruminant trade movement networks were also found to be highly connected, which could facilitate quick spread of infectious animal diseases across these networks. The findings from this study highlighted the significance of characterizing animal movement networks to inform surveillance, early detection, and subsequent control of infectious animal disease outbreaks., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Hasahya, Thakur, Dione, Kerfua, Mugezi and Lee.)

Simulation models are useful tools to predict and elucidate the effects of factors influencing the occurrence and spread of epidemics in animal populations, evaluate the effectiveness of different control strategies and ultimately inform decision-makers about mitigations to reduce risk. There is a paucity of simulation models to study waterborne transmission of viral and bacterial pathogens in marine environments. We developed a stochastic, spatiotemporal hybrid simulation model (DTU-DADS-Aqua) that incorporates a compartmental model for infection spread within net-pens, an agent-based model for infection spread between net-pens within and between sites and uses seaway distance to inform farm-site hydroconnectivity. The model includes processes to simulate infection transmission and control over surveillance, detection and depopulation measures. Different what-if scenarios can be explored according to the input data provided and user-defined parameter values, such as daily surveillance and depopulation capacities or increased animal mortality that triggers diagnostic testing to detect infection. The latter can be easily defined in a software application, in which results are summarized after each simulation. To demonstrate capabilities of the model, we simulated the spread of infectious salmon anaemia virus (ISAv) for realistic scenarios in a transboundary population of farmed Atlantic salmon (Salmo salar L.) in New Brunswick, Canada and Maine, United States. We assessed the progression of infection in the different simulated outbreak scenarios, allowing for variation in the control strategies adopted for ISAv. Model results showed that improved disease detection, coupled with increasing surveillance visits to farm-sites and increased culling capacity for depopulation of infected net-pens reduced the number of infected net-pens and outbreak duration but the number of ISA-infected farm sites was minimally affected. DTU-DADS-Aqua is a flexible modelling framework, which can be applied to study different infectious diseases in the aquatic environment, allowing the incorporation of alternative transmission and control dynamics. The framework is open-source and available at https://github.com/upei-aqua/DTU-DADS-Aqua., (© 2021 Wiley-VCH GmbH.)

An incursion of infectious salmon anaemia virus (ISAV) was detected in 2020 in southern Newfoundland, Canada. This resulted in an outbreak affecting four marine farms stocking Atlantic salmon (Salmo salar L.) vaccinated against ISAV. This study provides the first description of epidemiologic characteristics of an ISAV outbreak in 2020 and 2021, and detected ISAV variants at the population level. Fish kidneys were screened for ISAV by real-time RT-PCR and non-negative samples were submitted for genotyping and further diagnostic testing. Nine distinct ISAV variants were identified: five European and three North American (NA) HPRΔ ISAV, and one NA-HPR0 ISAV variant. A notable finding was the concurrent detection of both an HPR0 and an HPRΔ ISAV variant in one individual fish. In two farms, both European and NA variants were simultaneously detected, while in the other two farms either NA or European variants were identified, but not both together. Generally, mortality increases followed rises in ISAV prevalence and cycle threshold values on RT-PCR decreased with time. Epidemiologic descriptions of ISAV outbreaks in Atlantic Canada contributes to the understanding of local disease dynamics and identification of changes thereof. Such insights are essential for the strengthening of disease management plans., (© 2022 John Wiley & Sons Ltd.)

Growth in salmon aquaculture over the past two decades has raised concerns regarding the potential impacts of the industry on neighboring ecosystems and wild fish productivity. Despite limited evidence, sea lice have been identified as a major cause for the decline in some wild Pacific salmon populations on the west coast of Canada. We used sea lice count and management data from farmed and wild salmon, collected over 10 years (2007-2016) in the Muchalat Inlet region of Canada, to evaluate the association between sea lice recorded on salmon farms with the infestation levels on wild out-migrating Chum salmon. Our analyses indicated a significant positive association between the sea lice abundance on farms and the likelihood that wild fish would be infested. However, increased abundance of lice on farms was not significantly associated with the levels of infestation observed on the wild salmon. Our results suggest that Atlantic salmon farms may be an important source for the introduction of sea lice to wild Pacific salmon populations, but that the absence of a dose response relationship indicates that any estimate of farm impact requires more careful evaluation of causal inference than is typically seen in the extant scientific literature.