Climate change impacts on oyster aquaculture - Part II: Impact assessment and adaptation measures.

The oyster aquaculture sector plays a major role in food security, providing a sustainable way to obtain food and livelihood for coastal and Island nations. Oysters are one of the preferred choices by aquaculturists because of their resilience to harsh climatic conditions. Nonetheless, climate change will continue to pose threats to its culture. Climate-induced hazards such as floods, storms, disease, and invasive species are some of the key factors limiting oyster production globally. A thriving aquaculture industry needs optimal conditions to maximize exploitation. Here, we continue with the review of the impacts of climate change on oyster aquaculture at the global scale, highlighting climate vulnerability assessment. We also propose a framework for modeling oyster responses to future climate scenarios. Furthermore, we explore the health implications of infected oysters on consumer's health. We also identify knowledge gaps and challenges for sustainable oyster production. Additionally, we document mitigation and adaptation measures and future research directions.

Retrospective study on the occurrence of Salmonella serotypes in veterinary specimens of Atlantic Canada (2012-2021).

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.

Differences in diversity and community composition of the shell microbiome of apparently healthy lobsters Homarus americanus across 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.

Climate change impacts on oyster aquaculture - Part I: Identification of key factors.

Oysters are enriched with high-quality protein and are widely known for their exquisite taste. The production of oysters plays an important role in the local economies of coastal communities in many countries, including Atlantic Canada, because of their high economic value. However, because of the changing climatic conditions in recent years, oyster aquaculture faces potentially negative impacts, such as increasing water acidification, rising water temperatures, high salinity, invasive species, algal blooms, and other environmental factors. Although a few isolated effects of climate change on oyster aquaculture have been reported in recent years, it is not well understood how climate change will affect oyster aquaculture from a systematic perspective. In the first part of this study, we present a systematic review of the impacts of climate change and some key environmental factors affecting oyster production on a global scale. The study also identifies knowledge gaps and challenges. In addition, we present key research directions that will facilitate future investigations.

Observed size distribution changes in American lobsters over a 12-year period in southwestern Nova Scotia, Canada.

Size distribution and size frequency information of American lobsters (Homarus americanus) are often used to help estimate the age distributions, and reproductive output for the species and to guide the determination of appropriate minimum legal sizes for the fishery. This study used truncated linear regression models to estimate the effects of sampling year, sampling month, lobster sex and water depth on the lobster size. A dataset of almost 130,000 trap-caught lobsters from the two most important lobster fishing areas of Atlantic Canada collected over a 12-year period (2004-2015) was analyzed. It was shown that truncated models can help to account for biases due to the trap sampling method from vessels and from wharf samplings. There were significant annual and seasonal changes in size distribution, and data collected outside the fishing season showed a significant increase in carapace length in 2014 and 2015, potentially reflecting a northward shift of the range of lobster populations due to more favourable settlement and recruitment habitats. Size also increased in late summer, likely due to moult. Our results demonstrated that landed lobsters, especially females, were smaller than the predicted size-at-maturity in the region (96.5 mm carapace length), which could have long-term repercussions for the stock's reproductive potential.

Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.

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.

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.

Fisheries dataset on moulting patterns and shell quality of American lobsters H. americanus in Atlantic Canada.

Monitoring the moulting phenology of American lobsters (Homarus americanus) is important for maintaining sustainable lobster stocks. Changes in lobster landings can affect reproduction and disease susceptibility. Data on lobster moult indicators and on life-history traits (sex, size) were collated from a twelve-year monitoring program (2004-2015) in six lobster fishing areas in Atlantic Canada. A total of 141,659 lobsters were sampled over 1,195 sampling events using a standardized protocol and commercial lobster fishing traps. The dataset contains pleopod stages, estimated hemolymph protein levels (°Brix values) and shell hardness as well as lobster sex and size. Evaluation of sex ratio dynamics is also possible but existing biases in sampling males and females needs to be noted. This dataset is valuable in terms of inferring spatio-temporal trends in the life history of lobsters, as well as in the analysis of their moult cycle, and hence more generally for fisheries science and marine ecology.

Modeling the Spread of Porcine Reproductive and Respiratory Syndrome Among Pig Farms in Lira District of Northern Uganda.

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.

A stochastic network-based model to simulate farm-level transmission of African swine fever virus in Vietnam.

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.

A stochastic simulation model of African swine fever transmission in domestic pig farms in the Red River Delta region in Vietnam.

The main objectives of this study were to model various scenarios of African swine fever (ASF) virus transmission among farms in Vietnam and to evaluate the impact of control strategies using North American Animal Disease Spread Model (NAADSM). A total of 7,882 pig farms in the Red River Delta (RRD) region were obtained from the General Statistics Office, and then, random points corresponding to the number of farms in each province were generated as exact farm locations were not available. A total of 10 models were developed, including movement control scenarios. In addition, we conducted sensitivity analysis to assess the impact of indirect contact transmission probability (TP). Overall, the indirect contact exhibited an important role in transmitting the ASF virus. In order to minimize ASF transmission between farms, we found that movement restriction needed to reach a certain level (approximately between 50% and 75%) and that the restriction had to be applied in a timely manner. This study offers valuable insight into how ASF virus can be transmitted via direct and indirect contact and controlled among farms under the various simulation scenarios. Our results suggest that the enforcement of movement restriction was an effective control measure as soon as the outbreaks were reported. In addition, this study provided evidence that high standards of biosecurity can contribute to the reduction of disease spread.

Microbiome Profiling Reveals a Microbial Dysbiosis During a Natural Outbreak of Tenacibaculosis (Yellow Mouth) in Atlantic Salmon.

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.

Prevalence and phylogenetic analysis of hepatitis E virus in pigs in Vietnam.

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.

Seroprevalence of leptospirosis and Japanese encephalitis in swine in ten provinces of Vietnam.

BACKGROUND: Leptospirosis 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. METHODS: Samples 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). FINDINGS: A 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. CONCLUSION: Our 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.

Simulation of control scenarios of porcine reproductive and respiratory syndrome in Nghe An Province in Vietnam.

The main objective of this study was to develop various models using North American Animal Disease Spread Model (NAADSM) to simulate the transmission of Porcine reproductive and respiratory syndrome (PRRS) virus between farms in Nghe An Province in Vietnam in order to inform the prevention and control of this important disease. Using real data from the household survey, credible parameters for direct/indirect mean contact rates between different farms were estimated. A total of eleven models were developed, including immunization scenarios. In addition, we conducted sensitive analysis on how the mean contact rates influenced the results. The immunization scenarios showed that a high proportion of pigs in medium size farms needs to be vaccinated in order to reduce the transmission to pigs in small farms under the Vietnamese pig production system. In order to promote the use of vaccinations, incentives (such as a vaccine subsidy) for medium size farms may be needed. It could be the most cost-effective control and prevention strategy for pig diseases in Vietnam. Our study provides insights on how pig diseases can be spread between pig farms via direct and indirect contact in Nghe An under the various hypothetical scenarios. Our results suggest that medium/large farms may play an important role in the transmission of pig diseases.

Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia, Canada (1985-94).

In response to concerns that novel infectious agents were introduced through the movement of eggs as Atlantic salmon aquaculture developed in British Columbia (BC), Canada, we estimated the prevalence of infectious agents in archived return-migrating Sockeye salmon, from before and during aquaculture expansion in BC (1985-94). Of 45 infectious agents assessed through molecular assays in 652 samples, 23 (7 bacterial, 2 viral and 14 parasitic) were detected in liver tissue from six regions in BC. Prevalence ranged from 0.005 to 0.83 and varied significantly by region and year. Agent diversity ranged from 0 to 12 per fish (median 4), with the lowest diversity observed in fish from the Trans-Boundary and Central Coast regions. Agents known to be endemic in Sockeye salmon in BC, including Flavobacterium psychrophilum, Infectious haematopoietic necrosis virus, Ceratonova shasta and Parvicapsula minibicornis, were commonly observed. Others, such as Kudoa thyrsites and Piscirikettsia salmonis, were also detected. Surprisingly, infectious agents described only recently in BC salmon, Ca. Branchiomonas cysticola, Parvicapsula pseudobranchicola and Paranucleospora theridion, were also detected, indicating their potential presence prior to the expansion of the aquaculture industry. In general, our data suggest that agent distributions may not have substantially changed because of the salmon aquaculture industry.

Development of a network based model to simulate the between-farm transmission of the porcine reproductive and respiratory syndrome virus.

Contact structure within a population can significantly affect the outcomes of infectious disease spread models. The objective of this study was to develop a network based simulation model for the between-farm spread of porcine reproductive and respiratory syndrome virus to assess the impact of contact structure on between-farm transmission of PRRS virus. For these farm level models, a hypothetical population of 500 swine farms following a multistage production system was used. The contact rates between farms were based on a study analyzing movement of pigs in Canada, while disease spread parameters were extracted from published literature. Eighteen distinct scenarios were designed and simulated by varying the mode of transmission (direct versus direct and indirect contact), type of index herd (farrowing, nursery and finishing), and the presumed network structures among swine farms (random, scale-free and small-world). PRRS virus was seeded in a randomly selected farm and 500 iterations of each scenario were simulated for 52 weeks. The median epidemic size by the end of the simulated period and percentage die-out for each scenario, were the key outcomes captured. Scenarios with scale-free network models resulted in the largest epidemic sizes, while scenarios with random and small-world network models resulted in smaller and similar epidemic sizes. Similarly, stochastic die-out percentage was least for scenarios with scale-free networks followed by random and small-world networks. Findings of the study indicated that incorporating network structures among the swine farms had a considerable impact on the spread of PRRS virus, highlighting the importance of understanding and incorporating realistic contact structures when developing infectious disease spread models for similar populations.

Simulation of between-farm transmission of porcine reproductive and respiratory syndrome virus in Ontario, Canada using the North American Animal Disease Spread Model.

Porcine reproductive and respiratory syndrome (PRRS), a viral disease of swine, has major economic impacts on the swine industry. The North American Animal Disease Spread Model (NAADSM) is a spatial, stochastic, farm level state-transition modeling framework originally developed to simulate highly contagious and foreign livestock diseases. The objectives of this study were to develop a model to simulate between-farm spread of a homologous strain of PRRS virus in Ontario swine farms via direct (animal movement) and indirect (sharing of trucks between farms) contacts using the NAADSM and to compare the patterns and extent of outbreak under different simulated conditions. A total of 2552 swine farms in Ontario province were allocated to each census division of Ontario and geo-locations of the farms were randomly generated within the agriculture land of each Census Division. Contact rates among different production types were obtained using pig movement information from four regions in Canada. A total of 24 scenarios were developed involving various direct (movement of infected animals) and indirect (pig transportation trucks) contact parameters in combination with alternating the production type of the farm in which the infection was seeded. Outbreaks were simulated for one year with 1000 replications. The median number of farms infected, proportion of farms with multiple outbreaks and time to reach the peak epidemic were used to compare the size, progression and extent of outbreaks. Scenarios involving spread only by direct contact between farms resulted in outbreaks where the median percentage of infected farms ranged from 31.5 to 37% of all farms. In scenarios with both direct and indirect contact, the median percentage of infected farms increased to a range from 41.6 to 48.6%. Furthermore, scenarios with both direct and indirect contact resulted in a 44% increase in median epidemic size when compared to the direct contact scenarios. Incorporation of both animal movements and the sharing of trucks within the model indicated that the effect of direct and indirect contact may be nonlinear on outbreak progression. The increase of 44% in epidemic size when indirect contact, via sharing of trucks, was incorporated into the model highlights the importance of proper biosecurity measures in preventing transmission of the PRRS virus. Simulation of between-farm spread of the PRRS virus in swine farms has highlighted the relative importance of direct and indirect contact and provides important insights regarding the possible patterns and extent of spread of the PRRS virus in a completely susceptible population with herd demographics similar to those found in Ontario, Canada.