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Antimicrobial resistance (AMR) is a growing threat to human and animal health. However, in aquatic animals—the fastest growing food animal sector globally—AMR trends are seldom documented, particularly in Asia, which contributes two-thirds of global food fish production. Here, we present a systematic review and meta-analysis of 749 point prevalence surveys reporting antibiotic-resistant bacteria from aquatic food animals in Asia, extracted from 343 articles published in 2000–2019. We find concerning levels of resistance to medically important antimicrobials in foodborne pathogens. In aquaculture, the percentage of antimicrobial compounds per survey with resistance exceeding 50% (P50) plateaued at 33% [95% confidence interval (CI) 28 to 37%] between 2000 and 2018. In fisheries, P50 decreased from 52% [95% CI 39 to 65%] to 22% [95% CI 14 to 30%]. We map AMR at 10-kilometer resolution, finding resistance hotspots along Asia’s major river systems and coastal waters of China and India. Regions benefitting most from future surveillance efforts are eastern China and India. Scaling up surveillance to strengthen epidemiological evidence on AMR and inform aquaculture and fisheries interventions is needed to mitigate the impact of AMR globally. Trends in antimicrobial resistance (AMR) in aquatic food animals are seldom documented, particularly in Asia. Here, Schar et al. review 749 point prevalence surveys, describing AMR trends in Asian aquaculture and fisheries over two decades, and identifying resistance hotspots as well as regions that would benefit most from future surveillance efforts.

Mycobacterium marinum is an opportunistic pathogen inducing infection in fresh and marine water fish. This pathogen causes necrotizing granuloma like tuberculosis, morbidity and mortality in fish. The cell wall-associated lipid phthiocerol dimycocerosates, phenolic glycolipids and ESAT-6 secretion system 1 (ESX-1) are the conserved virulence determinant of the organism. Human infections with Mycobacterium marinum hypothetically are classified into four clinical categories (type I-type IV) and have been associated with the exposure of damaged skin to polluted water from fish pools or contacting objects contaminated with infected fish. Fish mycobacteriosis is clinically manifested and characterized in man by purple painless nodules, liable to develop into superficial crusting ulceration with scar formation. Early laboratory diagnosis of M. marinum including histopathology, culture and PCR is essential and critical as the clinical response to antibiotics requires months to be attained. The pathogenicity and virulence determinants of M. marinum need to be thoroughly and comprehensively investigated and understood. In spite of accumulating information on this pathogen, the different relevant data should be compared, connected and globally compiled. This article is reviewing the epidemiology, virulence factors, diagnosis and disease management in fish while casting light on the potential associated public health hazards.

In 2015, Singapore had the first and only reported foodborne outbreak of invasive disease caused by the group B Streptococcus (GBS; Streptococcus agalactiae). Disease, predominantly septic arthritis and meningitis, was associated with sequence type (ST)283, acquired from eating raw farmed freshwater fish. Although GBS sepsis is well-described in neonates and older adults with co-morbidities, this outbreak affected non-pregnant and younger adults with fewer co-morbidities, suggesting greater virulence. Before 2015 ST283 had only been reported from twenty humans in Hong Kong and two in France, and from one fish in Thailand. We hypothesised that ST283 was causing region-wide infection in Southeast Asia. We performed a literature review, whole genome sequencing on 145 GBS isolates collected from six Southeast Asian countries, and phylogenetic analysis on 7,468 GBS sequences including 227 variants of ST283 from humans and animals. Although almost absent outside Asia, ST283 was found in all invasive Asian collections analysed, from 1995 to 2017. It accounted for 29/38 (76%) human isolates in Lao PDR, 102/139 (73%) in Thailand, 4/13 (31%) in Vietnam, and 167/739 (23%) in Singapore. ST283 and its variants were found in 62/62 (100%) tilapia from 14 outbreak sites in Malaysia and Vietnam, in seven fish species in Singapore markets, and a diseased frog in China. GBS ST283 is widespread in Southeast Asia, where it accounts for a large proportion of bacteraemic GBS, and causes disease and economic loss in aquaculture. If human ST283 is fishborne, as in the Singapore outbreak, then GBS sepsis in Thailand and Lao PDR is predominantly a foodborne disease. However, whether transmission is from aquaculture to humans, or vice versa, or involves an unidentified reservoir remains unknown. Creation of cross-border collaborations in human and animal health are needed to complete the epidemiological picture.

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.

Tilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses. In situ hybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease. IMPORTANCE The economic impact of worldwide trade in tilapia is estimated at$7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development. The economic impact of worldwide trade in tilapia is estimated at $ 7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development.

Understanding the effects of anthropogenic changes on fish disease is vital for supporting mitigative actions for fisheries population recovery. The Lake Washington watershed in the Pacific Northwestern United States is influenced by high urban development and climate change, compromising the sustainability of anadromous salmon. We investigated Ceratonova shasta , a myxozoan parasite, in Chinook Salmon Oncorhynchus tshawytscha to determine the impacts of C. shasta -induced enteronecrosis during salmon freshwater migrations within this watershed. All sampled adult Chinook Salmon returning to an enhancement hatchery to spawn were infected with genotype I C. shasta with a high prevalence of severe enteritis and enteronecrosis. Parasite loads and associated pathology were more severe in adult fish succumbing to prespawn mortality than in fish that spawned. Natural prespawn mortality of Chinook Salmon in the Cedar River was also associated with high C. shasta loads. Sentinel exposure studies with Chinook Salmon juveniles in the spring and fall demonstrated high levels of C. shasta genotype II actinospores in the Lake Washington Ship Canal, a human engineered canal that salmon must traverse in their freshwater migrations from the Puget Sound. The sentinel juvenile Chinook Salmon succumbed to clinical disease and high mortality from genotype II C. shasta , suggesting that these stocks have high susceptibility to this genotype. The results show that both genotypes I and II pose disease risks to adult and juvenile stages of Chinook Salmon in the watershed, and that the Lake Washington Ship Canal could be a C. shasta ‘hot spot’ for genotype II that may increase disease risk for juveniles during smolt emigration.

The infective stage of Anisakidae nematodes responsible for allergic reactions in humans is found in a variety of edible fish and cephalopods. The identification of geographical regions that are high risk for infected seafood may help prevent allergic reactions in humans. Despite an abundance of published literature which has identified anisakid larvae in an array of edible seafood as well as scattered reports of human allergic anisakiasis, the relationship between the two has not been fully explored. Therefore, a systematic spatio-temporal study was conducted to determine the prevalence of Anisakis spp. in fish from January 2000 to August 2020 firstly to explore the relationship between fish infection and cases of allergic anisakiasis and secondly to use fish infection data to map potential allergic anisakiasis ‘hot spots’. A systematic literature search for original English text articles was conducted through search engines, Web of Science, Scopus, PubMed, Science Direct and Google Scholar. Out of 3228 articles which describe anisakid infection in fish, 264 were used for data extraction. Of 904 articles describing allergic anisakiasis, 37 were used for data extraction. A qualitative summary of the extracted data was performed using equal interval method (ArcMap software) in order to compare the global distribution of Anisakis-infected fish. Of the 152-identified fish hosts, five families were most commonly infected with Anisakis spp. These included Lophiidae (86.9%), Trichiuridae (77.05%), Zeidae (70.9%), Merlucciidae (67.8%) and Gadidae (56.8%). The hot spot areas for allergic anisakiasis were North and northeast of Atlantic Ocean, southwest of USA, west of Mexico, south of Chile, east of Argentina, Norway, UK and west of Iceland (confidence 99%). The highest rate of allergic anisakiasis was in Portugal and Norway with the prevalence rate of 18.45–22.50%. Allergologists should consider allergic anisakiasis as a public health issue particularly in high-risk countries where high prevalences in fish have been demonstrated.

Infectious hematopoietic necrosis virus (IHNV, Rhabdoviridae), is the causative agent of infectious hematopoietic necrosis (IHN), a disease notifiable to the World Organisation for Animal Health, and various countries and trading areas (including the European Union). IHNV is an economically important pathogen causing clinical disease and mortalities in a wide variety of salmonid species, including the main salmonid species produced in aquaculture, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). We reviewed the scientific literature on IHNV on a range of topics, including geographic distribution; host range; conditions required for infection and clinical disease; minimum infectious dose; subclinical infection; shedding of virus by infected fish; transmission via eggs; diagnostic tests; pathogen load and survival of IHNV in host tissues. This information is required for a range of purposes including import risk assessments; parameterisation of disease models; for surveillance planning; and evaluation of the chances of eradication of the pathogen to name just a few. The review focuses on issues that are of relevance for the European context, but many of the data summarised have relevance to IHN globally. Examples for application of the information is presented and data gaps highlighted.

Climate change affects marine ecosystems by promoting pathogens that threaten key fish populations. To protect these, monitoring programs must adapt to manage threats and sustain fisheries. Here, we combined traditional PCR methods and transcriptomic analysis from a single drop of blood stored on FTA cards to determine the prevalence of erythrocytic necrosis virus (ENV) and the Ichthyophonus parasite in the Atlantic herring population. Across 2023–2024, 33% of individual blood samples tested positive for ENV and 10% for Ichthyophonus by PCR, with ENV-positive fish more frequently found in estuarine and coastal areas. Spatial analyses revealed a clustered distribution for ENV and a more sporadic occurrence of Ichthyophonus . RNA-Seq detected viral RNA fragments in ENV PCR-positive fish, revealing high levels of viral transcripts consistent with active viral replication. However, no significant changes were observed in the host blood transcriptome between infected and uninfected individuals, suggesting that ENV replication may proceed with limited systemic host transcriptional response under subclinical conditions. Overall, our study provides the first comprehensive baseline on the prevalence and molecular activity of ENV and Ichthyophonus in Atlantic herring, demonstrating the power of FTA-based RNA-Seq diagnostics to uncover hidden infections and informing future surveillance and management of wild fish populations.

The Norwegian government has decided that the aquaculture industry shall grow, provided that the growth is environmentally sustainable. Sustainability is scored based on the mortality of wild salmonids caused by the parasitic salmon lice. Salmon lice infestation pressure has traditionally been monitored through catching wild sea trout and Arctic char using nets or traps or by trawling after Atlantic salmon postsmolts. However, due to that the Norwegian mainland coastline is nearly 25 000 km, complementary methods that may be used in order to give complete results are needed. We have therefore developed an operational salmon lice model, which calculates the infestation pressure all along the coast in near real-time based on a hydrodynamical ocean model and a salmon lice particle tracking model. The hydrodynamic model generally shows a negative temperature bias and a positive salinity bias compared to observations. The modeled salmon lice dispersion correlates with measured lice on wild salmonids caught using traps or nets. This allows for using two complementary data sources in order to determine the infestation pressure of lice originating from fish farms on wild salmonids, and thereby provide an improved monitoring system for assessing risk and sustainability which forms the basis for knowledge-based advice to management authorities.