Antimicrobial resistance in Chilean marine-farmed salmon: Improving food safety through One Health

Microchloropsis gaditana as a Natural Antimicrobial with a One Health Approach to Food Safety in Farmed Salmon

Sustainably farmed Atlantic salmon could drive global food system solutions by contributing essential nutrients to the human diet while delivering high-quality protein. One of the biggest obstacles to sustainable salmon aquaculture in Chile is the prevalence of piscirickettsiosis disease caused by the Gram-negative bacteria Piscirickettsia salmonis and the excessive amount of antibiotics used to eradicate this disease. Farmed salmon products can be consumed without prior processing and therefore present a substantial risk for the transfer of resistant pathogens to humans. Antibiotics also carry the risk of antibiotic residues and damage to the environment. An alternative to antibiotics is the use of natural antimicrobials without the negative influence on the consumer's microbiome. Here, we evaluate the potential antimicrobial activity against P. salmonis of the marine microalgae Microchloropsis gaditana. A non-genetically modified M. gaditana was grown with nitrogen deprivation to improve the synthesis of the eicosapentaenoic fatty acid (EPA). A spray-dried M. gaditana concentrate (Mg) was elaborated and given to Atlantic salmon for a period of 49 days, and serum and fillet samples were collected. Our results showed a significant increase in the nutritional quality improving the levels of EPA+ Docosapentaenoic acid (DPA) (23%) and Vitamin D3 (106%) of the fillets treated with Mg. Fish fed serum were challenged with P. salmonis, and serum antibacterial activity was measured. Sera from fish fed Mg-enriched diets showed a significant increase in antibacterial activity (85.68%) against P. salmonis. Our results indicate that Mg can be used as a viable alternative to address the critical problem of microbial resistance and to assure consumers that farm-raised Atlantic salmon is safe.

From Metagenomes to Functional Expression of Resistance: floR Gene Diversity in Bacteria from Salmon Farms

Background. The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. Methods. Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover floR gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. Results. Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The floR gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference floR. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the floR sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. Conclusions. This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms.

Fishy business in Seattle: Salmon mislabeling fraud in sushi restaurants vs grocery stores

Salmon is the most commonly consumed finfish in the United States of America (USA), and the mislabeling of salmon is a widespread problem. Washington State is a global supplier of wild-caught Pacific salmon and local salmon mislabeling results in substantial economic, ecological, and cultural impacts. Previous studies in Washington State identified high levels of mislabeled salmon in both markets and restaurants, resulting in local legislation being passed that requires proper labeling of salmon products, including identifying it as wild-caught or farm-raised. To investigate whether recent legislative efforts reduced salmon fraud rates, we acquired and genetically barcoded salmon samples from 67 grocery stores and 52 sushi restaurants in Seattle, Washington. DNA from each salmon sample was isolated and the cytochrome c oxidase gene was sequenced to identify the fish species. Our study, conducted from 2022-2023, revealed 18% of salmon samples from both grocery stores and sushi restaurants were mislabeled. While most samples were acquired during the fall months when wild salmon is in season, we still observed a high salmon mislabeling rate. Unlike grocery stores, Seattle sushi restaurants often sold farmed salmon mislabeled as wild salmon. Specifically, substitutions of vendor-claimed wild salmon with farmed salmon occurred in 32.3% of sushi restaurant samples compared to 0% of grocery store samples. Additionally, occurrences of wild salmon being substituted with another salmon species (wild or farmed) occurred in 38.7% of sushi restaurant samples compared to 11.1% of grocery store samples. All salmon substitutions in sushi restaurants harmed the customer financially as they were given a cheaper market-priced fish. In grocery stores, however, we did not detect significant economic loss to customers due to salmon mislabeling. Taken together, it is important to continue to develop and enforce legislation in Washington State that prevents salmon fraud and promotes ecologically sustainable fishing practices.

Interactive impact of residual pyrethroid compounds used in the Chilean salmon farming industry and coastal acidification conditions on the feeding performance of farmed mussels in northern Patagonia

The use of pyrethroids in aquaculture has been an important component of achieving a thriving salmon farming industry in Chile. While the residual presence of such substances is known to depend on environmental conditions, most ecotoxicological studies to date have not considered environmental context. Here, we conducted oceanographic monitoring combined with experiments aiming to estimate the effects of two pyrethroids on the feeding rates of larvae of farmed mussels, Mytilus chilensis. In additional experiments, mussel spats were exposed to both pyrethroids, but under contrasting temperature/pH so as to mimic winter and summer conditions. Experiments mimicking spring conditions revealed that both pyrethroid substances affected the feeding of mussel larvae as a function of concentration. Conversely, significant impact of pyrethroids on adults were not observed with regard to temperature and pH, but a significant impact of low temperature/low pH condition on ingestion rates was confirmed. Given the current status of increasing ocean acidification, the results of this study are expected to provide useful information with regard to achieving sustainable mussel aquaculture, especially considering both activities occur in similar geographic areas, and the expansion of salmon farming areas is ongoing in Chile.

Drivers of virulence and antimicrobial resistance in Gram-negative bacteria in different settings: A genomic perspective

The human gut presents a complex ecosystem harboring trillions of microorganisms living in close association with each other and the host body. Any perturbation or imbalance of the normal gut microbiota may prove detrimental to human health. Enteric infections and treatment with antibiotics pose major threats to gut microbiota health. Recent genomics-driven research has provided insights into the transmission and evolutionary dynamics of major enteric pathogens such as Escherichia coli, Klebsiella pneumoniae, Vibrio cholerae, Helicobacter pylori and Salmonella spp. Studies entailing the identification of various dominant lineages of some of these organisms based on artificial intelligence and machine learning point to the possibility of a system for prediction of antimicrobial resistance (AMR) as some lineages have a higher propensity to acquire virulence and fitness advantages. This is pertinent in the light of emerging AMR being one of the immediate threats posed by pathogenic bacteria in the form of a multi-layered fitness manifesting as phenotypic drug resistance at the level of clinics and field settings. To develop a holistic or systems-level understanding of such devastating traits, present methodologies need to be advanced with the high throughput techniques integrating community and ecosystem/niche level data across different omics platforms. The next major challenge for public health epidemiologists is understanding the interactions and functioning of these pathogens at the community level, both in the gut and outside. This would provide new insights into the dimensions of enteric bacteria in different environments and niches and would have a plausible impact on infection control strategies in terms of tackling AMR. Hence, the aim of this review is to discuss virulence and AMR in Gram-negative pathogens, the spillover of AMR and methodological advancements aimed at addressing it through a unified One Health framework applicable to the farms, the environment, different clinical settings and the human gut.

Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes

Humans are radically altering global ecology, and one of the most apparent human-induced effects is urbanization, where high-density human habitats disrupt long-established ecotones. Changes to these transitional areas between organisms, especially enhanced contact among humans and wild animals, provide new opportunities for the spread of zoonotic pathogens. This poses a serious threat to global public health, but little is known about how habitat disruption impacts cross-species pathogen spread. Here, we investigated variation in the zoonotic enteric pathogen Campylobacter jejuni. The ubiquity of C. jejuni in wild bird gut microbiomes makes it an ideal organism for understanding how host behavior and ecology influence pathogen transition and spread. We analyzed 700 C. jejuni isolate genomes from 30 bird species in eight countries using a scalable generalized linear model approach. Comparing multiple behavioral and ecological traits showed that proximity to human habitation promotes lineage diversity and is associated with antimicrobial-resistant (AMR) strains in natural populations. Specifically, wild birds from urban areas harbored up to three times more C. jejuni genotypes and AMR genes. This study provides novel methodology and much-needed quantitative evidence linking urbanization to gene pool spread and zoonoses.

Array-based specific classification of bacterial species via ligands with dimethylamino/amino groups

The early detection of bacterial species plays a crucial role in patient prognosis and the development of effective therapeutic regimens. This study introduces an accessible and promising colorimetric sensor array designed to classify gram-positive (G+) and gram-negative (G-) bacterial species. The classification relies on 6 chemical ligands with dimethylamino/amino groups as sensing elements and silver nanotriangles as colorimetric probes. Using these specific sensor arrays, we successfully differentiated G- and G+ bacterial species and discriminated individual bacterial strains, and the sensors exhibited remarkable reproducibility and high sensitivity. Moreover, the sensor array can identify bacterial mixtures and bacteria at varying concentrations, underscoring its versatility. In summary, this sensor array offers an effective tool for bacterial analysis with promising applications in the field of biomedical diagnostics.

The development and validation of the One Health Community Assessment

Interdisciplinary collaborations to address human, animal, and environmental health have been emphasized since the inception of the One Health framework. A quantitative survey instrument was developed to measure perceptions of the impacts of pets on One Health. Using the exploratory sequential mixed methods approach, 20 interviews were conducted with individuals from a racially diverse and low-socioeconomic status community in the U.S. to understand their perceptions of One Health. Data from those interviews informed the development of a Likert scale survey measuring individual perceptions of community, human, pet, and environmental health and welfare, as well as the connections between the domains of the One Health triad (human, animal, and environment). The resulting One Health Community Assessment (OHCA) was administered in two urban and two rural underserved U.S. communities longitudinally (2018-2021) through door-to-door data collection as well as phone, email, and text surveys. Validation of the instrument was completed using data collected in the third and fourth years of the study (n = 654). Factor analysis with orthogonal varimax rotation was used to assess the structure and internal consistency of the OHCA. Five subscales explained 42.4% of the variance in our 92-item instrument: community health (Cronbach's α = 0.897), human health (α = 0.842), pet health (α = 0.899), environmental health (α = 0.789), and connections between domains of One Health (α = 0.762). The OHCA represents the first reliable and validated instrument to measure the impacts of pets on One Health.

Triple-crises-induced food insecurity: systematic understanding and resilience building approaches in Africa

The triple crises of the COVID-19 pandemic, conflict and climate change have severely impacted food systems, leading to socio-economic consequences and undermining food and nutrition security across Africa. To address the malnutrition and poverty affecting approximately 700 million people in Africa, there is potential for the One Health approach implementation and operationalization to bring together multidisciplinary solutions for tackling food insecurity and ensuring food safety net. However, there is limited documentation on the potential of the One Health approach system thinking implementation to guide responses to triple crises-induced food insecurity. Therefore, this article aims to systematically understand the triple crises-induced food insecurity, connect existing solutions, and explore the role of the One Health approach in strengthening food and agriculture systems in Africa. Our finding showed the impact of triple crises exacerbating food system vulnerability in Africa and worldwide. Mitigating and resilient actions are urgently needed in tackling the emerging and persisting challenges, and infectious diseases menace and burden across Africa. We present a conceptual model illustrating the complex nature of triple crises-induced food insecurity, vulnerability areas within the food system, and actionable strategies for building community food resilience. Additionally, recommendations are provided to create an enabling environment that supports One Health approach implementation and addresses food insecurity challenges through innovative partnerships, local-led initiatives, and enhanced governance and artificial intelligence technology capacities in achieving sustainable and inclusive growth to reduce socio-economic inequalities. Stepping up integrated, actionable, and sustainable food systems programs and innovative long-lasting solutions requires investing in promoting new partnership and research collaboration in building conflict resolution and peace towards strengthening and reshaping local and global food security related climate change adaptations actions for most vulnerable communities' benefits. These are ingredients in fastening preparedness, prevention and control of infectious diseases prevention and control, reducing food supply chains disruption towards accelerating equitable benefits of Universal Health Coverage and Sustainable Development Goals, 2030 across Africa.

Misunderstandings and misinterpretations: Antimicrobial use and resistance in salmon aquaculture

The exponential growth of aquaculture over the past 30 years has been accompanied by a parallel increase in the use of antimicrobials. This widespread use has had negative effects on animal, human and environmental health and affected the biodiversity of the environments where aquaculture takes place. Results showing these harmful effects have been resisted and made light of by the aquaculture industry and their scientific supporters through introduction of misunderstandings and misinterpretations of concepts developed in the evolution, genetics, and molecular epidemiology of antimicrobial resistance. We focus on a few of the most obvious scientific shortcomings and biases of two recent attempts to minimise the negative impacts of excessive antimicrobial use in Chilean salmon aquaculture on human and piscine health and on the environment. Such open debate is critical to timely implementation of effective regulation of antimicrobial usage in salmon aquaculture in Chile, if the negative local and worldwide impacts of this usage are to be avoided.

Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon

Background: Worldwide, aquaculture is considered as a hotspot environment for antimicrobial resistance (AMR) due to the intense use of antibiotics in its productive systems. Chile is the second largest producer of farmed salmon worldwide, and tons of antibiotics are used to control bacterial diseases, such as Salmon Rickettsial Syndrome (SRS) and Bacterial Kidney Disease (BKD). However, studies determining the risk of consuming salmon fillets that have been treated with antibiotics during the salmon production are limited. Consulting leading experts in the field could provide a knowledge base to identify and address this question and research gaps. Methods: Multisectoral risk perception of AMR through salmon fillet consumption was evaluated by eliciting expert data obtained through discussions during a workshop and from questionnaires given to experts from academia (n = 15, 63%), the public sector (n = 5, 21%), and the salmon industry (n = 4, 17%). Results: The qualitative risk analysis suggested an overall ‘low’ probability of AMR acquisition by consumption of salmon fillet that had been treated during the production cycle. The risk perception varied slightly between production stages in freshwater and seawater. In consensus with all sectors, this overall ‘low’, but existing, risk was probably associated with bacterial infections and the use of antibiotics. Conclusions: As it is essential to reduce the use of antibiotics in the Chilean salmon industry, this intersectoral approach and consensual results could favor effective implementation of targeted initiatives for the control and prevention of major bacterial diseases.

The High Risk of Bivalve Farming in Coastal Areas With Heavy Metal Pollution and Antibiotic-Resistant Bacteria: A Chilean Perspective

Anthropogenic pollution has a huge impact on the water quality of marine ecosystems. Heavy metals and antibiotics are anthropogenic stressors that have a major effect on the health of the marine organisms. Although heavy metals are also associate with volcanic eruptions, wind erosion or evaporation, most of them come from industrial and urban waste. Such contamination, coupled to the use and subsequent misuse of antimicrobials in aquatic environments, is an important stress factor capable of affecting the marine communities in the ecosystem. Bivalves are important ecological components of the oceanic environments and can bioaccumulate pollutants during their feeding through water filtration, acting as environmental sentinels. However, heavy metals and antibiotics pollution can affect several of their physiologic and immunological processes, including their microbiome. In fact, heavy metals and antibiotics have the potential to select resistance genes in bacteria, including those that are part of the microbiota of bivalves, such as Vibrio spp. Worryingly, antibiotic-resistant phenotypes have been shown to be more tolerant to heavy metals, and vice versa, which probably occurs through co- and cross-resistance pathways. In this regard, a crucial role of heavy metal resistance genes in the spread of mobile element-mediated antibiotic resistance has been suggested. Thus, it might be expected that antibiotic resistance of Vibrio spp. associated with bivalves would be higher in contaminated environments. In this review, we focused on co-occurrence of heavy metal and antibiotic resistance in Vibrio spp. In addition, we explore the Chilean situation with respect to the contaminants described above, focusing on the main bivalves-producing region for human consumption, considering bivalves as potential vehicles of antibiotic resistance genes to humans through the ingestion of contaminated seafood.

Anthropogenic Activities and the Problem of Antibiotic Resistance in Latin America: A Water Issue

Antibiotics revolutionized modern medicine and have been an excellent tool to fight infections. However, their overuse and misuse in different human activities such as health care, food production and agriculture has resulted in a global antimicrobial resistance crisis. Some regions such as Latin America present a more complex scenario because of the lack of resources, systematic studies and legislation to control the use of antimicrobials, thus increasing the spread of antibiotic resistance. This review aims to summarize the state of environmental antibiotic resistance in Latin America, focusing on water resources. Three databases were searched to identify publications on antimicrobial resistance and anthropogenic activities in relation to natural and artificial water ecosystems. We found that antibiotic resistant bacteria, mainly against beta lactam antibiotics, have been reported in several Latin American countries, and that resistant bacteria as well as resistant genes can be isolated from a wide variety of aquatic environments, including drinking, surface, irrigation, sea and wastewater. It is urgent to establish policies and regulations for antibiotic use to prevent the increase of multi-drug resistant microorganisms in the environment.

Screening the Presence of Non-Typhoidal Salmonella in Different Animal Systems and the Assessment of Antimicrobial Resistance

Salmonella is a major bacterial foodborne pathogen that causes the majority of worldwide food-related outbreaks and hospitalizations. Salmonellosis outbreaks can be caused by multidrug-resistant (MDR) strains, emphasizing the importance of maintaining public health and safer food production. Nevertheless, the drivers of MDR Salmonella serovars have remained poorly understood. In this study, we compare the resistance profiles of Salmonella strains isolated from 4047 samples from domestic and wild animals in Chile. A total of 106 Salmonella strains (2.61%) are isolated, and their serogroups are characterized and tested for susceptibility to 16 different antimicrobials. The association between antimicrobial resistance (AMR) and a subset of independent variables is evaluated using multivariate logistic models. Our results show that 47 antimicrobial-resistant strains were found (44.3% of the total strains). Of the 47, 28 correspond to single-drug resistance (SDR = 26.4%) and 19 are MDR (17.9%). S. Enteritidis is highly persistent in animal production systems; however, we report that serogroup D strains are 18 times less likely to be resistant to at least one antimicrobial agent than the most common serogroup (serogroup B). The antimicrobials presenting the greatest contributions to AMR are ampicillin, streptomycin and tetracycline. Additionally, equines and industrial swine are more likely to acquire Salmonella strains with AMR. This study reports antimicrobial-susceptible and resistant Salmonella in Chile by expanding the extant literature on the potential variables affecting antimicrobial-resistant Salmonella.