Investigation of the Correlation between the Use of Antibiotics in Aquaculture Systems and Their Detection in Aquatic Environments: A Case Study of the Nera River Aquafarms in Italy

Effects of environmentally relevant concentrations of florfenicol on the glucose metabolism system, intestinal microbiome, and liver metabolome of zebrafish

Florfenicol, a widely used veterinary antibiotic, has now been frequently detected in various water environments and human urines, with high concentrations. Accordingly, the ecological risks and health hazards of florfenicol are attracting increasing attention. In recent years, antibiotic exposure has been implicated in the disruption of animal glucose metabolism. However, the specific effects of florfenicol on the glucose metabolism system and the underlying mechanisms are largely unknown. Herein, zebrafish as an animal model were exposed to environmentally relevant concentrations of florfenicol for 28 days. Using biochemical and molecular analyses, we found that exposure to florfenicol disturbed glucose homeostasis, as evidenced by the abnormal levels of blood glucose and hepatic/muscular glycogen, and the altered expression of genes involved in glycogenolysis, gluconeogenesis, glycogenesis, and glycolysis. Considering the efficient antibacterial activity of florfenicol and the crucial role of intestinal flora in host glucose metabolism, we then analyzed changes in the gut microbiome and its key metabolite short-chain fatty acids (SCFAs). Results indicated that exposure to florfenicol caused gut microbiota dysbiosis, inhibited the production of intestinal SCFAs, and ultimately affected the downstream signaling pathways of SCFA involved in glucose metabolism. Moreover, non-targeted metabolomics revealed that arachidonic acid and linoleic acid metabolic pathways may be associated with insulin sensitivity changes in florfenicol-exposed livers. Overall, this study highlighted a crucial aspect of the environmental risks of florfenicol to both non-target organisms and humans, and presented novel insights into the mechanistic elucidation of metabolic toxicity of antibiotics.

Understanding the toxicity risk of antibiotic emissions of aquaculture from the perspective of fluctuations concentration

Organisms are generally exposed to target contaminant with stable concentrations in traditional ecotoxicological studies. However, it is difficult to truly represent the dynamics and complexity of actual aquatic pollution for risk management. Contaminants may enter nearby aquatic systems in pulsed exposure, thus resulting in that aquatic organisms will be exposed to contaminants at fluctuating concentrations. Especially during the season of summer, due to the changes in displacement or periodic emissions of veterinary antibiotics in aquaculture, algal blooms occur frequently in surrounding waters, thus leading to eutrophication of the water. Florfenicol (FFC) is currently widely used as a veterinary antibiotic, but the aquatic ecological risks of FFC under concentration fluctuations are still unknown. Therefore, the acute exposure, chronic exposure and pulsed exposure effects of FFC on Microcystis aeruginosa were investigated to comprehensively evaluate the ecological risk of FFC and raise awareness of the pulsed exposure mode. Results indicated that the toxic effects of FFC on M. aeruginosa were dominated by exposure mode, exposure duration, exposure frequency, and exposure concentration. The maximum growth inhibition rate of the 10 μg/L FFC treatment amounted to 4.07% during chronic exposure of 18 days. However, the growth inhibition rate decreased from 55.1% to 19.31% when algae was exposure to 10 μg/L FFC during the first pulsed exposure (8 h). Therefore, when the concentration of FFC was equal under chronic and pulsed exposure, FFC exhibited greater toxicity on M. aeruginosa in short pulsed exposure than in continuous exposure. In addition, repetitive pulsed exposure strengthened the resistance of M. aeruginosa on FFC. The adaptive regulation of algae was related to the duration and frequency of exposure. Above results suggested that traditional toxicity assessments lacked consideration for fluctuating concentrations during pollutant emissions, thus underestimating the environmental risk of contaminant. This investigation aims to facilitate the standardization of pulsed exposure.

Target and suspect screening approaches for the identification of emerging and other contaminants in fish feeds using high resolution mass spectrometry

Fish feed is essential in aquaculture fish production because, along with beneficial nutrients and components, many suspected compounds can be transferred to fish and ultimately to humans. In this context, a comprehensive analysis was conducted to monitor various pesticides and pharmaceutical compounds in aquaculture fish feed through target analysis and many other groups of chemicals via suspect screening approaches. In this study, the QuEChERS extraction method was optimized, validated, and applied to fifty-four fish feed samples collected from different production batches. This was followed by liquid chromatography-high-resolution linear ion trap/Orbitrap mass spectrometry (LC-HR-IT/Orbitrap-MS) for targeted and suspect screening purposes. In general, pesticides provided satisfactory recoveries (70-105.5 %), with quantification limits lower than 5 ng g-1, whereas pharmaceuticals displayed recoveries ranging from 70.5 to 120.2 %, with quantification limits below 25 ng g-1. In addition, the matrix effects and measurement uncertainty were assessed to provide more accurate and high-confidence results. Pirimiphos-methyl was detected and quantified in 20 of 54 fish feed samples (37 %) at concentrations <77 ng g-1. Finally, suspect screening revealed the occurrence of 10 mycotoxins (e.g., citrinin, aflatoxin G2, zearalenone, and alternariol), two pesticides excluding the target pesticides (tebuconazole and fenazaquin), perfluorooctane sulfonic acid (PFOS) in almost 2 % of the samples, and ethoxyquin (antioxidant), with 12 of its Transformation Products (TPs). Finally, suspect analysis incorporated in routine analyses have proven to have great potential for complete monitoring.

Unraveling the nexus: Microplastics, antibiotics, and ARGs interactions, threats and control in aquaculture - A review

In recent years, aquaculture has expanded rapidly to address food scarcity and provides high-quality aquatic products. However, this growth has led to the release of significant effluents, containing emerging contaminants like antibiotics, microplastics (MPs), and antibiotic resistance genes (ARGs). This study investigated the occurrence and interactions of these pollutants in aquaculture environment. Combined pollutants, such as MPs and coexisting adsorbents, were widespread and could include antibiotics, heavy metals, resistance genes, and pathogens. Elevated levels of chemical pollutants on MPs could lead to the emergence of resistance genes under selective pressure, facilitated by bacterial communities and horizontal gene transfer (HGT). MPs acted as vectors, transferring pollutants into the food web. Various technologies, including membrane technology, coagulation, and advanced oxidation, have been trialed for pollutants removal, each with its benefits and drawbacks. Future research should focus on ecologically friendly treatment technologies for emerging contaminants in aquaculture wastewater. This review provided insights into understanding and addressing newly developing toxins, aiming to develop integrated systems for effective aquaculture wastewater treatment.

Impact of Soil Fertilization with Pig Slurry on Antibiotic Residues and Resistance Genes: A Longitudinal Study

The impact of soil fertilization with animal manure on the spread and persistence of antibiotic resistance in the environment is far from being fully understood. To add knowledge about persistence and correlations between antibiotic residues and antibiotic resistance genes (ARGs) in fertilized soil, a longitudinal soil mesocosm study was conducted. Soil samples were collected from the mesocosms immediately before spreading and then afterward at fifteen time points during a 320-day observation period. Eight ARGs (ermB, sul1, tetA, tetG, tetM, cfr, fexA, and optrA) and the class 1 integron-integrase gene, intI1, were determined in both pig slurry and soil, as well as residues of 36 antibiotics. Soil chemical and biochemical parameters were also measured. Twelve antibiotics were detected in the slurry in the range of 3 µg kg-1-3605 µg kg-1, with doxycycline, lincomycin, and tiamulin being the most abundant, whereas ermB, sul1, and tetM were the predominant ARGs. Before spreading, neither antibiotic residues nor ARGs were detectable in the soil; afterwards, their concentrations mirrored those in the slurry, with a gradual decline over the duration of the experiment. After about three months, the effect of the amendment was almost over, and no further evolution was observed.

Assessment of the combined inputs of antimicrobials from top soil improvers and irrigation waters on green leafy vegetable fields

Sustainable food systems involve the recycling of biowaste and water. This study characterizes thirty-one top soil improvers of anthropogenic, animal, and green waste origin, along with eleven irrigation waters from rivers, channels, and civil wastewater treatment plants (cWWTPs) for the presence of antimicrobials. Liquid chromatography coupled with hybrid High-Resolution Mass Spectrometry (LC-HRMS/MS) was employed to identify forty-eight drugs belonging to the classes of sulfonamides (11), tetracyclines (7), fluoroquinolones (10), macrolides (12), amphenicols (3), pleuromutilins (2), diaminopyrimidines (1), rifamycins (1) and licosamides (1). Sludge from cWWTPs, animal manure, slurry, and poultry litter exhibited the highest loads for sulfonamides, tetracyclines, fluoroquinolones and macrolides (80, 470, 885, and 4,487 ng g-1 wet weight, respectively) with nor- and ciprofloxacin serving as markers for anthropogenic sources. In compost and digestate, antimicrobials were found to be almost always below the limits of quantification. Reused water from cWWTPs for irrigation in open-field lettuce production were contaminated in the range of 12-221 ng L-1 with sulfonamides, tetracyclines, and fluoroquinolones, compared to very few detected in channels and surface waters. The Antimicrobials Hazard Index (HI), based on the Predicted No Effect Concentration for Antimicrobial Resistance (PNECAMR), was significantly >100 in contaminated topsoil improvers from urban and animal sources. Accounting for worst-case inputs from topsoil improvers and irrigation water, as well as dilution factors in amended soil, fluoroquinolones only exhibited an HI around 1 in open fields for lettuce production. The origin of topsoil improvers plays a pivotal role in ensuring safe and sustainable leafy vegetable production, thereby mitigating the risk of Antimicrobial Resistance (AMR) onset in food-borne diseases and the transfer of AMR elements to the human gut flora.

In vitro determination of probiotic efficacy of Bacillus subtilis TLDK301120C24 isolated from tilapia against warm water fish pathogens and in vivo validation using gnotobiotic zebrafish model

Eco-friendly alternatives such as probiotics are needed to prevent economically relevant infectious diseases for a successful disease-free harvest in aquaculture. The use of antibiotics has been the favored practice, but its empirical and indiscriminate use has led to antibiotic resistance in the aquatic environment and residues in the food fish. With this rationale, a probiotic was isolated from tilapia, a commercially important cultured fish worldwide. The characteristics of the probiotic were checked against common bacterial pathogens affecting aquaculture. In vitro tests demonstrated the inhibitory effects of the isolated probiotic on the growth of Aeromonas hydrophila, Edwardsiella tarda, Vibrio anguillarum, and V. alginolyticus. The candidate probiotic, referred to as TLDK301120C24, was identified as Bacillus subtilis by a battery of biochemical tests and genotypic confirmation by 16S rDNA sequencing. The in vitro results revealed the ability of the probiotic to withstand the gut conditions that included pH range of 3-9, salt concentration of 0.5-6%, and bile salt concentration of up to 6%. The isolate could hydrolyze starch (12-14 mm clearance zone), protein (20-22 mm clearance zone), and cellulose (22-24 mm clearance zone). Further, the inhibitory ability of the probiotic against aquatic pathogens was determined in vivo using gnotobiotic zebrafish by employing a novel approach that involved tagging the probiotic with a red fluorescent protein and the pathogens with a green fluorescent protein, respectively. The colonizing ability of probiotics and its inhibitory effects against the pathogens were evaluated by fluorescence microscopy, PCR, and estimation of viable counts in LBA + Amp plates. Finally, the competitive inhibition and exclusion of fish pathogens A. hydrophila and E. tarda by B. subtilis was confirmed semi-quantitatively, through challenge experiments. This study shows the potential of B. subtilis as a probiotic and its excellent ability to inhibit major fish pathogens in vivo and in vitro. It also shows promise as a potent substitute for antibiotics.

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC-MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.

Occurrence, distribution and risk assessment of antibiotics at various aquaculture stages in typical aquaculture areas surrounding the Yellow Sea

The pollution of antibiotics commonly existed throughout the entire aquaculture process, but the residues of antibiotics at different aquaculture stages have rarely been studied. This study investigated the occurrence, distribution and risk assessment of antibiotics at different aquaculture stages (the non-aquaculture stage, the early aquaculture stage, the middle aquaculture stage, and the late aquaculture stage) in two typical marine aquaculture areas (Mahegang River and Dingzi Bay) surrounding the Yellow Sea. Fluoroquinolones and tetracyclines were commonly used antibiotics in the aquaculture of these areas with high detection frequencies (17% to 83%). Compared among four aquaculture stages, the highest concentration of antibiotics (9032.08 ng/L) in aquaculture ponds was detected at the late aquaculture stage. And the antibiotic pollution level of natural water was directly related to the aquaculture stages. Similarly, at the aquaculture stages, the detection frequency of antibiotics in sediments was higher than that at the non-aquaculture stage. Based on the correlation analysis, the concentration of main antibiotics in water showed a positive correlation with total nitrogen (p<0.05) and chlorophyll a (p<0.01), while it showed a negative correlation with salinity (p<0.01) in coastal water of the Dingzi Bay. According to the risk assessment, with the development of aquaculture stages, the selection pressure of fluoroquinolones and tetracyclines on resistant bacteria had increased. And the ecological risks caused by sulfonamides and tetracyclines to aquatic organisms had also increased markedly. Overall, this study may provide a reference for formulating regulatory policies regarding antibiotic use at different aquaculture stages.

Review of Medicinal Plants and Active Pharmaceutical Ingredients against Aquatic Pathogenic Viruses

Aquaculture offers a promising source of economic and healthy protein for human consumption, which can improve wellbeing. Viral diseases are the most serious type of diseases affecting aquatic animals and a major obstacle to the development of the aquaculture industry. In the background of antibiotic-free farming, the development and application of antibiotic alternatives has become one of the most important issues in aquaculture. In recent years, many medicinal plants and their active pharmaceutical ingredients have been found to be effective in the treatment and prevention of viral diseases in aquatic animals. Compared with chemical drugs and antibiotics, medicinal plants have fewer side-effects, produce little drug resistance, and exhibit low toxicity to the water environment. Most medicinal plants can effectively improve the growth performance of aquatic animals; thus, they are becoming increasingly valued and widely used in aquaculture. The present review summarizes the promising antiviral activities of medicinal plants and their active pharmaceutical ingredients against aquatic viruses. Furthermore, it also explains their possible mechanisms of action and possible implications in the prevention or treatment of viral diseases in aquaculture. This article could lay the foundation for the future development of harmless drugs for the prevention and control of viral disease outbreaks in aquaculture.

Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures

The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.

The Impact of Intensive Fish Farming on Pond Sediment Microbiome and Antibiotic Resistance Gene Composition

Aquaculture is a fast-growing animal food sector, and freshwater fish farming is particularly common in Central and Eastern Europe. As the biodiversity of fishery ponds is changed toward fulfilling the industrial needs, precautions should be taken to keep the system sustainable and protect the adjacent environment from possible damage. Due to risk of infectious diseases, antibiotics are used in aquaculture production systems. The constant exposure to antimicrobials can contribute to the rise of antibiotic resistance in aquaculture products and the adjacent ecosystems, with possibility of dissemination to the wider environment as well as between animals and humans. Even though previous studies have found antibiotic resistance genes in the sediments and water of farming ponds, the tendency and direction of spreading is not clear yet. The objective of this project was to evaluate the influence of intensive fish farming on the condition of water bodies used for the aquaculture and the environment, concentrating on the impact of the aquaculture on the surrounding water ecosystems as well as the possibility of transferring the pollutants and antibiotic resistance genes to both environment and the human hosts. Combined measurement of antibiotic and heavy metal contamination, toxicity assessment, microorganism diversity, and the detection of common antibiotic resistance genes was performed in the sediments of one fishery farm ponds as well as sampling points upstream and downstream. All the tested sediment samples did not show significantly elevated heavy metal concentrations and no substantial veterinary antibiotic pollution. From the antibiotic resistance genes tested, the presence of aminoglycoside and β-lactam resistance determinants as well as the presence of integrons could be of concern for the possibility of transfer to humans. However, despite the lack of heavy metal and antibiotic pollution, the sediments showed toxicity, the cause of which should be explored more.