Unpacking factors influencing antimicrobial use in global aquaculture and their implication for management: a review from a systems perspective

Antimicrobial Resistance in Aquaculture: Risk Mitigation within the One Health Context

The application of antimicrobials in aquaculture primarily aims to prevent and treat bacterial infections in fish, but their inappropriate use may result in the emergence of zoonotic antibiotic-resistant bacteria and the subsequent transmission of resistant strains to humans via food consumption. The aquatic environment serves as a potential reservoir for resistant bacteria, providing an ideal breeding ground for development of antimicrobial resistance (AMR). The mutual inter-connection of intensive fish-farming systems with terrestrial environments, the food processing industry and human population creates pathways for the transmission of resistant bacteria, exacerbating the problem further. The aim of this study was to provide an overview of the most effective and available risk mitigation strategies to tackle AMR in aquaculture, based on the One Health (OH) concept. The stringent antimicrobial use guidelines, promoting disease control methods like enhanced farm biosecurity measures and vaccinations, alternatives to antibiotics (ABs) (prebiotics, probiotics, immunostimulants, essential oils (EOs), peptides and phage therapy), feeding practices, genetics, monitoring water quality, and improving wastewater treatment, rather than applying excessive use of antimicrobials, can effectively prevent the development of AMR and release of resistant bacteria into the environment and food. The contribution of the environment to AMR development traditionally receives less attention, and, therefore, environmental aspects should be included more prominently in OH efforts to predict, detect and prevent the risks to health. This is of particular importance for low and middle-income countries with a lack of integration of the national AMR action plans (NAPs) with the aquaculture-producing environment. Integrated control of AMR in fisheries based on the OH approach can contribute to substantial decrease in resistance, and such is the case in Asia, where in aquaculture, the percentage of antimicrobial compounds with resistance exceeding 50% (P50) decreased from 52% to 22% within the period of the previous two decades.

Spatiotemporal dynamics, bioaccumulation, and critical influencing factors of antibiotics in tilapia aquaculture: A study on source identification and environmental fate within typical farming systems

This study investigated the spatiotemporal dynamics, bioaccumulation, and critical influencing factors of antibiotics in tilapia aquaculture, focusing on source identification and environmental fate within typical farming systems. The results revealed a progressive increase in antibiotic concentrations in pond water and sediments over the cultivation period, with suspended solids and chemical oxygen demand identified as significant environmental factors influencing the distribution and dissemination of antibiotics. The aquaculture water source was the primary contributor of antibiotics in the farming system. Furthermore, the bioaccumulation factor (BAF) calculations indicated varying degrees of antibiotic enrichment in tilapia tissues, with sulfadimethoxine exhibiting the highest BAFs. Correlation analyses, redundancy analysis, and multivariate linear regression analysis provided insights into the relationship between environmental factors and antibiotics, identifying key antibiotics and influencing factors. The study highlighted the importance of managing and treating water sources to reduce the inflow of antibiotics into aquaculture systems and emphasized the need for non-antibiotic aquaculture practices to minimize the impact on the environment and public health. In conclusion, this research contributes valuable information for the development of effective management strategies and policies aimed at curbing antibiotic pollution in aquaculture environments, ensuring the sustainability of the aquaculture industry, and protecting ecosystem and consumer health.

Technical specifications for a EU-wide baseline survey of antimicrobial resistance in bacteria from aquaculture animals

The European Commission requested scientific and technical assistance in the preparation of a EU-wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in Aeromonas spp. isolated from Atlantic Salmon (Salmo salar), European seabass (Dicentrarchus labrax) and trout (Salmo trutta, Salvelinus fontinalis, Oncorhynchus mykiss) intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Vibrio parahaemolyticus and Vibrio alginolyticus in blue mussel (Mytilus edulis) and Mediterranean mussel (Mytilus galloprovincialis) from production areas and at dispatch centres at the EU level. These technical specifications define the target populations, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic analysis of some of the bacteria targeted) and the data reporting requirements. The data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA reporting system.

Knowledge, Attitudes, and Practices of Antibiotic Use among Small-, Medium-, and Large-Scale Fish Farmers of the Stratum II of the Volta Lake of Ghana

BACKGROUND

Antibiotic residue in food products and the resulting antibiotic-resistant bacteria represent a significant global public health threat. The misuse of antibiotics is a primary contributor to this issue. This study investigated the knowledge, attitudes, and practices (KAP) regarding antibiotic use among cage fish farmers on Ghana's Volta Lake.

METHOD

We conducted a cross-sectional survey with 91 cage fish farmers across three scales: small, medium, and large. A semi-structured questionnaire complemented by personal observations provided comprehensive data. We used several statistical methods for analysis: Pearson Chi-Square and Spearman correlation tests to examine relationships and trends among variables, logistic regression to analyze variable interactions, and Cronbach's alpha to check internal consistency. Additionally, Kendall's coefficient was used to rank challenges, utilizing STATA and SPSS for these calculations.

RESULTS

The survey revealed that 58.55% of cage fish farmers earn an average of 10,000 USD annually, with 35.16% having over 16 years of experience. From the survey, all sampled populations admitted to antibiotic applications in their farming operation. Knowledge of antibiotic types was mainly influenced by peers (46.15%), with tetracycline being the most recognized and used. There was a significant reliance on the empirical use of antibiotics, with 52.75% of farmers using them based on personal experience and 40.66% without a prescription. When initial treatments failed, 41.76% of the farmers would change or combine drugs. Older farmers (over 51 years) and those with tertiary education demonstrated significantly better KAP scores regarding antibiotic use. Strong correlations were also found among knowledge, attitudes, and practices in antibiotic usage.

CONCLUSIONS

The findings indicate a need for improved education on antibiotic use among fish farmers to reduce misuse and enhance awareness of the potential consequences. This study provides foundational data for designing interventions to address these issues in the context of cage fish farming on Volta Lake.

A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources

Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.

Effects of Shrimp Shell-Derived Chitosan on Growth, Immunity, Intestinal Morphology, and Gene Expression of Nile Tilapia (Oreochromis niloticus) Reared in a Biofloc System

Chitosan (CH) shows great potential as an immunostimulatory feed additive in aquaculture. This study evaluates the effects of varying dietary CH levels on the growth, immunity, intestinal morphology, and antioxidant status of Nile tilapia (Oreochromis niloticus) reared in a biofloc system. Tilapia fingerlings (mean weight 13.54 ± 0.05 g) were fed diets supplemented with 0 (CH0), 5 (CH5), 10 (CH10), 20 (CH20), and 40 (CH40) mL·kg-1 of CH for 8 weeks. Parameters were assessed after 4 and 8 weeks. Their final weight was not affected by CH supplementation, but CH at 10 mL·kg-1 significantly improved weight gain (WG) and specific growth rate (SGR) compared to the control (p < 0.05) at 8 weeks. Skin mucus lysozyme and peroxidase activities were lower in the chitosan-treated groups at weeks 4 and 8. Intestinal villi length and width were enhanced by 10 and 20 mL·kg-1 CH compared to the control. However, 40 mL·kg-1 CH caused detrimental impacts on the villi and muscular layer. CH supplementation, especially 5-10 mL·kg-1, increased liver and intestinal expressions of interleukin 1 (IL-1), interleukin 8 (IL-8), LPS-binding protein (LBP), glutathione reductase (GSR), glutathione peroxidase (GPX), and glutathione S-transferase (GST-α) compared to the control group. Overall, dietary CH at 10 mL·kg-1 can effectively promote growth, intestinal morphology, innate immunity, and antioxidant capacity in Nile tilapia fingerlings reared in biofloc systems.

Novel insights into the co-selection of metal-driven antibiotic resistance in bacteria: a study of arsenic and antibiotic co-exposure

The simultaneous development of antibiotic resistance in bacteria due to metal exposure poses a significant threat to the environment and human health. This study explored how exposure to both arsenic and antibiotics affects the ability of an arsenite oxidizer, Achromobacter xylosoxidans CAW4, to transform arsenite and its antibiotic resistance patterns. The bacterium was isolated from arsenic-contaminated groundwater in the Chandpur district of Bangladesh. We determined the minimum inhibitory concentration (MIC) of arsenite, cefotaxime, and tetracycline for A. xylosoxidans CAW4, demonstrating a multidrug resistance (MDR) trait. Following this determination, we aimed to mimic an environment where A. xylosoxidans CAW4 was exposed to both arsenite and antibiotics. We enabled the strain to grow in sub-MIC concentrations of 1 mM arsenite, 40 µg/mL cefotaxime, and 20 µg/mL tetracycline. The expression dynamics of the arsenite oxidase (aioA) gene in the presence or absence of antibiotics were analyzed. The findings indicated that simultaneous exposure to arsenite and antibiotics adversely affected the bacteria's capacity to metabolize arsenic. However, when arsenite was present in antibiotics-containing media, it promoted bacterial growth. The study observed a global downregulation of the aioA gene in arsenic-antibiotic conditions, indicating the possibility of increased susceptibility through co-resistance across the entire bacterial population of the environment. This study interprets that bacterial arsenic-metabolizing ability can rescue the bacteria from antibiotic stress, further disseminating environmental cross-resistance. Therefore, the co-selection of metal-driven antibiotic resistance in bacteria highlights the need for effective measures to address this emerging threat to human health and the environment.

Impacts of florfenicol on immunity, antioxidant activity, and histopathology of Oreochromis niloticus: a potential protective effect of dietary spirulina platensis

The misuse of antibiotics enhances the development of resistant microorganisms and decreases the efficacy of treatments. Florfenicol (FF) is one of the antibiotics approved for use in aquaculture in Egypt. Because of its extensive usage, potential negative impacts on aquatic creatures are a major concern. This motivates us to search for an appropriate neoadjuvant to work synergistically with FF and reduce adverse effects. Results from this study will contribute towards improving the understanding of the impacts of FF on Oreochromis niloticus and the possible amelioratory effects of Spirulina platensis algae (SP). O. niloticus (n = 240; 40 ± 2.5 g) were fed on two diets supplemented with or without SP for 4 weeks, then divided into four treatments each in three replicates (n = 60/treatment). G1; was fed a control diet, and the other groups were fed diets supplemented with FF (10 mg /kg of BW, G2), SP (2 g/kg of diet, G3), or FF + SP (G4) for 10 days. Among the four groups, the SP group (G3) had the best immunostimulatory effects as observed by a significant (p < 0.05) elevation in phagocytic activity, phagocytic index, IL6, and TNF-α. The treatment with FF had significantly impacted hepatic and renal tissues, as the values of liver enzymes and creatinine demonstrated tissue deterioration and also resulted in oxidative stress, which was expressed by an increase of GPx, CAT, and SOD in (G2). Additionally, the combined FF + SP improved the hematological parameters and decreased the oxidative damage induced by FF (G4). Thus, it was clear that FF has harmful effects on O. niloticus and that SP can modulate such impacts. These data recommend the use of SP as an effective immunostimulant and a probable adjuvant to FF in O. niloticus diets to attain maximum disease resistance.

Immune responses and protective efficacy of American eel (Anguilla rostrata) immunized with a formalin-inactivated vaccine against Anguillid herpesvirus

Anguillid herpesvirus 1 (AngHV), the causative agent of "mucus sloughing and hemorrhagic septicemia disease", causes serious infectious diseases in farmed eel. Among the effective prevention and control strategies, vaccination is one of the most effective approaches. However, no vaccine for AngHV is available. Our study developed a formalin-inactivated AngHV vaccine and evaluated its performance in American eels. Initially, AngHV-FJ, a strain of AngHV, was inactivated completely by 0.1 % formaldehyde, mixed with adjuvant Montanide ISA 763 A VG (763A). Then, vaccines containing different amount of antigen (3 × 106 PFU, 3 × 105 PFU, 3 × 104 PFU, 3 × 103 PFU) were immunized in each American eels. The results showed that the 3 × 105 PFU/fish was the proper dose. The inactivated AngHV vaccine was proven safe for American eels by back intramuscular injection. The results of twice immunization showed that antibody production peaked in the 8th week after the first immunization, and the antibody titer was 1:64,000. Furthermore, the immunized fishes challenged with AngHV (105 PFU/ml immersion) showed a significantly lower incidence rate (33.33 %) than the control group (95.65 %). The survival of the fish in the vaccine group (94.44 %) was significantly higher than the control group (60.87 %). The relative survival rate of the vaccinated group was 85.80 %. Also, vaccine group tissue collected at 7th d post-challenge showed reduced tissue damage and a lower virus load than the control group. The expression of cytokines of IL-1β, IFN-α, IFN-γ, Mx1, RIG-1, and IRF-3, were significantly lower in the vaccine group than the control group at the 7th and 14th d post-challenge. Overall, the formalin-inactivated AngHV vaccine was safe and had immune protective effects against AngHV infection.

Dietary β-Glucan Alleviates Antibiotic-Associated Side Effects by Increasing the Levels of Antioxidant Enzyme Activities and Modifying Intestinal Microbiota in Pacific White Shrimp (Litopenaeus vannamei)

Antibiotics and their secondary metabolites are commonly found in aquatic ecosystems, leading to the passive exposure of many aquatic animals to low doses of antibiotics, which can affect their health. However, there is limited information available on how to mitigate the side effects of antibiotics on normal aquatic animals. This study aimed to investigate the potential of dietary β-glucan to alleviate the side effects induced by antibiotics in Pacific white shrimp (Litopenaeus vannamei) (0.37 ± 0.02 g). A six-week feeding trial was conducted with four dietary treatments including a control, 1 g/kg β-glucan (β-glucan), 50 mg/kg oxytetracycline (OTC), and a combination of 50 mg/kg OTC and 1 g/kg β-glucan (Mix) groups. At the end of the trial, the growth performance, intestinal microbial composition, antioxidant capacity, and immune response of the shrimp were assessed. There were no significant differences in growth performance among the groups, but the condition factor of the shrimp in the Mix group was significantly decreased when compared to the control and β-glucan groups. The activities of hepatopancreas catalase (CAT) and serum phenol oxidase in the OTC group were significantly lower than those in the control group. On the other hand, the activities of hepatopancreas superoxide dismutase and CAT enzymes in the β-glucan group were significantly higher than those in the OTC group. The supplementation of β-glucan in combination with antibiotics significantly increased the CAT activity and bacteriolytic activity compared to the OTC and control groups, respectively. Moreover, an analysis of the intestinal microbiota revealed that the Observed_species estimator in the Mix group was significantly higher than that in the control group. Dietary antibiotics significantly increased the abundance of Actinobacteria at the phylum level, but the Mix group showed no significant difference. The supplementation of β-glucan in combination with antibiotics also significantly increased the relative abundance of Meridianimaribacter compared to the control group. Additionally, the synergistic influence of β-glucan with antibiotics increased the beta diversity of intestinal microbiotas. These findings suggest that the supplementation of β-glucan in combination with antibiotics on Pacific white shrimp can alleviate the low antioxidant capacity and immune response caused by antibiotics while enhancing the intestinal microbial composition. This provides a potential solution to mitigate the negative impacts of antibiotics in aquaculture.

A Scoping Review on GIS Technologies Applied to Farmed Fish Health Management

Finfish aquaculture, one of the fastest growing intensive sectors worldwide, is threatened by numerous transmissible diseases that may have devastating impacts on its economic sustainability. This review (2010-2022) used a PRISMA extension for scoping reviews and a text mining approach to explore the extent to which geographical information systems (GIS) are used in farmed fish health management and to unveil the main GIS technologies, databases, and functions used to update the spatiotemporal data underpinning risk and predictive models in aquatic surveillance programmes. After filtering for eligibility criteria, the literature search provided 54 records, highlighting the limited use of GIS technologies for disease prevention and control, as well as the prevalence of GIS application in marine salmonid farming, especially for viruses and parasitic diseases typically associated with these species. The text mining generated five main research areas, underlining a limited range of investigated species, rearing environments, and diseases, as well as highlighting the lack of GIS-based methodologies at the core of such publications. This scoping review provides a source of information for future more detailed literature analyses and outcomes to support the development of geospatial disease spread models and expand in-field GIS technologies for the prevention and mitigation of fish disease epidemics.

Current Status of Probiotics in European Sea Bass Aquaculture as One Important Mediterranean and Atlantic Commercial Species: A Review

European sea bass production has increased in recent decades. This increase is associated with an annually rising demand for sea bass, which encourages the aquaculture industries to increase their production to meet that demand. However, this intensification has repercussions on the animals, causing stress that is usually accompanied by dysbiosis, low feed-conversion rates, and immunodepression, among other factors. Therefore, the appearance of pathogenic diseases is common in these industries after immunodepression. Seeking to enhance animal welfare, researchers have focused on alternative approaches such as probiotic application. The use of probiotics in European sea bass production is presented as an ecological, safe, and viable alternative in addition to enhancing different host parameters such as growth performance, feed utilization, immunity, disease resistance, and fish survival against different pathogens through inclusion in fish diets through vectors and/or in water columns. Accordingly, the aim of this review is to present recent research findings on the application of probiotics in European sea bass aquaculture and their effect on growth performance, microbial diversity, enzyme production, immunity, disease resistance, and survival in order to help future research.

Antimicrobial Resistance, Virulence Properties and Genetic Diversity of Salmonella Typhimurium Recovered from Domestic and Imported Seafood

The quantity of seafood imported and produced by domestic aquaculture farming has increased. Recently, it has been reported that multidrug-resistant (MDR) Salmonella Typhimurium may be associated with seafood. However, information is limited to the antimicrobial resistance, virulence properties, and genetic diversity of S. Typhimurium recovered from imported and domestic seafood. This study investigated the antimicrobial resistance, virulence properties, and genetic diversity of S. Typhimurium isolated from domestic and imported catfish, shrimp, and tilapia. A total of 127 isolates were tested for the presence of multidrug-resistance (MDR), virulence genes (invA, pagC, spvC, spvR), and genetic diversity using the Sensititre micro-broth dilution method, PCR, and pulsed-field gel electrophoresis (PFGE), respectively. All isolates were uniformly susceptible to six (amoxicillin/clavulanic acid, ceftiofur, ceftriaxone, imipenem, nitrofurantoin, and trimethoprim/sulfamethoxazole) of the 17 tested antimicrobials and genetically diverse. Fifty-three percent of the Salmonella isolates were resistant to at least one antimicrobial and 49% were multidrug resistant. Ninety-five percent of the isolates possessed the invA gene, 67% pagC, and 43% for both spvC, and spvR. The results suggest that S. Typhimurium recovered from seafood is frequently MDR, virulent, and have the ability to cause salmonellosis.

Impact of antibiotics on microbial community in aquatic environment and biodegradation mechanism: a review and bibliometric analysis

Antibiotic residues in aquatic environments pose a potential hazard, and microbes, which play important roles in aquatic ecosystems, are vulnerable to the impacts of antibiotics. This study aimed to analyze the research progress, trends, and hot topics of the impact of antibiotics on microbial community and biodegradation mechanism using bibliometric analysis. An in-depth analysis of the publication characteristics of 6143 articles published between 1990 and 2021 revealed that the number of articles published increased exponentially. The research sites have been mainly concentrated in the Yamuna River, Pearl River, Lake Taihu, Lake Michigan, Danjiangkou Reservoir, etc., illustrating that research around the world is not even. Antibiotics could change the diversity, structure, and ecological functions of bacterial communities, stimulate a widespread abundance of antibiotic-resistant bacteria and antibiotic-resistant genes, and increase the diversity of eukaryotes, thus triggering the shift of food web structure to predatory and pathogenic. Latent Dirichlet allocation theme model analysis showed three clusters, and the research hotspots mainly included the effect of antibiotics on the denitrification process, microplastics combined with antibiotics, and methods for removing antibiotics. Furthermore, the mechanisms of microbe-mediated antibiotic degradation were unraveled, and importantly, we provided bottlenecks and future research perspectives on antibiotics and microbial diversity research.

Synergistic degradation of trimethoprim and its phytotoxicity via the UV/chlorine process: Influencing factors on removal and kinetic

Occurrence of trimethoprim (TMP), recalcitrant antibiotic, and its adverse effect on ecosystem have been reported in several countries. The study aims to remove the TMP and its phytotoxicity via a UV/chlorine process, compared with chlorination and UV irradiation alone. Various treatment conditions including chlorine doses, pHs, and TMP concentrations was conducted with synthetic waters and effluent waters. The UV/chlorine process exhibited a synergistic effect on the TMP removal, compared with chlorination and UV irradiation alone. The UV/chlorine process was the most effective in removing TMP, followed by chlorination. The UV irradiation slightly affected the TMP removal (less than 5%). The UV/chlorine process completely removed TMP by 15 min contact time, while chlorination for 60 min could achieve 71% of TMP removal. The TMP removal fitted well with the pseudo first-order kinetics, and the rate constant (k') increased with higher chlorine doses, lower TMP concentrations and low pH. HO• was the major oxidant affecting the TMP removal and its degradation rate, compared with other reactive chlorine species (e.g., Cl•, OCl•). The TMP exposure increased the phytotoxicity by decreasing a germination rate of Lactuca sativa and Vigna radiata seeds. The use of UV/chlorine process could effectively detoxify the TMP, resulting in the phytotoxicity level of treated waters equivalent or lower than those of TMP-free effluent water. The detoxification level depended on the TMP removal, and it was about 0.43-0.56 times of TMP removal. The findings indicated the potential use of UV/chlorine process in removing TMP residual and its phytotoxicity.

Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors

The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.

Diversity of enterobacterales in sediments of lagoons with fish farming activity and analysis of antibiotic resistance

The use of antibiotics in fish production can induce bacterial populations to develop resistance to multiple antibiotics and transfer antibiotic resistance genes to other bacteria, including clinically relevant bacteria. This study evaluated the diversity of Enterobacterales in sediment from lagoons with fish farming activity and analyzed antibiotic resistance in the central region of Peru. Sediment samples were collected from four fish-active ponds and transported to the laboratory for analysis. Bacterial diversity was analyzed using DNA sequencing and antibiotic resistance was tested using the disk diffusion method. The results showed variability of bacterial diversity in the ponds with fish farming activity. Simpson's index indicated that the Habascocha lagoon is the most diverse in bacterial species of the order Enterobacterales (0.8), but the least dominant. The Shannon-Wiener index revealed that it is the most diverse (2.93) and the Margalef index revealed that species richness in this lagoon is high (5.72). Similarity percentage analysis (SIMPER) allowed the identification of the main Enterobacterales with the highest percentage contribution in the frequencies of individuals. In general, the Enterobacterales species isolated showed multi-resistance to the antibiotics used and Escherichia coli was the most resistant.

Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water

Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.

Versatile lifestyles of Edwardsiella: Free-living, pathogen, and core bacterium of the aquatic resistome

Edwardsiella species in aquatic environments exist either as individual planktonic cells or in communal biofilms. These organisms encounter multiple stresses, include changes in salinity, pH, temperature, and nutrients. Pathogenic species such as E. piscicida, can multiply within the fish hosts. Additionally, Edwardsiella species (E. tarda), can carry antibiotic resistance genes (ARGs) on chromosomes and/or plasmids, that can be transmitted to the microbiome via horizontal gene transfer. E. tarda serves as a core in the aquatic resistome. Edwardsiela uses molecular switches (RpoS and EsrB) to control gene expression for survival in different environments. We speculate that free-living Edwardsiella can transition to host-living and vice versa, using similar molecular switches. Understanding such transitions can help us understand how other similar aquatic bacteria switch from free-living to become pathogens. This knowledge can be used to devise ways to slow down the spread of ARGs and prevent disease outbreaks in aquaculture and clinical settings.

Antibiotics usage practices in aquaculture in Bangladesh and their associated factors

Background

Irrational and inappropriate use of antibiotics in aquaculture can contribute to the development of antibiotic resistance.

Objectives

In this study, we aimed to assess antibiotic usage in inland and coastal fish farms in Bangladesh and identify factors associated with this practice.

Methods

We conducted a cross-sectional study to collect antibiotic usage information from 672 fish farmers in Bangladesh. The frequency of use, the types of antibiotics, the purpose of usage, and antibiotic prescribing practices were estimated. Adjusted odds ratios (aOR) were calculated to measure the association between antibiotic usage and factors related to the characteristics of the farms and farmers using multivariable logistic regression models.

Results

Twenty-two farms reported using antibiotics in the last 24 h preceding the interview (3%, 95% CI: 2-5%); 36 farms (5%, 95% CI: 4-7%) in the last 72 h, 141 farms (21%, 95% CI: 18-24%) in the last 14 days, and 478 farms (71%, 68-75%) reported antibiotic usage at least once since the start of their production cycle. Antibiotics usage in the last 14 days preceding the interviews was higher in freshwater fish farms (98%) than in brackish water farms (2%). Oxytetracycline, ciprofloxacin, and amoxicillin were the most frequently used antibiotics. Most of the antibiotics were reported to be used for both therapeutic and prophylactic purposes (71%, 95% CI: 63-78%). Antibiotics used within the last 14 days were mainly advised by feed dealers or drug sellers (51%, 95% CI: 43-60%), followed by farmers themselves (31%, 95% CI: 23-38%) and local service providers (18%, 95% CI, 12-25%). Fish farms having history of antibiotic use within the last 14 days preceding interviews was significantly associated with illness in fish (aOR 1.98, 95% CI:1.21-3.29) compared to farms with healthy fish and fishes cultured in ponds (aOR 9.34, 95% CI: 3.69-23.62) compared to enclosure cultures.

Conclusions

Improvement of fish health through better farming practices and changes in feed dealers' and farmers' attitudes towards self-prescription of antibiotic without veterinarian diagnostics may help to reduce the levels of antibiotic usage and thus contribute to mitigating antimicrobial resistance.

Effects of g-C3N4 on bacterial community and tetracycline resistance genes in two typical sediments in tetracycline pollution remediation

Photocatalysis, as a novel technique, has been widely used for antibiotic pollution remediation in wastewater. In the processes of degradation and removal of antibiotics, the impact of photocatalysts on microenvironment is very important but remains poorly understood. In the present study, the effect of typical photocatalyst g-C3N4 (Graphitic carbon nitride) on microbial community was investigated in two sediment types (riverbed sediment and pig-farm sediment) polluted by tetracycline (TC) in central southern China. The riverbed sediment and pig farm sediment samples were respectively exposed to g-C3N4 (25, 75, 125 mg⋅kg-1) and TC (60, 120, 180 mg⋅L-1) treatments alone or combination for 30 days, respectively. The bacterial community and antibiotic resistance genes (ARGs) of the treated sediments were analyzed by Illumina sequencing and metagenomic sequencing. Studies had shown that: TC, g-C3N4, and TC/g-C3N4 have significant effects on the changes of microbial communities and components in riverbed sediment, but they do not exist in pig farm sediment. The most alterations of microbial taxa were Acidobacteriota, Actinobacteriota, and Desulfobacterota in riverbed sediment, and Elusimicrobiota in the pig farm sediment under various treatments. Through network analysis, it was found that the distribution of microorganisms in the pig farm sediment is more complex and more stable. The addition of g-C3N4 reduced the absolute abundance of ARGs in the two examined sediments, but not significantly changed their relative abundance of ARGs. The g-C3N4 application was beneficial to the removal of TC residues and to the prevention of the generation and transmission of ARGs in sediments. Our results suggested that g-C3N4 was a suitable photocatalyst with excellent application prospect for the removal of TC residues and the control of ARGs in environment.

Development of an inactivated whole cell vaccine through immersion for immunoprophylaxis of Francisella orientalis infections in Nile tilapia (Oreochromis niloticus L.) fingerlings and juveniles

Francisella orientalis infections, known as francisellosis, are one of the most important diseases affecting the production of Nile tilapia, causing high mortality rates in the most susceptible fish stages: fingerlings and juveniles. Antibiotic therapy is the method of choice for treating the disease, as there are no commercially available vaccines. In this study, we developed an inactivated whole-cell vaccine using an isolate of F. orientalis in combination with the aqueous adjuvant Montanide IMS 1312 VG, which was administered to Nile tilapia through immersion. Two immunization trials (1 and 2) were conducted with fish at the fingerling and juvenile stages. For each trial, five different experimental groups were established: a complete vaccine (bacterin in combination with aqueous adjuvant), bacterin, aqueous adjuvant, and positive and negative controls. Thirty days after vaccination, an experimental challenge was performed through intraperitoneal injection of the same F. orientalis isolate. As a result, the vaccinated fingerlings were the only group in which mortality and progression of clinical signs of francisellosis were statistically significantly reduced, although relative percentage of survival (RPS) was low at 50%. In the juvenile group, RPS was higher at 63%, but not statistically significant. Nevertheless, an RPS of only 50% is acceptable for using vaccines in the field. The bacterin and adjuvant treatments alone were not effective, showing an RPS of 37% and 0%, respectively. Post-vaccination mortality was observed in the group exposed only to the adjuvant, which may indicate excessive immune stimulation at this stage. Interestingly, the immune response elicited by the vaccine was unable to eliminate the pathogen from the host; therefore, the surviving animals became carriers. Although the immune response elicited by the vaccine was unable to eliminate the pathogen from the host, this vaccine formulation could be a viable alternative for use in the field and serve as another means of controlling the mortality caused by the pathogen. Our study provides the first report of vaccination, using immersion, against francisellosis at the most susceptible stages of farmed Nile tilapia. Future studies should address the efficiency of immersion vaccines under field conditions.

Governing Antimicrobial Resistance (AMR) in a Changing Climate: A Participatory Scenario Planning Approach Applied to Sweden in 2050

Background

Antimicrobial resistance (AMR) is a growing global crisis with long-term and unpredictable health, social and economic impacts, with which climate change is likely to interact. Understanding how to govern AMR amidst evolving climatic changes is critical. Scenario planning offers a suitable approach. By envisioning alternative futures, stakeholders more effectively can identify consequences, anticipate problems, and better determine how to intervene. This study explored future worlds and actions that may successfully address AMR in a changing climate in a high-income country, using Sweden as the case.

Methods

We conducted online scenario-building workshops and interviews with eight experts who explored: (1) how promising interventions (taxation of antimicrobials at point of sale, and infection prevention measures) could each combat AMR in 2050 in Sweden given our changing climate; and (2) actions to take starting in 2030 to ensure success in 2050. Transcripts were thematically analyzed to produce a narrative of participant validated alternative futures.

Results

Recognizing AMR to be a global problem requiring global solutions, participants looked beyond Sweden to construct three alternative futures: (1) "Tax Burn Out" revealed taxation of antimicrobials as a low-impact intervention that creates inequities and thus would fail to address AMR without other interventions, such as infection prevention measures. (2) "Addressing the Basics" identified infection prevention measures as highly impactful at containing AMR in 2050 because they would contribute to achieving the Sustainable Development Goals (SDGs), which would be essential to tackling inequities underpinning AMR and climate change, and help to stabilize climate-induced mass migration and conflicts; and (3) "Siloed Nations" described a movement toward nationalism and protectionism that would derail the "Addressing the Basics" scenario, threatening health and wellbeing of all. Several urgent actions were identified to combat AMR long-term regardless which future un-folds, such as global collaboration, and a holistic approach where AMR and climate change are addressed as interlinked issues.

Conclusion

Our participatory scenario planning approach enabled participants from different sectors to create shared future visions and identify urgent actions to take that hinge on global collaboration, addressing AMR and climate change together, and achieving the SDGs to combat AMR under a changing climate.

Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as 'High Priority Critically Important Antimicrobials'. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.

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.

Atlantic Salmon (Salmo salar) bacterial and viral innate immune responses are not impaired by florfenicol or tetracycline administration

Antibiotics are used to treat bacterial infections in fish aquaculture, and these drugs can interact with immune cells/the immune system and potentially leave fish vulnerable to viral, fungal, parasitic, or other bacterial infections. However, the effects of antibiotics on fish immunity have largely been overlooked by the aquaculture industry. We tested, at 12 and 20 °C, whether tetracycline and florfenicol (the most commonly used antibiotics in commercial aquaculture), affected the Atlantic salmon's capacity to respond to bacterial or viral stimulation. Atlantic salmon were acclimated to 12 or 20 °C and fed with tetracycline or florfenicol (100 and 10 mg kg of body weight^-1 day^-1, respectively) medicated feed for 15 or 10 days, respectively. Thereafter, we evaluated their immune function prior to, and after, an intraperitoneal injection of Forte Micro (containing inactivated cultures of Aeromonas salmonicida, Vibrio anguillarum, Vibrio ordalii and Vibrio salmonicida) or the viral mimic polyriboinosinic polyribocytidylic acid (pIC). We measured the transcript expression levels of 8 anti-bacterial and 8 anti-viral putative biomarker genes, and the innate (leukocyte respiratory burst, plasma lysozyme activity and hemolytic activity of the alternative complement pathway) and cellular (relative number of erythrocytes, lymphocytes and thrombocytes, and granulocytes such as monocytes and neutrophils) responses to these challenges. Overall, we only found a few minor effects of either tetracycline or florfenicol on immune gene expression or function at either temperature. Although several studies have reported that antibiotics may negatively affect fish immune responses, our results show that industry-relevant dietary tetracycline and florfenicol treatments do not substantially impact the salmon's innate immune responses. Currently, this is the most comprehensive study on the effects of antibiotics administrated according to industry protocols on immune function in Atlantic salmon.

Factors influencing antimicrobial resistance in the European food system and potential leverage points for intervention: A participatory, One Health study

Introduction

Antimicrobial resistance (AMR) is a global crisis that evolves from a complex system of factors. Understanding what factors interact is key to finding solutions. Our objective was to identify the factors influencing AMR in the European food system and places to intervene.

Materials and methods

We conducted two workshops involving participants with diverse perspectives to identify the factors influencing AMR and leverage points (places) to target interventions. Transcripts were open coded for factors and connections, then transcribed into Vensim 8.0.4 to develop a causal loop diagram (CLD) and compute the number of feedback loops. Thematic analysis followed to describe AMR dynamics in Europe’s food system and places for intervention. The CLD and themes were confirmed via participant feedback.

Results

Seventeen participants representing human, animal and agricultural sectors identified 91 CLD factors and 331 connections. Seven themes (e.g., social and economic conditions) describing AMR dynamics in Europe’s food system, five ‘overarching factors’ that impact the entire CLD system (e.g., leadership) and fourteen places for intervention (e.g., consumer demand) emerged from workshop discussions. Most leverage points fell on highly networked feedback loops suggesting that intervening at these places may create unpredictable consequences.

Conclusions

Our study produced a CLD of factors influencing AMR in Europe’s food system that implicates sectors across the One Health spectrum. The high connectivity between the CLD factors described by participants and our finding that factors are connected with many feedback mechanisms underscores the complexity of the AMR problem and the challenge with finding long-term solutions. Identifying factors and feedbacks helped identify relevant leverage points in the system. Some actions, such as government’s setting AMU standards may be easier to implement. These actions in turn can support multi-pronged actions that can help redefine the vision, values and goals of the system to sustainably tackle AMR.

A Risk-Based Approach for Managing Aquaculture Used Oxytetracycline-Induced TetR in Surface Water Across Taiwan Regions

Oxytetracycline (OTC), one of the most important antibiotics in aquaculture industry, has been linked to emergence of antibiotic resistant genes in the aquatic environment. Given rapid growth of the aquaculture industry and unregulated use of antibiotics, it is necessary to implement measures to mitigate the impact of antibiotic resistance risk on environmental and human health. However, there is a lack of quantitative models to properly assess risk of antibiotic resistance associated with environmentally relevant antibiotic residues. To address this issue, here we developed a computational framework to assess antibiotic resistance risk posed by low-concentration OTC in aquaculture ponds and rivers across Taiwan regions. To this end, estimated amount of aquaculture used OTC as a crucial input parameter was incorporated into a multimedia fugacity model to predict environmental concentrations of OTC in surface water/sediment. A pharmacodynamic-based dose–response model was used to characterize the OTC concentration–antibiotic resistance relationships. The risk of antibiotic resistance selection in an aquatic environment could be assessed based on a probabilistic risk model. We also established a control measure model to manage the risks of substantial OTC-induced antibiotic resistance impacts. We found that OTC residues were likely to pose a high risk of tetracycline resistance (tetR) genes selection in aquaculture ponds among all the study basins, whereas risk of tetR genes selection in rivers experienced a variably changing fashion. We also showed that it was extremely difficult to moderate the tetR genes selection rates to less than 10% increase in aquaculture ponds situated at northeastern river basins in that the minimum reductions on OTC emission rates during spring, summer, and autumn were greater than 90%. On the other hand, water concentrations of OTC during spring and summer in southwestern rivers should be prioritized to be severely limited by reducing 67 and 25% of OTC emission rate, respectively. Overall, incorporating a computational fugacity model into a risk assessment framework can identify relative higher risk regions to provide the risk-based control strategies for public health decision-making and development of robust quantitative methods to zero-in on environment with high risk of tetR genes selection in relation to aquaculture-used pharmaceutical residues.

Autogenous vaccines in aquaculture: Tool to combat resistance of bacteria to antibiotics?

New technological progress and increased demands for fish as a source of animal protein are driving significant growth of aquaculture production. Intensification of production increases the severity and frequency of infectious disease outbreaks, and so requires significant effort to prevent and control disease. Because of the global crisis of bacterial resistance to antibiotics, the use of antibiotics in aquaculture is increasingly subjected to strict control and regulatory measures, leading to potential misuse. The lack of availability of approved veterinary medical products for use in aquaculture, combined with the risk of drug resistance development and antibiotic residues in fish flesh or water, support the development of preventive actions, including vaccines. However, the diversity of species and aquaculture production methods, including epidemiological units and their links, results in economic challenges for commercial vaccine development and authorization. As a possible response to the increasing demand for less antibiotic use in fish farms, and to the expenses associated with novel veterinary product development, there is a need for increased use of safe and effective autogenous vaccines in aquaculture. Regulatory processes for autogenous vaccine production, approval and application should recognize the specificities of epidemiological units and their links in aquatic animal production facilities. The joint efforts of regulatory authorities, producers, and veterinary services to follow veterinary biosecurity principles, including risk analysis, surveillance, and selection/prioritization of pathogens, are essential to provide maximum safety and efficacy of autogenous vaccines as disease prevention and control tools within larger areas, such as compartments and zones, and allow for reductions in antibiotic use.

A hybrid DNA sequencing approach is needed to properly link genotype to phenotype in multi-drug resistant bacteria

Antibiotic resistance genes (ARGs) are now viewed as emerging contaminants posing a potential worldwide human health risk. The degree to which ARGs are transferred to other bacteria via mobile genetic elements (MGEs), including insertion sequences (ISs), plasmids, and phages, has a strong association with their likelihood to function as resistance transfer determinants. Consequently, understanding the structure and function of MGEs is paramount to assessing future health risks associated with ARGs in an environment subjected to strong antibiotic pressure. In this study we used whole genome sequencing, done using MinION and HiSeq platforms, to examine antibiotic resistance determinants among four multidrug resistant bacteria isolated from fish farm effluent in Jeju, South Korea. The combined data was used to ascertain the association between ARGs and MGEs. Hybrid assembly using HiSeq and MinION reads revealed the presence of IncFIB(K) and pVPH2 plasmids, whose sizes were verified using pulsed field gel electrophoresis. Twenty four ARGs and 95 MGEs were identified among the 955 coding sequences annotated on these plasmids. More importantly, 22 of 24 ARGs conferring resistance to various antibiotics were found to be located near MGEs, whereas about a half of the ARGs (11 out of 21) were so in chromosomes. Our results also suggest that the total phenotypic resistance exhibited by the isolates was mainly contributed by these putatively mobilizable ARGs. The study gives genomic insights into the origins of putatively mobilizable ARGs in bacteria subjected to selection pressure.

Updating the Role of Probiotics, Prebiotics, and Synbiotics for Tilapia Aquaculture as Leading Candidates for Food Sustainability: a Review

Tilapia production has significantly increased over the past few years due to the adoption of semi-intensive and intensive aquaculture technologies. However, these farming systems have subjected the fish to stressful conditions that suppress their immunity, hence exposing them to various pathogens. The application of antibiotics and therapeutics to enhance disease resistance, survival, and growth performance in aquaculture has been recently banned due to the emergence of antibiotic-resistant bacteria that pose a serious threat to the environment and consumers of aquatic organisms. Hence, the need for an alternative approach based on sustainable farming practices is warranted. Probiotic, prebiotic, and synbiotic use in tilapia production is considered a viable, safe, and environmentally friendly alternative that enhances growth performance, feed utilization, immunity, disease resistance, and fish survival against pathogens and environmental stress. Their inclusion in fish diets and or rearing water improves the general wellbeing of fish. Hence, this review aims at presenting research findings from the use of probiotics, prebiotics, and synbiotics and their effect on survival, growth, growth performance, gut morphology, microbial abundance, enzyme production, immunity, and disease resistance in tilapia aquaculture, while highlighting several hematological, blood biochemical parameters, and omics techniques that have been used to assess fish health. Furthermore, gaps in existing knowledge are addressed and future research studies have been recommended.

Impact of cinnamaldehyde on innate immunity and immune gene expression in Channa striatus against Aphanomyces invadans

The effect of cinnamaldehyde (CM) enriched diet on immunity and cytokine gene expression in Channa striatus against Aphanomyces invadans is reported. C. striatus was uniformly divided into eight groups (n = 25 fish each) and fed with formulated diets with 0, 5, 10, and 15 mg kg^-1 CM enriched diet. In healthy and infected groups fed with 5 mg kg^-1 diet the leukocytes count increased significantly after 4th week; with 10 mg kg^-1 CM diet the increase manifested after 6th week, but with 15 mg kg^-1 not even after 8th week. In both groups, 5 mg kg^-1 CM diet resulted in a significant increase in the serum total protein, albumin, and globulin levels after 4th week, whereas with other diets this effect was observed only after 6th week. Similarly, with any enriched diet the lysozyme activity increased significantly, but with 15 mg kg^-1 CM diet only after 6th week. In both groups the complement activity and lymphocyte production increased significantly when fed with 5 mg kg^-1 CM diet after 4th week while with other enriched diets only after 6th week. The phagocytic activity increased significantly in both groups fed with 5 mg kg^-1 CM diet after 6th week, whereas the SOD activity increased after 4th week. The IgM production increased significantly in both groups fed with 5 mg kg^-1 CM diet after 2nd week, while with 5 and 10 mg kg^-1 CM diet after 4th week. In both groups, the expression of CXCR3α was significant on 4th week when fed with 10 mg kg^-1 CM diet, while in the healthy group fed with 15 mg kg^-1 CM diet the expression manifested earlier than 4th week. However, when fed with 10 and 15 mg kg^-1 CM diets the increase was observed on 6th week; whereas, the expression of MHC-I reached the maximum on 6th week with any enriched diet. The results indicate that in C. striatus the innate immunity and expression of cytokine and immune related genes were significantly modulated when fed with 5 mg kg^-1 CM diet on 4th week against A. invadans.

Water volume influences antibiotic resistomes and microbiomes during fish corpse decomposition

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.

Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail

Consumption of prawns as a protein source has been on the rise worldwide with seafood identified as the predominant attributable source of human vibriosis. However, surveillance of non-cholera Vibrio is limited both in public health and in food. Using a population- and market share-weighted study design, 211 prawn samples were collected and cultured for Vibrio spp. Contamination was detected in 46 % of samples, and multiple diverse Vibrio isolates were obtained from 34 % of positive samples. Whole genome sequencing (WGS) and phylogenetic analysis illustrated a comprehensive view of Vibrio species diversity in prawns available at retail, with no known pathogenicity markers identified in Vibrio parahaemolyticus and V. cholerae. Antimicrobial resistance genes were found in 77 % of isolates, and 12 % carried genes conferring resistance to three or more drug classes. Resistance genes were found predominantly in V. parahaemolyticus, though multiple resistance genes were also identified in V. cholerae and V. vulnificus. This study highlights the large diversity in Vibrio derived from prawns at retail, even within a single sample. Although there was little evidence in this study that prawns are a major source of vibriosis in the UK, surveillance of non-cholera Vibrio is very limited. This study illustrates the value of expanding WGS surveillance efforts of non-cholera Vibrios in the food chain to identify critical control points for food safety through the production system and to determine the full extent of the public health impact.

Langmuir Monolayer Techniques for the Investigation of Model Bacterial Membranes and Antibiotic Biodegradation Mechanisms

The amounts of antibiotics of anthropogenic origin released and accumulated in the environment are known to have a negative impact on local communities of microorganisms, which leads to disturbances in the course of the biodegradation process and to growing antimicrobial resistance. This mini-review covers up-to-date information regarding problems related to the omnipresence of antibiotics and their consequences for the world of bacteria. In order to understand the interaction of antibiotics with bacterial membranes, it is necessary to explain their interaction mechanism at the molecular level. Such molecular-level interactions can be probed with Langmuir monolayers representing the cell membrane. This mini-review describes monolayer experiments undertaken to investigate the impact of selected antibiotics on components of biomembranes, with particular emphasis on the role and content of individual phospholipids and lipopolysaccharides (LPS). It is shown that the Langmuir technique may provide information about the interactions between antibiotics and lipids at the mixed film surface (π–A isotherm) and about the penetration of the active substances into the phospholipid monolayer model membranes (relaxation of the monolayer). Effects induced by antibiotics on the bacterial membrane may be correlated with their bactericidal activity, which may be vital for the selection of appropriate bacterial consortia that would ensure a high degradation efficiency of pharmaceuticals in the environment.

Twenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia

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.

Environmental performance of blue foods

Fish and other aquatic foods (blue foods) present an opportunity for more sustainable diets^1,2. Yet comprehensive comparison has been limited due to sparse inclusion of blue foods in environmental impact studies^3,4 relative to the vast diversity of production⁵. Here we provide standardized estimates of greenhouse gas, nitrogen, phosphorus, freshwater and land stressors for species groups covering nearly three quarters of global production. We find that across all blue foods, farmed bivalves and seaweeds generate the lowest stressors. Capture fisheries predominantly generate greenhouse gas emissions, with small pelagic fishes generating lower emissions than all fed aquaculture, but flatfish and crustaceans generating the highest. Among farmed finfish and crustaceans, silver and bighead carps have the lowest greenhouse gas, nitrogen and phosphorus emissions, but highest water use, while farmed salmon and trout use the least land and water. Finally, we model intervention scenarios and find improving feed conversion ratios reduces stressors across all fed groups, increasing fish yield reduces land and water use by up to half, and optimizing gears reduces capture fishery emissions by more than half for some groups. Collectively, our analysis identifies high-performing blue foods, highlights opportunities to improve environmental performance, advances data-poor environmental assessments, and informs sustainable diets.

Granulomatous bacterial diseases in fish: An overview of the host's immune response

Bacterial diseases represent the main impediment to the development of fish aquaculture. Granulomatous diseases caused by bacteria lead to fish culture losses by high mortality rates and slow growth. Bacteria belonging to genera Streptococcus spp., Mycobacterium sp., Nocardia sp., Francisella sp., and Staphylococcus sp. have been implicated in the development of granulomatous processes. The granuloma formation and the fish's immune response continue to be the subject of scientific research. In fish, the first defense line is constituted by non-specific humoral factors through growth-inhibiting substances such as transferrin and antiproteases, or lytic effectors as lysozyme and antimicrobial peptides, and linking with non-specific phagocyte responses. If the first line is breached, fish produce antibody constituents for a specific humoral defense inhibiting bacterial adherence, as well as the mobilization of non-phagocytic host cells and counteracting toxins from bacteria. However, bacteria causing granulomatous diseases can be persistent microorganisms, difficult to eliminate that can cause chronic diseases, even using some immune system components to survive. Understanding the infectious process leading to granulomatosis and how the host's immune system responds against granulomatous diseases is crucial to know more about fish immunology and develop strategies to overcome granulomatous diseases.

Characteristics of bacterial community and ARGs profile in engineered goldfish tanks with stresses of sulfanilamide and copper

Abuse of antibiotics in aquaculture have been alarming and might aggravate spread of resistance genes in the environment. Holistic ARGs proliferation checks require deeper analyses of coupled absolute abundances in 16S rRNA bacteria communities at the phylum level to detect biomarkers. Sulfanilamide (sul) and copper II sulfate (CuSO₄ II) were, therefore, designed and added as separate or combined treatments in 9 replicate engineered goldfish tanks comprising 3 individual sul, 3 CuSO₄ II, 3 (sul + CuSO₄ II) combinations, and 3 controls within 180 days. The DNA from water and fish guts was sequenced under qPCR to determine 16S rRNA bacteria biomarkers co-occurring with the correspondent ARGs. Combined chemical addition at 0.8-1.5 mg sul + 0.5-1.0 mg CuSO₄ II/3 L of tank waters reduced sequenced 16S rRNA bacteria absolute abundances in fish gut and water samples while portraying the biomarkers. Absolute abundances of the entire 16S rRNA bacteria was higher in fish guts (3.4 × 10¹⁴-4.9 × 10⁸ copies/g) than water samples (1.5 × 10⁹-2.6 × 10¹⁵ copies/L), respectively. Much as sul 1(log) were dominant over intl 1(log) genes, and their fundamental profiles were also higher in the fish guts than water samples; the Spearman's correlation analyses revealed positive relationship (p < 0.01 and r = 0.873) among the biomarkers of both ARG pairs at the phylum level and the physicochemical parameters. In the fish gut and water samples ratios, Bacteroidetes (10-85:12-85%) > Proteobacteria (10-50:15-65%) > Planktomycetes (10-52:8-25%) featured prominently based on LEfSe use as the hot-spotted biomarkers, hence justifying its higher prospects towards innovative environmental microbiological and biotechnological studies.

Systems-thinking approach to identify and assess feasibility of potential interventions to reduce antibiotic use in tilapia farming in Egypt

Antibiotics are used in aquaculture to maintain the health and welfare of stocks; however, the emergence and selection of antibiotic resistance in bacteria poses threats to humans, animals and the environment. Mitigation of antibiotic resistance relies on understanding the flow of antibiotics, residues, resistant bacteria and resistance genes through interconnecting systems, so that potential solutions can be identified and issues around their implementation evaluated. Participatory systems-thinking can capture the deep complexity of a system while integrating stakeholder perspectives. In this present study, such an approach was applied to Nile tilapia (Oreochromis niloticus) production in the Nile Delta of Egypt, where disease events caused by antibiotic-resistant pathogens have been reported. A system map was co-produced with aquaculture stakeholders at a workshop in May 2018 and used to identify hotspots of antibiotic use, exposure and fate and to describe approaches that would promote fish health and thus reduce antibiotic use. Antibiotics are introduced into the aquaculture system via direct application for example in medicated feed, but residues may also be introduced into the system through agricultural drainage water, which is the primary source of water for most fish farms in Egypt. A follow-up survey of stakeholders assessed the perceived feasibility, advantages and disadvantages of potential interventions. Interventions that respondents felt could be implemented in the short-term to reduce antibiotic usage effectively included: more frequent water exchanges, regular monitoring of culture water quality parameters, improved storage conditions for feed, use of probiotics and greater access to farmer and service providers training programmes. Other potential interventions included greater access to suitable and rapid diagnostics, high quality feeds, improved biosecurity measures and genetically-improved fish, but these solutions were expected to be achieved as long-term goals, with cost being of one of the noted barriers to implementation. Identifying feasible and sustainable interventions that can be taken to reduce antibiotic use, and understanding implementation barriers, are important for addressing antibiotic resistance and ensuring the continued efficacy of antibiotics. This is vital to ensuring the productivity of the tilapia sector in Egypt. The approach taken in the present study provides a means to identify points in the system where the effectiveness of interventions can be evaluated and thus it may be applied to other food production systems to combat the problem of antibiotic resistance.

Characterisation of Colistin -Resistant Enterobacterales and Acinetobacter Strains Carrying mcr Genes from Asian Aquaculture Products

Aquaculture systems are widely recognised as hotspots for horizontal gene transfer, and the need for screening for bacteria carrying antimicrobial resistance genes in aquaculture systems is becoming more important. In this study, we characterised seventeen bacterial strains (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and A. nosocomialis) resistant to colistin originating from retailed aquaculture products imported from Vietnam to the Czech Republic. The mcr-1.1 gene was found located on plasmid types IncHI2, IncI2, and IncX4, as well as on the rarely described plasmid types IncFIB-FIC and IncFIB(K), phage-like plasmid p0111, and on the chromosome of E. coli. One E. coli strain carried the mcr-3.5 gene on IncFII(pCoo) plasmid in addition to the mcr-1.1 gene located on IncHI2 plasmid. K. pneumoniae was found to carry the mcr-1.1 and mcr-8.2 genes on IncFIA(HI1) plasmid. The mcr-4.3 gene was found on similar untypeable plasmids of A. baumannii and A. nosocomialis strains, pointing to the possible interspecies transfer of plasmids carrying the mcr-4 gene. Our results highlight that some aquaculture products of Asian origin can represent an important source of variable plasmids carrying mcr genes. The results showed an involvement of phages in the incorporation of the mcr-1 gene into plasmids or the chromosome in E. coli strains from aquaculture. The detection of E. coli with the mcr-1 gene in the chromosome points to the risks associated with the stabilisation of the mcr genes in the bacterial chromosome.

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.

AMR-Intervene: a social-ecological framework to capture the diversity of actions to tackle antimicrobial resistance from a One Health perspective

The global threat of antimicrobial resistance (AMR) requires coordinated actions by and across different sectors. Increasing attention at the global and national levels has led to different strategies to tackle the challenge. The diversity of possible actions to address AMR is currently not well understood from a One Health perspective. AMR-Intervene, an interdisciplinary social-ecological framework, describes interventions to tackle AMR in terms of six components: (i) core information about the publication; (ii) social system; (iii) bio-ecological system; (iv) triggers and goals; (v) implementation and governance; and (vi) assessment. AMR-Intervene provides a broadly applicable framework, which can inform the design, implementation, assessment and reporting of interventions to tackle AMR and, in turn, enable faster uptake of successful interventions to build societal resilience to AMR.