Antibiotic resistance genes and their links with bacteria and environmental factors in three predominant freshwater aquaculture modes

Review of quorum-quenching probiotics: A promising non-antibiotic-based strategy for sustainable aquaculture

The emergence of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquaculture underscores the urgent need for alternative veterinary strategies to combat antimicrobial resistance (AMR). These measures are vital to reduce the likelihood of entering a post-antibiotic era. Identifying environmentally friendly biotechnological solutions to prevent and treat bacterial diseases is crucial for the sustainability of aquaculture and for minimizing the use of antimicrobials, especially antibiotics. The development of probiotics with quorum-quenching (QQ) capabilities presents a promising non-antibiotic strategy for sustainable aquaculture. Recent research has demonstrated the effectiveness of QQ probiotics (QQPs) against a range of significant fish pathogens in aquaculture. QQ disrupts microbial communication (quorum sensing, QS) by inhibiting the production, replication, and detection of signalling molecules, thereby reducing bacterial virulence factors. With their targeted anti-virulence approach, QQPs have substantial promise as a potential alternative to antibiotics. The application of QQPs in aquaculture, however, is still in its early stages and requires additional research. Key challenges include determining the optimal dosage and treatment regimens, understanding the long-term effects, and integrating QQPs with other disease control methods in diverse aquaculture systems. This review scrutinizes the current literature on antibiotic usage, AMR prevalence in aquaculture, QQ mechanisms and the application of QQPs as a sustainable alternative to antibiotics.

Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria

Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of Pseudomonodota and Bacteriodota, notably the genera Flavobacterium, Aquirufa, Acidovorax, Polynucleobacter, and Limnohabitans. The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with Flavobacterium exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of Polynucleobacter and Limnohabitans. There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes erm(B), erm(F), mph(E), msr(E) (macrolides); tet(C), tet(O), tet(W), tet(Q) and tet(X) (tetracyclines); sul1 and sul2 (sulphonamides); and cfxA3, cfxA6 (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems blaOXA-58 and blaIMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring.

Source Attribution of Antibiotic Resistance Genes in Estuarine Aquaculture: A Machine Learning Approach

Aquaculture located in urban river estuaries, where other anthropogenic activities may occur, has an impact on and may be affected by the environment where they are inserted, namely by the exchange of antimicrobial resistance genes. The latter may ultimately, through the food chain, represent a source of resistance genes to the human resistome. In an exploratory study of the presence of resistance genes in aquaculture sediments located in urban river estuaries, two machine learning models were applied to predict the source of 34 resistome observations in the aquaculture sediments of oysters and gilt-head sea bream, located in the estuaries of the Sado and Lima Rivers and in the Aveiro Lagoon, as well as in the sediments of the Tejo River estuary, where Japanese clams and mussels are collected. The first model included all 34 resistomes, amounting to 53 different antimicrobial resistance genes used as source predictors. The most important antimicrobial genes for source attribution were tetracycline resistance genes tet(51) and tet(L); aminoglycoside resistance gene aadA6; beta-lactam resistance gene blaBRO-2; and amphenicol resistance gene cmx_1. The second model included only oyster sediment resistomes, amounting to 30 antimicrobial resistance genes as predictors. The most important antimicrobial genes for source attribution were the aminoglycoside resistance gene aadA6, followed by the tetracycline genes tet(L) and tet(33). This exploratory study provides the first information about antimicrobial resistance genes in intensive and semi-intensive aquaculture in Portugal, helping to recognize the importance of environmental control to maintain the integrity and the sustainability of aquaculture farms.

Dynamic Evolution of Aquaculture along the Bohai Sea Coastline and Implications for Eco-Coastal Vegetation Restoration Based on Remote Sensing

The expansion and intensification of coastal aquaculture around the Bohai Sea in China has reduced the tidal flats and damaged the coastal vegetation environment. However, there are few studies on the relationship between the evolution of coastal aquaculture and the variability of coastal vegetation, which limits our understanding of the impact of human activities on the coastal ecosystem. In this study, based on remote sensing technology, we firstly used a combination of a neural network classifier and manual correction to monitor the long-term dynamic changes in aquaculture in the Bohai Sea from 1984 to 2022. We then analyzed its evolution, as well as the relationship between the evolution of coastal aquaculture and the variability of coastal vegetation, in detail. Our study had three main conclusions. Firstly, the aquaculture along the coast of the Bohai Sea showed an expanding trend from 1984 to 2022, with an increase of 538%. Secondly, the spatiotemporal changes in the aquaculture centroids in different provinces and cities varied. The centroid of aquaculture in Liaoning Province was mainly distributed in the Liaodong Peninsula, and moved northwest; that in Hebei Province was distributed in the northeast and moved with no apparent pattern; the centroid of aquaculture in Tianjin was mainly distributed in the southeast and moved westward; and the centroid of aquaculture in Shandong Province was mainly distributed in the northwest and moved in a northwesterly direction. Finally, the expansion of aquaculture of the Bohai Sea has increased the regional NDVI and length of the corresponding coastline, and has made coastlines move toward the sea. Our results provide reliable data support and reference for ecologically managing aquaculture and coastal environmental protection in the Bohai Sea.

Bacterial heavy metal resistance related to environmental conditions

Contaminated water bodies such as rivers provide reservoirs for bacterial resistance. This field study tested the water quality and the bacterial resistance to heavy metals of Qishan River water pollution. Wastewater discharged to environmental surface waters is a major pathway of heavy metals and heavy metal-resistant bacteria. Contaminated water bodies such as rivers provide reservoirs for bacterial resistance. This field study tested the water quality and bacterial resistance to heavy metals of Qishan River water pollution. Guided by our research hypothesis that an overall increase in downstream heavy metal resistance levels was following an increase in human settlements were eight sites sampled along the Qishan River. These were situated upstream and downstream to the confluence of the Qishan River with the Kaoping River. In the laboratory bacterial heavy metal resistance was bio-assayed by disk diffusion and micro-dilution with six widely used heavy metals. The comparison of bacterial resistance was among Qishan River upstream sites (sites 1-6) and downstream sites (sites 7-9). Multi-drug-resistant bacteria and co-resistance against heavy metals and antibacterials appeared at site 8. This research discusses the correlation between environmental factors, and antibacterial and heavy metal resistance. The results provide stakeholders and authorities responsible for environmental pollution with a reference for risk assessment and management of bacterial resistance.

Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: Geographical differentiation and corresponding drivers

Antibiotic resistance genes (ARGs), emerging environmental contaminants, have become challenges of public health security. However, the distribution and drivers of ARGs, especially high-risk ARGs, in large-scale aquaculture sediments remain unknown. Here, we collected sediment samples from 40 crayfish ponds in seven main crayfish culture provinces in China and then investigated the distribution and risk of ARGs based on high-throughput sequencing and quantitative PCR techniques. Our results suggested that aquaculture sediment was potential reservoir of ARGs and the abundance of aadA-02 was the highest. High-risk ARG (floR) was also prevalent in the sediment and was the most abundant in Jiangsu Province, where opportunistic pathogens were also enriched. The abundance of floR was positively correlated with different environmental factors, such as total phosphorus in water and total carbon in sediment. In addition, Mycobacterium sp., opportunistic pathogenic bacteria, might be potential host for floR. Furthermore, the potential propagation pathway of ARGs was from sediment to crayfish gut, and Bacteroidetes and Proteobacteria might be the main bacterial groups responsible for the proliferation of ARGs. Generally, our results illustrate that pond sediment may be an ARG reservoir of aquatic animals. Meanwhile, our study helps develop valuable strategies for accessing risks and managing ARGs.

Are microplastics in aquaculture an undeniable driver in accelerating the spread of antibiotic resistance genes?

Aquaculture products have been a key source of protein in the human food supply. Contamination by microplastics and antibiotic resistance genes (ARGs) directly affects food quality and safety. Plastic fishing gear and the long-term misuse of antibiotics result in the persistent residue, migration, and spread of microplastics and ARGs in the aquaculture environment, causing in ecological imbalance and endangering human security. Microplastics can act as "petri dishes" for the reproduction, communication, and spread of ARGs, which adds an additional layer of complexity to the global issues surrounding microplastics and ARGs. Aquaculture has become an important source of microplastics and ARGs in natural waters. Accordingly, this paper mainly discusses the contribution of aquaculture to the presence of microplastics and ARGs in aquatic ecosystems. Microplastics and ARGs can (1) affect the production and quality of aquatic products; (2) influence the development and reproduction of aquatic organisms; and (3) accelerate the spread of resistant bacteria. How to eliminate microplastics and ARGs and block their transmission has become a worldwide problem. Actually, further research is required to understand the scale and scope of these effects.

Degradation of Sulfonamides by UV/Electrochemical Oxidation and the Effects of Treated Effluents on the Bacterial Community in Surface Water

This study evaluated the effects of ultraviolet (UV) photolysis combined with electrochemical oxidation on sulfonamides (SAs) as well as its treated effluent on the bacterial community in surface water. In terms of degradation rate, the best anode material for electrochemical oxidation was Ti/RuO2-IrO2, which had the highest degradation kinetic constant compared to Ti/Ta2O5-IrO2 and Ti/Pt. Experiments showed the highest degradation rate of SAs at 8.3 pH. Similarly, increasing the current leads to stronger degradation due to the promotion of free chlorine production, and its energy consumption rate decreases slightly from 73 to 67 W h/mmol. Compared with tap water, the kinetic constants decreased by 20-62% for SAs in three different surface water samples, which was related to the decrease in free chlorine. When extending the reaction time to 24 h, the concentrations of chemical oxygen demand and total organic carbon decreased by approximately 30-40%, indicating that the SAs and their products could be mineralized. The diversity analysis showed that the effluents influenced the richness and diversity of the bacterial community, particularly in the 4 h sample. Additionally, there were 86 operational taxonomic units common to all samples, excluding the 4 h sample; significant differences were derived from changes in the Actinobacteriota and Bacteroidota phyla. The toxicity of the products might explain these changes, and these products could be mineralized, as observed in the 24 h sample. Therefore, the extension of treatment time would greatly reduce the ecological harm of treated effluent and ensure that the UV/electrochemical process is a feasible treatment option. Overall, this study provides valuable insight into the optimization and feasibility of UV/electrochemical processes as a sustainable treatment option for sulfonamide-contaminated water sources, emphasizing the importance of considering ecological impacts and the need for extended treatment times that address environmental concerns and ensuring improved water quality.

Linking pharmaceutical residues to dissolved organic matter and aquatic bacterial communities in a highly urbanized bay

Pharmaceuticals are causing environmental concerns associated with their widespread distribution in aquatic ecosystems. The environmental fate and behavior of pharmaceutical residues are related to dissolved organic matter and bacterial communities, both of which are strongly influenced by human activities. However, the relationships among pharmaceutical pollution, dissolved organic matter pool, and bacterial community structure under the pressure of human activities are still unclear, especially in highly urbanized bay areas. In this study, we investigated the occurrence and distribution of 35 pharmaceuticals in a typical urbanized bay (Hangzhou Bay) in Eastern China, and analyzed their relationships with dissolved organic matter and aquatic bacterial community structure. The target pharmaceuticals were ubiquitously detected in surface water samples, with their concentrations ranging from undetectable to 263 ng/L. The detected pharmaceuticals were mostly sulfonamides, macrolides, antidepressants, and metabolites of stimulants. Significant positive correlations were observed between the concentrations of pharmaceuticals and the intensity of human activities. Strong correlations also emerged between the concentration of antidepressants and the speed of urban expansion, as well as between the concentration of cardiovascular drugs and the population density or nightlight index. Three fluorescent components (protein-like C1, terrestrial humic-like C2, protein tryptophan-like C3) were significantly positively correlated with the total concentration of pharmaceuticals. Pharmaceutical pollution reshaped aquatic bacterial communities, based on the close correlation observed between pharmaceutical concentration and bacterial community structure. The results elucidate the potential dynamics of dissolved organic matter pool and aquatic bacterial communities in response to pharmaceutical pollution in urbanized bay ecosystems.

Distribution and drivers of antibiotic resistance genes in brackish water aquaculture sediment

Brackish water aquaculture has brought numerous economic benefits, whereas anthropogenic activities in aquaculture may cause the dissemination of antibiotic resistance genes (ARGs) in brackish water sediments. The intricate relationships between environmental factors and microbial communities as well as their role in ARGs dissemination in brackish water aquaculture remain unclear. This study applied PCR and 16S sequencing to identify the variations in ARGs, class 1 integron gene (intI1) and microbial communities in brackish water aquaculture sediment. The distribution of ARGs in brackish water aquaculture sediment was similar to that in freshwater aquaculture, and the sulfonamide resistance gene sul1 was the indicator of ARGs. Proteobacteria and Firmicutes were the dominant phyla, and Paenisporosarcina (p_ Firmicutes) was the dominant genus. The results of correlation, network and redundancy analysis indicated that the microbial community in the brackish water aquaculture sediment was function-driven. The neutral model and variation partitioning analysis were used to verify the ecological processes of the bacterial community. The normalized stochasticity ratio showed that pond bacteria community was dominated by determinacy, which was affected by aquaculture activities. The total nitrogen and organic matter influenced the abundance of ARGs, while Proteobacteria and Thiobacillus (p_Proteobacteria) were the key antibiotic-resistant hosts. Our study provides insight into the prevalence of ARGs in brackish water aquaculture sediments, and indicates that brackish water aquaculture is a reservoir of ARGs.