Prevalence and distribution analysis of antibiotic resistance genes in a large-scale aquaculture environment

The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs

In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.

Microplastics enhance the prevalence of antibiotic resistance genes in mariculture sediments by enriching host bacteria and promoting horizontal gene transfer

Microplastics (MPs) and antibiotic resistance genes (ARGs) pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts. However, the understanding of how MP properties influence ARG prevalence in mariculture sediments remains limited. Herein, the polystyrene (PS) and polyvinyl chloride (PVC) MPs with different sizes (20-120 μm and 0.5-2.0 mm) were selected to evaluate their impacts and underlying mechanisms driving ARGs dissemination. The results showed that PS and PVC MPs increased the relative abundance of ARGs by 1.41-2.50-fold and 2.01-2.84-fold, respectively, compared with control, particularly high-risk genes. The polymer type effect was identified as more influential than the size effect in driving the sediment resistome evolution. PVC shifted the microbial community assembly from stochastic to deterministic processes, thus enriching ARG host pathogens. Furthermore, the highly hydrophobic PS not only recruited the host bacteria colonization but also facilitated ARG exchange within the plastisphere. The exogenous additives released by PVC (e.g., heavy metals, bisphenol A, and tridecyl ester) and the particles synergistically promoted ARG conjugative transfer by inducing oxidative stress and enhancing cell membrane permeability. These findings revealed how MPs characteristics facilitated the spread of ARGs in marine benthic ecosystems, underscoring the importance of mitigating MPs pollution to maintain mariculture ecosystem health, prevent zoonotic diseases, and balance global mariculture with ecological health.

Automatic detection of multi-antibiotic residues simultaneously in aquatic products by visual protein microarray chips

A 96-well microplate-based protein microarray chip which can simultaneously detect three different families of antibiotics using a multiplexed approach has been developed for the first time. All steps in the microarray chip can be completed through an automated biochip analyzer, enabling high throughput analysis of 96 samples within 60 min according to the set program. The microarray chip can be visually evaluated by the color depth of array points, and can also be quantified through a scanner. Under the optimal conditions, the limits of detection (LODs) of nitrofuran metabolites (NFMs), chloramphenicol (CAP), and fluoroquinolones (FQs) were 0.11-0.15 μg/kg, 0.07 μg/kg and 6.42 μg/kg, respectively. This microarray chip can be applied to different aquatic products, including crucian carp, shrimp, and scallops, with the recovery ranged from 89.4 % to 111.2 %. These results demonstrate new strategies for the high-throughput detection of multi-antibiotic residues and present potential of protein chip technologies for daily supervision.

National antibiotic consumption is strongly related to the prevalence of antibiotic resistance across bacterial clades

The impact of societal antibiotic consumption on the prevalence of antibiotic resistance across microbial taxa in natural environments has not yet been assessed at global scales. Here, I examine the prevalence of 155 antibiotic resistance genes (ARGs) in 300,209 bacterial genomes, from non-clinical non-human-associated terrestrial environments at over 9,600 locations in 44 countries. I then compare ARG prevalences to nationwide antibiotic consumption rates, distinguishing between different ARG types. I find that depending on country and ARG type, ARG prevalences can be extremely high; for example, the probability that a given quinolone resistance gene is present in a given strain in Thailand was estimated at 42%. Further, I find strong positive correlations between nationwide antibiotic consumption rates and mean ARG prevalences for nearly all ARG types. Thus, national antibiotic consumption leaves a signal on the prevalence of ARGs across the bacterial tree, even in non-clinical environments.

Comparative genomic analysis reveals distinct virulence and resistance mechanisms in 21 bacterial fish pathogens

The rising bacterial infections threaten world aquaculture and wild fish populations, making it imperative to increase the understanding of the mechanisms of pathogenic virulence and resistance. This study applies comparative genomic analysis to 21 bacterial fish pathogens, using whole-genome sequences from public genomic resources and sophisticated bioinformatics tools for screening of virulence factors, mobile genetic elements, antibiotic resistance genes, anti-phage defense mechanisms and secretory systems. We have seen that the different pathogens depict a wide range of variability regarding virulence and resistance potential, which may be attributed to species-specific adaptation. Notably, Streptococcus agalactiae and Mycobacterium salmoniphilum were found to possess high offensive and defensive virulence potential, but at different regulative controls. We also found diverse secretion systems and intricate mechanisms for antibiotic resistance, which have provided very important insights into how pathogens adapt to their environments. By categorizing functional genes and finding anti-phage systems, our analysis has revealed new insights into the complex interactions among bacterial virulence, resistance, and host defense mechanisms. These findings not only shed new light on the bacterial pathogenesis process in aquaculture but also provide the bases for focused, therapeutically-based strategies and genomic surveillance programs able to improve disease management and sustainability in aquaculture environments.

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human

BACKGROUND

Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.

RESULTS

The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.

CONCLUSIONS

The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

Characteristics and driving factors of antibiotic resistance genes in aquaculture products from freshwater ponds in China Yangtze River Delta

Antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a huge threat to aquaculture organisms and human health. In this study, occurrences and relative abundances of ARGs were analysed in the guts of products cultured in freshwater ponds in the Yangtze River Delta region in China. A total of 29 ARGs were found in the gut samples, with detection frequencies ranging from 4.8% to 81%, and the relative abundances (ARGs/16S rRNA) ranging from 10-7 to 1. In addition, the human dietary intake of ARGs via aquaculture products was assessed, where the daily intake of most ARGs via aquaculture products was higher than those via PM2.5 and drinking water, but lower than that via vegetables. The relative abundances of MGE (IS613, Tp614, tnpA and int1) were significantly correlated with those of multiple ARGs, indicating the horizontal gene transfer (HGT) of ARGs among gut microorganisms. Proteobacteria, Firmicutes and Actinobacteria were the dominated microbial communities found in the guts of aquaculture products. In addition, significant correlations were found between Cyanobacteria and int1, between Nitrospira and tetE, and between sul2 and aadA2, indicating potential same hosts of these genes. In addition, results from co-correlation indicated both HGT (dominated by MGEs) of ARGs and the enrichment of ARGs in bacteria. MGEs, mostly int1, were more effective than bacteria in increasing the ARG abundance. This study could provide a better understanding of the transmission of ARGs in the aquaculture environment and improve the quality of aquaculture products and the ecology.

The effect of bulk-biochar and nano-biochar amendment on the removal of antibiotic resistance genes in microplastic contaminated soil

Biochar amendment has significant benefits in removing antibiotic resistance genes (ARGs) in the soil. Nevertheless, there is little information on ARGs removal in microplastic contaminated soil. Herein, a 42-day soil microcosm experiment were carried out to study how two coconut shell biochars (bulk- and nano-size) eliminate soil ARGs with/without microplastic presence. The results showed that microplastic increased significantly the numbers and abundances of ARGs in soil at 14d of cultivation. And, two biochars amendment effectively inhibited soil ARGs spread whether or not microplastic was present, especially for nano-biochar which had more effective removal compared to bulk-biochar. However, microplastic weakened soil ARGs removal after applying same biochar. Two biochars removed ARGs through decreasing horizontal gene transfer (HGT) of ARGs, potential host-bacteria abundances, some bacteria crowding the eco-niche of hosts and promoting soil properties. The adverse effect of microplastic on ARGs removal was mainly caused by weakening mobile genetic elements (MGEs) removal, and by changing soil properties. Structural equation modeling (SEM) analysis indicated that biochar's effect on ARGs profile was changed by its size and microplastic presence through altering MGEs abundances. These results highlight that biochar amendment is still an effective method for ARGs removal in microplastic contaminated soil.

Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture

Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g-1, and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.

Concentrations, distribution, and key influencing factors of antibiotic resistance genes and bacterial community in water and reared fish tissues in a typical tilapia farm in South China

Although previous studies have investigated the occurrence of antibiotic resistance genes (ARGs) in aquaculture, few have monitored the concentrations and propagation of ARGs in biological tissues or investigated the key factors influencing their spread in aquaculture. This study investigated the concentration, propagation, and distribution of ARGs and bacterial communities in water sources, pond water, and tilapia tissues, and their key influencing factors, in a typical tilapia farm. ErmF, sul1, and sul2 were the dominant ARGs with high concentrations. The total concentrations of ARGs (TCAs) in tilapia tissues decreased in the following order: stomach > scales > intestine > gills (P < 0.05). Redundancy analysis and multiple linear regression revealed that suspended solids (SS) and chemical oxygen demand (COD) were positively correlated with the dominant ARGs ermF sul2, and the TCAs (P < 0.05); additionally, Chloroflexi and Bacteroidetes in tilapia aquaculture water were positively correlated with the dominant ARGs ermF and sul2, as well as the TCAs (P < 0.05). This study suggests that SS and COD were the key factors driving the distribution and spread of ARGs in tilapia aquaculture water. Additionally, Chloroflexi and Bacteroidetes were the key bacterial flora affecting the propagation of ARGs in tilapia aquaculture systems.

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.

Characterization and fitness cost analysis of two plasmids carrying different subtypes of blaNDM in aquaculture farming

In recent years, the blaNDM gene, which mediate resistance to carbapenems, has disseminated all over the world, and has also been detected in animals. Understanding the dissemination and accumulation of antibiotic resistance genes (ARGs) in a human-impacted environment is essential to solve the food safety problems caused by antibiotics. In this study, two strains of carbapenem bacteria carrying blaNDM were screened from 244 strains isolated from two T. sinensis farms in Zhejiang province, China. After their plasmids were isolated and sequenced, their structure and gene environment were analyzed and the mechanism of blaNDM gene transfer was explored. The study measured the fitness cost of plasmids carrying different blaNDM subtypes by four biological characteristics experiments. The results showed that the fitness cost of IncC plasmid carrying blaNDM-1 was higher than that of IncX3 plasmid carrying blaNDM-5. Furthermore, the real-time PCR showed that the decrease of transcription level of fitness-related genes lead to the different fitness cost of plasmids carrying different blaNDM subtypes. Fitness of many blaNDM-harboring plasmids enhanced the further dissemination of this gene and increase the risk of blaNDM gene spreading in aquatic environment, and thus further investigation of carbapenem-resistant bacterias among food animals are in urgent need.

Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments

Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10^-2 to 1.90 × 10^-1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

Temporal variations, distribution, and dissemination of antibiotic resistance genes and changes of bacterial communities in a biofloc-based zero-water-exchange mariculture system

Antibiotic resistance genes (ARGs) have obtained an increasing number of global concerns for the severe risks they pose to food safety and public health. Studies have investigated the concentrations and distribution of ARGs in the environment. However, the distribution and dissemination of ARGs, the bacterial communities, and the key influencing factors during the entire rearing period in the biofloc-based zero-water-exchange mariculture system (BBZWEMS) remain unclear. The current study investigated the concentrations, temporal variations, distribution, and dissemination of ARGs, the changes in the bacterial communities, as well as the key influencing factors during the rearing period in the BBZWEMS. Sul1 and sul2 were dominant ARGs. Total concentrations of ARGs followed a trend of decrease in pond water, while they followed a trend of increase in source water, biofloc, and shrimp gut. Total concentrations of targeted ARGs in the water source were higher than those in the pond water and biofloc samples for each corresponding rearing stage by 2.25-122.97-fold (p < 0.05). The bacterial communities in biofloc and pond water did not change much, while they changed considerably in the shrimp gut samples during the rearing period. Pearson correlation, redundancy analysis, and multivariable linear regression analysis showed that suspended substances and Planctomycetes were positively correlated with the concentrations of ARGs (p < 0.05). The current study indicates that the water source may be a critical source of ARGs, and that suspended substances is a key factor influencing the distribution and dissemination of ARGs in the BBZWEMS. Early intervention measures on ARGs in water sources should be implemented to aid in the prevention and control of resistance genes in aquaculture industry, and reduce the potential risks of ARGs to public health and food safety.

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

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

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.

Distribution and migration of antibiotic resistance genes, as well as their correlation with microbial communities in swine farm and its surrounding environments

The prevalence and correlation of antibiotic resistance genes (ARGs) in pig farm wastewater treatment plants (WWTPs) and surrounding environment were investigated using metagenomics and real time quantitative PCR (q-PCR). The hosts of ARGs were also studied in this study. The abundance of ARGs decreased significantly in the anoxic/oxic (A/O) process and disinfection tank of WWTPs. New ARGs emerged in wastewater that passed though the anaerobic reactor. The abundances of ARGs in the soils and water near pig farm were 10- and 35-fold higher than those in the control, respectively. The abundance of ARGs in wells near pig farm were an order of magnitude higher than that in the control. Similarly, a high abundance of ARGs was detected in swine manure. After composting, most of the ARGs were eliminated, but sul1 increased 10.5-fold. A high-throughput analysis revealed that the pig farm altered the microbial community structure in the surrounding environment, with 52% and 37% of the operational taxonomic units (OTUs) endemic to the soil and water samples near pig farm in comparison with these data in the control, respectively. The phyla Proteobacteria, Choroflexi, and Actinobacteriota dominated the water and soil samples. In addition, three pathogenic genera were found in the surrounding soil and water samples. A metagenomic analysis identified 14 types of ARGs (>1%), with the highest proportion of multidrug ARGs at 47%. A total of 28 subtypes of ARGs were detected (>1%), with macB the most prevalent. The correlation analysis revealed that several key phyla, including Proteobacteria, Actinobacteria and Acidobacteria, were the main potential hosts and posed a positive correlation with the ARGs. Efflux pumps (60-66%) were the primary resistance mechanism, and each resistance mechanism was distributed in similar proportions in the microbial community.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Size-dependent effects of microplastics on antibiotic resistance genes fate in wastewater treatment systems: The role of changed surface property and microbial assemblages in a continuous exposure mode

Microplastics (MPs) were continuously transported to wastewater treatment systems and accumulated in sludge constantly, potentially affecting systems function and co-occurrent contaminants fate. However, previous studies were based on acute exposure of MPs, which could not reflect the dynamics of MPs accumulation. Herein, this study firstly raised a more realistic method to evaluate the practical impacts of MPs on systems purification efficiency and antibiotic resistance genes (ARGs) fate. Continuous exposure of MPs did not pose negative effects on nutrients removal, but significantly changed the occurrence patterns of ARGs. ARGs abundances increased by 42.8 % and 54.3 % when exposed to millimeter-size MPs (mm-MPs) polyamide and polyethylene terephthalate, but increased by 31.3 % and 39.4 % to micron-size MPs (μm-MPs), respectively. Thus, mm-MPs posed severer effects on ARGs than μm-MPs. Further, mm-MPs surface properties were obviously altered after long-term exposure (higher specific surface area and O-containing species), which benefited microbes attachment. More importantly, more taxa linkages and changed topological properties (higher average degree and average weight) of co-occurrent network were observed in sludge with mm-MPs than with μm-MPs, as well as totally different potential host bacteria of ARGs. Rough surface of MPs and closer relations between ARGs and bacteria taxa contributed to the propagation of ARGs, which accounted for the observed higher ARGs abundances of mm-MPs. This study demonstrated that long-term accumulation of MPs in wastewater treatment systems affected ARGs fate, and mm-MPs caused severer risk due to their enrichment of ARGs. The results would promote the understanding of MPs real environmental behavior and influences.

Suspect screening of pharmaceuticals, illicit drugs, pesticides, and other emerging contaminants in Argentinean Piaractus mesopotamicus, a fish species used for local consumption and export

The widespread distribution of contaminants of emerging concern (CECs) is a major concern due to their potential effects on human health and the environment. The insufficient sewage treatment plant infrastructures is a global problem most accentuated in less developed countries and results in the discharge of CECs to water bodies. Pacu (Piaractus mesopotamicus) is a ray-finned freshwater fish species native to the Paraná basin. It is also the most produced aquaculture fish species in Argentina since 2012. Though uninvestigated to date, the occurrence of CECs in pacu may be of high relevance due to production volumes and relevance to human exposure through fish consumption. In this study, we applied a high-resolution mass spectrometry screening method to qualitatively analyze over 100 CECs in pacu. Four extraction/cleanup methods were tested on pooled pacu fillet, including solid-phase extraction and QuEChERS. The method that produced the highest number of detections was selected for further analysis of pacu purchased in supermarkets and fish markets in Argentina between 2017 and 2020. Residues of pesticides, antibiotics, pharmaceuticals, personal care products, plasticizers, sweeteners, drug metabolites, stimulants, and illegal drugs were detected in the samples. A total of 38 CECs were detected, ranging between 24 and 35 CECs per individual sample. 100% of the samples had positive detections of caffeine, 1,7-dimethylxanthine, xanthine, benzoylecgonine, methylparaben, ethylparaben, bis(2-ethylhexyl) phthalate (DEHP), metolachlor, carbendazim, salicylic acid, 2,4-D, saccharin, cyclamate, and dodecanedioic acid. Mappings generated with correspondence analysis were used to explore similarities/dissimilarities among the detected compounds. To our knowledge this is the first report of saccharin, cyclamate, 2,4 - D, carbendazim, metolachlor, ethylparaben, propylparben, bisphenol A, DEHP, and benzotriazole in fish from Argentina, and the first report on the presence of lisinopril, metropolol acid and dodecanedioic acid in fish worldwide.

Antimicrobial resistance in fish and poultry: Public health implications for animal source food production in Nigeria, Egypt, and South Africa

Antimicrobial resistance (AMR) is a significant threat to global public health. Specifically, excessive usage of antimicrobials in food animal production is one significant reason for AMR development in humans. Therefore, it is essential to identify the trends of AMR in fish and poultry and develop better surveillance strategies for the future. Despite this imperative need, such information is not well documented, especially in Africa. This study used a systematic review to assess AMR trend, spatial distribution, and incidence in fish and poultry research in Nigeria, Egypt, and South Africa. A literature assessment was conducted for published studies on AMR between 1989 and 2021 using the Scopus and Web of Science databases. One hundred and seventy-three relevant articles were obtained from the database search. Egypt was the leading exponent of antimicrobial resistance research (43.35%, 75 studies), followed by Nigeria (39.31%, 68 studies), then South Africa (17.34%, 30 studies). The majority of the antimicrobial resistance studies were on poultry in Egypt (81%, 61 studies), Nigeria (87%, 59 studies), and South Africa (80%, 24 studies). Studies on fish were 17% (13 studies), 9% (6 studies), and 10% (3 studies) in Egypt, Nigeria, and South Africa, respectively. Antimicrobial resistance patterns showed multiple drug resistance and variations in resistant genes. AMR research focused on sulfamethoxazole groups, chloramphenicol, trimethoprim, tetracycline, erythromycin, and ampicillin. Most studies employed the disk diffusion method for antimicrobial susceptibility tests. Among the four mechanisms of AMR, limiting drug uptake was the most reported in this study (both in fish and poultry). The findings reveal public and environmental health threats and suggest that it would be useful to promote and advance AMR research, particularly for countries on the global hotspot for antimicrobial use.

Metagenomic insights into the spatiotemporal responses of antibiotic resistance genes and microbial communities in aquaculture sediments

The dissemination of antibiotic resistance genes (ARGs) in aquaculture systems is a potential threat to environmental safety and human health. However, the spatiotemporal distribution pattern of ARGs and key factors associated with their dissemination in aquaculture sediments remain unclear. In this study, ARGs, mobile genetic elements, microbial community composition, heavy metal contents, and nutrient contents of samples collected from a whole culture cycle of fish in a representative aquaculture farm were characterized. The distribution patterns of nine subtypes of ARGs (tetW, tetM, tetA, ermC, ermB, sul1, sul2, floR, and qnrS) showed clear spatiotemporal differences. The absolute abundance of ARGs in aquaculture sediments was higher in winter and in rivers of the aquaculture farm. Proteobacteria was the dominant phylum in all sediment samples. The results of network and redundancy analyses confirmed that the Dechloromonas, Candidatus Accumulibacter, Smithella, Geobacter, and Anaeromyxobacter belonging to Proteobacteria were positively correlated with ARGs, suggesting that these microbial species are potential hosts of corresponding ARGs. Our study highlights that the microbial community is the determining factor for ARG dissemination. Strategies for inhibiting these potential hosts of ARGs should be developed based on controllable factors.

Metagenomic analysis of the abundances, diversity, and distribution of antibiotic resistance genes and their potential bacterial hosts in two types of shrimp-rearing farms in South China

Antibiotic resistance genes (ARGs) are attracting increasing concern worldwide. Many previous studies have investigated the occurrence and concentrations of ARGs in aquaculture. However, the sources of ARGs and the links with their potential bacterial hosts have not yet been explored. This study investigated the abundances and diversity of ARGs in two types of shrimp farms in South China through metagenomic sequencing. In total, 14 ARG types were detected. Tetracycline was the dominant ARG type. The abundances of ARGs in samples decreased in the order of duck feces > water source > sediment > shrimp gut > pond water. The samples from the duck-shrimp integrated farm contained 1.29-3.81-fold more abundant ARGs than those from the shrimp monoculture farm (p < 0.05). Several ARGs, that were most predominant in the duck feces samples, were also the most predominant in the shrimp gut samples from the duck-shrimp integrated farm. Redundancy analysis indicated that the abundances and distribution of ARGs formed three clusters: duck feces, water samples, and sediment and shrimp gut samples. The dominant genera in duck feces known as human pathogenic bacteria were potential hosts of ARGs, and were also dominant in the shrimp gut samples in the duck-shrimp integrated farm. Additionally, the abundances of dominant genera in the shrimp gut samples of the duck-shrimp integrated farm were 1.74-35.07-fold higher than those in the shrimp monoculture farm (p < 0.01). The duck-shrimp integrated farm had 3.36-fold and 4.94-fold higher abundances of ARGs and mobile genetic elements in the shrimp gut samples than those from the shrimp monoculture farm, respectively (p < 0.05). The results indicate that duck feces may be a crucial source of diverse and abundant ARGs spreading to reared shrimps in duck-shrimp integrated farms, posing a severe risk to public health.

The dynamic of the potential pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic resistance genes in the water at different growth stages of grass carp pond

Pond aquaculture has become the most important and broadest breeding model in China, and an extremely important source of aquatic products, but the potential hazard factors of potential pathogenic bacteria (PPB), antibiotic resistance bacteria (ARB), and antibiotic resistance genes (ARGs) in aquaculture environment are largely invisible. In the present study, the bacterial communities in the larvae, juvenile, rearing, and harvesting culture stages of great grass carp (Ctenopharyngodon idellus) ponds were investigated and the structure of microbial flora analysis showed that the larvae culture stage has the highest abundance and the most dominant phyla were Proteobacteria (27.8%). A total of 123 significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations and the relative abundance of nine bacterial phenotypes implied that the larvae culture stage had the most abundance of pathogenic potential and mobile elements. The correlation analyses of environmental factors showed that temperature, stocking density, pH, and transparency showed the significant impacts on both the distribution of microbiome and the PPB. More importantly, a total of 40 ARB were identified, and 16 ARGs have the detection rates of 100%, which revealed that they are widely distributed and highly enriched in the aquaculture production. Notably, this is the first robust report to analyze and understand the PPB, ARB, and ARGs characteristics and dynamic changes in the pond aquaculture.

Antibiotic Resistance in the Drinking Water: Old and New Strategies to Remove Antibiotics, Resistant Bacteria, and Resistance Genes

Bacterial resistance is a naturally occurring process. However, bacterial antibiotic resistance has emerged as a major public health problem in recent years. The accumulation of antibiotics in the environment, including in wastewaters and drinking water, has contributed to the development of antibiotic resistant bacteria and the dissemination of antibiotic resistance genes (ARGs). Such can be justified by the growing consumption of antibiotics and their inadequate elimination. The conventional water treatments are ineffective in promoting the complete elimination of antibiotics and bacteria, mainly in removing ARGs. Therefore, ARGs can be horizontally transferred to other microorganisms within the aquatic environment, thus promoting the dissemination of antibiotic resistance. In this review, we discuss the efficiency of conventional water treatment processes in removing agents that can spread/stimulate the development of antibiotic resistance and the promising strategies for water remediation, mainly those based on nanotechnology and microalgae. Despite the potential of some of these approaches, the elimination of ARGs remains a challenge that requires further research. Moreover, the development of new processes must avoid the release of new contaminants for the environment, such as the chemicals resulting from nanomaterials synthesis, and consider the utilization of green and eco-friendly alternatives such as biogenic nanomaterials and microalgae-based technologies.

Bacteriophage therapy in aquaculture: current status and future challenges

The escalation of antibiotic resistance has revitalized bacteriophage (phage) therapy. Recently, phage therapy has been gradually applied in medicine, agriculture, food, and environmental fields due to its distinctive features of high efficiency, specificity, and environmental friendliness compared to antibiotics. Likewise, phage therapy also holds great promise in controlling pathogenic bacteria in aquaculture. The application of phage therapy instead of antibiotics to eliminate pathogenic bacteria such as Vibrio, Pseudomonas, Aeromonas, and Flavobacterium and to reduce fish mortality in aquaculture has been frequently reported. In this context, the present review summarizes and analyzes the current status of phage therapy in aquaculture, focusing on the key parameters of phage application, such as phage isolation, selection, dosage, and administration modes, and introducing the strategies and methods to boost efficacy and restrain the emergence of resistance. In addition, we discussed the human safety, environmental friendliness, and techno-economic practicability of phage therapy in aquaculture. Finally, this review outlines the current challenges of phage therapy application in aquaculture from the perspectives of phage resistance, phage-mediated resistance gene transfer, and effects on the host immune system.

Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system

To meet the rapidly growing global demand for aquaculture products, large amounts of antibiotics were used in aquaculture, which might accelerate the evolution of antibiotic-resistant bacteria (ARB) and the propagation of antibiotic genes (ARGs). In our research, we revealed the ARGs profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis. The residual antibiotic seems to increase the propagation of ARGs in the crab pond, but there was no clear relationship between a given antibiotic type and the corresponding resistance genes. The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities, but increased the relative abundance of sulfonamide resistance gene. A higher abundance of MGEs, especially plasmid, increased the potential ARGs dissemination risk in crab and purification ponds. Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs. The horizontal gene transfer was likely to occur among a variety of microorganisms, and various ARGs hosts including Pseudomonas, Acinetobacter, Escherichia, and Klebsiella were identified. Bacterial community influenced the composition of ARG hosts, and Proteobacteria was the predominant hosts. Overall, our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.

Ecological response to antibiotics re-entering the aquaculture environment with possible long-term antibiotics selection based on enzyme activity in sediment

Antibiotics are frequently applied in aquaculture to control infectious diseases and promote aquaculture production. The long-term application of antibiotics can lead to antibiotic resistance within an ecosystem. Herein, we assessed the ecological responses to two antibiotics (oxytetracycline (OTC) and sulfadiazine (SD)) at three concentrations (0 mg/kg (control), 10 mg/kg, and 1000 mg/kg) re-entering the aquaculture sediments of shrimp ponds with an approximately long-term drug application history (5, 15, and more than 30 years) for 2 and 4 months. For the newly reclaimed aquaculture ponds (approximately 5 years), the re-entered OTC significantly promoted urease activity (UA) and peroxidase activity (POA), while inhibited dehydrogenase activity (DHA) and fluorescein diacetate esterase activity (FDA). Meanwhile, the re-entered SD showed promotional effects on POA and DHA, and inhibitory effects on UA and FDA. For ponds with 15 years of aquaculture history, re-entered OTC promoted POA, inhibited FDA, and changed the influencing effects of UA and DHA with exposure time. The re-entered SD showed promotional effects on UA, POA and DHA, and inhibitory effects on FDA. For long-term aquaculture ponds (more than 30 years of aquaculture history), re-entered OTC promoted POA, DHA, and FDA, while it inhibited UA. Meanwhile, SD promoted all four enzyme activities. Pearson correlation analysis indicated that the variances of enzyme responses to the re-entry of antibiotics in the three sediment environments were related with the type, concentration, and exposure time of antibiotics, as well as the sediment properties and aquaculture history. The enzyme activities in the sediment environment from newly reclaimed aquaculture ponds were more sensitive to the re-entered antibiotics, while the enzyme activities displayed a clear tolerance in the sediment environment with more than 30 years of aquaculture history. However, in the sediment environment with 15 years of aquaculture history, the response of the enzyme activities to re-entered antibiotics demonstrated time processes of antibiotic adaptation during antibiotic resistance selection. This study has illustrated the effects of re-entered antibiotics on enzyme activities in the aquaculture environment with long-term antibiotic resistance/tolerance profiles, and further establishes the possible effects on ecosystem functioning in continuous antibiotic selection pressure.

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals

Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.

Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment

The increasing pollution of urban drinking water sources by antibiotic resistance genes (ARGs) threatens human health worldwide. However, the distribution and influencing factors of ARGs, especially how to reveal the risks of ARGs in this environment remains unclear. Hence, Chaohu Lake was selected as an example to investigate the characteristics of ARGs and explore the interactions among physicochemical factors, microorganisms, and ARGs by metagenomic approach. In this work, 75 ARG subtypes with an average of 30.4 × /Gb (ranging from 15.2 ×/Gb to 57.9 ×/Gb) were identified, and multidrug and bacA were most frequent in Chaohu Lake. Non-random co-occurrence patterns and potential host bacteria of ARGs were revealed through co-occurrence networks. Microbial community and mobile genetic elements (MGEs) were the major direct factors in ARG profiles. The dissemination of ARGs was mainly driven by plasmids. Considering the interactions among MGEs, human bacterial pathogens, and ARGs, antibiotic resistome risk index (ARRI) was proposed to manifest the risks of ARGs. Overall, our work systemically investigated the composition and associated factors of ARGs and built ARRI to estimate the potential risks of ARGs in a typical urban drinking water source, providing an intuitive indicator for managing similar lakes.

The response of sediment microbial communities to temporal and site-specific variations of pollution in interconnected aquaculture pond and ditch systems

Sediment microbial communities play critical roles in the health of fish and the biogeochemical cycling of elements in aquaculture ecosystems. However, the response of microbial communities to temporal and spatial variations in interconnected aquaculture pond and ditch systems remains unclear. In this study, 61 sediment bacterial samples were collected over one year from 11 sites (including five ponds and six ditches) in a 30-year-old fish aquaculture farm. The 16S rRNA approach was used to determine the relative abundances of microbial communities in the sediment samples. The relationships among nutrients, heavy metals, and abundant microorganisms were analyzed. Our results showed that Proteobacteria, Bacteroides and Chloroflexi were the predominant phyla in the sediments of aquaculture pond, with average abundances of 36.33%, 18.60%, and 14.58%, respectively. The microbial diversity in aquaculture sediments was negatively correlated (P < 0.05) with the concentrations of total nitrogen and total phosphorus in sediments, indicating that the microbial diversity is highly associated with the remediation of nutrients in sediments. The sediment samples with high similarities were discovered by the t-distributed stochastic neighbor embedding (t-SNE) method. The site-specific correlations between specific microorganisms and heavy metals were explored. The network analysis revealed that the microbial diversities in aquaculture ponds were more stable than that in aquaculture ditches. The network analysis also illustrated that the microbial genera with low relative abundances may become key groups of microbial communities in sediment ecosystems. Our work deepens the understanding of the relationships between microbial communities and the spatiotemporal characteristics of surface water and sediments in aquaculture farms.

Antibiotics, antibiotic-resistant bacteria, and resistance genes in aquaculture: risks, current concern, and future thinking

Aquaculture is remarkably one of the most promising industries among the food-producing industries in the world. Aquaculture production as well as fish consumption per capita have been dramatically increasing over the past two decades. Shifting of culture method from semi-intensive to intensive technique and applying of antibiotics to control the disease outbreak are the major factors for the increasing trend of aquaculture production. Antibiotics are usually present at subtherapeutic levels in the aquaculture environment, which increases the selective pressure to the resistant bacteria and stimulates resistant gene transfer in the aquatic environment. It is now widely documented that antibiotic resistance genes and resistant bacteria are transported from the aquatic environment to the terrestrial environment and may pose adverse effects on human and animal health. However, data related to antibiotic usage and bacterial resistance in aquaculture is very limited or even absent in major aquaculture-producing countries. In particular, residual levels of antibiotics in fish and shellfish are not well documented. Recently, some of the countries have already decided the maximum residue levels (MRLs) of antibiotics in fish muscle or skin; however, many antibiotics are yet not to be decided. Therefore, an urgent universal effort needs to be taken to monitor antibiotic concentration and resistant bacteria particularly multiple antibiotic-resistant bacteria and to assess the associated risks in aquaculture. Finally, we suggest to take an initiative to make a uniform antibiotic registration process, to establish the MRLs for fish/shrimp and to ensure the use of only aquaculture antibiotics in fish and shellfish farming globally.

Is rice-crayfish co-culture a better aquaculture model: From the perspective of antibiotic resistome profiles

Aquaculture ecosystem is a hot-spot for antibiotic resistance genes (ARGs). Rice-crayfish co-culture was considered an eco-friendly aquaculture model and has been widely adopted in China. However, it is unclear whether rice-crayfish co-culture is one of the most eco-friendly models from the perspective of antibiotic resistance profiles. In this study, we evaluated the eco-friendliness of rice-crayfish co-culture, and compared this model with other aquaculture models, from the perspectives of antibiotics and ARG patterns, based on multi-omics and antibiotic profiles. Results showed that the nutrient levels, antibiotic concentrations, dominant microbial genera and ARG patterns in the rice-crayfish co-culture model were profoundly different from the other three aquaculture models (crab only aquaculture model, crayfish only aquaculture model, and crab-crayfish co-culture models). Specifically, the rice-crayfish co-culture model has significantly lower diversity of ARGs and lower potential risks of ARGs when compared to the other aquaculture models. Nutrient and antibiotic concentrations were the important environmental factors for shaping ARG patterns, but compared with environmental factors, the effects of mobile genes and bacteria community on the proliferation and transmission of ARGs were stronger. This study has deepened our understanding of ARGs in freshwater aquaculture ecosystem, and suggested that rice-crayfish co-culture model is a relatively eco-friendly aquaculture model when compared with the other aquaculture models.

Hormetic dose responses induced by antibiotics in bacteria: A phantom menace to be thoroughly evaluated to address the environmental risk and tackle the antibiotic resistance phenomenon

The environmental contamination of antibiotics caused by their over or inappropriate use is a major issue for environmental and human health since it can adversely impact the ecosystems and promote the antimicrobial resistance. Indeed, considering that in the environmental matrices these drugs are present at low levels, the possibility that bacteria exhibit a hormetic response to increase their resilience when exposed to antibiotic subinhibitory concentrations might represent a serious threat. Information reported in this review showed that exposure to different types of antibiotics, either administered individually or in mixtures, is capable of exerting hormetic effects on bacteria at environmentally relevant concentrations. These responses have been reported regardless of the type of bacterium or antibiotic, thus suggesting that hormesis would be a generalized adaptive mechanism implemented by bacteria to strengthen their resistance to antibiotics. Hormetic effects included growth, bioluminescence and motility of bacteria, their ability to produce biofilm, but also the frequency of mutation and plasmid conjugative transfer. The evaluation of quantitative features of antibiotic-induced hormesis showed that these responses have both maximum stimulation and dose width characteristics similar to those already reported in the literature for other stressors. Notably, mixtures comprising individual antibiotic inducing stimulatory responses might have distinct combined effects based on antagonistic, synergistic or additive interactions between components. Regarding the molecular mechanisms of action underlying the aforementioned effects, we put forward the hypothesis that the adoption of adaptive/defensive responses would be driven by the ability of antibiotic low doses to modulate the transcriptional activity of bacteria. Overall, our findings suggest that hormesis plays a pivotal role in affecting the bacterial behavior in order to acquire a survival advantage. Therefore, a proactive and effective risk assessment should necessarily take due account of the hormesis concept to adequately evaluate the risks to ecosystems and human health posed by antibiotic environmental contamination.

Whole-genome epidemiology and characterisation of mcr-1-encoding Escherichia coli in aquatic bird farms from the Pearl River Delta, China, 2019-2020

Due to their unique breeding pattern, aquatic bird farms are increasingly considered as hotspots in the development and spread of antimicrobial resistance. However, comprehensive studies addressing the whole-genomic features of colistin-resistant bacteria in aquatic bird farms are scarce. Over a 2-year period, we conducted surveillance to determine the whole-genome epidemiology and characterisation of mcr-1-positive Escherichia coli in aquatic bird farms in southeastern coastal China. A total of 100 mcr-1-producing isolates among 654 E. coli strains were recovered from 781 samples collected in 11 aquatic bird farms and 1 veterinary clinic in the Pearl River Delta area. Higher resistance phenotypes to 17 antibiotics were found in mcr-1-positive isolates compared with other isolates. Subsequently, 20 mcr-1-carrying isolates were sequenced to analyse the whole-genomic features. Molecular typing as well as antimicrobial resistance gene and virulence factor profiles of the isolates showed considerable diversity. Three types of genetic backbones of mcr-1 in the isolates were assembled and were identified in diverse broad-host-range plasmids and bacterial species. Pangenome analyses revealed a large genetic pool composed of the isolates. Furthermore, phylogenetic trees both of the isolates in this study and a global data set were built, indicating the spread of the three mcr-1 backbones and the mcr-1-positive isolates among different habitats, farms and even countries. This study highlights that aquatic bird farms may act as an important reservoir for mcr-1-producing E. coli, from which colistin resistance may be spread to diverse habitats, different geographical locations and even across bacterial species.

Antibiotic resistant bacteria and genes in shrimp aquaculture water: Identification and removal by ferrate(VI)

Enclosed shrimp culturing ponds are breeding environments for the spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the aquatic environment. This paper surveyed the presence of antibiotics, ARB, and ARGs in aquaculture waters and demonstrated their removal by ferrate (Fe(VI), FeO₄^2-). Tetracyclines were the most prevalent antibiotics, followed by quinolones and β-lactam. The bacterial resistance rates to three antibiotics were ordered as follows: amoxicillin (AMX) > oxytetracycline (OTC) > enrofloxacin (ENR). Proteobacteria, Verrucomicrobia, and Bacteroidetes were the predominant phyla, while sul1 and sul2 were the predominant ARGs. sul2 was positively correlated with Proteobacteria. Water quality parameters significantly influenced the dissemination of tetracycline resistance genes in aquacultures due to high organic waste accumulation. The removal efficiency of antibiotics by Fe(VI) depended on the structural moieties of antibiotics, with phenol-containing antibiotics more thoroughly oxidized (i.e., OTC) than amine-containing (ENR and AMX) antibiotics. Greater removal of antibiotics in aquaculture waters suggested that the constituents of farming water enhances the efficacy of antibiotics removal by Fe(VI). An acidic pH environment enhanced Fe(VI) inactivation of ARB over the circumneutral pH. The presented results are intended to improve aquaculture managing practices to minimize the antibiotic proliferation in aquaculture waters and the environment.

Occurrence, Distribution, and Ecological Risk Assessment of Antibiotics in Different Environmental Media in Anqing, Anhui Province, China

The widespread usage of antibiotics in human and animal medication has brought global concerns over environmental contamination of antibiotic residues. In this study, 16 kinds of antibiotics in different environmental media of water, sediments, and soils in Anqing city, Anhui province were determined by ultra-performance liquid chromatography tandem mass spectrometry. A total of fourteen kinds of antibiotics were detected in surface water, with a total concentration up to 479 ng·L⁻¹, while six kinds of antibiotics were detected in sediment and soil with concentrations ranging from 15.1 to 108 μg·kg⁻¹. Ciprofloxacin (12.8–99.5 ng·L⁻¹) and tetracycline (17.2–225 μg·kg⁻¹) antibiotics exhibited the highest concentration in water and soil, respectively. In spatial distribution, the total concentration of antibiotics in surface water from the highest to the lowest followed the order of urban area, mainstream of Wan River, suburbs, tributaries of Wan River, indicating that the level of antibiotic concentration in surface water is positively associated with the frequency of human activities. In addition, the antibiotic mass fraction in agriculture land and fishpond were found higher than that in other sampling sites. Moreover, the environmental risk assessment results showed that ciprofloxacin, erythromycin, ofloxacin, enrofloxacin and tetracycline might pose medium to high risks to algae and bacteria in aquatic ecosystem.

Impacts of pineapple peel powder on growth performance, innate immunity, disease resistance, and relative immune gene expression of Nile tilapia, Oreochromis niloticus

An 8-week growth trial was conducted to examine the efficacy of pineapple peel powder (PAPP) on growth rate and immunity of Nile tilapia, O. niloticus. Three hundred Nile tilapia (20.91 ± 0.11 g) were fed five diets containing different levels of PAPP at 0, 10, 20, 30 and 40 g kg^-1 PAPP, respectively. After four and eight weeks of the feeding trial, growth rates, and immune responses were tested. A challenge test using Streptococcus agalactiae and relative immune gene expression were performed after eight weeks of PAPP feeding. It was found that skin mucus and serum lysozyme, skin mucus and serum peroxidase, alternative complement, phagocytosis, and respiratory burst activities were significantly increased with the addition of PAPP. The maximum (P ≤ 0.05) innate immune values were noted in fish fed 10 g kg^-1 PAPP. Similarly, the up-regulation of IL1, IL8, and LBP gene expressions were also detected in fish fed PAPP diets, with the maximum value was found in 10 g kg^-1 PAPP fed fish. The relative percentage of survival (RPS) of Oreochromis niloticus after the challenge test were (56.00%, 72.00%, 60.00%, and 44.00%) for the 5, 10, 20 and 40 g kg^-1 PAPP diets, respectively. Fish fed the 10 g kg^-1 PAPP supplemented diet achieved the highest (P < 0.05) survival rate against S. agalactiae. Growth and feed efficiency were outstandingly (P < 0.05) enhanced in the PAPP groups. In conclusion, PAPP can be potentially used as a feed additive in Nile tilapia culture under Biofloc system.

Analysis of Antibiotic Resistance Genes, Environmental Factors, and Microbial Community From Aquaculture Farms in Five Provinces, China

The excessive use of antibiotics speeds up the dissemination and aggregation of antibiotic resistance genes (ARGs) in the environment. The ARGs have been regarded as a contaminant of serious environmental threats on a global scale. The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat bacterial infections; there is a universal concern about the environmental risk of ARGs in the aquaculture environment. In this study, a survey was conducted to evaluate the abundance and distributions of 10 ARGs, bacterial community, and environmental factors in sediment samples from aquatic farms distributed in Anhui (AP1, AP2, and AP3), Fujian (FP1, FP2, and FP3), Guangxi (GP1, GP2, and GP3), Hainan (HP1, HP2, and HP3), and Shaanxi (SP1, SP2, and SP3) Province in China. The results showed that the relative abundance of total ARGs was higher in AP1, AP2, AP3, FP3, GP3, HP1, HP2, and HP3 than that in FP1, FP2, GP1, GP2, SP1, SP2, and SP3. The sul1 and tetW genes of all sediment samples had the highest abundance. The class 1 integron (intl1) was detected in all samples, and the result of Pearson correlation analysis showed that the intl1 has a positive correlation with the sul1, sul2, sul3, bla_OXA, qnrS, tetM, tetQ, and tetW genes. Correlation analysis of the bacterial community diversity and environmental factors showed that the Ca²⁺ concentration has a negative correlation with richness and diversity of the bacterial community in these samples. Of the identified bacterial community, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the predominant phyla in these samples. Redundancy analysis showed that environmental factors (TN, TP, Cl^–, and Ca²⁺) have a positive correlation with the bacterial community (AP1, GP1, GP2, GP3, SP1, SP2, and SP3), and the abundance of ARGs (sul1, tetW, qnrS, and intl1) has a positive correlation with the bacterial community (AP2, AP3, HP1, HP2, and HP3). Based on the network analysis, the ARGs (sul1, sul2, bla_CMY, bla_OXA, qnrS, tetW, tetQ, tetM, and intl1) were found to co-occur with bacterial taxa from the phyla Chloroflexi, Euryarchaeota, Firmicutes, Halobacterota, and Proteobacteria. In conclusion, this study provides an important reference for understanding the environmental risk associated with aquaculture activities in China.

Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater

Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.

Hormetic dose-dependent response about typical antibiotics and their mixtures on plasmid conjugative transfer of Escherichia coli and its relationship with toxic effects on growth

Bacterial resistance caused by the abuse of antibiotics has attracted worldwide attention. However, there are few studies exploring bacterial resistance under the environmental exposure condition of antibiotics that is featured by low-dose and mixture. In this study, sulfonamides (SAs), sulfonamide potentiators (SAPs) and tetracyclines (TCs) were used to determine the effects of antibiotics on plasmid RP4 conjugative transfer of Escherichia coli (E. coli) under single or combined exposure, and the relationship between the effects of antibiotics on conjugative transfer and growth was investigated. The results show that the effects of single or binary antibiotics on plasmid RP4 conjugative transfer all exhibit a hormetic phenomenon. The linear regression reveals that the concentrations of the three antibiotics promoting conjugative transfer are correlated with the concentrations promoting growth and the physicochemical properties of the compounds. The combined effects of SAs-SAPs and SAs-TCs on plasmid conjugative transfer are mainly synergistic and antagonistic. While SAPs provide more effective concentrations for the promotion of conjugative transfer in SAs-SAPs mixtures, SAs play a more important role in promoting conjugative transfer in SAs-TCs mixtures. Mechanism explanation shows that SAs, SAPs and TCs inhibit bacterial growth by acting on their target proteins DHPS, DHFR and 30S ribosomal subunit, respectively. This study indicates that toxic stress stimulates the occurrence of conjugative transfer and promotes the development of bacterial resistance, which will provide a reference for resistance risk assessment of antibiotic exposure.

Characteristics of microbial community of soil subjected to industrial production of antibiotics

Ecosystems worldwide are exposed to pollutants connected to the industrial production of pharmaceuticals. The objective of this study was to study the composition and characteristics of the soil microbial communities that had been exposed to long-term selection pressure caused by the industrial production of penicillin G. Soil samples from four sites among the penicillin G production plant were analysed using 16S rRNA profiling via Illumina MiSeq platform and were compared with the control samples from four sites outside the plant. Total metagenomic DNA from the impacted soil was also used for the preparation of E. coli T1R-based fosmid library which was consequently qualitatively tested for the presence of penicillin G acylase (PGA)-encoding genes using the method of sequence homology. Analyses of alpha diversity revealed that the long-term antibiotic presence in the soil significantly increased the microbial diversity and richness in terms of Shannon diversity index (p = 0.002) and Chao estimates (p = 0.004). Principal component analysis showed that the two types of communities (on-site and control) could be separated at the phylum, class and genus level. The on-site soil was enriched in Betaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetia, while a significant decrease in Actinobacteria was observed. Metagenomic fosmid library revealed high hit rates in identifying PGAs (14 different genes identified) and confirmed the biotechnological potential of soils impacted by anthropogenic activity. This study offers new insights into the changes in microbial communities of soils exposed to anthropogenic activity as well as indicates that those soils may represent a hotspot for biotechnologically interesting targets.

Spread of resistance genes from duck manure to fish intestine in simulated fish-duck pond and the promotion of cefotaxime and As

Integrated culture is a widespread culture mode in South China, in which resistance genes (RGs) also spread in the circulation system with nutrients. Accordingly, the aim of the present study was to investigate the spread of RGs in a fish-duck pond and the RGs and bacterial community of fish intestines. Five fish tanks, including a control tank and four experimental tanks (duck manure, duck manure + cefotaxime, duck manure + As, and duck manure + cefotaxime + As), were tested for 100 days. The results showed that duck manure increased both the diversity and relative abundance of RGs in fish intestines, and the addition of stress factors (cefotaxime, As) increased the relative abundance of RGs by one to two orders of magnitude. The stress-inducing effect of cefotaxime was greater than that of As. Tetracycline resistance genes were more sensitive to stress factors and were the predominant RGs in fish intestines. RGs in duck manure preferentially spread from the water to biofilm and then to fish intestines, whereas co-stress of cefotaxime and As obviously promoted the spread of RGs to fish intestines. In comparison to the control tank, duck manure and stress factors significantly changed the bacterial community of fish intestines. Correlation analysis also revealed that arsB, MOX, tetA and sul1 were significantly correlated with intI1 (P < 0.01), which hinted a potentially dissemination risk of RGs in fish intestines. These findings provide a theoretical basis for further investigating the dissemination of RGs in integrated culture systems and for evaluating the ecological risk of antibiotic and As use in aquaculture.

Evaluation and Analysis of Water Quality of Marine Aquaculture Area

In the rapid development of marine aquaculture, the water quality of aquatic environments is regarded as a main limiting factor. Therefore, it is necessary to assess the water quality and environmental conditions in marine aquaculture areas and find out the main influencing factors regarding damage to the water quality environment. In the present research, pond aquaculture and cage aquaculture areas were sampled in May, August and November in 2018. Nine water quality indicators were detected, including pH, temperature, salinity, dissolved oxygen, molybdate-reactive phosphorus, chemical oxygen demand, chlorophyll a, inorganic nitrogen and antibiotic resistance genes (ARGs). Principal component analysis (PCA) was used to analyze the water quality conditions, spatial-temporal changes, and the driving factors in pond and cage aquaculture areas. The results showed that three main components were extracted from the pond aquaculture area, which explained 66.82% of the results, the most relevant factors are salinity, dissolved oxygen and ARGs. For the cage aquaculture area, three main components were extracted which can account for 72.99% of the results, the most relevant factors are chlorophyll a, salinity and dissolved oxygen. The comprehensive scores of the principal components indicated that the heaviest polluted months in pond and aquaculture areas were August and November, respectively. The water quality of the pond aquaculture area is mainly limited by the volume of the pond, while aquaculture activities and seasonality are the main factors for cage aquaculture. ARGs in cage culture areas showed more variety and frequency compared with pond culture areas, which indicated that terrestrial input might be one of the sources for ARGs occurrence. The results would be helpful for the relevant authorities to select water quality monitoring parameters in marine aquaculture areas.