Metagenomic analysis revealed the prevalence of antibiotic resistance genes in the gut and living environment of freshwater shrimp

Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1

Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn Macrobrachiumrosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.

Integrating metagenomic and isolation strategies revealed high contamination of pathogenies and resistome in market shrimps

This study employs a comprehensive approach combining metagenomic analysis and bacterial isolation to elucidate the microbial composition, antibiotic resistance genes (ARGs), and virulence factors (VFGs) present in shrimps from market and supermarket. Metagenomic analysis of shrimps revealed a dominance of Proteobacteria and Bacteroidetes with Firmicutes notably enriched in some samples. On the other hand, the dominant bacteria isolated included Citrobacter portucalensis, Escherichia coli, Salmonella enterica, Vibrio species and Klebsiella pneumonaie. Metagenomic analysis unveiled a diverse spectrum of 23 main types and 380 subtypes of ARGs in shrimp samples including many clinical significant ARGs such as blaKPC, blaNDM, mcr, tet(X4) etc. Genomic analysis of isolated bacterial strains identified 14 ARG types with 109 subtype genes, which complemented the metagenomic data. Genomic analysis also allowed us to identify a rich amount of MDR plasmids, which provided further insights into the dissemination of resistance genes in different species of bacteria in the same samples. Examination of VFGs and mobile genetic elements (MGEs) in both metagenomic and bacterial genomes revealed a complex landscape of factors contributing to bacterial virulence and genetic mobility. Potential co-occurrence patterns of ARGs and VFGs within human pathogenic bacteria underlined the intricate interplay between antibiotic resistance and virulence. In conclusion, this integrated analysis for the first time provides a comprehensive view and sheds new light on the potential hazards associated with shrimp products in the markets. The findings underscore the necessity of ongoing surveillance and intervention strategies to mitigate risks posed by antibiotic-resistant bacteria in the food supply chain using the novel comprehensive approaches.

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.

Antibiotic Resistance in Plant Pathogenic Bacteria: Recent Data and Environmental Impact of Unchecked Use and the Potential of Biocontrol Agents as an Eco-Friendly Alternative

The economic impact of phytopathogenic bacteria on agriculture is staggering, costing billions of US dollars globally. Pseudomonas syringae is the top most phytopathogenic bacteria, having more than 60 pathovars, which cause bacteria speck in tomatoes, halo blight in beans, and so on. Although antibiotics or a combination of antibiotics are used to manage infectious diseases in plants, they are employed far less in agriculture compared to human and animal populations. Moreover, the majority of antibiotics used in plants are immediately washed away, leading to environmental damage to ecosystems and food chains. Due to the serious risk of antibiotic resistance (AR) and the potential for environmental contamination with antibiotic residues and resistance genes, the use of unchecked antibiotics against phytopathogenic bacteria is not advisable. Despite the significant concern regarding AR in the world today, there are inadequate and outdated data on the AR of phytopathogenic bacteria. This review presents recent AR data on plant pathogenic bacteria (PPB), along with their environmental impact. In light of these findings, we suggest the use of biocontrol agents as a sustainable, eco-friendly, and effective alternative to controlling phytopathogenic bacteria.

Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.

Simultaneous suppression of As mobilization and N2O emission from NH4+/As-rich paddy soils by combined nitrate and birnessite amendment

The environmental impacts of As mobilization and nitrous oxide (N2O) emission in flooded paddy soils are serious issues for food safety and agricultural greenhouse gas emissions. Several As immobilization strategies utilizing microbially-mediated nitrate reducing-As(III) oxidation (NRAO) and birnessite (δ-MnO2)-induced oxidation/adsorption have proven effective for mitigating As bioavailability in flooded paddy soils. However, several inefficiency and unsustainability issues still exist in these remediation approaches. In this study, the effects of a combined treatment of nitrate and birnessite were assessed for the simultaneous suppression of As(III) mobilization and N2O emission from flooded paddy soils. Microcosm incubations confirmed that the combined treatment achieved an effective suppression of As(III) mobilization and N2O emission, with virtually no As(T) released and at least a 87% decrease in N2O emission compared to nitrate treatment alone after incubating for 8 days. When nitrate and birnessite are co-amended to flooded paddy soils, the activities of denitrifying enzymes within the denitrification electron transport pathway were suppressed by MnO2. As a result, the majority of applied nitrate participated in nitrate-dependent microbial Mn(II) oxidation. The regenerated biogenetic MnO2 was available to facilitate subsequent cycles of As(III) immobilization and concomitant N2O emission suppression, sustainable remediation strategy. Moreover, the combined nitrate-birnessite amendment promoted the enrichment of Pseudomonas, Achromobacter and Cupriavidu, which are known to participate in the oxidation of As(III)/Mn(II). Our findings document strong efficacy for the combined nitrate/birnessite treatment as a remediation strategy to simultaneously mitigate As-pollution and N2O emission, thereby improving food safety and reducing greenhouse gas emissions from flooded paddy soils enriched with NH4+ and As.

Emerging contaminants and their potential impacts on estuarine ecosystems: Are we aware of it?

Emerging contaminants (ECs) are becoming more prevalent in estuaries and constitute a danger to both human health and ecosystems. These pollutants can infiltrate the ecosystem and spread throughout the food chain. Because of the diversified sources and extensive human activities, estuaries are particularly susceptible to increased pollution levels. A thorough review on recent ECs (platinum group elements, pharmaceuticals and personal care products, pesticides, siloxanes, liquid crystal monomers, cationic surfactant, antibiotic resistance genes, and microplastics) in estuaries, including their incidence, detection levels, and toxic effects, was performed. The inclusion of studies from different regions highlights the global nature of this issue, with each location having its unique set of contaminants. The diverse range of contaminants detected in estuary samples worldwide underscores the intricacy of ECs. A significant drawback is the scarcity of research on the toxic mechanisms of ECs on estuarine organisms, the prospect of unidentified ECs, warrant research scopes.

Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land

Soils, especially in farmlands, are key media for the transmission of antibiotic resistance genes (ARGs) and their hosts from the environment to humans. Sloping farmland is an important agricultural resource, but there lack of studies on the fate and risk of ARGs in sloping land. Also, the behavior and drivers of ARGs in response to slope gradient and position are unclear. Here, metagenomics was used to investigate the profiles of ARGs, mobile genetic elements, and microbial communities in soils from lands of five slope gradients (5°, 10°, 15°, 20°, and 25°) with two slope positions (uphill and downhill). Results showed that while the abundance (except 15°) and diversity (except 20°) of ARGs increased as the slope gradient increased, the diversity of ARGs with health risk, especially the high-risk ones, decreased. For slope positions, abundant and diverse ARGs were more likely to accumulate at downhill. Furthermore, 52 bacterial genera and 12 human pathogenic bacteria (HPB) species were identified as the potential hosts for ARGs with high risk, and abundant HPB species were also detected in the soils with low gradients at downhill. Moreover, the structural equation model analysis revealed that the slope gradient and the slope position have both direct and indirect effects on the abundance of ARGs. Further correlation analysis revealed that the slope gradient has a positive effect (p < 0.05) on nitrite nitrogen in the soils. Also, the slope position has a negative effect (p < 0.05) on total phosphorus and microbial nitrogen, while positively affected (p < 0.05) on particulate nitrogen and microbial carbon, which were the key factors driving the behavior of ARGs. Overall, this study provided comprehensive information on ARGs with health risks and their potential pathogenic hosts in sloping farmland. It can be important for controlling antibiotic resistance transmission and be consistent with the One Health framework.

Gross yield driving the mass fluxes of fishery drugs: Evidence of occurrence from full aquaculture cycle in lower Yangtze River Basin

Expanding aquaculture has generated pollutants like fishery drugs in wastewater, which affects the aquatic environments and hinders sustainable development of aquaculture. To evaluate the occurrence, mass fluxes and production factors of fishery drugs in aquaculture, full-aquaculture-cycle monitoring in finfish and crustacean wastewater was conducted in the lower Yangtze River Basin, and 28 pesticides and 15 antibiotics were detected. The results showed that individual fishery drugs varied from ppt to ppb levels. Among them, sulfonamides were dominant with a mean concentration of 105.95 ± 4.13 ng·L-1 in finfish aquacultural wastewater, and insecticides were prevailing in crustacean aquacultural wastewater with a content of 146.56 ± 0.66 ng·L-1. Since the susceptibility to finfish disease determined the aquaculture practice, there were significant differences between two types of aquacultural wastewater. Finfish aquacultural wastewater contained more drugs and reached peak earlier in rapid-growth period, yet crustacean aquacultural wastewater peaked at the harvest period, to prevent against disease. Meanwhile, higher ecological risk, especially for florfenicol, were found in finfish wastewater. With 6 production factors from Good Aquaculture Practice, the gross yield was the most influential factor of drug mass flux, explaining 98 % variance by stepwise regression. Apart from increasing concentrations of fishery drugs in wastewater, regional high-yield aquaculture also significantly impacted the corresponding mass flux. As estimated by linear regression, 1.63 tons of target drugs would be discharged by 1 Mt. aquatic products, and 7.77 tons were discharged from aquaculture in the lower Yangtze River Basin in 2021. This is the first report to quantify mass fluxes of fishery drugs and to highlight gross yield as the most influential factor, which provides guidance for the supervision and regulation of sustainable aquaculture.

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.

A decennial study of the trend of antibiotic studies in China

Antibiotics are one of the greatest inventions in human history and are used worldwide on an enormous scale. Besides its extensive usage in medical and veterinary arenas to treat and prevent the infection, its application is very prominent in other fields, including agriculture, aquaculture, and horticulture. In recent decades, the increased consumption of antibiotics in China saw a vast increase in its production and disposal in various environments. However, in this post-antibiotic era, the abuse and misuse of these valuable compounds could lead to the unreversible consequence of drug resistance. In China, antibiotics are given a broad discussion in various fields to reveal their impact on both human/animals health and the environment. To our knowledge, we are the first paper to look back at the development trend of antibiotic-related studies in China with qualitative and quantitative bibliometric analysis from the past decades. Our study identified and analyzed 5559 papers from its inception (1991) to December 6, 2021, from the Web of Science Core Collection database. However, with few authors and institutions focusing on long-term studies, we found the quality of contributions was uneven. Studies mainly focused on areas such as food science, clinical research, and environmental studies, including molecular biology, genetics and environmental, ecotoxicology, and nutrition, which indicate possible primary future trends. Our study reports on including potentially new keywords, studies' milestones, and their contribution to antibiotic research. We offer potential topics that may be important in upcoming years that could help guide future research.

Metagenomic analysis of antimicrobial resistance in ducks, workers, and the environment in duck farms, southern China

Duck farms are one of the important reservoirs of antimicrobial resistance genes (ARGs) that spread to humans and the environment. However, few studies have focused on the characteristics of antimicrobial profiles in duck farms. Here we explored the distribution characteristics and potential transmission mechanisms of ARGs in ducks, farm workers, and the environment in duck farms by a metagenomic approach. The results showed that the highest abundance and diversity of ARGs were found in duck manure. The abundance and diversity of ARGs in workers and environmental samples were higher than those in the control group. tet(X) and its variants were prevalent in duck farms, with tet(X10) being the most abundant. The genetic structure "tet(X)-like + α/β hydrolase" was found in ducks, workers, and the environment, implying that tet(X) and its variants have been widely spread in duck farms. Network analysis indicated that ISVsa3 and IS5075 might play an important role in the coexistence of ARGs and metal resistance genes (MRGs). The Mantel tests showed that mobile genetic elements (MGEs) were significantly correlated with ARG profiles. The results suggest that duck manure may be a potential hotspot source of ARGs, including tet(X) variants that spread to the surrounding environment and workers via MGEs. These results help us optimize the antimicrobials strategy and deepen our understanding of ARG spread in duck farms.

Chemical-microbial effects of acetic acid, oxalic acid and citric acid on arsenic transformation and migration in the rhizosphere of paddy soil

Low-molecular-weight organic acids (LMWOAs) are essential components of rice roots exudates and an important source of soil organic carbon. The chemical-microbial pathway by which LMWOA affects arsenic (As) cycling in the rhizosphere of paddy soils is still unclear. In this study, three typical LMWOAs (acetic acid (AA), oxalic acid (OA), and citric acid (CA)) in rice root exudates were added to As-contaminated soil at a concentration of 10 mM, mimicking the rhizosphere environment. The results showed that the addition of AA and OA inhibited the mobilization of As in the rhizosphere soil. After 14 days of incubation, the content of As in the porewater of AA and OA decreased by 40% and 22%, respectively, compared with the control. AA hindered the mobilization of As in soil via promoting the formation of secondary minerals. The addition of OA inhibits the mobilization of As via increasing the proportion of As (V) in porewater and promoting the formation of secondary minerals in soil. In addition, OA addition not only significantly increased the aioA gene abundance but also notably enriched the microorganisms containing As (III) methylation functional genes (arsM). The addition of CA greatly expedited the release of As from the soil solid phase through the solubilization of Fe/Mn minerals via the effects of both soil chemistry and microbial action. Furthermore, linear discriminant analysis effect size (LEfSe) revealed the possibility that bacteria such as Burkholderia, Magnetospirillum, and Mycobacterium were involved in the reduction or methylation of As in the rhizosphere of paddy soil. This study revealed the internal causes of LMWOAs regulating As transformation and mobilization in flooded paddy soil and provided theoretical support for reducing As accumulation in rice by breeding rice varieties with high AA and OA secretions.

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.

Sulfur: a neglected driver of the increased abundance of antibiotic resistance genes in agricultural reclaimed subsidence land located in coal mines with high phreatic water levels

Due to the shallow burial of groundwater in coal mines with a high phreatic water level, a large area of subsidence lakes is formed after the mine collapses. Agricultural and fishery reclamation activities have been carried out, which introduced antibiotics and exacerbated the contamination of antibiotic resistance genes (ARGs), but this has received limited attention. This study analyzed ARG occurrence in reclaimed mining areas, the key impact factors, and the underlying mechanism. The results show that sulfur is the most critical factor impacting the abundance of ARGs in reclaimed soil, which is due to changes in the microbial community. The species and abundance of ARGs in the reclaimed soil were higher than those in the controlled soil. The relative abundances of most ARGs increased with the depth of reclaimed soil (from 0 to 80 cm). In addition, the microbial structures of the reclaimed and controlled soils were significantly different. Proteobacteria, was the most dominant microbial phylum in the reclaimed soil. This difference is likely related to the high abundance of sulfur metabolism functional genes in the reclaimed soil. Correlation analysis showed that the differences in ARGs and microorganisms in the two soil types were highly correlated with the sulfur content. High levels of sulfur promoted the proliferation of sulfur-metabolizing microbial populations such as Proteobacteria and Gemmatimonadetes in the reclaimed soils. Remarkably, these microbial phyla were the main antibiotic-resistant bacteria in this study, and their proliferation created conditions for the enrichment of ARGs. Overall, this study underscores the risk of the abundance and spread of ARGs driven by high-level sulfur in reclaimed soils and reveals the mechanisms.

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.

Review of hospital effluents: special emphasis on characterization, impact, and treatment of pollutants and antibiotic resistance

Health care institutions generate large volumes of liquid effluents from specific activities related to healthcare, analysis, and research. Their direct discharge into the environment has various negative effects on aquatic environments and human health, due to their high organic matter charges and the presence of various emerging contaminants such as disinfectants, drugs, bacteria, viruses, and parasites. Moreover, hospital effluents, by carrying antibiotics, contribute to the development of antibiotic-resistant microorganisms in the environment. This resistance has become a global issue that manifests itself variously in different countries, causing the transmission of different infections. In this respect, an effort is provided to protect water resources by current treatment methods that imply physical-chemical processes such as adsorption and advanced oxidation processes, biological processes such as activated sludge and membrane bioreactors and other hybrid techniques. The purpose of this review is to improve the knowledge on the composition and impact of hospital wastewater on man and the environment, highlighting the different treatment techniques appropriate to this type of disposal before discharge into the environment.

Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments

Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.

Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO₃-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.

Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis

Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people's lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.

ARGs distribution and high-risk ARGs identification based on continuous application of manure in purple soil

Tetracyclines (TCs) are one of the most widely used antibiotics in livestock and poultry industry. Sichuan province and Chongqing city are the provinces and cities with the most concentrated purple soil distribution in China, as well as the largest livestock and poultry breeding scale. Purple soils with low organic carbon content and poor structure, and manure fertilizers were heavily applied to improve soil quality. However, the research on antibiotic resistance genes (ARGs) dispersal in purple soils is limited. Overall, 234 ARGs subtypes belonging to 15 types were detected in all soils. Long-term application of livestock manures significantly changed the characteristics of ARGs, mobile genetic elements (MGEs), pathogen species and bacterial communities in the soil, and increased by 103.2 %, 13.1 %, 188.6 % and 43.7 % in chicken manure treatments compared with the control, respectively. Partial equation PLS-PM analysis further reveals that the main driving factor of ARGs is bacterial abundance, while bacterial diversity has a negative effect on ARGs abundance. Through ANOVA and network analysis, it was found that 30 ARGs were significantly affected by manure, its relative abundance is 0.8-1.4 times that of the control treatment. The qPCR results also proved that the relative abundance of ARGs including sul2, etc. increased with the increase of manure application and these resistance genes in chicken manure treatments were higher than in pig manure treatments. These resistance genes pose a high risk to public health, and chicken manure application posed a higher risk than pig manure. The TC content in the 40-60 cm soil layer was higher in medium- and high-volume pig manure, which was at risk of being transported to groundwater. Our research results deepen the understanding of ARGs transmission in purple soil under agricultural activities and emphasize the species and distribution of antibiotic resistance genes may differ across soil and manure types.

Reduction of antibiotic resistance genes (ARGs) in swine manure-fertilized soil via fermentation broth from fruit and vegetable waste

The issue of growing increase of antibiotic resistance genes (ARGs) in manure-fertilized soil needs urgently addressing. In this study, fermentation broth from fruit and vegetable waste was prepared to reduce ARG abundance in swine manure-fertilized soils. With a six-month field experiment, we found that swine manure-fertilized soil had significantly higher ARG abundance than soil applied with chemical fertilizer. As expected, the homemade fermentation broth significantly reduced ARG abundance in swine manure-fertilized soil, possibly through the decrease of abundance of Actinomyces, in which there was a 48.0%, 51.9%, and 66.7% decrease in the abundance of Nocardioides, Streptomyces, and Nonomuraea, respectively. With the bacteriostatic experiment, we observed that fermentation broth (5 mL/L) significantly inhibited the growth and metabolism in Actinomycetes spp. and Nocardioides sp., in terms of ATPase and PDH activity. These findings confirmed that the inhibition of Actinobacteria, some of the most dominant ARG hosts, was one of the main mechanisms responsible for the decrease in ARG abundance in fermentation broth-treated soil. This study provides field-scale evidence of a feasible strategy for controlling farmland ARG pollution, which is of utmost importance for soil health in the context of sustainable agriculture.

Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences

Wild birds are known to harbor and discharge antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). However, assessments of their contribution to the dissemination of antibiotic resistance in the environment are limited to culture-dependent bacterial snapshots. Here, we present a high-throughput sequencing study that corroborates extensive ARG exchange between wild bird feces and their habitats and implies the need to scrutinize high-mobility birds as potential vectors for global propagation of ARGs. We characterized the resistome (281 ARGs) and microbiome of seven wild bird species and their terrestrial and aquatic habitats. The resistomes of bird feces were influenced by the microbial community structure, mobile genetic elements (MGEs), and residual antibiotics. We designated 33 ARGs found in more than 90% of the bird fecal samples as core ARGs of wild bird feces, among which 16 ARGs were shared as core ARGs in both wild bird feces and their habitats; these genes represent a large proportion of both the bird feces (35.0 ± 15.9%) and the environmental resistome (29.9 ± 21.4%). One of the most detected β-lactam resistance genes (bla_TEM, commonly harbored by multidrug resistant "superbugs") was used as molecular marker to demonstrate the high interconnectivity of ARGs between the microbiomes of wild birds and their habitats. Overall, this work provides a comprehensive analysis of the wild bird resistome and underscores the importance to consider genetic exchange between animals and the environment in the One Health approach.

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.

Metagenomics highlights the impact of climate and human activities on antibiotic resistance genes in China's estuaries

Estuarine environments faced with contaminations from coastal zones and the inland are vital sinks of antibiotic resistance genes (ARGs). However, little is known about the temporal-spatial pattern of ARGs and its predominant constraints in estuarine environments. Here, we leveraged metagenomics to investigate ARG profiles from 16 China's estuaries across 6 climate zones in dry and wet seasons, and disentangled their relationships with environmental constraints. Our results revealed that ARG abundance, richness, and diversity in dry season were higher than those in wet season, and ARG abundance exhibited an increasing trend with latitude. The prevalence of ARGs was significantly driven by human activities, mobile gene elements, microbial communities, antibiotic residuals, physicochemical properties, and climatic variables. Among which, climatic variables and human activities ranked the most important factors, contributing 44% and 36% of the total variance of observed ARGs, respectively. The most important climatic variable shaping ARGs is temperature, where increasing temperature is associated with decreased ARGs. Our results highlight that the prevalence of ARGs in estuarine environments would be co-driven by anthropogenic activities and climate, and suggest the dynamics of ARGs under future changing climate and socioeconomic development.

Multi-drug resistance, integron and transposon-mediated gene transfer in heterotrophic bacteria from Penaeus vannamei and its culture environment

Multi-drug resistance (MDR) in bacteria is regarded as an emerging pollutant in different food production avenues including aquaculture. One hundred and sixty out of 2304 bacterial isolates from shrimp farm samples (n = 192) of Andhra Pradesh, India, were MDR. Based on biochemical identification and 16S rRNA sequencing, they were grouped into 35 bacterial species with the predominance of Vibrio parahaemolyticus (12.5%). The MDR isolates showed highest resistance toward oxytetracycline (89%) with more than 0.2 MAR (multiple antibiotic resistance), demonstrates a high-risk source. The most prevalent antibiotic-resistance gene (ARG) and mobile genetic element (MGE) detected were tetA (47.5%) and int1 (46.2%), respectively. In conjugation experiments, overall transfer frequency was found to be in the range of 1.1 × 10^-9 to 1.8 × 10^-3 with the transconjugants harbouring ARGs and MGEs. This study exposed the wide distribution of MDR bacteria in shrimp and its environment, which can further aggravate the already raised concerns of antibiotic residues in the absence of proper mitigation measures.

Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China

With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.

Distribution and Transfer of Antibiotic Resistance Genes in Coastal Aquatic Ecosystems of Bohai Bay

Antibiotic resistance genes (ARGs) are abundant in diverse ecosystems and the resistome may constitute a health threat for humans and animals. It is necessary to uncover ARGs and the accumulation mechanisms from different environmental sources. Various habitats, such as soil, seawater and fish intestines, could overflow a considerable amount of ARGs and the horizontal transfer of ARGs may occur in these environments. Thus, we assessed the composition and abundance of ARGs in seawater, soil and intestinal tracts of Cynoglossus semilaevis collected from different sites in Bohai Bay (China), including a natural area and three fish farms, through a high-throughput qPCR array. In total, 243 ARGs were uncovered, governing the resistance to aminoglycoside, multidrug, beta-lactamase, macrolide lincosamide streptomycin B (MLSB), chloramphenicol, sulfonamide, tetracycline, vancomycin and other antibiotics. The action mechanisms of these ARGs were mainly antibiotic deactivation, efflux pump and cellular protection. Importantly, similar ARGs were detected in different samples but show dissimilar enrichment levels. ARGs were highly enriched in the fish farms compared to the natural sea area, with more genes detected, while some ARGs were detected only in the natural sea area samples, such as bacA-02, tetL-01 and ampC-06. Regarding sample types, water samples from all locations shared more ARGs in common and held the highest average level of ARGs detected than in the soil and fish samples. Mobile genetic elements (MGEs) were also detected in three sample types, in the same trend as ARGs. This is the first study comparing the resistome of different samples of seawater, soil and intestines of C. semilaevis. This study contributes to a better understanding of ARG dissemination in water sources and could facilitate the effective control of ARG contamination in the aquatic environment.

Earthworms reduce the dissemination potential of antibiotic resistance genes by changing bacterial co-occurrence patterns in soil

Globally distributed earthworms affect compositions of soil compounds, microbial community structures, as well as antibiotic resistance genes (ARGs). Compared to their surroundings, earthworm gut is a simpler environment which could filter out microbes when soil passes through it. However, little is known about how earthworms affect the dissemination of ARGs in soil, and the understanding of the relationship between microbe-microbe interactions and ARGs is still lacking. Here, we designed a microcosm experiment with earthworm addition, and determined bacterial and fungal community compositions based on amplicon sequencing. We also examined mobile genetic elements (MGEs) and ARGs in earthworm gut and soils using high-throughput qPCR. The results showed significant differences of bacterial, fungal and ARG patterns between gut and soil. Earthworms indirectly impacted the patterns of ARGs in soils by affecting bacterial communities and soil properties, which play key roles in the distribution of ARGs and MGEs. The absolute abundances of MGEs in earthworm gut were significantly lower than those in soils, and earthworms reduce the absolute abundance of MGEs in soils. Earthworms changed the microbial co-occurrence patterns, and reduced bacterial connectivity, which were significantly and positively correlated with MGE abundance. These results highlight the importance of earthworm on the distribution and dissemination of ARGs in soils.

Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment

The prevalence of antibiotic resistance genes (ARGs) in livestock and poultry manure is a severe threat to human health. However, the comprehensive characterization of antibiotic resistance in swine, workers, and the receiving environment is still lacking in the actual breeding environment. Hence, the ARG profile and the potential bacterial hosts producing among swine manure (including sows, piglets, finishing pigs, and nursery pigs), worker feces, and the receiving environment (including sediment and vegetable soil) were comprehensively analyzed based on the metagenomic method. The results showed that swine manure exhibited the high levels of richness and diversity of ARGs. Inactivating tetracycline resistance genes such as tet(X), tet(X1), and tet(X10) were prevalent on swine farms. Workers and the environment were the primary recipients of ARGs, and shared ARGs accounted for at least 90% of their ARG abundances. Network analysis revealed that Escherichia, Acinetobacter, and Erysipelothrix were the most dominant genera co-occurring with specific shared ARGs. The abundance of coexisting ARGs in swine at different developmental stages accounted for 76.4% to 90.8% of the shared ARGs in swine, workers, and environmental samples. The Mantel test revealed that Firmicutes and Proteobacteria had a significant correlation with the ARG profiles. In addition, variation partitioning analysis (VPA) showed that the joint effects of mobile genetic elements (MGEs) and bacterial communities accounted for 24.7% of the resistome variation and played a significant role in the ARG profiles. These results improve our understanding of the transmission and persistence of ARGs in the actual breeding environment.

The fate and behavior mechanism of antibiotic resistance genes and microbial communities in anaerobic reactors treating oxytetracycline manufacturing wastewater

In this study, two parallel-operated expanded granular sludge bed (EGSB) reactors, one used to treat oxytetracycline (OTC) manufacturing wastewater with gradual increase of OTC concentration as experimental reactor and the other fed with the same wastewater without OTC as control reactor, were operated to investigate the behavior of antibiotics resistance genes (ARGs) and mobile genetic elements (MGEs) and their possible relationships with bacterial community among influent, sludge and effluent environments. Though the average absolute abundance of ARGs slightly decreased (0.26 - log), the ARGs' relative abundance normalized to 16S-rRNA gene copy numbers showed a significant upward trend in effluent (2 multiples - increase) and the absolute and relative abundances both extremely increased in anaerobic sludge, indicating that anaerobic treatment process cannot reduce ARGs efficiently, inversely can increase the risk of ARGs through the proliferation of antibiotics resistance bacteria (ARB) under the suppression of OTC. MGEs, bacterial communities and OTC concentration mainly impacted the ARGs profiles, which contributed 88.4% to the variation of ARGs. The differences and correlations of hosts in influent, effluent and sludge were further confirmed by network analysis. Overall, this study enhanced the understanding of the prevalence and transfer of ARGs in OTC production effluents during anaerobic treatment.

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.

Performance and mechanism in degradation of typical antibiotics and antibiotic resistance genes by magnetic resin-mediated UV-Fenton process

Incomplete removal of antibiotics and antibiotic resistance genes (ARGs) has often been reported in wastewater treatment plants. More efficient treatment processes are needed to reduce their risks to the environment. Herein, we evaluated the degradation of antibiotics and ARGs by using magnetic anion exchange resin (MAER) as UV-Fenton catalyst. Sulfamethoxazole (SMZ), ofloxacin (OFX), and amoxicillin (AMX) were selected as the target compounds. The three antibiotics were almost completely degraded (> 99%) following the MAER UV-Fenton reaction for 30 min. From the degradation mechanism study, it was found that Fe³⁺/Fe²⁺ could be cyclically transferred from the catalyst at permeable interface, and the photo-generated electrons could be effectively separated. The dominant reactive radicals for antibiotics degradation were hydroxide during the MAER UV-Fenton reaction. The degradation pathway for sulfamethoxazole was proposed. In addition, wastewater samples from a wastewater treatment plant were applied to investigate the removal efficiency of antibiotics and their ARGs by the MAER UV-Fenton system. A rapid decrease in antibiotics and ARGs level was observed with this reaction system. The results from this study suggest that the MAER-mediated UV-Fenton reaction could be applied for the effective removal of antibiotics and ARGs in wastewater.

A case study on the distribution of the environmental resistome in Korean shrimp farms

Hundreds of tons of antibiotics are widely used in aquaculture to prevent microbial infections and promote fish growth. However, the overuse of antibiotics and chemical products can lead to the selection and spreading of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), which are of great concern considering the threat to public health worldwide. Here, in-depth metagenome sequencing was performed to explore the environmental resistome and ARB distribution across farming stages in shrimp farms and examine anthropogenic effects in nearby coastal waters. A genome-centric analysis using a metagenome binning approach allowed us to accurately investigate the distribution of pathogens and ARG hosts in shrimp farms. The diversity of resistomes was higher in shrimp farms than in coastal waters, and the distribution of resistomes was dependent on the farming stage. In particular, the tetracycline resistance gene was found mainly at the early post-larval stage regardless of the farm. The metagenome-assembled genomes of Vibrio spp. were dominant at this stage and harbored tet34, which is known to confer resistance to oxytetracycline. In addition, opportunistic pathogens such as Francisella, Mycoplasma, Photobacterium, and Vibrio were found in abundance in shrimp farms, which had multiple virulence factors. This study highlights the increased resistance diversity and environmental selection of pathogens in shrimp farms. The use of environmental pollutants on farms may cause an increase in resistome diversity/abundance and the transmission of pathogens to the surrounding environment, which may pose future risks to public health and aquatic organisms.

Responses of sediment resistome, virulence factors and potential pathogens to decades of antibiotics pollution in a shrimp aquafarm

Aquaculture ecosystem has become a hotspot of antibiotics resistance genes (ARGs) dissemination, owing to the abuse of prophylactic antibiotics. However, it is still unclear how and to what extent ARGs respond to the increasing antibiotic pollution, a trend as expected and as has occurred. Herein, a significant sediment antibiotic pollution gradient was detected along a drainage ditch after decades of shrimp aquaculture. The increasing antibiotic pollution evidently promoted the diversities and tailored the community structures of ARGs, mobile genetic elements (MGEs), virulence factors and pathogens. The profiles of ARGs and MGEs were directly altered by the concentrations of terramycin and sulphadimidine. By contrast, virulence factors were primarily affected by nutrient variables in sediment. The pathogens potentially hosted diverse virulence factors and ARGs. More than half of the detected ARGs subtypes non-linearly responded to increasing antibiotic pollution, as supported by significant tipping points. However, we screened seven antibiotic concentration discriminatory ARGs that could serve as independent variable for quantitatively diagnosing total antibiotic concentration. Co-occurrence analysis depicted that notorious aquaculture pathogens of Vibrio harveyi and V. parahaemolyticus potentially hosted ARGs that confer resistance to multiple antibiotics, while priority pathogens for humankind, e.g., Helicobacter pylori and Staphylococcus aureus, could have harbored redundant virulence factors. Collectively, the significant tipping points and antibiotic concentration-discriminatory ARGs may translate into warning index and diagnostic approach for diagnosing antibiotic pollution. Our findings provided novel insights into the interplay among ARGs, MGEs, pathogens, virulence factors and geochemical variables under the scenario of increasing antibiotic pollution.

Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes

Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.

Distribution of antibiotic resistance genes in the environment

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990-2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept.

Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination

Insight into the distribution of antibiotic resistance genes (ARGs) in phytoplankton-zooplankton communities (PZCs) is essential for the management and control of antibiotic resistance in aquatic ecosystems. This study characterized the profiles of PZCs and their carried ARGs in a typical urban river and ranked the factors (water physicochemical parameters, PZCs, bacterial abundance, and mobile genetic elements) influencing the dynamic of ARG profiles by the partial least squares path modeling. Results showed Cyanobacteria, Bacillariophyta and Chlorophyta were dominant phyla of phytoplankton, and Rotifera was with the highest abundance in zooplankton. River contamination markedly altered the structure of PZCs, increasing the abundance of phytoplankton and zooplankton, decreasing the diversity of phytoplankton while elevating in zooplankton. PZCs harbored large amounts of ARGs with average relative abundance of 2.35 × 10^-2/copies nearly an order magnitude higher than the living water and most ARGs exhibited significant accumulation in PZCs with the aggravated environmental pollution. The partial least squares path modeling predicted the water parameters as the most important factor mainly playing indirect effects on ARGs via PZCs and bacterial communities, followed by mobile genetic elements as the most essential direct factor for ARGs profiles. Besides, PZCs were also important drivers for the carried ARGs via direct effects on the ARGs' composition and indirect effects on host bacterial communities of ARGs and their mobile genetic elements. The present study fills the gaps in knowledge about the distribution of ARGs in PZCs and provided a new perspective to decipher the key roles of PZCs in the maintenance and dissemination of ARGs in urban river ecosystems.

Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG's proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material is available in the online version of this article at 10.1007/s11783-021-1469-4 and is accessible for authorized users.

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

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

Metagenomic Insights Into the Structure and Function of Intestinal Microbiota of the Hadal Amphipods

Hadal trenches are the deepest known areas of the ocean. Amphipods are considered to be the dominant scavengers in the hadal food webs. The studies on the structure and function of the hadal intestinal microbiotas are largely lacking. Here, the intestinal microbiotas of three hadal amphipods, Hirondellea gigas, Scopelocheirus schellenbergi, and Alicella gigantea, from Mariana Trench, Marceau Trench, and New Britain Trench, respectively, were investigated. The taxonomic analysis identified 358 microbial genera commonly shared within the three amphipods. Different amphipod species possessed their own characteristic dominant microbial component, Psychromonas in H. gigas and Candidatus Hepatoplasma in A. gigantea and S. schellenbergi. Functional composition analysis showed that “Carbohydrate Metabolism,” “Lipid Metabolism,” “Cell Motility,” “Replication and Repair,” and “Membrane Transport” were among the most represented Gene Ontology (GO) Categories in the gut microbiotas. To test the possible functions of “Bacterial Chemotaxis” within the “Cell Motility” category, the methyl-accepting chemotaxis protein (MCP) gene involved in the “Bacterial Chemotaxis” pathway was obtained and used for swarming motility assays. Results showed that bacteria transformed with the gut bacterial MCP gene showed significantly faster growths compared with the control group, suggesting MCP promoted the bacterial swimming capability and nutrient utilization ability. This result suggested that hadal gut microbes could promote their survival in poor nutrient conditions by enhancing chemotaxis and motility. In addition, large quantities of probiotic genera were detected in the hadal amphipod gut microbiotas, which indicated that those probiotics would be possible contributors for promoting the host’s growth and development, which could facilitate adaptation of hadal amphipods to the extreme environment.

Removal of extracellular antibiotic resistance genes using magnetic biochar/quaternary phosphonium salt in aquatic environments: A mechanistic study

The proliferation and spread of antibiotic resistance genes (ARGs) is becoming a worldwide crisis. Extracellular DNA encoding ARGs (eARGs) in aquatic environment plays a critical role in the dispersion of antimicrobial resistance genes. Strategies to control the dissemination of eARGs are urgently required for ecological safety and human health. Towards this goal, magnetic biochar/quaternary phosphonium salt (MBQ), was used to investigate the efficiency and removal mechanism for eARGs. Magnetic biochar modified by quaternary phosphonium salt enhanced the adsorption capacity of extracellular DNA to approximately 9 folds, compared to that of the unmodified. DNA adsorption by MBQ was mainly dominated by chemisorption in heterogeneous systems and was promoted in acidic and low-salt environment. The generation of •OH and MBQ colloid jointly cleaved DNA into fragments, facilitating the adsorption of the phosphate backbone of DNA onto MBQ through electrostatic force as well as the conformational transition of DNA. Furthermore, quantification of extracellular DNA after MBQ was applied in water demonstrated that over 92.7% of resistance genes were removed, indicating a significantly reduced risk of propagation of antimicrobial resistance in aquatic environments. These findings have a practical significance in the application of MBQ in mitigating the spread of ARGs in aquatic environment.

Deposition of resistant bacteria and resistome through FMT in germ-free piglets

Faecal microbiota transplantation (FMT) has received considerable attention in recent years due to its remarkable efficacy in restoring a normal gut microbiome. Here, we established the groups of post-FMT recipient piglets using germ-free piglets during early life to characterize the colonization of gut microbiota composition and the enrichment of resistance gene acquisition. By metagenomic analysis, we identified 115 bacterial phyla and 2111 bacterial genera that were acquired by the FMT recipients. We found that early-life microbial colonization and the spread of resistomes in recipient piglets were age dependent. A total of 425, 425 and 358 AR genes primarily belonging to 114, 114 and 102 different types were detected in the donors, post-FMT recipients in the FMT-3D group and post-FMT recipients in the FMT-15D group respectively. Genes that encoded tetracycline, macrolide and chloramphenicol resistance proteins were the most dominant AR genes, and the results corresponded with the exposure of antibiotic consumption at farm. Bacteroides, Escherichia, Clostridium, Parabacteroides, Treponema, Lactobacillus and Enterococcus were significantly correlated with the distribution of AR genes. More importantly, the relative abundance of AR genes was positively correlated with the levels of mobile genetic elements. Our results indicate that early-life microbial colonization can persistently shape the gut microbiota and antibiotic resistome.

Shifts in bacterial communities and antibiotic resistance genes in surface water and gut microbiota of guppies (Poecilia reticulata) in the upper Rio Uberabinha, Brazil

Anthropogenic activities especially water pollution can affect the diversity and composition of microbial communities and promote the spread of antibiotic resistance genes (ARGs). In this study, water samples and guppies (Poecilia reticulata) were sampled from six sampling sites along the Uberabinha River in southeastern Brazil, both microbial communities and ARGs of surface waters and intestinal microbiota of guppies (Poecilia reticulata) were detected. According to the results of 16S rRNA amplicon sequencing, Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria were dominant phyla in both water and intestinal microbiota, but the abundance of putative pathogens was higher at heavily polluted sites. Up to 83% of bacteria in intestinal microbiota originated from water microbiota; this proportion was relatively higher in less polluted compared to polluted environments. ARGs providing resistance of tetracyclines and quinolones were dominant in both water and gut microbiota. The relative abundances of class I integrons and ARGs were as high as 1.74 × 10^-1/16S rRNA copies and 3.61 × 10^-1/16S rRNA copies, respectively, at heavily polluted sites. Correlation analysis suggests that integrons and bacteria play key roles in explaining the widespread occurrence of ARGs in the surface, but not in intestinal microbiota. We could rule out the class I integrons a potential intermediary bridge for ARGs between both types of microbiomes. Our results highlight the tight link in microbial communities and ARGs between ambient microbiota of stream ecosystems and intestinal microbiota of fish. Our study could have far-reaching consequences for fisheries and consumer safety and calls for investigations of gut microbiota of target species of both commercial fisheries and recreational (hobby) angling.

Prevalence and hazardous impact of pharmaceutical and personal care products and antibiotics in environment: A review on emerging contaminants

Antibiotic resistance is a global health emergency linked to unrestrained use of pharmaceutical and personal care products (PPCPs) as prophylactic agent and therapeutic purposes across various industries. Occurrence of pharmaceuticals are identified in ground water, surface water, soils, and wastewater treatment plants (WWTPs) in ng/L to μg/L concentration range. The prevalence of organic compounds including antimicrobial agents, hormones, antibiotics, preservatives, disinfectants, synthetic musks etc. in environment have posed serious health concerns. The aim of this review is to elucidate the major sources accountable for emergence of antibiotic resistance. For this purpose, variety of introductory sources and fate of PPCPs in aquatic environment including human and veterinary wastes, aquaculture and agriculture related wastes, and other anthropogenic activities have been discussed. Furthermore, genetic and enzymatic factors responsible for transfer and appearance of antibiotic resistance genes are presented. Ecotoxicity of PPCPs has been studied in environment in order to present risk imposed to human and ecological health. As per published literature reports, the removal of antibiotics and related traces being difficult, couples the possibility of emergence of antibiotic resistance and hence sustainability in global water resources. Therefore, research on environmental behavior and control strategies should be conducted along with assessing their chronic toxicity to identify potential human and ecological risks.

Heterotrophic nitrification-aerobic denitrification characteristics and antibiotic resistance of two bacterial consortia from Marinomonas and Halomonas with effective nitrogen removal in mariculture wastewater

Heterotrophic nitrification-aerobic denitrification (HNAD) characteristics and antibiotic resistance of two bacterial consortia, Marinomonas communis & Halomonas titanicae (MCH) and Marinomonas aquimarina & Halomonas titanicae (MAH), and their single isolates (MC, MA, and H) were determinated in this study. When cultured in sole and mixed N-source media (NH₄⁺-N and/or NO₂^--N of 10 mg/L), MCH and MAH exhibited greater efficiency and stability of inorganic-N removal than single isolates, and these strains preferred to remove NH₄⁺-N by simultaneous HNAD in mixed N-source media. Meanwhile, 45%-70% of NH₄⁺-N and/or NO₂^--N was mainly converted to organic nitrogen (15%-25%) and gaseous nitrogen (30%-40%) by these strains, and more inorganic-N was transformed to intracellular-N by MCH and MAH via assimilation instead of gaseous-N production by denitrification. Both isolates and their consortia had the maximal NH₄⁺-N or NO₂^--N removal efficiency above 95% under the optimum conditions including temperature of 20-30 °C, C/N ratios of 15-20, and sucrose as carbon source. Interestingly, bacterial consortia performed greater nitrogen removal than single isolates under the low temperature of 10 °C or C/N ratios of 2-5. In real mariculture wastewater, MCH and MAH also showed higher NH₄⁺-N removal efficiency (65%-68%) and more stable cell quantity (4.2-5.2 × 10⁸ CFU/mL) than single strains, due to the interspecific coexistence detected by bacterial quantitation with indirect immunoassay. Additionally, these isolates and consortia had stronger resistances to polypeptides, tetracyclines, sulfonamides, furanes, and macrolides than other antibiotics. These findings will be conducive to the applications of HNAD bacteria of Marinomonas and Halomonas on reducing nitrogen pollution in mariculture or other saline environments.

River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus)

Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10^-1/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.

Degradation of sulfamethoxazole by cobalt-nickel powder composite catalyst coupled with peroxymonosulfate: Performance, degradation pathways and mechanistic consideration

In this work, cobalt-nickel powder (Co-NP) synthesized through electroless plating was used as a heterogeneous bimetallic catalyst for peroxymonosulfate (PMS) activation to degrade sulfamethoxazole (SMX) in the aqueous phase. Compared with different oxidation systems and different catalysts, it was proved that Co-NP had excellent catalytic ability, fast electron transfer rate and good stability. The effects of key parameters (initial pH, SMX concentration, catalyst and PMS dosages) on SMX degradation and ion leaching were studied in detail. Furthermore, the sensitivity of inorganic anions and different pollutants towards the Co-NP/PMS system was studied to investigate its application in natural water bodies. Quenching test showed that the main reactive oxygen species generated during the reaction were OH and SO₄^-, of which SO₄^- played a predominating role. Combined with XPS analysis, the activation mechanism was concluded that free radicals were mainly generated through the valence change of Co and Ni. Based on the seven intermediates measured through ultrahigh performance liquid chromatograph-mass spectrometry (UPLC-QTOF-MS/MS), the possible degradation pathways of SMX were proposed. Notably, this study provided a new kind of supporter for advanced oxidation processes and electroless plating technology.

Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context

The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 μg L^-1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.

Characterization of a gill-abundant crustin with microbiota modulating function in Litopenaeus vannamei

Gills as the respiratory tissue of crustacean encounter various threats in the environment. The immune defense in gills is essential to the health of shrimp. In the present study, we identified a novel gill-abundant crustin, LvCrustin Ⅱ-1, from the shrimp Litopenaeus vannamei. The full-length open reading frame of LvCrustin Ⅱ-1 is 522 bp, which encodes 173 amino acid residues. The amino acid sequence of LvCrustin Ⅱ-1 contained a signal peptide, a glycine rich region, a cysteine rich region and a whey acidic protein (WAP) domain. The expression level of LvCrustin Ⅱ-1 was significantly up-regulated at different time points after Vibrio parahaemolyticus immersion. When LvCrustin Ⅱ-1 was silenced by dsRNA interference, the count of bacteria colonies increased significantly in the hepatopancreas of shrimp after V. parahaemolyticus immersion, which indicated that the infection progress of pathogenic bacteria was accelerated after LvCrustin Ⅱ-1 knockdown. Compared with the microbiota of seawater, the lower proportion of aquatic bacteria and higher proportion of symbiont in the gills microbiota of shrimp indicated the bacterial colonization was modulated by the host. Knockdown of LvCrustin Ⅱ-1 changed the proportion of some potential pathogens and aquatic bacteria, which supported the idea that the new identified crustin in the gills played important roles in modulation of the microbiota community in shrimp. The present data provided new insights into the multiple functions of crustin in the immunity of shrimp.