Seasonal variations in antibiotic resistance genes in estuarine sediments and the driving mechanisms

Optimizing entropy weight model to accurately predict variation of pharmaceuticals and personal care products in the estuaries and coasts of the South China

Pharmaceuticals and personal care products (PPCPs) have raised increasing concern worldwide due to their continuous release and potential hazards to the ecosystem and human health. This study optimized the entropy weight model (EW-WRSR) that combines entropy weight with multi-criteria decision analysis to investigate pollution patterns of PPCPs in the coasts and estuaries. The results revealed that occurrences of PPCPs from the 1940s to the present were consistent with using PPCPs, different types of human activities, and local urban development. This helped better understand the history of PPCP contamination and evaluate the uncertainty of EW-WRSR. The model predicted hotspots of PPCPs that were consistent with the actual situation, indicating that PPCPs mainly enter the nearshore ecosystem by the form of sewage discharge and residual aquaculture. This study can provide method that identifying highly contaminated regions on a global scale.

Seasonal hydrological dynamics affected the diversity and assembly process of the antibiotic resistome in a canal network

The significant threat of antibiotic resistance genes (ARGs) to aquatic environments health has been widely acknowledged. To date, several studies have focused on the distribution and diversity of ARGs in a single river while their profiles in complex river networks are largely known. Here, the spatiotemporal dynamics of ARG profiles in a canal network were examined using high-throughput quantitative PCR, and the underlying assembly processes and its main environmental influencing factors were elucidated using multiple statistical analyses. The results demonstrated significant seasonal dynamics with greater richness and relative abundance of ARGs observed during the dry season compared to the wet season. ARG profiles exhibited a pronounced distance-decay pattern in the dry season, whereas no such pattern was evident in the wet season. Null model analysis indicated that deterministic processes, in contrast to stochastic processes, had a significant impact on shaping the ARG profiles. Furthermore, it was found that Firmicutes and pH emerged as the foremost factors influencing these profiles. This study enhanced our comprehension of the variations in ARG profiles within canal networks, which may contribute to the design of efficient management approaches aimed at restraining the propagation of ARGs.

Tire particles and its leachates: Impact on antibiotic resistance genes in coastal sediments

Tire particles (TPs), a significant group of microplastics, can be discharged into the coastal environments in various ways. However, our understanding of how TPs impact the antibiotic resistance and pathogenic risks of microorganisms in coastal sediments remains limited. In this study, we used metagenomics to investigate how TPs and their leachates could affect the prevalence of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their potential risks to the living creatures such as soil invertebrates and microorganisms in the coastal sediments. We discovered that TP addition significantly increased the abundance and diversity of ARGs and VFGs in coastal sediments, with raw TPs displayed higher impacts than TP leachates and TPs after leaching on ARGs and VFGs. With increasing TP exposure concentrations, the co-occurrence frequency of ARGs and mobile genetic elements (MGEs) in the same contig also increased, suggesting that TPs could enhance the dispersal risk of ARGs. Our metagenome-based binning analysis further revealed that exposure to TPs increased the abundance of potentially pathogenic antibiotic-resistant bacteria (PARB). In addition, chemical additives of TP leachates (e.g., Zn and N-cyclohexylformamide) significantly affected the changes of ARGs in the pore water. In summary, our study provides novel insights into the adverse effects of TP pollutions on aggravating the dissemination and pathogenic risks of ARGs and PARB in the coastal environment.

Antimicrobial Susceptibility in Respiratory Pathogens and Farm and Animal Variables in Weaned California Dairy Heifers: Logistic Regression and Bayesian Network Analyses

Weaned dairy heifers are a relatively understudied production group. Bovine respiratory disease (BRD) is the most common cause of antimicrobial drug (AMD) use, morbidity, and mortality in this production group. The study of antimicrobial resistance (AMR) is complicated because many variables that may affect AMR are related. This study generates hypotheses regarding the farm- and animal-level variables (e.g., vaccination, lane cleaning, and AMD use practices) that may be associated with AMR in respiratory isolates from weaned dairy heifers. A cross-sectional study was performed using survey data and respiratory isolates (Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni) collected from 341 weaned dairy heifers on six farms in California. Logistic regression and Bayesian network analyses were used to evaluate the associations between farm- and animal-level variables with minimum inhibitory concentration (MIC) classification of respiratory isolates against 11 AMDs. Farm-level variables associated with MIC classification of respiratory isolates included the number of source farms of a calf-rearing facility, whether the farm practiced onsite milking, the use of lagoon water for flush lane cleaning, and respiratory and pinkeye vaccination practices. Animal-level variables associated with a MIC classification included whether the calf was BRD-score-positive and time since the last phenicol treatment.

Microcosm experiments revealed resistome coalescence of sewage treatment plant effluents in river environment

Sewage treatment plant (STP) effluents are important contributors of antibiotic resistance (AR) pollution in rivers. Effluent discharging into rivers causes resistome coalescence. However, their mechanisms and dynamic processes are poorly understood, especially for the effects of dilution, diffusion, and sunlight-induced attenuation on coalescence. In this study, we have constructed microcosmic experiments based on in-situ investigation to explore these issues. The first batch experiment revealed the effects of dilution and diffusion. The coverage of water coalesced resistomes ranged 66.26∼152.18 × /Gb and was positively correlated with effluent volume (Mann-Kendall test, p < 0.01). Principal coordinate analysis (PCoA) and source tracking analysis demonstrated that dilution and diffusion stepwise reduced AR pollution. The second batch experiment explored the temporal dynamics and sunlight attenuation on coalesced resistomes. Under natural light, the coverage and diversity of water resistomes posed decreasing trends, primarily attributed to drastic erasure of effluent traces. The proportion of effluent-specific ARGs in coalesced resistomes significantly declined over time (Spearman's r = -0.83 and -0.94 in coverage and richness). While under dark condition, the coverage and diversity increased. Sunlight radiation intensified the interactions between water and sediment resistomes, as evidenced by more shared ARGs and less dissimilarities across niches. Network analysis, metagenome-assembled genome (MAG) analysis and variation partitioning analysis (VPA) showed that microbiome controlled resistome coalescence, explaining 56.5% and 58.4% of resistomes in water and sediment, respectively. Biotic and abiotic factors synergistically explained 40% of water resistomes. This study offers a comprehensive understanding of AR transmission and provides theoretical bases for grasping AR pollution and developing effective suppression strategies.

Antibiotic resistance genes in constructed wetlands: Driving indicators and risk assessment

Constructed wetlands (CWs) were responsible for the in-depth purification of wastewater, providing an ideal environment for the transport, acquisition, and dissemination of antibiotic resistance genes (ARGs). A better understanding of influencing factors and risks of ARGs in CWs was deemed indispensable. In this research, the abundance of ARGs and mobile genetic elements (MGEs) was determined to be higher in summer and spring, ranging from 53.7 to 8.51 × 106 and 30.9-6.02 × 106 copies/mL, respectively. Seasonal variation significantly influenced the abundance of ARGs and MGEs, as well as the co-occurrence patterns among ARGs, MGEs and bacteria. However, the environmental gradients, from the influent (CW01) to the effluent (CW10), did not impose significant effects on the abundance of ARGs and MGEs. Furthermore, the ratios of pathogenic bacteria to ARG hosts and ARG risks index decreased by 50.4% and 88.54% along with the environmental gradients, indicating that CWs could act as barriers to the transfer of ARGs. Partial least squares-path modeling (PLSPM) revealed that temperature was the main driving factor of ARGs, followed by MGEs, stable and differential bacteria. This finding effectively and innovatively explored the driving indicators for the variations and risks of ARGs caused by spatial-temporal variations, providing new insights into the evaluation and control of ARGs in CWs.

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.

Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem

Aquatic ecosystems in anthropogenically impacted areas are important reservoirs of antibiotic resistance genes (ARGs) of allochthonous origin. However, the dynamics of the different ARGs within the bacterial communities of lakes and rivers, as well as the factors that drive their selection, are not completely understood. In this study, we analysed the fate of the bacterial resistome (total content of ARGs and of metal resistance genes, MRGs) for a period of six months (summer-winter) in a continuum lake-river-lake system (Lake Varese, River Bardello, Lake Maggiore) in Northern Italy, by shotgun metagenomics. The metagenomic data were then compared with chemical, physical and microbiological data, to infer the role of anthropogenic pressure in the different sampling stations. ARGs and MRGs were more abundant and diverse in the River Bardello, characterised by the highest anthropogenic pollution. The date of sampling influenced ARGs and MRGs, with higher abundances in summer (August) than in fall or in winter, when the impact of the treated wastewater discharge in the river was limited by a higher water flow from Lake Varese. ARG and MRG abundances were significantly correlated and they co-occurred in the main network analysis modules with potential pathogenic bacteria. Different levels of anthropogenic impact selectively promoted specific ARGs while others, generally abundant in waters, were not affected by anthropogenic pressure. Reducing the level of anthropogenic pressure resulted in a rapid decrease of most ARGs. From our results, the role of anthropogenic pressure in promoting the spread of specific antibiotic resistances and of potential pathogens in aquatic ecosystem becomes clear. Finally we highlight the strict correlation between ARGs and MRGs suggesting their potential co-selection in stressed aquatic bacterial communities.

Fate of antibiotic resistance genes and bacteria in a coupled water-processing system with wastewater treatment plants and constructed wetlands in coastal eco-industrial parks

In coastal eco-industrial zones, wastewater treatment plants (WWTPs) and constructed wetlands (CWs) can alleviate the challenge of water shortage and the negative effect of sewage discharge, while the problems of antibiotic resistance genes (ARGs) have not attracted enough attention. In this research, the Wafergen SmartChip system was adopted to investigate the ARG profiles in a coupled system combined WWTPs and CWs in a coastal industrial park. Potential risks of antibiotic resistance in chemical industrial wastewater were confirmed due to the higher abundance of target ARGs (> 10⁷ copies/mL). General decline with partial enrichment in absolute and relative abundance of ARGs from the WWTPs to CWs revealed the effective removal of ARGs in the coupled system, while the fate of different ARG types varied greatly. Aminoglycoside and sulfonamide ARGs were detected with higher abundance (up to 5.34 ×10⁷ and 3.61 ×10⁷ copies/mL), especially aac(6')-Ib and sul1. Denitrification, secondary sedimentation, and acid hydrolysis contributed to the removal of aminoglycoside, sulfonamide, β-lactamase, chloramphenicol, and multidrug ARGs. Catalytic ozonation contributed to the removal of tetracycline and MLSB ARGs. Subsurface CWs worked effectively for the removal of sulfonamide, tetracycline, and multidrug ARGs, especially tetX, cphA, tetG, and strB. Close correlations between ARGs and MGEs emphasized the vital roles of anthropogenic pollutants and horizontal gene transfer on the diffusion of ARGs. Actinobacteria, Bacteroidota, and Cyanobacteria were dominant in the CWs, while Proteobacteria, Firmicutes, and Planctomycetota were prevalent in the WWTPs. Redundancy analysis and variance partitioning analysis indicated that transposase and water quality posed greater influences on the distribution of ARGs. Co-occurrence network revealed that potential multiple antibiotic resistant pathogenic bacteria decreased in the CWs. The coupled system has a limited effect on the reduction of ARGs and potential ARG hosts, providing a comprehensive insight into the fate of ARGs in conventional water-processing systems.

The reasons for the spatial and media distribution variations of ARGs in a typical semi-enclosed bay

Antibiotic resistance genes (ARGs) are considered a newly emerging contaminant. This study aimed to investigate the spatial and media distribution patterns of ARGs in Jiaozhou Bay, as well as the reasons behind these patterns. The results revealed that aminoglycoside and MLSB resistant genes predominated in all samples, and the relative abundance of ARGs ranging from 10^-6 to 10^-2, 10^-6 to 10^-3 and 10^-5 to 10^-2 copies/16S rRNA in coastal water, bay water, and sediments, respectively. The significant spatial variation of ARGs was explained by the fact that the coastal water was more susceptible to human activities, whereas environmental physicochemical factors played a crucial role in the bay water. The intrinsic reason for the media distribution variation was the different assembly processes in the two media, while the external reason was that the ARGs in the water and sediments were mainly influenced by environmental physicochemical factors and heavy metals, respectively.

Distribution of antibiotic resistance genes in the sediments of Erhai Lake, Yunnan-Kweichow Plateau, China: Their linear relations with nonpoint source pollution discharges from 26 tributaries

Erhai Lake, a typical plateau deep water lake, experienced long-term nonpoint source (NPS) pollution discharge from 26 tributaries, which significantly affected the abundance and spread of resistance genes. In this study, 25 antibiotic resistance genes (ARGs), classified into six types, and NPS pollution discharges were investigated throughout around the Erhai basin. FCA (mexF) and sulfonamide resistance genes (sul1, sul2 and sul3) were the most common. Although the absolute overall abundance of ARGs there was low so far, the individual gene like sulfonamide resistance gene was high. Regression analysis using an ordinary least squares model (OLS) showed that the discharge of NPS pollution into Erhai Lake would have an obvious effect on the distribution of ARGs. And the relations between them were linear. Concretely speaking, the total nitrogen (TN) pollution input from tributaries could significantly correlated with the increasing of ARG abundance, while the total phosphorus (TP) pollution input showed the opposite correlation, and ultimately affect the distribution of ARGs. Moreover, the effect of TP on ARG distribution was more significant than TN. This study provides a geographical profile of ARG distribution in a subtropical deep lake on Yunnan-Kweichow Plateau. The results are beneficial for predicting the distribution characteristics of ARGs and controlling their pollution in plateau lakes.

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a  ~  200  km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

The variations of antibiotics and antibiotic resistance genes in two subtropical large river basins of south China: Anthropogenic impacts and environmental risks

Emission of antibiotics into riverine environments affects aquatic ecosystem functions and leads to the development of antibiotic resistance. Here, the profiles of forty-four antibiotics and eighteen antibiotic resistance genes (ARGs) were analyzed in two large rivers of the Pearl River System. In addition, the risks of ecotoxicity and resistance selection posed by the antibiotics were estimated. As compared to the reservoirs, the river sections close to the urban and livestock areas contained more antibiotics and ARGs. Seasonal variations of antibiotics (higher in the dry season) and relative ARGs (normalized by 16S rRNA gene, higher in the wet season) were found in the water, but not in the sediment. Sulfonamide resistance genes were the most prevalent ARGs in both river water and sediment. Antibiotic concentration was correlated with ARG abundance in the water, indicating that antibiotics play a critical role in ARG spread. In addition, oxytetracycline was the most abundant antibiotic with concentrations up to 2030 ng/L in the water and 2100 ng/g in the sediment respectively, and posed the highest risks for resistance selection. Oxytetracycline, tetracycline and sulfamethoxazole were expected to be more ecotoxicologically harmful to aquatic organisms, while ofloxacin, enrofloxacin, norfloxacin, chlortetracycline, oxytetracycline and tetracycline posed ecotoxicological risks in the sediment. The Nanliujiang river with intensive livestock activities was contaminated by antibiotics and ARGs and faced high ecotoxicological and resistance selection risks. Collectively, these findings reflect the impacts of anthropogenic activities on the spread of antibiotic resistance in large river basins.

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.

Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms

The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.

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.

The panorama of antibiotics and the related antibiotic resistance genes (ARGs) in landfill leachate

Landfill leachate is an important source and sink of antibiotics and antibiotic resistance genes (ARGs), which poses a potential threat to human health and ecological environment. Ten antibiotics and 8 ARGs in leachates collected from Zhejiang Province, China, were systematically investigated. The effects of multiple factors were considered: leachate age, season when the leachate was sampled (dry or rainy), heavy metal concentrations, and leachate quality parameters. Leachate age was crucial to the profile of the detectable antibiotics and ARGs. The total concentration of antibiotics were in the order of macrolides > sulfonamides > tetracyclines and they decreased significantly with leachate age. Similarly, fewer ARGs were harbored in aged leachate; the order of abundance of the ARGs was mexF (11.92 ± 0.22 log₁₀ gene copies/L) > sul2 > Intl1 > sul1 > ermB > mefA > tetM > tetQ (9.57 ± 1.32 log₁₀ gene copies/L). The extreme abundances (i.e., the maxima and minima) of ARGs relating to the same class of antibiotic were always surprisingly similar and appeared in leachate of the same age. Seasonal variation greatly affected the concentrations of antibiotics in the leachate-the concentration difference between the dry and rainy seasons could reach two orders of magnitude. Heavy metal concentrations and leachate quality parameters also had important effects on the distribution of antibiotics and ARGs. Overall, the profile of antibiotics and ARGs in leachates was influenced by numerous factors, and the pollution of antibiotics and ARGs may be reduced and controlled by adjusting the environmental factors.

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.

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors

Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.

Antibiotic resistance genes on the Qinghai-Tibet Plateau above an elevation of 5,000 m

Antibiotic resistance genes (ARGs) widely occur in both anthropogenic and remote environments. Several studies have investigated the distribution of antibiotic resistance in natural environments. However, the occurrence and diversity of ARGs in remote environments at high elevations have not yet been well elucidated. Abundance, diversity, as well as influencing factors of ARGs in different ecosystems on the Qinghai-Tibet Plateau beyond elevation 5,000 m were explored, using high-throughput quantitative PCR. Totally, 197 ARGs and 12 mobile genetic elements (MGEs) were determined with abundances ranging from 3.75 × 10⁶ to 2.39 × 10⁷ and from 2.21 × 10⁴ to 1.62 × 10⁶ copies g^-1, respectively. Both the absolute and relative abundances of ARGs in farmland were lower than those in wetland and grassland. The diversity and dominant resistance mechanism of ARG profiles showed obvious differences among these ecosystems. Bacterial communities and MGEs significantly correlated with ARG profiles, while physico-chemical factors showed little impact. The high abundance and strong positive correlation between integron intI-1 and ARGs suggested a high potential horizontal ARG transfer. Based on the results, the Qinghai-Tibet Plateau can be regarded as a considerable ARG gene pool. This study provides insights into the provenance of ARGs at high elevations.

Distribution of Metal Resistance Genes in Estuarine Sediments and Associated Key Impact Factors

Currently, little is known about the distribution of metal resistance genes (MRGs) in estuarine sediments. In this study, we used the high-throughput quantitative real-time polymerase chain reaction (HT-qPCR) to determine the distribution of MRGs in the sediments of an estuary system and the associated key impact factors. The relative abundance of the detected MRGs showed a decreasing trend from the river inlet toward the sea and a decrease from the middle area of the estuary to the near-shore areas on both sides; these decreases were higher in the summer than in the winter. In the estuary system during the summer, the abundance of Zn- and Cu-MRGs from the river inlet to the sea decreased by 99.5% and 93.6%, whereas those of Hg- and Cd-Zn-Co-MRGs increased by 51.5% and 16.7%, respectively. Moreover, the abundance of Zn- and Cu-MRGs in the winter decreased by 88.6% and 97.7%, respectively, whereas that of Cd-Bi-Zn-Pb-MRGs increased by 729.6%. Furthermore, the abundances of MRGs and mobile genetic elements (MGEs) were significantly positively correlated with the levels of antibiotic residues and heavy metals as well as with the particle size and total organic carbon content of the sediment; however, they were significantly negatively correlated with seawater salinity and the oxidation and reduction potential (E_h) and pH of the sediment. The abundance of MGEs was significantly positively correlated with the abundance of MRGs in the sediment. Our findings suggest that antibiotic residues facilitated the proliferation and propagation of MRGs by promoting MGEs in estuarine sediments.

Spatiotemporal distribution, source apportionment and combined pollution of antibiotics in natural waters adjacent to mariculture areas in the Laizhou Bay, Bohai Sea

The spatiotemporal distribution, source apportionment and combined pollution of 14 antibiotics in natural waters adjacent to mariculture farms of Laizhou Bay in the Bohai Sea were studied. The contribution proportion and quantity of each potential pollution source to antibiotics in natural water bodies were quantitatively described. The correlations between heavy metals and antibiotics and their underlying mechanisms in natural and aquaculture water environment were analyzed. Fourteen antibiotics were detected in natural water and sediment in the coastal area of Laizhou Bay. The maximum concentrations of sulfamethazine and trimethoprim in water reached tens or even hundreds of μg/L in winter. Trimethoprim was the main antibiotic in natural water bodies in winter and summer, and enrofloxacin was the principal antibiotic in sediments. Enrofloxacin, ciprofloxacin and oxytetracycline were detected in all underground water samples; thus, control of these antibiotics needs to be made a priority to mitigate groundwater contamination. PCA-MLR revealed that the potential sources of antibiotics in natural waters of Laizhou Bay include the mariculture wastewater (18.3%), the domestic sewage (63.3%) and the livestock wastewater (18.4%). Therefore, the antibiotic burden of Laizhou Bay was principally from the domestic sewage. In natural water, the concentration of Cu was positively correlated with antibiotics, which might be related to the common sources, the competitive adsorption in sediments and the easy complexation characteristic of Cu and antibiotics. Positive correlations among antibiotics and heavy metals were observed in mariculture sediments, while negative relationships were observed in natural sediments.

Distance dilution of antibiotic resistance genes of sediments in an estuary system in relation to coastal cities

Coastal tourist and industrial cities are most likely to have differential effects on the distance dilution of antibiotic resistance genes (ARGs) in an estuary system. This study used high-throughput fluorescence quantitative polymerase chain reaction to identify sediment ARGs in two typical estuaries of coastal tourist and industrial cities (Xiamen and Taizhou) in China. The distance dilution of ARGs and its relationship with key environmental factors were analysed. The results indicated that along the river inlet towards the sea, the distance dilution effect on ARG abundance in estuary sediments of Taizhou was approximately double that in Xiamen, and the macrolide, lincosamide, and streptogramin B (MLSB) and vancomycin genes were replaced by the fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) and β-lactam genes in Taizhou, whereas β-lactam genes succeeded the MLSB and sul genes in Xiamen. The abundance and number of ARGs and mobile genetic elements (MGEs) were positively correlated with the particle size and total organic carbon (TOC) contents of sediments, whereas they were negatively associated with the oxidation and reduction potential (E_h) and pH of sediments, as well as the seawater salinity. The sediment particle size (SPZ) was the dominant physicochemical factor affecting the abundance of ARGs (r = 0.826, p < 0.05) and MGEs (r = 0.850, p < 0.01). These findings suggest that although the distance dilution effect on the ARG abundance of estuary sediments of the industrial city is greater than that of the tourist city, the larger SPZ, higher TOC content, and lower salinity, pH, and E_h in estuary regions adjacent to the industrial city can more significantly facilitate the proliferation and propagation of ARGs in the sediments.

The prevalence of ampicillin-resistant opportunistic pathogenic bacteria undergoing selective stress of heavy metal pollutants in the Xiangjiang River, China

The emergence of clinically relevant β-lactam-resistant bacteria poses a serious threat to human health and presents a major challenge for medical treatment. How opportunistic pathogenic bacteria acquire antibiotic resistance and the prevalence of antibiotic-resistant opportunistic pathogenic bacteria in the environment are still unclear. In this study, we further confirmed that the selective pressure of heavy metals contributes to the increase in ampicillin-resistant opportunistic pathogens in the Xiangjiang River. Four ampicillin-resistant opportunistic pathogenic bacteria (Pseudomonas monteilii, Aeromonas hydrophila, Acinetobacter baumannii, and Staphylococcus epidermidis) were isolated on Luria-Bertani (LB) agar plates and identified by 16S rRNA sequencing. The abundance of these opportunistic pathogenic bacteria significantly increased in the sites downstream of the Xiangjiang River that were heavily influenced by metal mining activities. A microcosm experiment showed that the abundance of β-lactam resistance genes carried by opportunistic pathogenic bacteria in the heavy metal (Cu²⁺ and Zn²⁺) treatment group was 2-10 times higher than that in the control. Moreover, heavy metals (Cu²⁺ and Zn²⁺) significantly increased the horizontal transfer of plasmids in pathogenic bacteria. Of particular interest is that heavy metals facilitated the horizontal transfer of conjugative plasmids, which may lead to the prevalence of multidrug-resistant pathogenic bacteria in the Xiangjiang River.

Antibiotic resistance genes, bacterial communities, and functions in constructed wetland-microbial fuel cells: Responses to the co-stresses of antibiotics and zinc

The effects of the continuous accumulation of Zinc (Zn) on the fate of antibiotic resistance genes (ARGs) in constructed wetland-microbial fuel cells (CW-MFCs) remain unclear. In this study, the impacts of Zn addition and a circuit mode on antibiotic removal, occurrence of ARGs, the bacterial community, and bacterial functions were investigated in three groups of CW-MFCs. The results showed that continuous Zn exposure enriched the target ARGs during the initial stage, while excessive Zn accumulation decreased antibiotic removal and the abundance of ARGs. A principal component analysis demonstrated that ARGs and the bacterial community distribution characteristics were significantly impacted by the mass accumulation of antibiotics and Zn, as well as the circuit mode. A redundancy analysis, partial least squares path modeling, and Procrustes analysis revealed that the accumulation of antibiotics and Zn, the composition of the bacterial community, the circuit mode, and the abundance of intI associated with horizontal gene transfer jointly contributed to the distributions of ARGs in the electrodes and effluent. Moreover, continuous exposure to Zn decreased the bacterial diversity and changed the composition and function of the bacterial community predicted using PICRUSt tool. The co-occurrence of ARGs, their potential hosts and bacterial functions were further revealed using a network analysis. A variation partition analysis also showed that the accumulation of target pollutants and the circuit mode had a significant impact on the bacterial community composition and functions. Therefore, the interaction among ARGs, the bacterial community, bacterial functions, and pollutant accumulations in the CW-MFC was complex. This study provides useful implications for the application of CW-MFCs for the treatment of wastewater contaminated with antibiotics and heavy metals.

Occurrence and distribution of antibiotic resistance genes in sediments in a semi-enclosed continental shelf sea

Extensive and improper overuse of antibiotics resulted in the prevalence of antibiotic resistance genes (ARGs). As the typical semi-enclosed continental shelf sea, the Bohai Sea has been considered as one of the most polluted marine areas in China. However, no comprehensive investigation on the spatial distribution of ARGs in sediments from the Bohai Sea has been reported. A large-scale sampling was performed in the Bohai Sea areas. The abundances of ARGs (6 classes, 29 ARG subtypes), class 1 integron-integrase gene (intI1), hmt-DNA and 16S rRNA gene were evaluated. IntI1 was detected with higher abundances in coastal areas ranging from 2.8 × 10⁵ to 2.5 × 10⁸ copies/g. The total ARGs abundances varied over 3 orders of magnitude in different sampling sites with the maximum at 4.9 × 10⁸ copies/g. Sulfonamides resistance genes were ubiquitous and abundant with the abundances ranging from 5.7 × 10⁴ to 1.8 × 10⁷ copies/g, and quinolones resistance genes varied greatly in different samples. The contour map demonstrated that ARGs were more abundant in the Laizhou Bay, the south of Bohai Bay and the eastern of central sea basin. Most of the target ARG subtypes were detected with 100% detection frequencies. The genes of sul1, sul2 and tetX were detected with both higher absolute and relative abundance, while the abundance of β-lactams ARG subtypes was lower. Principal component analysis (PCA) and redundancy analysis (RDA) indicated that no significant differences in the ARGs abundance existed in different samples, and the sediment qualities played important roles in the distribution of ARGs. Bacterial communities were investigated and 768 strong and significant connections between ARGs and bacteria were identified. The possible hosts of ARGs were revealed by network analysis with higher relative abundance in coastal areas than the sea.

Characterization of antibiotic resistance genes and bacterial community in selected municipal and industrial sewage treatment plants beside Poyang Lake

Sewage treatment plants (STPs) are significant reservoirs of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Municipal STPs (MSTPs) and industrial STPs (ISTPs) are the two most important STP types in cities. In this study, the ARGs, mobile genetic elements (MGEs), and bacterial communities of selected STPs, including two MSTPs and one ISTP, in the vicinity of Poyang Lake were comprehensively investigated through high-throughput qPCR and high-throughput Illumina sequencing. The results showed that the profiles of ARGs, MGEs and bacteria differed between the ISTP and the two MSTPs, most likely due to differences in influent water quality, such as the Pb that characterized in the ISTP's influent. The longer hydraulic retention times (HRTs) of the two MSTPs than of the ISTP may also have accounted for the different profiles. Thus, a prolonged HRT in the CASS process seems to allow a more extensive removal of ARGs and bacteria in ISTPs with similar treatment process. By providing comprehensive insights into the characteristics of ARGs, MGEs and the bacterial communities of the selected MSTPs and ISTP, our study provides a scientific basis for controlling the propagation and diffusion of ARGs and ARB in different types of STPs.