Antibiotic resistance gene abundances associated with antibiotics and heavy metals in animal manures and agricultural soils adjacent to feedlots in Shanghai; China

Technologies towards antibiotic resistance genes (ARGs) removal from aquatic environment: A critical review

Antibiotic resistance genes (ARGs) have been recognized as emerging pollutants that are widely distributed and accumulated in most of aquatic environment. Although many ARGs-removal technologies are employed, a corresponding discussion of merits and limitations of known technologies is still currently lacking. More importantly, the removal mechanisms of ARGs remain unclear, hindering their ecological feasibility. Thus, further in-depth studies are highly required. In this review, the occurrence and risk of ARGs in aquatic environment are introduced, and the main routes and potential impacts of ARGs dissemination are enumerated. In addition, several novel ARGs detection methods are critically reviewed. Notably, to ensure greater applicability of these technologies, systematic information on how recent technologies impact the ARGs removal and control are comprehensively compared and summarized. Finally, future research directions to alleviate the risk of ARGs in aquatic environment are briefly introduced. Taken together, this review provides useful information to facilitate the development of innovative and feasible ARGs removal technologies and increase their economic viability and ecological sustainability.

Removal of antibiotic-resistant genes during drinking water treatment: A review

Once contaminate the drinking water source, antibiotic resistance genes (ARGs) will propagate in drinking water systems and pose a serious risk to human health. Therefore, the drinking water treatment processes (DWTPs) are critical to manage the risks posed by ARGs. This study summarizes the prevalence of ARGs in raw water sources and treated drinking water worldwide. In addition, the removal efficiency of ARGs and related mechanisms by different DWTPs are reviewed. Abiotic and biotic factors that affect ARGs elimination are also discussed. The data on presence of ARGs in drinking water help come to the conclusion that ARGs pollution is prevalent and deserves a high priority. Generally, DWTPs indeed achieve ARGs removal, but some biological treatment processes such as biological activated carbon filtration may promote antibiotic resistance due to the enrichment of ARGs in the biofilm. The finding that disinfection and membrane filtration are superior to other DWTPs adds weight to the advice that DWTPs should adopt multiple disinfection barriers, as well as keep sufficient chlorine residuals to inhibit re-growth of ARGs during subsequent distribution. Mechanistically, DWTPs obtain direct and inderect ARGs reduction through DNA damage and interception of host bacterias of ARGs. Thus, escaping of intracellular ARGs to extracellular environment, induced by DWTPs, should be advoided. This review provides the theoretical support for developping efficient reduction technologies of ARGs. Future study should focus on ARGs controlling in terms of transmissibility or persistence through DWTPs due to their biological related nature and ubiquitous presence of biofilm in the treatment unit.

Pathways and mechanisms of nitrogen transformation during co-composting of pig manure and diatomite

The aim of this study was to investigate the pathways and mechanisms of nitrogen transformation during the composting process, by adding diatomite (0%, 2.5%, 5%, 10%, 15% and 20%) into initial mixtures of pig manure and sawdust. The results revealed that diatomite facilitated the conversion from NH₄⁺-N to amino acid nitrogen and hydrolysis undefined nitrogen, then reduced NH₃ and N₂O emission by 8.63-35.29% and 14.34-73.21%, respectively. Moreover, the structure and abundance of nitrogen functional genes provided evidence for nitrogen loss. Furthermore, compared with the control (0.03), the treatment blended with 10% diatomite (T3) had the highest value in composting score (-1.27). Additionally, the ratio of carbon and nitrogen (57.30%) was vital for reducing nitrogen loss among all physio-chemical parameters in this study. In conclusion, adding diatomite was a practical way to enhance nitrogen conservation and increase quality of end products, and the optimum added dosage was at 10%.

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

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

Fitness reduction of antibiotic resistome by an extra carbon source during swine manure composting

This study employed high-throughput quantitative polymerase chain reaction to evaluate the effects of specific co-substrate and additive on the fitness of antibiotic resistome during swine manure composting. The results showed that corncob particle as a co-substrate significantly reduced the relative abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) simultaneously. The diversity of ARGs was also reduced more effectively by corncob addition. Brick granule as an additive reduced the concentrations of bioavailable Cu and Zn. However, the relative abundances of ARGs and MGEs were not reduced by the addition of brick granule subsequently. Redundancy analysis indicated a negative effect of the C content and positive effects of class I integrase gene (intI) and bioavailable metals on the variation of the relative abundance of ARGs (p < 0.01). The Procrustes test showed a higher goodness-of-fit between the relative abundance of ARGs and 16S rRNA genes (r = 0.8166; p < 0.0001). Our results suggests that the effect of corncob particle on the relative abundance of ARGs was achieved by driving the changes in physicochemical properties and microbial communities. This study confirmed the hypothesis of fitness cost and demonstrated the contribution of extra C source to ARG attenuation during composting.

Pollution by Antibiotics and Antimicrobial Resistance in LiveStock and Poultry Manure in China, and Countermeasures

The demand for animal protein has increased considerably worldwide, especially in China, where large numbers of livestock and poultry are produced. Antibiotics have been widely applied to promote growth and prevent diseases. However, the overuse of antibiotics in animal feed has caused serious environmental and health risks, especially the wide spread of antimicrobial resistance (AMR), which seriously affects animal and human health, food safety, ecosystems, and the sustainable future development of animal protein production. Unfortunately, AMR has already become a worldwide challenge, so international cooperation is becoming more important for combatting it. China’s efforts and determination to restrict antibiotic usage through law enforcement and effective management are of significance. In this review, we address the pollution problems of antibiotics; in particular, the AMR in water, soil, and plants caused by livestock and poultry manure in China. The negative impact of widespread and intensive use of antibiotics in livestock production is discussed. To reduce and mitigate AMR problems, we emphasize in this review the development of antibiotic substitutes for the era of antibiotic prohibition.

Designing a marine outfall to reduce microbial risk on a recreational beach: Field experiment and modeling

A marine outfall can be a wastewater management system that discharges sewage and stormwater into the sea; hence, it is a source of microbial pollution on recreational beaches, including antibiotic resistant genes (ARGs), which lead to an increase in untreatable diseases. In this regard, a marine outfall must be efficiently located to mitigate these risks. This study aimed to 1) investigate the spatiotemporal variability of Escherichia coli (E. coli) and ARGs on a recreational beach and 2) design marine outfalls to reduce microbial risks. For this purpose, E. coli and ARGs with influential environmental variables were intensively monitored on Gwangalli beach, South Korea in this study. Environmental fluid dynamic code (EFDC) was used and calibrated using the monitoring data, and 12 outfall extension scenarios were explored (6 locations at 2 depths). The results revealed that repositioning the marine outfall can significantly reduce the concentrations of E. coli and ARGs on the beach by 46-99%. Offshore extended outfalls at the bottom of the sea reduced concentrations of E. coli and ARGs on the beach more effectively than onshore outfalls at the sea surface. These findings could be helpful in establishing microbial pollution management plans at recreational beaches in the future.

Pollution characteristics of livestock faeces and the key driver of the spread of antibiotic resistance genes

The increasing prevalence of antibiotic resistance genes (ARGs) in livestock and poultry faeces has attracted considerable amounts of attention. However, in the actual breeding environment, the key driver of the spread of ARGs and which bacteria are involved remain unclear. This study investigated 19 antibiotics and 4 heavy metals in 147 animal faeces. The results showed that piglet faeces exhibited the highest levels of antibiotics and heavy metals. Twelve ARGs, 4 mobile genetic elements (MGEs) and bacterial communities of piglet faeces from 6 pig farms were further assessed to determine the key driver and relevant mechanism of the spread of ARGs. Sulphonamides (SAs) explained 36.5% of the variance (P < 0.05) of the bacterial community and were significantly related to 8 genes (P < 0.01), indicating that SAs dominated the spread of ARGs and should be tightly supervised. Structural equation modelling (SEM) indicated that SAs increased the abundance of ARGs via two pathways: horizontal transfer of ARGs (involving 10 genera) and vertical transfer of ARGs (involving 26 genera). These results improve our understanding of the potential hosts involved in the spread of ARGs, suggesting that monitoring of the above potential hosts is also important in animal feeding practice.

Effects on microbiomes and resistomes and the source-specific ecological risks of heavy metals in the sediments of an urban river

This study aims to better understand the effects of heavy metal enrichment on microbiomes and resistomes and the source-specific ecological risks of metals in the sediments of an urban river. Geo-accumulation index and enrichment factor suggested the river sediments were contaminated by Cd, Cu, Pb, and Zn in varying degrees. High-throughput sequencing-based metagenomics analysis identified 430 types of antibiotic resistance genes (ARGs), dominated by the multidrug, MLS, bacitracin, quinolone, and aminoglycoside ARGs, and 52 metal resistance genes (MRGs) mainly conferring resistance to zinc, copper, cadmium, lead, mercury and multiple metals. Spearman correlation analysis and Mantel test showed the heavy metal enrichment exerted significant effects on the microbial community, ARGs and MRGs. Source apportionment using positive matrix factorization revealed that natural source (42.8%) was the largest contributor of metals in the river sediments, followed by urban activities (35.4%) and a mixed source (21.7%). However, when incorporating the apportionment results into a modified risk model to evaluate the source-specific ecological risks, results showed human activities dominated the risks of metals. Comparatively, the urban activities majorly caused moderate- and considerable- ecological risks, while the mixed source with respect to agricultural and industrial activities contributed higher percentages on high- and extremely high- ecological risks.

Interactions Between Microplastics and Heavy Metals in Aquatic Environments: A Review

Microplastics (MPs), tiny particles broken down from larger pieces of plastics, have accumulated everywhere on the earth. As an inert carbon stream in aquatic environment, they have been reported as carriers for heavy metals and exhibit diverse interactive effects. However, these interactions are still poorly understood, especially mechanisms driving these interactions and how they pose risks on living organisms. In this mini review, a bibliometric analysis in this field was conducted and then the mechanisms driving these interactions were examined, especially emphasizing the important roles of microorganisms on the interactions. Their combined toxic effects and the potential hazards to human health were also discussed. Finally, the future research directions in this field were suggested. This review summarized the recent research progress in this field and highlighted the essential roles of the microbes on the interactions between MPs and heavy metals with the hope to promote more studies to unveil action mechanisms and reduce/eliminate the risks associated with MP presence.

Fate of antibiotic resistance genes and metal resistance genes during the thermophilic fermentation of solid and liquid swine manures in an ectopic fermentation system

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44-97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.

Quantifying the occurrence and transformation potential of extracellular polymeric substances (EPS)-associated antibiotic resistance genes in activated sludge

Antibiotic resistance has been regarded as a global concern and biological wastewater treatment plants (WWTPs) are ideal hotbeds for the emergence and propagation of antibiotic resistance genes (ARGs). Extracellular polymeric substances (EPS), one of the primary components of activated sludge, might affect the distribution of extracellular ARGs in supernatant and EPS matrix, and thus alter their uptake potential by microbial cells. Herein, the presence and significance of EPS-associated ARGs in activated sludge from four WWTPs were assessed. Seven typical ARGs (sulI, sulII, bla_TEM-1, tetA, tetO, tetQ, tetW) and class I integron (intI1) in EPS-associated, cell-free, and intracellular DNA were quantified. Results show that the absolute abundances of EPS-associated, cell-free, and intracellular ARGs were 5.90 × 10⁶-6.45 × 10⁹, 5.53 × 10⁴-4.58 × 10⁶, and 2.68 × 10⁸-1.79 × 10¹¹ copies/g-volatile suspended solids, respectively. The absolute abundances of EPS-associated ARGs were 0.2-4.6 orders of magnitude higher than those of the corresponding cell-free ARGs. Considering the higher DNA contents in EPS, the transformation abilities of EPS-associated ARGs were 3.3-236.3 folds higher than those of cell-free ARGs. Therefore, EPS-associated ARGs are an important source of extracellular ARGs, and it may play a crucial role in horizontal gene transfer via transformation in WWTPs.

Tracking high-risk β-lactamase gene (bla gene) transfers in two Chinese intensive dairy farms

Extended-spectrum β-lactam antibiotics are critically important antibiotics for humans, but their use in food-animals poses a potential threat for public health. This paper addressed the occurrence of high-risk β-lactamase genes (bla genes) in intensive dairy farms, and assessed the effects of different waste treatment technologies at dairies on the propagation and dissemination of bla genes. Results showed that ESBL genes (bla_TEM-1, bla_OXA-1), ampC β-lactamase genes (bla_ampC) and carbapenemase genes (bla_GES-1, bla_NDM) were prevalent in dairy cow waste, and even prevailed through each processing stage of solid manure and dairy wastewater. Significant levels of bla genes were present in the final lagoon (from 10⁴ to 10⁶ copies/mL, representing from 10% to 151%, of raw influent levels), raising the possibility of dissemination to the receiving environment. This concern was validated by the investigation on farmland that had long-term undergone wastewater irrigation, where causing an increase in bla gene levels in soils (approximately 1-3 orders of magnitude). More troublesomely, considerable levels of certain bla genes were still observed in the bedding material (up to 10⁵ and 10⁷ copies/g), which would directly threaten the dairy cow health. Otherwise, correlation analysis showed that both bacterial community and environmental factors played important roles in the bla genes abundances in dairy farms. This study demonstrated the prevalence of high-risk bla genes in dairy farms, and also underscored that dairy waste was a non-ignored great source of multidrug resistance for their surroundings.

Synergistic impacts of Cu2+ on simultaneous removal of tetracycline and tetracycline resistance genes by PSF/TPU/UiO forward osmosis membrane

Cu²⁺, tetracycline (TC), and corresponding tetracycline resistance genes (TRGs) are common micropollutants in aquaculture wastewater, which have great impact on environment and human health. In this study, we developed a thin-film nanocomposite (TFN) forward osmosis (FO) membrane with an electrospinning thermoplastic polyurethane/polysulfone (PSF/TPU) substrate and a UiO-66-NH₂ particle interlayer modified active layer. The effects of Cu²⁺ concentration on the synergetic removal of TC and TRGs (e.g., tetA/M/X/O/C, int1, and 16 S rRNA gene) were analyzed to determine the role of Cu²⁺ in FO process. The rejection mechanism was also analyzed in depth. Results demonstrated that the rejection of TC and Cu²⁺ was 99.53% and 97.99%. The rejection of TRGs exceeded 90% (specifically, over 99% for tetC) at a Cu²⁺ concentration of 500 μg/L when 0.5 M (NH₄)₂HPO₄ was used as draw solution. Complexation reaction between Cu²⁺ and TC, electrostatic interaction, and the adsorption of Cu²⁺ on membrane surface were the main contributing factors for the high rejection efficiencies. Altogether, the as-prepared FO membrane holds great potential for simultaneously removing heavy metals, antibiotics, and resistance genes in real wastewater.

The behavior of antibiotic-resistance genes and their relationships with the bacterial community and heavy metals during sewage sludge composting

The main contributors to antibiotic resistance genes (ARGs) profiles during the composting process under the addition of biochar (BC) and peat (PT) were not fully explored. This study investigated the influence of BC and PT amendment on ARGs fate, the bacterial community and heavy metals in sewage sludge compost. Compared to control, BC and PT declined the total abundances of ARGs by 17.6% and 43.0% after composting. Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla across the composting process, among which, members of Firmicutes (mainly Bacillaceae) were the potential hosts for multiple ARGs. BC and PT addition declined the abundance of bacterial pathogens such as Bacteroides and Pseudomonas. Besides, the concentrations of copper (Cu), zinc (Zn) and lead (Pb) were less in BC and PT treatments than control on day 40, and these metals displayed significant positive correlations to sul1 and intI1. Furthermore, variation partitioning analysis (VPA) revealed that the bacterial community exhibited the most contribution to the ARG patterns, as much as 34.0%, followed by heavy metals (10.8%) and intI1 gene (1.5%). These results suggested that biochar and peat can reduce the risks of ARGs in sewage sludge mainly by sharping the bacterial composition.

The response of copper resistance genes, antibiotic resistance genes, and intl1/2 to copper addition during anaerobic digestion in laboratory

Heavy metal pollution can serve as a selective pressure for antibiotic resistance genes in polluted environments. Anaerobic fermentation, as a recommended wastewater treatment method, is an effective mitigation measure of antibiotic resistance diffusion. To explore the influence of copper on anaerobic fermentation, we exposed the fermentation substrate to copper in a laboratory setup. We found that the relative abundance of 8 genes (pcoD, tetT, tetA, tetB, tetO, qnrS, ermA and ermB) increased at the late stage of fermentation and their abundance was linked to copper content. Corynebacterium and Streptococcus were significantly positively correlated with ermA, ermB, tetA and tetB (P < 0.05). The relative abundance of tetT was significantly positively correlated with Terrisporobacter, Clostridium_sensu_stricto_1 and Turicibacter (P < 0.05). We screened 90 strains of copper resistant bacteria from blank, medium and high copper test groups on days 25, 31 and 37. The number of fragments carried by a single strain increased with time while intl1, ermA and ermB existed in almost all combinations of the multiple fragments we identified. The relative abundance of these three genes were linearly correlated with Corynebacterium and Streptococcus. The antibiotic resistance genes carried by class 1 integrons gradually increased with time in the fermentation system and integrons carrying ermA and ermB most likely contributed to host survival through the late stages of fermentation. The genera Corynebacterium and Streptococcus may be the primary carriers of such integrated mobile gene element and this was most likely the reason for their rebound in relative abundance during the late fermentation stages.

Effects of substrate types on the transformation of heavy metal speciation and bioavailability in an anaerobic digestion system

Chemical speciation can fundamentally affect the potential toxicity and bioavailability of heavy metals. The transformation of heavy metal speciation and change of bioavailability were investigated in an anaerobic digestion (AD) system using four different substrates (pig manure (PM), cattle manure (CAM), chicken manure (CHM) and rice straw (RS)). The results obtained indicated that the total contents of heavy metals in PM, CHM and CAM were higher than in RS and decreased in the order Zn > Cu > Ni > Pb > As > Cd in all substrates. Moreover, the speciation with the largest proportion for each heavy metal was the same both in the different substrates and the biogas residues. Among them, Zn, Ni, Cd and As were mainly in the reducible fraction (F2), while Cu was mainly in the oxidizable fraction (F3) and Pb occurred predominantly in the residual fraction (F4). Our results further indicated that the AD process had a greater effect on the speciation of heavy metals in CHM and PM, but less on CAM and RS. The rates of change in bioavailability followed the order PM > CHM > CAM > RS. Changes in organic matter, humic acid or local metal ion environment as a result of AD were inferred as likely mechanisms leading to the transformation of heavy metal speciation. These results enhanced our understanding of the behavior of heavy metals in AD and provided a new perspective for the treatment and disposal of the substrates.

Antibiotic resistance contamination in four Italian municipal solid waste landfills sites spanning 34 years

Municipal solid waste landfill is now recognized as a significant reservoir of antibiotics and antibiotic resistance genes (ARGs). This study investigates the contamination of antibiotics resistance, in 10 leachate samples collected from four MSW landfills in north Italy spanning 34 years, including ARGs as well as mobile genetic element (MGEs). Antibiotics (0-434740 ng/L) and ARGs (5.56-6.85 × 10⁵copies/μL leachate) were found in leachate. Abundances of the measured ARGs were found to be clustered into two groups with different changing tendencies with landfilling age in different landfills. Even though some antibiotics were banned or limited in Italy, they were found to still occur in landfills and drive the long-term contamination of ARGs indirectly, indicating the persistence of antibiotic resistance. What's more, the complexity of antibiotic resistance in leachate was found to synthetically relate to antibiotics, metals, microbes and MGEs presenting that Mn, SMX and EFC influence positively (p < 0.01) the contamination of tetW, tetQ, tetM, tetA, ermB, and cat, contributing importantly in new leachate. This study discusses the AR pollution of leachate in Italy where antibiotics are used the most in Europe, less reported in literatures. Our results suggest that a full-scale view for landfill antibiotics resistance should be considered with history of landfills, use of antibiotics and different phase in landfills, with both "relative static" and "dynamic tracking" perspective to focus on the principal antibiotic-resistance pollutants for leachate treatment, and raise the attention for landfill post-closure care and landfill mining.

Removal of antibiotic resistance genes from swine wastewater by membrane filtration treatment

Antibiotic resistance genes (ARGs) have attracted extensive attention as an emerging environmental contaminant potentially threatening humans. One of the main emission sources of ARGs is swine wastewater. In this study, integrated membrane filtration including ultrafiltration and two-stage reverse osmosis was conducted for swine wastewater treatment. The abundances of 16 target ARGs, which accounted for 72.64% of the total ARGs in swine wastewater according to metagenomic sequencing, were quantified by quantitative real-time PCR (qPCR) during each stage of the membrane filtration process. The results showed that integrated membrane filtration could reduce more than 99.0% of conventional pollutants and 99.79% of ARGs (from 3.02 × 10⁸ copy numbers/mL to 6.45 × 10⁵ copy numbers/mL). Principal component analysis (PCA) indicated that the removal efficiency of ARGs subtype by membrane filtration did not depend on ARGs type. However, strong correlations were found between ARGs and the wastewater quality indicators TP, SS and EC according to Cooccurrence patterns, indicating that ARG removal was closely associated with insoluble solid particles and soluble ions in swine wastewater. These results showed that membrane filtration could not only remove conventional pollutants such as nitrogen and phosphorus but also reduce the emerging pollutant of ARGs and decrease the risk of ARGs flowing into natural water.

Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments

Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.

Negative effects of oxytetracycline and copper on nitrogen metabolism in an aerobic fermentation system: Characteristics and mechanisms

Aerobic fermentation is a sustainable option for livestock waste treatment, but little is known about the microbial mechanism that allows oxytetracycline (OTC) and copper (Cu) to affect nitrogen metabolism during aerobic fermentation. In this study, contamination with OTC and Cu alone or in combination reduced the total nitrogen (TN) content of the fermentation products. Metagenomic analysis demonstrated that the contribution of microorganisms to nitrogen metabolism changed significantly in different stages of fermentation. OTC and Cu affected the formation and utilization pattern of NO₂^--N by microorganisms, which were mainly responsible for the reduced N₂O emissions. In the presence of OTC and/or Cu, Myxococcus_stipitatus, Myxococcus_xanthus, and Gimesia_maris were evidently enriched at the end of fermentation, and their increased roles in the dissimilatory reduction of nitrite to ammonium were confirmed by network analysis. Ardenticatena_maritima was the main contributor to denitrification (NO₃^--N to NO). Furthermore, organic matter (OM) was the most important factor responsible for driving the variation in nitrogen-transforming microorganisms and controlling denitrification. OTC affected the formation of OM, which can directly affect TN (λ = -0.37, p < 0.001), and the adverse impact of Cu on nirK- and nifH-dominant microorganisms was validated (p < 0.05).

Novel PVDF-PVP Hollow Fiber Membrane Augmented with TiO2 Nanoparticles: Preparation, Characterization and Application for Copper Removal from Leachate

High proportion of copper has become a global challenge owing to its negative impact on the environment and public health complications. The present study focuses on the fabrication of a polyvinylidene fluoride (PVDF)-polyvinyl pyrrolidone (PVP) fiber membrane incorporated with varying loading (0, 0.5, 1.0, 1.5, and 2.0 wt%) of titanium dioxide (TiO₂) nanoparticles via phase inversion technique to achieve hydrophilicity along with high selectivity for copper removal. The developed fibers were characterized based on scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), permeability, porosity, zeta potential, and contact angle. The improved membrane (with 1.0 wt% TiO₂) concentration recorded the maximum flux (223 L/m²·h) and copper rejection (98.18%). Similarly, 1.0 wt% concentration of TiO₂ nanoparticles made the membrane matrix more hydrophilic with the least contact angle of 50.01°. The maximum copper adsorption capacity of 69.68 mg/g was attained at 1.0 wt% TiO₂ concentration. The experimental data of adsorption capacity were best fitted to the Freundlich isotherm model with R² value of 0.99573. The hybrid membrane developed in this study has considerably eliminated copper from leachate and the concentration of copper in the permeate was substantially reduced to 0.044 mg/L, which is below standard discharge threshold.

Metagenomic Quantification of Genes with Internal Standards

qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume.

We demonstrate that an assembly-independent and spike-in facilitated metagenomic quantification approach can be used to screen and quantify over 2,000 genes simultaneously, while delivering absolute gene concentrations comparable to those for quantitative PCR (qPCR). DNA extracted from dairy manure slurry, digestate, and compost was spiked with genomic DNA from a marine bacterium and sequenced using the Illumina HiSeq4000. We compared gene copy concentrations, in gene copies per mass of sample, of five antimicrobial resistance genes (ARGs) generated with (i) our quantitative metagenomic approach, (ii) targeted qPCR, and (iii) a hybrid quantification approach involving metagenomics and qPCR-based 16S rRNA gene quantification. Although qPCR achieved lower quantification limits, the metagenomic method avoided biases caused by primer specificity inherent to qPCR-based methods and was able to detect orders of magnitude more genes than is possible with qPCR assays. We used the approach to simultaneously quantify ARGs in the Comprehensive Antimicrobial Resistance Database (CARD). We observed that the total abundance of tetracycline resistance genes was consistent across different stages of manure treatment on three farms, but different samples were dominated by different tetracycline resistance gene families.

Dissemination of the tet(X)-Variant Genes from Layer Farms to Manure-Receiving Soil and Corresponding Lettuce

The occurrence of high-level tigecycline resistance tet(X) variant genes represents a new transferable resistance crisis to food safety and human health. Here, we investigated the abundance of tet(X)-variant genes [tet(X), tet(X1) to tet(X6)] in 33 samples collected from layer manures, manured/un-manured soils, and corresponding lettuce from three provinces in China. The results showed the occurrence of tet(X)/(X2), tet(X3), and tet(X4) in 24 samples. The detection rate of tet(X)/(X2) (23/24) is higher than that of tet(X3) (7/24) and tet(X4) (2/24), and tet(X)/tet(X2) and tet(X3) were found to be enriched and more abundant in most manured soil and several lettuce samples from manured soils than that from manure samples. Twenty six tigecycline-resistant bacteria were isolated, and tet(X)-variant genes were found to be disseminated not only by bacterial clone spreading but also via multidrug resistance plasmids. The total concentrations of tet(X)-variant genes showed significantly positive correlations (R = 0.683, p < 0.001) with ISCR2. Two veterinary tetracyclines (tetracycline and oxytetracycline) and other classes of antimicrobials (enrofloxacin, azithromycin, thiamphenicol, and florfenicol) showed significant correlations with the total concentrations of tet(X)-variant genes (R = 0.35-0.516, p < 0.05). The findings indicate the transmission of tet(X)-variant genes from layer manures to their receiving environmental soils and lettuce and highlight the contribution of veterinary antimicrobials to the spread of tet(X)-variant genes.

Zero-valent iron enhanced in-situ advanced anaerobic digestion for the removal of antibiotics and antibiotic resistance genes in sewage sludge

The in-situ advanced anaerobic digestion (AAD) enhanced with zero-valent iron powder (ZVI) under mesophilic condition was investigated to remove 5 antibiotics (sulfamerazine (SMR), sulfamethoxazole (SMZ), ofloxacin (OFL), tetracycline (TC), and roxithromycin (ROX)) and 11 antibiotic resistance genes (ARGs) (AAC (6')-IB-CR, qnrS, ermF, ermT, ermX, sul1, sul2, sul3, tetA, tetB, and tetG) in sewage sludge. The effects of different ZVI dosages, antibiotic concentrations, and solid retention time (SRTs) on the removal were explored. Also, the correlation coefficient of antibiotics and ARGs, microbial community structure, biogas production and methane yield were analyzed. All conducted treatments operated stably, and the modified Gompertz model described the cumulative methane yield well. The antibiotics, with the exception of OFL, were effectively removed in the sewage sludge at a dosage of 1000 mg/L ZVI, SRT 20 d, and an antibiotic concentration of 20 μg/L during AAD. The removal rates of SMZ, SMR, TC, and ROX reached 97.39%, 74.54%, 78.61%, and 56.58%, respectively. AAC (6')-IB-CR and tetB could be effectively reduced during the in-situ AAD. Through the redundancy analysis, AAC (6')-IB-CR, ermT, ermX, sul2, tetB, and tetG had strong positive correlations with the antibiotics in the reactor. The principle component analysis revealed that the community structure was similar when the SRT was 10 d and 20 d at the same amount of ZVI and antibiotic concentrations in the sludge. Under the operating parameters of 1000 mg/L ZVI dosage, SRT 20 d, and an antibiotic concentration of 20 μg/L, Erysipelotrichia, Verrucomicrobia, Clostridia, Caldiserica, and Alphaproteobacteria of the class were dominated microorganisms in the anaerobic digestion.

Changes in the Impacts of Topographic Factors, Soil Texture, and Cropping Systems on Topsoil Chemical Properties in the Mountainous Areas of the Subtropical Monsoon Region from 2007 to 2017: A Case Study in Hefeng, China

Understanding the spatial pattern of soil chemical properties (SCPs) together with topological factors and soil management practices is essential for land management. This study examines the spatial changes in soil chemical properties and their impact on China's subtropical mountainous areas. In 2007 and 2017, 290 and 200 soil samples, respectively, were collected in Hefeng County, a mountainous county in central China. We used descriptive statistics and geostatistical methods, including ANOVA, semivariance, Moran's I, and fractal dimensions, to analyze the characteristics and spatial autocorrelation changes in soil organic matter (OM), available phosphorus (AP), available potassium (AK), and pH value from 2007 to 2017. We explored the relationship between each SCP and the relationship between SCPs with topographic parameters, soil texture, and cropping systems. The results show that the mean value of soil OM, AP, AK, and pH in Hefeng increased from 2007 to 2017. The spatial variation and spatial dependency of each SCP in 2007, excluding AP and AK in 2007, were higher than in 2017. The soil in areas with high topographic relief, profile curvature, and planform curvature had less AP, AK, and pH. Soil at higher elevation had lower OM (r = -0.197, p < 0.01; r = -0.334, p < 0.01) and AP (r = -0.043, p < 0.05; r = -0.121, p < 0.05) and higher AK (r = -0.305, p < 0.01; r =0.408, p < 0.01) in 2007 and 2017. Soil OM and AK in 2007 were significantly (p < 0.05) correlated with soil texture (p < 0.05). In contrast, oil AP and soil pH in 2007 and all SCPs in 2017 were poorly correlated with soil texture. The cropping systems played an important role in affecting all SCPs in 2007 (p < 0.01), while they only significantly affected AK in 2017 (p < 0.05). Our findings demonstrate that both topological factors, that is, the changes in cropping management and the changes in acid rain, impact soil chemical properties. The local government should place more focus on reducing soil acid amounts, soil AP content, and soil erosion by improving water conservancy facilities.

Evaluation of an OPEN Stewardship generated feedback intervention to improve antibiotic prescribing among primary care veterinarians in Ontario, Canada and Israel: protocol for evaluating usability and an interrupted time-series analysis

INTRODUCTION

Antimicrobial resistance (AMR) impacts the health and well-being of animals, affects animal owners both socially and economically, and contributes to AMR at the human and environmental interface. The overuse and/or inappropriate use of antibiotics in animals has been identified as one of the most important drivers of the development of AMR in animals. Effective antibiotic stewardship interventions such as feedback can be adopted in veterinary practices to improve antibiotic prescribing. However, the provision of dedicated financial and technical resources to implement such systems are challenging. The newly developed web-based Online Platform for Expanding Antibiotic Stewardship (OPEN Stewardship) platform aims to automate the generation of feedback reports and facilitate wider adoption of antibiotic stewardship. This paper describes a protocol to evaluate the usability and usefulness of a feedback intervention among veterinarians and assess its impact on individual antibiotic prescribing.

METHODS AND ANALYSIS

Approximately 80 veterinarians from Ontario, Canada and 60 veterinarians from Israel will be voluntarily enrolled in a controlled interrupted time-series study and their monthly antibiotic prescribing data accessed. The study intervention consists of targeted feedback reports generated using the OPEN Stewardship platform. After a 3-month preintervention period, a cohort of veterinarians (treatment cohort, n=120) will receive three feedback reports over the course of 6 months while the remainder of the veterinarians (n=20) will be the control cohort. A survey will be administered among the treatment cohort after each feedback cycle to assess the usability and usefulness of various elements of the feedback report. A multilevel negative-binomial regression analysis of the preintervention and postintervention antibiotic prescribing of the treatment cohort will be performed to evaluate the impact of the intervention.

ETHICS AND DISSEMINATION

Research ethics board approval was obtained at each participating site prior to the recruitment of the veterinarians. The study findings will be disseminated through open-access scientific publications, stakeholder networks and national/international meetings.

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.

Variation of heavy metal speciation, antibiotic degradation, and potential horizontal gene transfer during pig manure composting under different chlortetracycline concentration

Overuse of heavy metal and antibiotics in livestock husbandry has led to the accumulation of heavy metal resistance genes (HMRGs) and antibiotic resistance genes (ARGs) in environment. This research aims to reveal the variation of heavy metal speciation and potential horizontal gene transfer (HGT) of HMRGs and ARGs in manure composting under different initial chlortetracycline (CTC) concentrations. Treatments spiked with 20 mg/kg CTC (treatment P1), 100 mg/kg CTC (treatment P2), and the control (treatment CK) were operated. Results showed that CTC could be completely removed in the thermophilic phase of all the treatments despite of the initial concentrations. Bioavailable Cu in treatments CK, P1, and P2 declined by 14.5%, 27.1%, and 26.7% and bioavailable Zn declined by 15.3%, 29.5%, and 12.1%, respectively, after the composting, respectively. Relative abundance of HMRGs decreased by 6.49 log, 8.88 log, and 5.77 log, respectively, in treatments CK, P1, and P2. Relative abundance of ARGs decreased by 3.37 log, 4.86 log, and 3.32 log, respectively, in treatments CK, P1, and P2. Composting could effectively reduce genes pcoD, pcoA, zntA, tetQ, and tetA, which might locate on the same plasmid. CTC of 100 mg/kg promoted the co-selection of ARGs and HMRGs and increased the potential HGT of gene cusA.

Toxicological effects of single and joint sulfamethazine and cadmium stress in soil on pakchoi (Brassica chinensis L.)

The combined pollution of heavy metals and antibiotics in soil has attracted increasing attention due to their negative effects on plant growth. The aims of this study were to evaluate the phytotoxicity of single and combined sulfamethazine (SMT) and cadmium (Cd), selected as target pollutants in soil, on growth and physiological response of pakchoi (Brassica chinensis L.). Results revealed that the soil spiked with 10 mg kg^-1 Cd inhibited the pakchoi growth regardless of SMT addition. The combined effect of SMT and Cd stress on uptake of SMT or Cd by pakchoi were concerned with their combined concentration. The combined influence of high concentrations SMT and Cd (1 and 10 mg kg^-1) exposure on the Cd content of pakchoi showed antagonistic effects and synergistic effects, respectively. Besides, oxidative substances and enzyme activity of pakchoi tissue were affected by Cd and SMT exposure in the soil, particularly by their joint stress. This mainly expressed as the increase of malondialdehyde (MDA), H₂O₂ content and antioxidant enzyme activity (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT)), which could be ascribed to the induction of Cd and SMT stress. Additionally, the SMT-Cd combined stress caused more reduction in nutrients (vitamin C and sugar) of pakchoi than the correspondingly single Cd stress. In conclusion, the SMT and Cd in soil lead to their accumulation and oxidative damage in pakchoi, which disturb the antioxidant defense system and ultimately adversely affect growth and quality of pakchoi.

Occurrence of antibiotics and antibiotic resistance genes in the Fuxian Lake and antibiotic source analysis based on principal component analysis-multiple linear regression model

In recent years, the dramatic increase in antibiotic use has led to the evolution of antibiotic resistant genes (ARGs), posing a potential risk to human and aquatic ecological safety. In this study, source contribution and correlations between twelve antibiotics and their corresponding ARGs were firstly investigated in surface water in the Fuxian Lake. The results showed that sulfamethoxazole (SMX) (0.98-14.32 ng L^-1) and ofloxacin (OFL) (0.77-7.3 ng L^-1) were the dominant antibiotics in surface water, whereas erythromycin-H₂O (EM-H₂O), SMX and OFL posed the medium risk to aquatic organisms. Meanwhile, the mean concentrations of MLs in inflowing rivers were 5.6 times more than those in the lake, which was related to dilution and degradation. Moreover, the facter1 (co-sources L (Living quarters), M (Mining area), A (Agricultural district) and T (tourist area)) contributed 78% of antibiotic concentrations, and the source L was predominant. The results also revealed the prevalence of intL1, sul1 and sul2 in all the sampling sites, and that the abundance of ARGs in the lake was significantly lower (P < 0.01) than that in inflowing rives. Additionally, significant correlations (p < 0.0001) between intL1 and sulfanilamide resistance genes (sul1, sul2) were detected, indicating that intL1 promoted the propagation and they originated from the same anthropogenic sources. Overall, our findings revealed the presence of antibiotics and ARGs and their inconsistent correlations in the Fuxian Lake, which provides a foundation to support further exploration of the occurrence and transmission mechanisms of antibiotics and ARGs.

Cadmium enhances conjugative plasmid transfer to a fresh water microbial community

Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd²⁺) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd²⁺ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd²⁺ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd²⁺ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd²⁺ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd²⁺ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd²⁺ in aquatic environments.

Sources of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARGs) in the Soil: A Review of the Spreading Mechanism and Human Health Risks

Soil is an essential part of our ecosystem and plays a crucial role as a nutrient source, provides habitat for plants and other organisms. Overuse of antibiotics has accelerated the development and dissemination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). ARB and ARGs are recognized as emerging environmental contaminants causing soil pollution and serious risks to public health. ARB and ARGs are discharged into soils through several pathways. Application of manure in agriculture is one of the primary sources of ARB and ARGs dissemination in the soil. Different sources of contamination by ARB and ARGs were reviewed and analyzed as well as dissemination mechanisms in the soil. The effects of ARB and ARGs on soil bacterial community were evaluated. Furthermore, the impact of different sources of manure on soil microbial diversity as well as the effect of antibiotics on the development of ARB and ARGs in soils was analyzed. Human health risk assessments associated with the spreading of ARB and ARGs in soils were investigated. Finally, recommendations and mitigation strategies were proposed.

Changes and distributions of antibiotic resistance genes in liquid and solid fractions in mesophilic and thermophilic anaerobic digestion of dairy manure

This study mainly explored the changes and distributions of antibiotic resistance genes (ARGs) in liquid fraction (L_F) and solid fraction (S_F) in anaerobic digestion (AD) of dairy manure. After mesophilic and thermophilic AD, the copy numbers of ARGs in L_F decreased by 0.06-1.80 logs while those in S_F increased by 0.08-7.85 logs, suggesting the enrichment of ARGs in S_F. Statistical analysis elucidated that high total solids promoted the enrichment of ARGs in S_F. The increased abundances of genera such as Ruminofilibacter, Treponema and Sphaerochaeta in S_F were responsible for the enrichment of most ARGs. These insights demonstrated the digested solid had the potential risks to promote the spread of ARGs in the environment, and the digested solid of livestock manure should be post-treated before the application.

Impacts of cadmium addition on the alteration of microbial community and transport of antibiotic resistance genes in oxytetracycline contaminated soil

The large-scale development in livestock feed industry has increased the chances of antibiotics and heavy metals contamination in the soil. The fate of antibiotic resistance genes (ARGs) and microbial community in heavy metals and antibiotic contaminated soil is still unclear. In this study, we investigated the effect of cadmium (Cd) addition on the transport of ARGs, microbial community and human pathogenic bacteria in oxytetracycline (OTC) contaminated soil. Results showed that the addition of OTC significantly increased the abundance of ARGs and intI1 in the soil and lettuce tissues. The addition of Cd to OTC treated soil further increased the abundance and translocation of ARGs and intI1. Moreover, Cd promoted the transfer of potential human pathogenic bacteria (HPB) into lettuce tissues. Compared with O10 treatment, the addition of Cd decreased the concentration of OTC in soil and lettuce tissue, but slightly increased the fresh weight of lettuce tissues. Redundancy analysis indicated that bacterial community succession is a major factor in ARGs variation. Network analysis indicated that the main host bacteria of ARGs were mainly derived from Proteobacteria. Correlation analysis showed that intI1 was significantly correlated with tetG, tetC, sul1, sul2, ermX, and ermQ. Meanwhile, potential HPB (Clostridium, and Burkholderia) was significantly correlated with intI1 and eight ARGs (tetG, tetC, tetW, tetX, sul1, sul2, ermX, and ermQ.). The findings of this study suggest that the addition of heavy metals to agricultural fields must be considered in order to reduce the transfer of ARGs in the soil and crops.

Intracellular versus extracellular antibiotic resistance genes in the environment: Prevalence, horizontal transfer, and mitigation strategies

Antibiotic resistance genes (ARGs) are present as both intracellular and extracellular fractions of DNA in the environment. Due to the poor yield of extracellular DNA in conventional extraction methods, previous studies have mainly focused on intracellular ARGs (iARGs). In this review, we evaluate the prevalence/persistence and horizontal transfer of iARGs and extracellular ARGs (eARGs) in different environments, and then explore advanced mitigation strategies in wastewater treatment plants (WWTPs) for preventing the spread of antibiotic resistance in the environment. Although iARGs are the main fraction of ARGs in nutrient-rich environments, eARGs are predominant in receiving aquatic environments. In such environments, natural transformation of eARGs occurs with a comparable frequency to conjugation of iARGs. Further, eARGs can be adsorbed by soil and sediments particles, protected from DNase degradation, and consequently persist longer than iARGs. Collectively, these characteristics emphasize the crucial role of eARGs in the spread of antibiotic resistance in the environment. Fate of iARGs and eARGs through advanced treatment technologies (disinfection and membrane filtration) indicates that different mitigation strategies may be required for each ARG fraction to be significantly removed. Finally, comprehensive risk assessment is needed to evaluate/compare the effect of iARGs versus eARGs in the environment.

Environmentally Friendly Quinolones Design for a Two-Way Choice between Biotoxicity and Genotoxicity through Double-Activity 3D-QSAR Model Coupled with the Variation Weighting Method

Quinolone (QN) antibiotics are widely used, which lead to their accumulation in soil and toxic effects on ryegrass in pasture. In this study, we employed ryegrass as the research object and selected the total scores of 29 QN molecules docked with two resistant enzyme structures, superoxide dismutase (SOD, PDB ID: 1B06) and proline (Pro, PPEP-2, PDB ID: 6FPC), as dependent variables. The structural parameters of QNs were used as independent variables to construct a QN double-activity 3D-QSAR model for determining the biotoxicity on ryegrass by employing the variation weighting method. This model was constructed to determine modification sites and groups for designing QNs molecules. According to the 3D contour map of the model, by considering enrofloxacin (ENR) and sparfloxacin (SPA) as examples, 23 QN derivatives with low biotoxicity were designed, respectively. The functional properties and environmental friendliness of the QN derivatives were predicted through a two-way selection between biotoxicity and genotoxicity before and after modification; four environmentally friendly derivatives with low biotoxicity and high genotoxicity were screened out. Mixed toxicity index and molecular dynamics methods were used to verify the combined toxicity mechanism of QNs on ryegrass before and after modification. By simulating the combined pollution of ENR and its derivatives in different soils (farmland, garden, and woodland), the types of combined toxicity were determined as partial additive and synergistic. Binding energies were calculated using molecular dynamics. The designed QN derivatives with low biotoxicity, high genotoxicity, and environmental friendliness can highly reduce the combined toxicity on ryegrass and can be used as theoretic reserves to replace QN antibiotics.

Removal of sulfamethazine and Cu2+ by Sakaguchia cladiensis A5: Performance and transcriptome analysis

To reduce the potential risks of contamination of antibiotics and heavy metals to ecological environment and human safety, biological removal of these composite pollutants is the focus of much study. One previously identified isolate, Sakaguchia cladiensis A5, was used to decompose sulfamethazine (SMZ) and adsorb Cu²⁺. The ability of A5 to remove SMZ was enhanced by pre-induced culture, which reached 49.8% on day 9. The removal of SMZ could be also increased to 37.6% on day 3 in the presence of Cu²⁺, but only to 12.2% in the system without Cu²⁺. The biosorption of Cu²⁺ mainly occurred on the cell walls, while the biodegradation of SMZ was inside the cells. By comparative transcriptome analysis for A5, 1270 and 2220 differentially expressed genes (DEGs) were identified after treating single SMZ and SMZ/Cu²⁺, respectively. The Gene expression pattern analysis suggested a suppression of transcriptional changes in A5 responding to SMZ/Cu²⁺ as compared to under the sole stress of SMZ. The DEGs functional enrichment analysis suggested that the antioxidant and sulfate assimilation pathways played a key role on SMZ biodegradation and Cu²⁺ biosorption. The DEGs of proteins CAT, PRDX5, SAT, and CYSC were up-regulated to facilitate the resistance of A5 against oxidative toxicity of Cu²⁺. Moreover, the protein MET30 activated by Cu²⁺ was also overexpressed to promote the transmembrane transport of SMZ, such that A5 could decompose SMZ more effectively in SMZ/Cu²⁺ system. The results of this study would provide new insights into the mechanism of biodegradation and biosorption of SMZ/Cu²⁺.

Presence of veterinary antibiotics in livestock manure in two Southeastern Europe countries, Albania and Kosovo

Nowadays, veterinary drug application has become an integral practice in livestock farming. Veterinary antibiotics (VAs) are administered onto animals for therapeutic use; meanwhile, in some countries, they are used for growth promotion. To indicate the level of VAs use in livestock breeding in two countries, Albania and Kosovo, their presence was studied in the animal manure. In total, 38 manure samples, 22 from Kosovo and 16 samples from Albania, belonging to cattle, pig, and poultry, were collected and investigated for the presence of VAs. Seven VAs and 2 metabolites, from the groups of sulfonamides and tetracyclines, were identified by ultra-high pressure liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The detected antibiotics were sulfadiazine (SDZ), sulfathiazole (STZ), sulfamethazine (SMZ), oxytetracycline (OTC), tetracycline (TC), chlortetracycline (TC), and doxycycline (DOY). VAs were detected in 27% and 31.2% of the manure samples, from Kosovo and Albania, respectively, and the levels ranged from 0.04 to 10.1 mg kg^-1. VAs were widely detected (100%) in poultry manure from Kosovo, as well as poultry manure from Albania. The contamination rate ranged from pig manure (25%) to cow manure (66.6%). Sulfonamides were the most commonly detected VAs with maximum concentration of sulfadiazine (10.1 mg kg^-1) in poultry manure. Tetracyclines were most widely detected in poultry manure, as well as other animal manures. When it comes to the comparison between the two countries, VAs residues are more frequent per analyzed sample and higher in concentrations in the manure samples from Albania. Therefore, an environmental impact of VAs on both countries may be expected. These results indicate that VAs may enter the local ecosystem through manure application to agriculture and potentially may bring ecological risks.

High frequency of antibiotic tolerance in deep subsurface heterotrophic cultivable bacteria from the Rozália Gold Mine, Slovakia

The Rozália Mine, with its long mining history, could represent an environmental threat connected with metal contamination and associated antibiotic tolerance. Metal and antibiotic tolerance profiles of heterotrophic, cultivable bacteria isolated from the Rozália Gold Mine in Hodruša-Hámre, Slovakia, and the surrounding area were analysed. Subsurface samples were collected from different mine levels or an ore storage dump. As expected, heterotrophic cultivable bacteria showed high minimum inhibitory concentrations for metals (up to 1000 mg/l for zinc and nickel, 2000 mg/l for lead and 500 mg/l for copper). Surprisingly, very high minimum inhibitory concentrations of selected antibiotics were observed, e.g. > 10,000 μg/ml for ampicillin, up to 4800 μg/ml for kanamycin, 800 μg/ml for chloramphenicol and 50 μg/ml for tetracycline. Correlation analysis revealed a linkage between increased tolerance to the antibiotics ampicillin and chloramphenicol and metal tolerance to nickel and copper. A correlation was also observed between tetracycline-kanamycin tolerance and zinc-lead tolerance. Our data indicate that high levels of antibiotic tolerance occur in deep subsurface microbiota, which is probably connected with the increased level of metal concentrations in the mine environment.

Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats

Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in 55 000 bacterial genomes, 16 000 bacterial plasmid sequences, 3000 bacterial integron sequences and 850 metagenomes using a standard pipeline. We found that >80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation with the degree of anthropogenicity. These observations highlight the need to differentiate ARGs of high clinical relevance. This profile is published on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as a valuable resource for the most challenging topics in this field, i.e. the risk, evolution and emergence of ARGs.

Determination of trace levels of selenium in natural water, agriculture soil and food samples by vortex assisted liquid-liquid microextraction method: Multivariate techniques

A green vortex assisted based liquid-liquid microextraction (VA-LLME) method was developed for preconcentration of selenium. Ammonium pyrrolidine dithiocarbamate (APDC) was used to form a hydrophobic complex with selenium in natural water, agricultural soil and food samples by GFAAS. Whereas Triton X-114, a nonionic surfactant and 1-butyl-3-methylimidazolium hexafluorophosphate ionic liquid were used for Se extraction as a dispersing medium. The conical flasks contents were shack on a vortex mixer to increase the extraction efficiency. Multivariate techniques were used to evaluate extraction parameters; pH, vortex time, APDC amount, volume of ionic liquid and Triton X-114 and centrifugation rate on the recovery of Se. The central composite design (CCD) was used for further optimization of the essential extraction parameters. The enhancement factor and limit of detection were obtained as 98.7 and 0.07 µg L^-1. The certified reference materials was used for accuracy of method and the related standard deviation was found to be 3.51%. The resulted data indicated that concentrations of Se in all types of water samples were below the permissible limit recommended by WHO.

Plasmid-Mediated Ampicillin, Quinolone, and Heavy Metal Co-Resistance among ESBL-Producing Isolates from the Yamuna River, New Delhi, India

Antibiotic resistance is one of the major current global health crises. Because of increasing contamination with antimicrobials, pesticides, and heavy metals, the aquatic environment has become a hotspot for emergence, maintenance, and dissemination of antibiotic and heavy metal resistance genes among bacteria. The aim of the present study was to determine the co-resistance to quinolones, ampicillin, and heavy metals among the bacterial isolates harboring extended-spectrum β-lactamases (ESBLs) genes. Among 73 bacterial strains isolated from a highly polluted stretch of the Yamuna River in Delhi, those carrying blaCTX-M, blaTEM, or blaSHV genes were analyzed to detect the genetic determinants of resistance to quinolones, ampicillin, mercury, and arsenic. The plasmid-mediated quinolone resistance (PMQR) gene qnrS was found in 22 isolates; however, the qnrA, B, C, and qnrD genes could not be detected in any of the bacteria. Two variants of CMY, blaCMY-2 and blaCMY-42, were identified among eight and seven strains, respectively. Furthermore, merB, merP, merT, and arsC genes were detected in 40, 40, 44, and 24 bacterial strains, respectively. Co-transfer of different resistance genes was also investigated in a transconjugation experiment. Successful transconjugants had antibiotic and heavy metal resistance genes with similar tolerance toward antibiotics and heavy metals as did their donors. This study indicates that the aquatic environment is a major reservoir of bacteria harboring resistance genes to antibiotics and heavy metals and emphasizes the need to study the genetic basis of resistant microorganisms and their public health implications.

Antibiotic resistance gene transfer during anaerobic digestion with added copper: Important roles of mobile genetic elements

The abuse of heavy metals as feed additives in livestock is widespread and it might aggravate the spread of antibiotic resistance genes (ARGs) in the environment. However, the mechanisms that allow heavy metals to increase the transmission of ARGs in the environment remain unclear. Cu is the heavy metal present at the highest concentration in livestock manure, and thus Cu was selected to investigate the responses of ARGs to heavy metals. The effects of the microbial communities, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) on ARGs were determined in the presence of 75 and 227 mg L^-1 Cu in a swine manure anaerobic digestion (AD) system. In the AD products, the presence of residual Cu (75 and 227 mg L^-1) increased the total ARGs, HMRGs, and some MGEs, and the higher Cu selected more ARGs than the lower Cu treatment. The results demonstrated that Cu could promote the co-selection of HMRGs, ARGs, and MGEs. The different levels of Cu did not change the bacterial community composition, but they influenced the abundances of bacteria during AD. Network analysis showed that the presence of Cu increased the co-occurrence of specific bacteria containing ARGs, HMRGs, and MGEs. Furthermore, the co-occurrence of MGEs and ARGs increased greatly compared with that of HMRGs and ARGs. Therefore, compared HMRGs, the increased MGEs had the main effect on increasing of ARGs.

Swine Manure Composting With Compound Microbial Inoculants: Removal of Antibiotic Resistance Genes and Their Associations With Microbial Community

In this study, compound microbial inoculants, including three Bacillus strains and one Yeast strain, were inoculated into swine manure composting to explore the effects on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), microbial community structure, and pathogenic bacteria. The results indicated that the abundances of the detected ARGs ranged from 3.6 × 10³ to 1.13 × 10⁸ copies/g. The ARGs with the highest abundance was sul2, and the lowest was blaCTX. Composting removes most of the ARGs and MGEs by 22.8-99.7%. These ARGs were significantly reduced during the thermophilic phase of compost. The removal rate of ARGs at the different layers of compost pile was different as follows: middle layer > upper layer > lower layer. But some ARGs proliferated significantly in the maturation phase of compost, especially the sulfonamide resistance genes. Compound microbial inoculants increased the temperature of compost, accelerated water loss, nitrogen fixation, and increased the removal rate of β-lactamase resistance genes, the transposon gene tn916 and part of tetracycline resistance genes by 3.7-23.8% in compost. Compound microbial inoculants changed the community structure and increased the Bacillus abundance in the thermophilic phase of compost. And it was helpful for removing pathogens during composting. The addition of compound microbial inoculants causes the decrease of Firmicutes and the increase of Bacteroidetes, which may be related to the removal and proliferation of ARGs.

Struvite crystallization induced the discrepant transports of antibiotics and antibiotic resistance genes in phosphorus recovery from swine wastewater

Struvite (MgNH₄PO₃·6H₂O) crystallization is one of important methods of phosphorus recovery from wastewater. As to livestock wastewater, the high-strength occurrence of antibiotics and antibiotic resistance genes might induce struvite recovery to spread antibiotic resistance to the environment. However, limited information has been reported on the simultaneous transport of antibiotics and ARGs in struvite recovery. In the present study, tetracyclines (TCs) and tetracyclines antibiotic resistance genes (ARGs) were selected as the targeted pollutants, and their discrepant residues in struvite recovery from swine wastewater were investigated. TCs and ARGs were obviously detected, with their contents of 4.88-79.5 mg/kg and 6.99 × 10⁷-2.14 × 10¹¹ copies/g, notably higher than those of TCs 0.550-1.94 mg/kg and ARGs 3.98 × 10⁴-5.66 × 10⁷ copies/g obtained from synthetic wastewater. The correlational relationship revealed that predominant factors affecting TCs and ARGs transports were different. Results from network analyses indicated that among the total edges, the negative correlations between TCs and ARGs predominately occupied 18.0%. The redundancy analysis revealed that mineral components in the recovered products, including struvite, K-struvite and amorphous calcium phosphate, coupling with organic contents, displayed insignificant roles on TCs residues, where heavy metals exerted positive and remarkable functions to boost TCs migration. Unexpectedly, mineral components and heavy metals did not displayed significant promotion on ARGs transport as a whole.

Assessment of Bioavailability of Biochar-Sorbed Tetracycline to Escherichia coli for Activation of Antibiotic Resistance Genes

Human overuse and misuse of antibiotics have caused the wide dissemination of antibiotics in the environment, which has promoted the development and proliferation of antibiotic resistance genes (ARGs) in soils. Biochar (BC) with strong sorption affinity to many antibiotics is considered to sequester antibiotics and hence mitigate their impacts to bacterial communities in soils. However, little is known about whether BC-sorbed antibiotics are bioavailable and exert selective pressure on soil bacteria. In this study, we probed the bioavailability of tetracycline sorbed by BCs prepared from rice-, wheat-, maize-, and bean-straw feedstock using Escherichia coli MC4100/pTGM bioreporter strain. The results revealed that BC-sorbed tetracycline was still bioavailable to the E. coli attached to BC surfaces. Tetracycline sorbed by BCs prepared at 400 °C (BC400) demonstrated a higher bioavailability to bacteria compared to that sorbed by BCs prepared at 500 °C (BC500). Tetracycline could be sorbed primarily in the small pores of BC500 where bacteria could not access due to the size exclusion to bacteria. In contrast, tetracycline could be sorbed mainly on BC400 surfaces where bacteria could conveniently access tetracycline. Increasing the ambient humidity apparently enhanced the bioavailability of BC400-sorbed tetracycline. BC500-sorbed tetracycline exposed to varying levels of ambient humidity showed no significant changes in bioavailability, indicating that water could not effectively mobilize tetracycline from BC500 pores to surfaces where bacteria could access tetracycline. The results from this study suggest that BCs prepared at a higher pyrolysis temperature could be more effective to sequester tetracycline and mitigate the selective pressure on soil bacteria.

Antibiotic resistance genes (ARGs) in agricultural soils from the Yangtze River Delta, China

As an important reservoir of intrinsic antimicrobial resistance, soil is subjected to increasing anthropogenic activities that creates sustained selection pressure for the prevalence of antibiotic resistance genes (ARGs), thus constituting an important environmental dissemination pathway to human exposure. This study investigated the levels and spatial distributions of three classes of ARGs in relation to a range of co-occurring chemical mixtures and soil properties at a regional scale of the Yangtze River Delta (YRD), China. The selected eight ARGs were all detected in 241 agricultural soil samples with relative abundances ranging from 1.01 × 10^-7 to 2.31 × 10^-1 normalized to the 16S rRNA gene. The sulII and tetG were the dominant ARGs with a mean relative abundance of 6.67 × 10^-3 and 5.25 × 10^-3, respectively. The ARGs were mainly present in agricultural soils alongside Taihu Lake and Shanghai municipality, the most agriculturally and economically vibrant area of the YRD region. Antibiotics, rather than other co-occurring pollutants and soil properties, remain to be the dominant correlate to the ARGs, suggesting their co-introduction into the soils via irrigation and manure application or the sustained selection pressure of antibiotics from these sources for the proliferation of ARGs in the soils. While the current dataset provided useful information to assess the ARGs pollution for mitigation, future studies are warranted to reveal the complete picture on the potential transfer of antimicrobial resistance from soil to agricultural produces to human consumption and associated health implications.

Speciation, toxicity mechanism and remediation ways of heavy metals during composting: A novel theoretical microbial remediation method is proposed

Heavy metals (HM) pollution is a major limitation to the application of composting products. Therefore, mitigating the toxicity of HM has attracted wide attention during composting. The toxicity of HM is mainly acted on microorganisms during composting, and the toxicity of different HM speciation is obviously various. There are many pathways to change the speciation to reduce the toxicity during composting. Therefore, in this review, the speciation distribution, toxicity mechanism and remediation ways of HM during composting were discussed in order to better solve HM pollution. The microbial remediation technology holds enormous potential to remediate for HM without damaging composting, however, it is hard to extract HM. The innovation of this review was to outline microbial remediation strategies for HM during composting based on two mechanisms of microbial remediation: extracellular adsorption and intracellular sequestration, to solve the problem how to extract microbial agents from the compost. Ultimately, a novel theoretical method of microbial remediation was proposed to remove HM from the compost.