Application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil

Long-term rice-eel co-culture system effectively alleviated the accumulation of antibiotic resistance genes in soil

Alleviating the accumulation of antibiotic resistance genes (ARGs) in farmlands is crucial for restricting the transfer of ARGs to crops and controlling the soil-borne microbiological health risk. Rice and eel co-culture (REC) systems have recently been used as an emerging integrated farming model that can stabilize grain yields and improve fertilizer availability. However, the influence of long-term REC system concerning the aggregation and health risk of ARGs in rice fields is still unclear. Here, we deciphered firstly the profile, potential of pathogenicity and mobility, and bacterial hosts for soil ARGs in the long-term REC system compared to the mono-rice (MR) culture system by collecting soil samples from 12 rice fields in Shanghai. The long-term REC system alleviated the accumulation of ARGs in soil, which is manifested in the abundance decrease of total ARGs and 11 ARG types (e.g., multidrug and aminoglycoside). The frequency of ARGs co-occurring with VFGs and MGEs was lower in the long-term REC system than in the MR system, indicating the lower pathogenicity and mobility potential for ARGs. The soil microbial community was identified to primarily drive the ARG discrepancy between the long-term REC and MR systems. In comparison with the MR system, long-term REC weakened the competitive advantage of ARG bacterial hosts, which might contribute to the decreased prevalence of antibiotic resistance. Overall, these findings uncovered the important role of long-term REC system in alleviating the accumulation of soil ARGs, providing theoretical support for antibiotic resistance risk control and sustainable agricultural strategic management.

Alterations in microbial community structures and metabolic function in soil treated with biological and chemical insecticides

Entomopathogenic fungi show significant promise as effective and ecological friendly alternatives to chemical insecticides for insect pest control. However, little is known concerning their effects on soil ecosystems, especially in comparison to application of chemical insecticides. Here, we examined the effects of one biological and two chemical insecticides, Metarhizium anisopliae, imidacloprid (IMI) and emamectin benzoate (EMB) on microbial community structure, metabolic functioning, and soil biochemistry. Treatment with EMB and IMI, reduced Actinobacteriota populations, while increasing that of Acidobacteriota. However, these populations were not significantly altered under M. anisopliae treatment. Chemical pesticides also altered fungal communities including potential pathogens. Activities of soil beneficial nitrogen-cycling-related enzymes were reduced after application of IMI and EMB, but were increased after treatment with M. anisopliae. Metagenomics analysis showed that IMI treatment reduced levels of carbon and nitrogen-related metabolic pathways. However, M. anisopliae treatment increased representation of key enzymes involved in the carbon, nitrogen, and sulfur cycling important for maintenance of soil fertility. Insecticides treatments altered the abundance of a number antibiotic resistance genes (ARGs) but not virulence factors (VFs), whereas application of M. anisopliae resulted had only minimal effects. These findings highlight the consequences of use of biological vs. chemical pesticides on soil microbiology can affect plant and ecosystem health indicating that the fungal biological control agent, M. anisopliae likely has far less detrimental and potentially beneficial effects on soil ecology as compared to chemical pesticides.

Metagenomic analysis of the dichotomous role of uranium in regulating intracellular and extracellular antibiotic resistance genes in activated sludge

Antibiotic resistance genes (ARGs) in activated sludge include intracellular ARGs (iARGs) and extracellular ARGs (eARGs), both of which are recognized as emerging pollutants. While the activated sludge process has been commonly considered for treating wastewater contaminated with radionuclide, the effects and mechanisms of radioactive heavy metals on the fate of iARGs and eARGs (i/e-ARGs) in activated sludge are largely elusive. Here, the distribution, mobility, and hosts of i/e-ARGs in activated sludge during environmental concentrations (50 μg/L and 5000 μg/L) of radioactive uranium (U) stress were explored via metagenomics. The results revealed that the total relative abundance of iARGs and eARGs decreased by 11.62% and 10.41%, respectively, after 90 days of 50 μg/L of U treatment. In contrast, both i/e-multi- and tetracycline ARGs remarkably increased after being exposed to 5000 μg/L of U. Additionally, exposure to 5000 μg/L of U triggered notable decrease in i/e-insertion sequences and plasmids abundance, but significantly enriched i/e-integrons (p < 0.05). Partial least squares pathway modelling indicated that the prevalence of iARGs and eARGs in activated sludge was primarily driven by bacterial hosts and functional genes, respectively. Our findings revealed the dichotomous variation landscape and mechanisms of i/e-ARGs dynamics in activated sludge during U exposure, offering valuable insights for controlling ARGs risk during radioactive wastewater treatment.

Antibiotic resistome dynamics in agricultural river systems: Elucidating transmission mechanisms and associated risk to water security

Usage of antibiotics in agriculture has increased dramatically recently, significantly raising the influx of antibiotic resistance genes (ARGs) into river systems through organic manure runoff, seriously threatening water security. However, the dynamics, transmission mechanisms, and potential water security risk of ARGs, as well as their response to land use spatial scale and seasonal variations in agricultural river systems remain unclear. To address these challenges, this work employed metagenomic technique to systematically evaluate the pollution and dissemination of ARGs in overlying water and sediment within a typical agricultural catchment in China. The results demonstrated significant differences between overlying water and sediment ARGs. Overlying water dominated by multidrug ARGs exhibited higher diversity, whereas sediment predominantly containing sulfonamide ARGs had higher abundance. The dynamics of ARGs in overlying water were more responsive to seasonal variations compared to sediment due to greater changes in hydrodynamics and nutrient conditions. The profiles of ARGs in overlying water were largely regulated by microbiota, whereas mobile genetic elements (MGEs) were the main forces driving the dissemination of ARGs in sediment. The variation in dissemination mechanisms led to different resistance risks, with sediment presenting a higher resistance risk than overlying water. Furthermore, Mantel test was applied to discover the impact of land use spatial scale and composition on the transmission of ARGs in river systems. The findings showed that cultivated land within 5 km of the riverbank was the key influencing factor. Cultivated land exacerbated ARGs spread by increasing MGEs abundance and nutrient concentrations, resulting in the abundance of ARGs in high-cultivated sites being twice that in low-cultivated sites, and raising the regional water security risk, with a more pronounced effect in sediment. These findings contribute to a better understanding of ARGs dissemination in agricultural watersheds, providing a basis for implementing effective resistance control measures and ensuring water security.

Unveiling the impact of low-molecular-weight organic acids on enrofloxacin sorption in North China agricultural soil: Insights and implications

Low-molecular-weight organic acids (LMWOAs) play a crucial role as components of dissolved organic matter in soil, influencing the sorption/desorption, degradation, and plant uptake of diverse pollutants within the agricultural soil ecosystem. This study delves into the sorption behavior and mechanism of the fluoroquinolone antibiotic enrofloxacin (ENR) on agricultural soil in North China, focusing on the impact of LMWOAs. Through batch equilibrium experiments, we explored the sorption/desorption kinetics of ENR under varying conditions such as temperature, pH, ion strength, and ion type, with the addition of acetic acid, oxalic acid, and citric acid individually. Our findings reveal that the sorption and desorption kinetics of ENR-whether with or without LMWOAs-conformed well to the pseudo-second-order kinetic model (R2 ≥ 0.997). The presence of LMWOAs notably enhanced ENR sorption while impeding desorption in soil, with oxalic acid demonstrating the highest promotion effect followed by acetic acid and citric acid. Moreover, the sorption capacity and affinity of ENR decreased with rising solution pH, dropping from 96.8%-98.5% to 30.9%-34.4%. Acidic conditions favored ENR retention in soil, with inhibition of sorption escalating alongside increasing ionic strength. LMWOAs, soil solution pH, and coexisting ions emerge as pivotal factors shaping ENR sorption behavior. Furthermore, LMWOA presence intensified desorption hysteresis of ENR on soil, with a desorption hysteresis coefficient (HI) ≤ 0.124. These results suggest that LMWOAs restrict ENR mobility in the local soil environment, heightening the risk of its accumulation in soil and crops. This study offers valuable insights into the intricate interplay among LMWOAs, ENR sorption dynamics, and environmental outcomes, underscoring the importance of understanding such complexities in agricultural soil management.

Toxic effects of avermectin on liver function, gut microbiota, and colon barrier in the rat model

Avermectin (AVM), a compound derived from the fermentation of Avermectin Streptomyces, has insecticidal, acaricidal, and nematicidal properties. Widely employed in agriculture, it serves as an effective and broad-spectrum insecticide for pest control. Although the toxicity of AVM at low doses may not be readily apparent, prolonged and extensive exposure can result in poisoning. To investigate the toxic effects of AVM on the body, this study established rat models of AVM poisoning with both low and high concentrations of the compound. Fifteen male rats were randomly assigned to one of three groups (n=5 per group): a control group, a low-concentration group, and a high-concentration group. The low-concentration group was administered an oral dose of 2 mg/kg AVM once daily for a duration of seven days, while the high-concentration group received an oral dose of 10 mg/kg AVM once daily for the same period. This study examined the impact of AVM on liver function and gut microbiota in rats using weight monitoring, liver function indicator detection, liver metabolomics sequencing, colon barrier function testing, and gut microbiota sequencing. The findings of this study demonstrated that exposure to 2 or 10 mg/kg AVM for seven days can lead to a notable decrease in rat weight, as well as induce liver dysfunction and metabolic disturbances. Additionally, AVM exposure can disrupt the composition of the intestinal microbiota and impair the integrity of the colon mucosal barrier, causing downregulation of Occludin expression and upregulation of inflammation-related protein expression levels such as IL-1β, Myd88, and TLR4. Furthermore, bioinformatics analysis revealed a significant association between liver dysfunction and dysbiosis of the gut microbiota. These findings have implications for the agricultural use of AVM and its potential contribution to environmental pollution. Consequently, individuals involved in AVM usage should prioritize safety precautions and monitor liver function.

Assessing the removal of heavy metals and polycyclic aromatic hydrocarbons and occurrence of metal resistance genes and antibiotic resistance genes in a stormwater bioretention system

Bioretention basins are extensively used in urban areas to manage stormwater by reducing peak flows and pollution. This study evaluated the performance of a bioretention basin in removing heavy metals, polycyclic aromatic hydrocarbons (PAHs), and oil and grease. Using droplet digital PCR (ddPCR), the presence of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) in the basin's soil was analyzed. The results indicated effective removal of Zn (67%), but higher concentration of Mg was observed at the outlet. Cu, Fe and Pb showed no significant differences in the in- and outflow concentrations. The system successfully removed 82% of influent PAHs. Soil samples collected in summer and fall revealed higher MRG abundance in summer, with copA being the most prevalent MRG (1.2-4.8 log10 copies/g soil). Among the ARGs, sul1 was consistently found throughout the basin (2.5-6.7 log10 copies/g soil), while tetW was detected primarily at the basin's start and end in the topsoil layer. Rubellimicrobium and Geobacter were identified as potential carriers of ARGs/MRGs. Although the concentration of metals in soil was not measured in the current study, these findings emphasize the need to understand heavy metal distribution and the occurrence of MRGs and ARGs in stormwater control systems to improve their design and effectiveness.

Adsorption/desorption of enrofloxacin in farmland soil as the effect of pH and coexisting ions: implications for enrofloxacin fate and risk in loess soil

Fluoroquinolone antibiotics have been extensively used in clinical treatments for human and animal diseases. However, their long-term presence in the environment increases the risk of producing resistance genes and creates a potential threat to ecosystems and the health of humans and animals. Batch equilibrium experiments were utilized to investigate the adsorption and retention behavior and mechanism of the quinolone antibiotic enrofloxacin (ENR) in farmland soil in North China. The adsorption and desorption kinetics of ENR in soil were best fitted by pseudo-second-order model (R2 > 0.999). Both the adsorption and desorption processes of ENR in soil reached equilibrium in 1 h. The desorption amounts of ENR were significantly lower than the adsorption amounts, with the hysteresis coefficient (HI) being less than 0.7. The adsorption thermodynamic process of ENR followed the Linear and Freundlich models (0.965 < R2 < 0.985). Hydrophobic distribution and heterogeneous multimolecular layer adsorption were identified as critical factors in the adsorption process. The adsorption amount of ENR gradually decreased with increasing temperature and the initial concentration of ENR. The adsorption rate of ENR was above 80%, while the desorption rate remained below 15%, indicating strong retention ability. The adsorption rate of ENR in soil decreased with increasing pH, the adsorption rate reached 98.3% at pH 3.0 but only 31.5% at pH 11. The influence of coexisting ions on adsorption primarily depended on their properties, such as ion radius, ionic strength, and hydrolysis properties, and the inhibition of adsorption increased with increasing ionic strength. These findings contribute to understanding the fate and risk of veterinary antibiotics in loess soil in North China.

Silybin protected from avermectin-induced carp (Cyprinus carpio) nephrotoxicity by regulating PPAR-γ-involved inflammation, oxidative stress, ferroptosis and autophagy

Avermectin, a widely used deworming drug, poses a significant threat to fisheries. Silybin is recognized for its antioxidant and anti-inflammatory properties. The kidney, being crucial for fish survival, plays a vital role in maintaining ion balance, nitrogen metabolism, and hormone regulation. While residual avermectin in water could pose a risk to carp (Cyprinus carpio), it remains unclear whether silybin can alleviate the renal tissue toxicity induced by avermectin in this species. In current study, we developed a model of long-term exposure of carp to avermectin to investigate the potential protective effect of silybin against avermectin-induced nephrotoxicity. The results indicated that avermectin induced renal inflammation, oxidative stress, ferroptosis, and autophagy in carp. Silybin suppressed the mRNA transcript levels of pro-inflammatory factors, increased catalase (CAT) activity, reduced glutathione (GSH) activity, diminished reactive oxygen species (ROS) accumulation in renal tissues, and promoted the activation of the Nrf2-Keap1 signaling pathway. Furthermore, the transcript levels of ferroptosis-associated proteins, including gpx4 and slc7a11, were significantly reduced, while those of cox2, ftl, and ncoa4 were elevated. The transcript levels of autophagy-related genes, including p62 and atg5, were also regulated. Network pharmacological analysis revealed that silybin inhibited ROS accumulation and mitigated avermectin-induced renal inflammation, oxidative stress, ferroptosis, and autophagy in carp through the involvement of PPAR-γ. Silybin exerted its anti-inflammatory effect through the NF-κB pathway and antioxidant effect through the Nrf2-Keap1 pathway, induced renal cell iron efflux through the SLC7A11/GSH/GPX4, and suppressed autophagy initiation via the PI3K/AKT pathway. This study provides evidence of the protective effect of silybin against avermectin-induced nephrotoxicity in carp, highlighting its potential as a therapeutic agent to alleviate the adverse effects of avermectin exposure in fish.

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Urbanization influences the indoor transfer of airborne antibiotic resistance genes, which has a seasonally dependent pattern

Over the last few years, the cumulative use of antibiotics in healthcare institutions, as well as the rearing of livestock and poultry, has resulted in the accumulation of antibiotic resistance genes (ARGs). This presents a substantial danger to human health worldwide. The characteristics of airborne ARGs, especially those transferred from outdoors to indoors, remains largely unexplored in neighborhoods, even though a majority of human population spends most of their time there. We investigated airborne ARGs and mobile genetic element (MGE, IntI1), plant communities, and airborne microbiota transferred indoors, as well as respiratory disease (RD) prevalence using a combination of metabarcode sequencing, real-time quantitative PCR and questionnaires in 72 neighborhoods in Shanghai. We hypothesized that (i) urbanization regulates ARGs abundance, (ii) the urbanization effect on ARGs varies seasonally, and (iii) land use types are associated with ARGs abundance. Supporting these hypotheses, during the warm season, the abundance of ARGs in peri-urban areas was higher than in urban areas. The abundance of ARGs was also affected by the surrounding land use and plant communities: an increase in the proportion of gray infrastructure (e.g., residential area) around neighborhoods can lead to an increase in some ARGs (mecA, qnrA, ermB and mexD). Additionally, there were variations observed in the relationship between ARGs and bacterial genera in different seasons. Specifically, Stenotrophomonas and Campylobacter were positively correlated with vanA during warm seasons, whereas Pseudomonas, Bacteroides, Treponema and Stenotrophomonas positively correlated with tetX in the cold season. Interstingly, a noteworthy positive correlation was observed between the abundance of vanA and the occurrence of both rhinitis and rhinoconjunctivitis. Taken together, our study underlines the importance of urbanization and season in controlling the indoor transfer of airborne ARGs. Furthermore, we also highlight the augmentation of green-blue infrastructure in urban environments has the potential to mitigate an excess of ARGs.

Silybin mitigates chronic Avermectin exposure-induced intestinal damage and growth inhibition in carp

Avermectins, as a new type of environmental pollutant, have received significant attention in recent years. Previous research has shown that acute exposure to avermectins can induce oxidative stress and inflammation in non-target fish species, such as carp. Flavonoid lignans, particularly Silybin, have demonstrated promising biological activities, including regulation of non-alcoholic fatty liver and cerebral ischemia-reperfusion injury. This study aims to investigate the impact of dietary supplementation with Silybin on the intestinal damage in carp caused by chronic exposure to avermectins and to improve the health status and production of carp in aquaculture. Silybin was used as a dietary supplement by adding it to the experimental feed, and an animal experimental model was utilized to assess its effects on oxidative stress, inflammation, and cell apoptosis in carp intestine. Additionally, intestinal barrier integrity, digestive capacity, and fish growth were evaluated. The results indicated that dietary supplementation with Silybin effectively alleviated the oxidative stress induced by chronic exposure to avermectins in carp intestine. Furthermore, Silybin improved intestinal barrier integrity and digestive capacity by modulating the Nrf2/Keap1 pathway. This study demonstrates that dietary supplementation with Silybin can effectively mitigate the intestinal damage caused by chronic exposure to avermectins in carp, providing a sustainable solution for the aquaculture industry to enhance the overall health and production of cultured fish. The research expands our understanding of avermectin environmental pollution and offers a potential remediation approach.

Whole-transcriptome analysis after the acquisition of antibiotic resistance of Cronobacter sakazakii: Mechanisms of antibiotic resistance and virulence changes

The emergence of antibiotic-resistant bacteria led to the misuse of antibiotics, resulting in the emergence of more resistant bacteria and continuous improvement in their resistance ability. Cronobacter sakazakii (C. sakazakii) has been considered a pathogen that harms infants. Incidents of C. sakazakii contamination have continued globally, several studies have indicated that C. sakazakii is increasingly resistant to antibiotics. A few studies have explored the mechanism of antibiotic resistance in C. sakazakii, and some have examined the antibiotic resistance and changes in virulence levels. We aimed to investigate the antibiotic resistance mechanism and virulence differences in C. sakazakii. The level of virulence factors of C. sakazakii was modified after induction by antibiotics compared with the antibiotic-sensitive strains, and the XS001-Ofl group had the strongest capacity to produce enterotoxin (85.18 pg/mL) and hemolysin (1.47 ng/mL). The biofilm formation capacity after induction significantly improved. The number of bases and mapped reads in all groups accounted for more than 55 % and 70 %, as detected by transcriptomic analysis. The resistance mechanism of different antibiotics was more common in efflux pumps, cationic antimicrobial peptides, and biofilm formation pathways. The level of antibiotic resistance mainly affected the expression of virulence genes associated with flagella assembly and synthesis.