Enrichment Of Antibiotic Resistance Genes Research Articles

Effect of polyethylene microplastics on antibiotic resistance genes: A comparison based on different soil types and plant types

Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1–5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks.

Diel variations of airborne microbes and antibiotic resistance genes in Response to urban PM2.5 chemical properties during the heating season

Among the components of fine particulate matter (PM2.5), the contributions of airborne microorganisms and antibiotic resistance genes (ARGs) to health risks have been overlooked. Airborne microbial dynamics exhibit a unique diurnal cycle due to environmental influences. However, the specific roles of PM2.5 chemical properties resulting from fossil fuel combustion in driving circadian fluctuations in microbial populations and ARGs remain unclear. This study explored the interactions between toxic components and microbial communities during the heating period to understand the variations in ARGs. Bacterial and fungal communities showed a higher susceptibility to diel variations in PM2.5 compared to their chemical properties. Mantel tests revealed that chemical properties and microbial community interactions contribute differently to ARG variations, both directly and indirectly, during circadian fluctuations. Our findings highlight that, during the daytime, the enrichment of pathogenic microorganisms and ARGs increases the risk of PM2.5 toxicity. Conversely, during the nighttime, the utilization of water-soluble ions by the fungal community increased, leading to a significant increase in fungal biomass. Notably, Aspergillus exhibited a significant correlation with mobile genetic elements and ARGs, implying that this genus is a crucial driver of airborne ARGs. This study provides novel insights into the interplay between the chemical composition, microbial communities, and ARGs in PM, underscoring the urgent need for a comprehensive understanding of effective air pollution control strategies.

Pre-exposure of Triclosan compromise tetracycline-derived antibiotic resistance in methanogenic digestion microbiome

Triclosan (TCS) and tetracycline (TC) are commonly detected antibacterial agents in sewage and environment matrices. Nonetheless, the impact of sequential exposure to TCS and TC on the methanogenic digestion microbiome remains unknown. In this study, TCS was shown to reduce COD removal efficiency to 69.8%, but alleviated the inhibitive effect of consequent TC-amendment on the digestion microbiome. Interestingly, TCS pre-exposure resulted in abundance increase of acetotrophic Methanosaeta to 2.68%, being 2.91 folds higher than that without TCS amendment. Microbial network analyses showed that TCS pre-exposure caused microorganisms to establish a co-ecological relationship against TC disturbance. Further analyses of total antibiotic resistance genes (ARGs) showed the TCS-derived compromise of TC-induced ARGs enrichment in digestion microbiomes, e.g., 238.2% and 152.1% ARGs increase upon TC addition in digestion microbiomes without and with TCS pre-exposure, respectively. This study provides new insights into the impact of antibacterial agents on the methanogenic digestion microbiome.

Effect of microplastics on oxytetracycline trophic transfer: Immune, gut microbiota and antibiotic resistance gene responses

Microplastics and antibiotics are prevalent and emerging pollutants in aquatic ecosystems, but their interactions in aquatic food chains remain largely unexplored. This study investigated the impact of polypropylene microplastics (PP-MPs) on oxytetracycline (OTC) trophic transfer from the shrimp (Neocaridina denticulate) to crucian carp (Carassius auratus) by metagenomic sequencing. The carrier effects of PP-MPs promoted OTC bioaccumulation and trophic transfer, which exacerbated enterocyte vacuolation and hepatocyte eosinophilic necrosis. PP-MPs enhanced the inhibitory effect of OTC on intestinal lysozyme activities and complement C3 levels in shrimp and fish, and hepatic immunoglobulin M levels in fish (p < 0.05). Co-exposure of MPs and OTC markedly increased the abundance of Actinobacteria in shrimp and Firmicutes in fish, which caused disturbances in carbohydrate, amino acid, and energy metabolism. Moreover, OTC exacerbated the enrichment of antibiotic resistance genes (ARGs) in aquatic animals, and PP-MPs significantly increased the diversity and abundance of ARGs and facilitated the trophic transfer of teta and tetm. Our findings disclosed the impacts of PP-MPs on the mechanism of antibiotic toxicity in aquatic food chains and emphasized the importance of gut microbiota for ARGs trophic transfer, which contributed to a deeper understanding of potential risks posed by complex pollutants on aquatic ecosystems.

Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems

Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0–2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.

Involvement of functional metabolism promotes the enrichment of antibiotic resistome in drinking water: Based on the PICRUSt2 functional prediction

Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 102–103 CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Premise Plumbing Pipe Materials and In-Building Disinfectants Shape the Potential for Proliferation of Pathogens and Antibiotic Resistance Genes.

In-building disinfectants are commonly applied to control the growth of pathogens in plumbing, particularly in facilities such as hospitals that house vulnerable populations. However, their application has not been well optimized, especially with respect to interactive effects with pipe materials and potential unintended effects, such as enrichment of antibiotic resistance genes (ARGs) across the microbial community. Here, we used triplicate convectively mixed pipe reactors consisting of three pipe materials (PVC, copper, and iron) for replicated simulation of the distal reaches of premise plumbing and evaluated the effects of incrementally increased doses of chlorine, chloramine, chlorine dioxide, and copper-silver disinfectants. We used shotgun metagenomic sequencing to characterize the resulting succession of the corresponding microbiomes over the course of 37 weeks. We found that both disinfectants and pipe material affected ARG and microbial community taxonomic composition both independently and interactively. Water quality and total bacterial numbers were not found to be predictive of pathogenic species markers. One result of particular concern was the tendency of disinfectants, especially monochloramine, to enrich ARGs. Metagenome assembly indicated that many ARGs were enriched specifically among the pathogenic species. Functional gene analysis was indicative of a response of the microbes to oxidative stress, which is known to co/cross-select for antibiotic resistance. These findings emphasize the need for a holistic evaluation of pathogen control strategies for plumbing.

Chloroxylenol positively affects the aerobic sequencing batch reactor performance and reshapes microbial communities and antibiotic resistance genes

The antibacterial ingredient chloroxylenol (PCMX) has been frequently detected in various environments, raising increasing concerns about its potential risks to organisms and ecosystems. Herein, the impacts of PCMX on the performance and microbial communities of aerobic sequencing batch reactors were investigated. The results demonstrated that 0.1 and 1.0 mg/L PCMX did not affect the removal performance of COD and NH4+-N, as well as the production of extracellular polymeric substances. However, a notable enhancement in these performances was observed when the concentration of PCMX reached 10 mg/L. Analysis of microbial community revealed that exposure to PCMX did not alter α diversity but significantly shifted the community structure. Spirosoma and Ferruginibacter were identified as dominant genera across all stages in the sludge, with Ferruginibacter being inhibited by 10 mg/L PCMX (from 20.3 % to 11.1 %). Network analysis revealed that PCMX had a diminishing effect on the interaction and complexity of microbial. High throughput qPCR analysis indicated that PCMX reshaped the antibiotic resistance genes (ARGs). The relative gene copy number increased from 0.23 to 0.29 at a concentration of 0.1 mg/L PCMX, while it decreased from 0.51 to 0.40 by 10 mg/L PCMX. Genes tetX and sul2 were identified as dominant genes unaffected by 0.1 and 1.0 mg/L but significantly inhibited by 10 mg/L PCMX. These findings suggested that environmental levels of PCMX might promote the enrichment of ARGs, while higher concentrations impeded gene propagation. This study provides new information regarding the roles, potential risks, and removal strategies of PCMX in wastewater treatment processes.

Dynamic evolution of antibiotic resistance genes in plastisphere in the vertical profile of urban rivers

Microplastics (MPs) can vertically transport in the aquatic environment due to their aging and biofouling, forming distinct plastisphere in different water layers. However, even though MPs have been regarded as hotspots for antibiotic resistance genes (ARGs), little is known about the propagation and transfer of ARGs in plastisphere in waters, especially in the vertical profile. Therefore, this study investigated the dynamic responses and evolution of ARGs in different plastisphere distributed vertically in an urbanized river. The biofilm biomass in the polylactic acid (PLA) plastisphere was relatively higher than that in the polyethylene terephthalate (PET), showing depth-decay variations. The ARGs abundance in plastisphere were much higher than that in the surrounding waters, especially for the PLA. In the vertical profiles, the ARGs abundance in the PET plastisphere increased with water depths, while the highest abundance of ARGs in the PLA mostly appeared at intermediate waters. In the temporal dynamic, the ARGs abundance in plastisphere increased and then decreased, which may be dominated by the MP types at the initial periods. After long-term exposure, the influences of water depths seemed to be strengthened, especially in the PET plastisphere. Compared with surface waters, the microbiota attached in plastisphere in deep waters showed high species richness, strong diversity, and complex interactions, which was basically consistent with the changes of nutrient contents in different water layers. These vertical variations in microbiota and nutrients (e.g., nitrogen) may be responsible for the propagation of ARGs in plastisphere in deep waters. The host bacteria for ARGs in plastisphere was also developed as water depth increased, leading to an enrichment of ARGs in deep waters. In addition, the abundance of ARGs in plastisphere in bottom waters was positively correlated with the mobile genetic elements (MGEs) of intI1 and tnpA05, indicative of a frequent horizontal gene transfer of ARGs. Overall, water depth played a critical role in the propagation of ARGs in plastisphere, which should not be ignored in a long time series. This study provides new insights into the dynamic evolution of ARGs propagation in plastisphere under increasing global MPs pollution, especially in the vertical profile.

Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management

There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.

Deterministic effect of oxygen level variation on shaping antibiotic resistome

An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5–7 mg L−1), normoxic (2–4 mg L−1), and hypoxic (0.5–1 mg L−1) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L−1) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.

Carbamazepine facilitated horizontal transfer of antibiotic resistance genes by enhancing microbial communication and aggregation

Antimicrobial resistance is a global health security issue of widespread concern. Recent studies have unveiled the potential contribution of non-antibiotics to the emergence of antimicrobial resistance. This study investigated the effect of carbamazepine, a non-antibiotic pharmaceutical, on the fate of antibiotic resistance genes (ARGs) during anaerobic digestion. The results, as revealed by both metagenomic sequencing and absolute quantification, demonstrated that carbamazepine induced the enrichment of ARGs and increased the abundance of ARGs hosts by 1.2–2.1 times. Carbamazepine facilitated microbial aggregation and intercellular communication by upregulating functional genes associated with two-component systems, quorum sensing and type IV secretion systems, thereby increasing the frequency of ARGs conjugation. Furthermore, carbamazepine induced the acquisition of ARGs by pathogens and elevated the overall pathogenic abundance. This study revealed the mechanisms of microbial self-regulation and ARGs transmission under carbamazepine stress, highlighting the potential health risks posed by non-antibiotic pharmaceuticals during the safe disposal of sludge.

Spatial distribution of antibiotics and antibiotic resistance genes in tidal flat reclamation areas in China.

Tidal flat areas are important resources for land development and are becoming antibiotic resistance receivers that trigger major health concerns. The spatial distributions of forty-nine antibiotics, nine antibiotic resistance genes (ARGs), one mobile gene element (MGE) gene, and nine available metals in the soils and sediments along the coastlines of the Yellow Sea in China were quantified. Hierarchical linear model analysis was used to explore relationships between the antibiotics and ARGs across multiple effects resulting from human activities and environmental factors. Fish farm sediments and farmland soils showed high levels of quinolones (QNs) (maximum 637ng·g-1), sulfonamides (SAs) (maximum 221ng·g-1), and corresponding ARGs. Significant positive correlations (P from 5.47 × 10-14 to 0.0487) were observed between the antibiotics (QNs, SAs, and chlortetracycline) and their corresponding ARGs (qnrA, qnrD, aac(6')-Ib-cr, dfrA, sul2, and tetA), indicating the selective pressure from antibiotics in soils and sediments. Nine available metals had positive correlations with at least one ARG, indicating heavy metal pollution could enhance the ARGs. Sheep and poultry husbandry and marine aquaculture contribute the most to the antibiotic resistance in the coastlines. In conclusion, antibiotic pollutions have promoting effects at sub-inhibitory concentrations and more attention should be given to inhibit the enrichment of ARGs during tidal flat reclamation processes. The study also suggests the induction effects from metal pollutions, MGE spread, and the antibiotic pollutions from the usage in livestock and aquaculture.

Alteration of microbial mediated carbon cycle and antibiotic resistance genes during plastisphere formation in coastal area

Microorganisms can attach on the surface of microplastics (MPs) through biological fouling process to form a diverse community called the "plastisphere", which has attracted extensive attention. Although the microbial structure and composition of biofilm have been studied, the knowledge of its microbial function and ecological risk is still limited. In this study, we investigated how the surface properties of MPs affect the biofilm communities and metabolic features under different environmental conditions, and explored the biofilm enrichment of antibiotic resistance genes (ARGs). The results showed that the incubation time, habitat and MPs aging state significantly influenced the structure and composition of biofilm microbial communities, and a small amount of pathogens have been found in the MPs-attached biofilm. The microbial carbon utilization capacity of the biofilm in different incubation habitats varies greatly with highest metabolism capacity appear in the river. The utilization efficiency of different carbon sources is polymer > carbohydrate > amino acid > carboxylic acids > amine/amide, which indicates that the biofilm communities have selectivity between different types of carbon sources. More importantly, ARGs were detected in all the MPs samples and showed a trend of estuary > river > marine. The aged MPs can accumulate more ARGs than the virgin items. In general, MPs in the aquatic environment may become a carrier for pathogens and ARGs to spread to other environment, which may enhance their potential risks to the ecosystem and human health.

Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).

With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.

Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress

Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.

Occurrence and fate of antibiotic-resistance genes and their potential hosts in high-moisture alfalfa silage treated with or without formic acid bactericide

Silage as the main forage for ruminants could be a reservoir for antibiotic resistance genes (ARGs) through which these genes got access into the animals' system causing a latent health risk. This study employed metagenomics and investigated the ARGs’ fate and transmission mechanism in high-moisture alfalfa silage treated with formic acid bactericide. The results showed that there were 22 ARGs types, in which multidrug, macrolide-lincosamide-streptogramine, bacitracin, beta-lactam, fosmidomycin, kasugamycin, and polymycin resistance genes were the most prevalent ARGs types in the ensiled alfalfa. The natural ensiling process increased ARGs enrichment. Intriguingly, after 5 days of ensiling, formic acid-treated silage reduced ARGs abundances by inhibiting host bacterial and plasmids. Although formic acid bactericide enhanced the fermentation characteristics of the high-moisture alfalfa by lowering silage pH, butyric acid concentration, dry matter losses and proteolysis, it increased ARGs abundances in alfalfa silage owing to increases in abundances of ARGs carriers and transposase after 90 days of ensiling. Notably, several pathogens like Staphylococcus, Clostridium, and Pseudomonas were inferred as potential ARGs hosts in high-moisture alfalfa silage, and high-moisture alfalfa silage may harbor a portion of the clinical ARGs. Fundamentally, microbes were distinguished as the foremost driving factor of ARGs propagation in ensiling microecosystem. In conclusion, although formic acid bactericide improved the fermentation characteristics of high-moisture alfalfa during ensiling and reduced ARGs enrichment at the initial ensiling stage, it increased ARGs enrichment at the end of ensiling.

Response of viable bacteria to antibiotics in aerobic granular sludge: Resistance mechanisms and behaviors, bacterial communities, and driving factors

The assessment of antimicrobial resistance (AMR) risk by DNA-based techniques mainly relies on total bacterial DNA. In this case, AMR risk recognition is restricted to the genotype level, lacking crucial phenotypic information, such as the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in dead and viable bacteria. This limitation hinders the recognition of AMR behavior. Herein, based on propidium monoazide (PMA) shielding method, this work firstly quantified the intracellular ARGs/MGEs in viable and dead bacteria, and the impact of viable bacteria composition on the formation of intracellular/extracellular polymeric substance-related /cell-free ARGs (i/e/cARGs) and MGEs (i/e/cMGEs) in aerobic granular sludge (AGS). The shielding efficiency of PMA against dead bacteria was optimized to be as high as 97.5% when the MLSS of AGS was 2.0 g/L. Under antibiotic stimulation, 29.0% ∼ 49.0% of iARGs/iMGEs were carried by viable bacteria, and the remaining proportion were carried by dead bacteria. 18 out of the top 20 dominant genera showed a change in abundance by more than 1% after PMA treatment. 29 viable hosts were identified to associate with 52 iARGs, of which 28 and 15 hosts were also linked to 40 eARGs and 26 cARGs. Also, partial least-squares path model and variance partitioning analysis disclosed that viable bacteria and i/e/cMGEs had a positive effect on i/e/cARGs, with both contributing as much as 64.5% to the total ARGs enrichment. These results better visualized the AMR risk carried by viable bacteria and the categories of viable hosts. This work provides a novel insight into analyzing the actual AMR risk and viable hosts, helping to the reduction and control of AMR in wastewater treatment plants.

Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf

Aquacultures are the main reason for the environmental selection of antibiotic resistance genes (ARGs), resulting in the enrichment of ARGs. As a filter, a marine mangrove ecosystem can reduce antimicrobial resistance (AMR) or eliminate ARGs; however, its elimination mechanism remains unclear. This study investigated the spatiotemporal dynamic distribution of ARGs in two different types of mangrove habitats (shrimp ponds and virgin forests), within a subtropical gulf located in the Beibu Gulf, China, during dry and wet seasons by using metagenomics and real time quantitative polymerase chain reaction (RT-qPCR) analysis. As the key environmental factors, sulfide, salinity, and mobile genetic elements significantly were found to contribute to ARGs distribution, respectively. Wet and dry seasons influenced the dispersal of ARGs but did not affect the microbial community structure. Three potential biomarkers, TEM-116, smeD, and smeE, played key roles in seasonal differences. The key different genes in the biological relevance of absolute abundance were demonstrated by RT-qPCR. Co-occurrence network analysis indicated that high-abundance ARGs were distributed in a modular manner. For the first time, a risk index weighted by risk rank (RIR) was proposed and used to quantify the human risk of ARGs in the mangrove metagenome. The shrimp ponds during the wet season showed the highest RIR detected. In addition to offering a perspective on reducing AMR in mangrove wetlands, this study constructed the first spatiotemporal dynamic model of ARGs in the Beibu Gulf, China and contributed to revealing the global spread of ARGs. Meanwhile, this study proposes a new pipeline for assessing the risk of ARGs, while also exploring the concept of “One Health.”