Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants

Removal of intracellular and extracellular antibiotic resistance genes and virulence factor genes using electricity-intensified constructed wetlands

Constructed wetland (CW) is considered a promising technology for the removal of emerging contaminants. However, its removal performance for antibiotic resistance genes (ARGs) is not efficient and influence of virulence factor genes (VFGs) have not been elucidated. Here, removal of intracellular and extracellular ARGs as well as VFGs by electricity-intensified CWs was comprehensively evaluated. The two electrolysis-intensified CWs can improve the removal of intracellular ARGs and MGEs to 0.96- and 0.85-logs, respectively. But cell-free extracellular ARGs (CF-eARGs) were significantly enriched with 1.8-logs in the electrolysis-intensified CW. Interestingly, adding Fe-C microelectrolysis to the electrolysis-intensified CW is conducive to the reduction of CF-eARGs. However, the detected number and relative abundances of intracellular and extracellular VFGs were increased in all of the three CWs. The biofilms attached onto the substrates and rhizosphere are also hotspots of both intracellular and particle-associated extracellular ARGs and VFGs. Structural equation models and correlation analysis indicated that ARGs and VFGs were significantly cooccurred, suggesting that VFGs may affect the dynamics of ARGs. The phenotypes of VFGs, such as biofilm, may act as protective matrix for ARGs, hindering the removal of resistance genes. Our results provide novel insights into the ecological remediation technologies to enhance the removal of ARGs.

Unveiling the characteristics of free-living and particle-associated antibiotic resistance genes associated with bacterial communities along different processes in a full-scale drinking water treatment plant

Antibiotic resistance genes (ARGs) as emerging contaminants, often co-occur with mobile genetic elements (MGEs) and are prevalent in drinking water treatment plants (DWTPs). In this study, the characteristics of free-living (FL) and particle-associated (PA) ARGs associated with bacterial communities were investigated along two processes within a full-scale DWTP. A total of 13 ARGs and two MGEs were detected. FL-ARGs with diverse subtypes and PA-ARGs with high abundances displayed significantly different structures. PA-MGEs showed a strong positive correlation with PA-ARGs. Chlorine dioxide disinfection achieved 1.47-log reduction of FL-MGEs in process A and 0.24-log reduction of PA-MGEs in process B. Notably, PA-fraction virtually disappeared after treatment, while blaTEM, sul2, mexE, mexF and IntI1 of FL-fraction remained in the finished water. Moreover, Acinetobacter lwoffii (0.04 % ∼ 45.58 %) and Acinetobacter schindleri (0.00 % ∼ 18.54 %) dominated the 16 pathogens, which were more abundant in FL than PA bacterial communities. PA bacteria exhibited a more complex structure with more keystone species than FL bacteria. MGEs contributed 20.23 % and 19.31 % to the changes of FL-ARGs and PA-ARGs respectively, and water quality was a key driver (21.73 %) for PA-ARGs variation. This study provides novel insights into microbial risk control associated with size-fractionated ARGs in drinking water.

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human

BACKGROUND

Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.

RESULTS

The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.

CONCLUSIONS

The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

Strong suppression of silver nanoparticles on antibiotic resistome in anammox process

This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.

Microbial community and antimicrobial resistance niche differentiation in a multistage, surface flow constructed wetland

Free-living (FL) and particulate-associated (PA) communities are distinct bacterioplankton lifestyles with different mobility and dissemination routes. Understanding spatio-temporal dynamics of PA and FL fractions will allow improvement to wastewater treatment processes including pathogen and AMR bacteria removal. In this study, PA, FL and sediment community composition and antimicrobial resistance gene (ARG; tetW, ermB, sul1, intI1) dynamics were investigated in a full-scale municipal wastewater free-water surface polishing constructed wetland. Taxonomic composition of PA and FL microbial communities shifted towards less diverse communities (Shannon, Chao1) at the CW effluent but retained a distinct fraction-specific composition. Wastewater treatment plant derived PA communities introduced the bulk of AMR load (70 %) into the CW. However, the FL fraction was responsible for exporting over 60 % of the effluent AMR load given its high mobility and the effective immobilization (1-3 log removal) of PA communities. Strong correlations (r2>0.8, p < 0.05) were observed between the FL fraction, tetW and emrB dynamics, and amplicon sequence variants (ASVs) of potentially pathogenic taxa, including Bacteroides, Enterobacteriaceae, Aeromonadaceae, and Lachnospiraceae. This study reveals niche differentiation of microbial communities and associated AMR in CWs and shows that free-living bacteria are a primary escape route of pathogenic and ARG load from CWs under low-flow hydraulic conditions.

Deciphering the dynamics and driving mechanisms of high-risk antibiotic resistome in size-fractionated bacterial community during drinking water chlorination via metagenomic analysis

To reveal the impact of chlorination on the high-risk resistome in size-fractionated bacterial community, we employed metagenomic approaches to decipher dynamics of high-risk antibiotic resistance genes (ARGs) and driving mechanisms in the free-living and particle-associated fractions within a full-scale drinking water treatment system. Our results revealed that chlorination significantly increased the relative abundance of high-risk ARGs in the free-living fraction to 0.33 ± 0.005 copies/cell (cpc), bacitracin and chloramphenicol resistance types were major contributors. Furthermore, chlorination significantly increased the relative abundance of mobile genetic elements (MGEs) in the free-living fraction, while decreasing it in the particle-associated fraction. During chlorination, size-fractionated bacterial communities varied considerably. Multiple statistical analyses highlighted the pivotal role of the bacterial community in altering high-risk ARGs in both the free-living and particle-associated fractions, while MGEs had a more pronounced impact on high-risk ARGs in the free-living fraction. Specifically, the enrichment of pathogenic hosts, such as Comamonas and Pseudomonas, led to an increase in the abundance of high-risk ARGs. Concurrently, MGEs exhibited significant correlations with high-risk ARGs, indicating the potential of horizontal transfer of high-risk ARGs. These findings provide novel insights for mitigating antibiotic resistance risk by considering different bacterial fractions and respective risk ranks in drinking water.

Analysis of extracellular and intracellular antibiotic resistance genes in commercial organic fertilizers reveals a non-negligible risk posed by extracellular genes

Livestock manure is known to be a significant reservoir of antibiotic resistance genes (ARGs), posing a major threat to human health and animal safety. ARGs are found in both intracellular and extracellular DNA fractions. However, there has been no comprehensive analysis of these fractions in commercial organic fertilizers (COFs). The present study conducted a systematic survey of the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) and their contributing factor in COFs in Northern China. Results showed that the ARG diversity in COFs (i.e., 57 iARGs and 53 eARGs) was significantly lower than that in cow dung (i.e., 68 iARGs and 69 eARGs). The total abundance of iARGs and eARGs decreased by 85.7% and 75.8%, respectively, after compost processing, and there were no significant differences between iARGs and eARGs in COFs (P > 0.05). Notably, the relative abundance of Campilobacterota decreased significantly (99.1-100.0%) after composting, while that of Actinobacteriota and Firmicutes increased by 21.1% and 29.7%, respectively, becoming the dominant bacteria in COFs. Co-occurrence analysis showed that microorganisms and mobile genetic elements (MGEs) were more closely related to eARGs than iARGs in COFs. And structural equation models (SEMs) further verified that microbial community was an essential factor regulating iARGs and eARGs variation in COFs, with a direct influence (λ = 0.74 and 0.62, P < 0.01), following by similar effects of MGEs (λ = 0.59 and 0.43, P < 0.05). These findings indicate the need to separate eARGs and iARGs when assessing the risk of dissemination and during removal management in the environment.

Transfer, elimination and accumulation of antibiotic resistance genes in decentralized household wastewater treatment facility treating total wastewater from residential complex

The fate and behavior of antibiotic resistance genes (ARGs) in decentralized household wastewater treatment facilities (DHWWTFs) are unclear. In this study, targeting on a representative DHWWTF that receive all wastewater from a residential complex having 150 households, the transfer, elimination and accumulation of tetG, tetM, sul1, sul2 and intl1 were quantitively studied through real-time PCR-based quantification, mass balance evaluation and the existing state analysis based on size fractionation. Significant abundance changes of the genes were observed in involved biological reactions and the sedimentation process due to microbial growth and decomposition as well as the accumulation of the genes to sludge. tetG and sul1 increased in their fluxes against respective input in the influent. Although substantial portions of the increased genes were found in excess sludge compared to the flux of genes in the influent, those remaining in the discharge were still high, with an average about 3.4 × 1014 copies/d. The abundance of all four genes (tetG, tetM, sul1and sul2) in both water and sludge phases showed a general trend of reduction as sludge accumulated gradually in its storage tank within two months after desludging. Classification of ARGs based on particle sizes (>250 μm, 125-250 μm, 75-125 μm, 25-75 μm, 3-25 μm, <3 μm) indicated that while the major part of ARGs were distributed in particles with larger sizes (125-250 μm), ARGs in smaller particles (3-25 μm) and free ARGs (<3 μm) still existed, which may pose a greater threat to water environment due to their poor settleability. The results of this study can benefit the optimization of on-site maintenance and operation of decentralized wastewater treatment facility for elimination of the transfer of ARGs.

Bibliometric analysis of papers on antibiotic resistance genes in aquatic environments on a global scale from 2012 to 2022: Evidence from universality, development and harmfulness

Antibiotic resistance genes (ARGs), emerging pollutants, are widely distributed in aquatic environments, and are tightly linked to human health. However, the research progress and trends in recent years on ARGs of aquatic environments are still unclear. This paper made a comprehensive understanding of the research advance, study trends and key topics of 1592 ARGs articles from 2012 to 2022 by bibliometrics. Publications on ARGs increased rapidly from 2012 to 2022, and scholars paid closer attention to the field of Environmental Sciences & Ecology. The most influential country and institution was mainly China and Chinese Academy of Sciences, respectively. The most articles (14.64 %) were published in the journal Science of the total environment. China and USA had the most cooperation, and USA was more inclined to international cooperation. PCR-based methods for water ARG research were the most widely used, followed by metagenomics. The most studied ARG types were sulfonamides, tetracyclines. Moreover, ARGs from wastewater and rivers were popularly concerned. Current topics mainly included pollution investigation, characteristics, transmission, reduction and risk identification of ARGs. Additionally, future research directions were proposed. Generally, by bibliometrics, this paper reviews the research hotspots and future directions of ARGs on a global scale, and summarizes the more important categories of ARGs, the pollution degree of ARGs in the relevant water environment and the research methods, which can provide a more comprehensive information for the future breakthrough of resistance mechanism, prevention and control standard formulation of ARGs.

Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO₂ nanoparticles (SiO₂NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO₂NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO₂NPs to reduce the propagation of ARGs.

Field-realistic dose of cefotaxime enhances potential mobility of β-lactam resistance genes in the gut microbiota of zebrafish (Danio rerio)

With large amounts of cephalosporin end up in natural ecosystems, water has been acknowledged as the large reservoir of β-lactam resistance over the past decades. However, there is still insufficient knowledge available on the function of the living organisms to the transmission of antibiotic resistance. For this reason, in this study, using adult zebrafish (Danio rerio) as animal model, exposing them to environmentally relevant dose of cefotaxime for 150 days, we asked whether cefotaxime contamination accelerated β-lactam resistance in gut microbiota as well as its potential transmission. Results showed that some of β-lactam resistance genes (βRGs) were intrinsic embedded in intestinal microbiome of zebrafish even without antibiotic stressor. Across cefotaxime treatment, the abundance of most βRGs in fish gut microbiome decreased apparently in the short term firstly, and then increased with the prolonged exposure, forming distinctly divergent βRG profiles with antibiotic-untreated zebrafish. Meanwhile, with the rising concentration of cefotaxime, the range of βRGs' host-taxa expanded and the co-occurrence relationships of mobile genetics elements (MGEs) with βRGs intensified, indicating the enhancement of βRGs' mobility in gut microbiome when the fish suffered from cefotaxime contamination. Furthermore, the path of partial least squares path modeling (PLS-PM) gave an integral assessment on the specific causality of cefotaxime treatment to βRG profiles, showing that cefotaxime-mediated βRGs variation was most ascribed to the alteration of MGEs under cefotaxime stress, followed by bacterial community, functioning both direct influence as βRG-hosts and indirect effects via affecting MGEs. Finally, pathogenic bacteria Aeromonas was identified as the critical host for multiple βRGs in fish guts, and its β-lactam resistance increased over the duration time of cefotaxime exposure, suggesting the potential spreading risks for the antibiotic-resistant pathogens from environmental ecosystems to clinic. Overall, our finding emphasized cefotaxime contamination in aquatic surroundings could enhance the β-lactam resistance and its transmission mobility in fish bodies.

Unveiling the dynamics of antibiotic resistome, bacterial communities, and metals from the feces of patients in a typical hospital wastewater treatment system

Bacterial pathogens and antibiotic resistance genes (ARGs) are extensively disseminated into the environment via hospital wastewater (HWW), as it contains large quantities of feces from resident patients. However, studies on the antibiotic resistome and pathogenic bacteria from the gut of resident patients within the hospital wastewater treatment plant (hWWTP) are limited. Here, we examined and compared the occurrence and abundance of ARGs, mobile genetic elements (MGEs), metals, and bacterial communities from the feces of patients in a typical hWWTP system and determined the pathogenic hosts responsible for transferring ARGs. There were 176 ARGs and 43 MGEs detected in the feces of hospitalized patients, 129 genes were persistent, and 88 genes were enriched after HWW treatment, particularly for the bla_VEB, bla_NDM, and class 1 integron (intI1), with an average of 659-fold, 202-fold, and seven-fold enrichment, respectively. MGEs, especially Is613, in the feces of hospitalized patients were exceptionally abundant and even surpassed the abundance of total ARGs, which explained the persistence of ARGs in hWWTPs due to possible gene mobilization events. Bacteroidetes and Firmicutes were the most abundant phyla in these feces, accounting for 81 % of the total gut microbiota, while Epsilonbacteraeota and Proteobacteria dominated the hWWTPs. Additionally, 54 possible bacterial pathogens were found in the hospital environment, including four "ESKAPE" pathogens and 14 cancer-related pathogens. Many of them were strongly associated with different types of ARGs. Notably, Bacteroides was the major potential ARG-harboring pathogenic genus, as determined by the network analysis, and was highly abundant after the treatment. The altered microbial community was the major contributing factor shaping antibiotic resistome. This study might provide a comprehensive insight into the distribution profiles of ARGs and pathogens from the gut of inpatients throughout the HWW treatment system, which could be used as a reference for optimizing HWW treatment and monitoring public risk.

Deciphering the antibiotic resistome and microbial community in municipal wastewater treatment plants at different elevations in eastern and western China

Antibiotic resistance genes (ARGs) as emerging environmental contaminants pose severe global risks to public health and ecosystems. Municipal wastewater treatment plants (WWTPs) are crucial transmitters for the dissemination and propagation of ARGs into receiving water bodies via mobile genetic elements (MGEs). However, the comprehensive and deep deciphering of the diversity, abundance, and potential hosts of ARGs in two distinct altitudinal WWTPs is scarce. In this work, we revealed the elevational distribution characteristics of the resistance genes and microbial community of six WWTPs from two distinct geographical zones: a low-elevation (LE) region (Shandong, 10-22 m above sea level) and a high-elevation (HE) region (Gansu, 1,520-1,708 m above sea level). Significant elevational variations in the diversity and relative abundance of resistance genes were observed. Wastewater treatment could significantly reduce the concentrations of ARGs and MGEs by about 1-2 and 2-3 orders of magnitude, respectively. However, above 69.95% of resistance genes were enriched in effluent. In particular, 24 ARG subtype, 3 MGE subtypes, and 59 bacterial genera were persistent in all samples. More potential hosts for ARGs in LE region and more abundant human gut microbiota in HE region were identified. This work provides helpful information for controlling the spread of ARGs for their management and assessment, thereby mitigating the risks of ARGs in WWTPs.

Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome

Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.

The fate of antibiotic resistance genes and their association with bacterial and archaeal communities during advanced treatment of pig farm wastewater

Advanced wastewater treatment plants are widely used in most large-scale pig farms in southern China. However, the fate of antibiotic resistance genes (ARGs) and their association with bacterial and archaeal communities during advanced wastewater treatment remain unclear. In this study, the profiles of ARGs in typical advanced wastewater treatment plants were surveyed using metagenomic analysis. The results showed that 279- 326 different subtypes of ARGs were detected in raw wastewater, with a total abundance of 5.98 ± 0.48 copies per bacterial cell. During the advanced wastewater treatment, the abundance and number of ARGs were significantly reduced. Microbial communities (bacteria and archaea) contributed the most to the variation in ARG abundance and composition (PCA axis_1), accounting for 10.8 % and 15.7 %, respectively, followed by mobile genetic elements (MGEs) and physicochemical factors. Special attention should be given to potential pathogenic bacteria such as Escherichia, Streptococcus, Enterococcus and Staphylococcus and archaea such as Methanocorpusculum, Candidatus Methanoplasma and Candidatus Methanomethylophilus, which were important potential ARG hosts. Bacterial communities may indirectly affect ARG variation by affecting archaeal communities. These findings indicated that ARG levels in pig farm wastewater can be effectively reduced during advanced treatment and highlighted the important role played by archaea, which should not be ignored.

Size-dependent effects of microplastics on antibiotic resistance genes fate in wastewater treatment systems: The role of changed surface property and microbial assemblages in a continuous exposure mode

Microplastics (MPs) were continuously transported to wastewater treatment systems and accumulated in sludge constantly, potentially affecting systems function and co-occurrent contaminants fate. However, previous studies were based on acute exposure of MPs, which could not reflect the dynamics of MPs accumulation. Herein, this study firstly raised a more realistic method to evaluate the practical impacts of MPs on systems purification efficiency and antibiotic resistance genes (ARGs) fate. Continuous exposure of MPs did not pose negative effects on nutrients removal, but significantly changed the occurrence patterns of ARGs. ARGs abundances increased by 42.8 % and 54.3 % when exposed to millimeter-size MPs (mm-MPs) polyamide and polyethylene terephthalate, but increased by 31.3 % and 39.4 % to micron-size MPs (μm-MPs), respectively. Thus, mm-MPs posed severer effects on ARGs than μm-MPs. Further, mm-MPs surface properties were obviously altered after long-term exposure (higher specific surface area and O-containing species), which benefited microbes attachment. More importantly, more taxa linkages and changed topological properties (higher average degree and average weight) of co-occurrent network were observed in sludge with mm-MPs than with μm-MPs, as well as totally different potential host bacteria of ARGs. Rough surface of MPs and closer relations between ARGs and bacteria taxa contributed to the propagation of ARGs, which accounted for the observed higher ARGs abundances of mm-MPs. This study demonstrated that long-term accumulation of MPs in wastewater treatment systems affected ARGs fate, and mm-MPs caused severer risk due to their enrichment of ARGs. The results would promote the understanding of MPs real environmental behavior and influences.

Removal behavior and key drivers of antibiotic resistance genes in two full-scale leachate treatment plants

Leachate is a critical reservoir of antibiotic resistance genes (ARGs) and its proper treatment is closely related to human health and ecosystem safety. Here, we used high-throughput qPCR to explore the removal behavior of ARGs in two full-scale leachate treatment plants (LTPs) where biological treatment and membrane filtration processes were integrated. A total of 286 ARGs and 55 mobile genetic elements (MGEs) were detected, with aminoglycoside, multidrug and MLSB resistance genes being the most prevalent and abundant. Anaerobic digestion was found to be an important pretreatment process for leachate, while anoxic/aerobic tanks in membrane bioreactor (MBR) acted as incubators for ARGs due to their significant proliferation effect on ARGs. Integrated membrane filtration (UF-NF-RO) excelled in ARGs removal with absolute abundances reduced by 3 to 6 orders of magnitude, from about 10⁹ copies/mL in raw leachate to 10³-10⁵ copies/mL in effluents. Our results also showed that leachate treatment processes significantly altered the composition of ARGs and bacterial communities. Procrustes analysis and network analysis revealed strong associations between microbes and ARGs, with several hub genes and bacterial genera identified. Structural equation models (SEMs) indicated that bacterial composition, MGEs and basic water properties were the key drivers shaping ARGs dynamics in the raw leachate, biological system and filtration system, respectively. Notably, several pathogens (e.g., Klebsiella, Vibrio, Aeromonas) were closely correlated with ARGs in raw leachate and may amplify the dissemination risks of ARGs. Moreover, insertion sequences in biological systems would accelerate the horizontal gene transfer of ARGs. In short, this study provides new insights into the mechanisms of ARGs removal and dissemination behavior in industrial-scale LTPs.

Regionalization and Shaping Factors for Microbiomes and Core Resistomes in Atmospheric Particulate Matters

Antimicrobial resistance (AMR) seriously threatens public health by reducing antibiotic effectiveness in curing bacterial infections. Atmospheric particulate matter (APM) is a common environmental hazard that affects human health by causing various diseases and disseminating bacterial pathogenesis, of which pathogenic bacteria and AMR are essential parts. The properties of APM microbiomes and resistomes, along with their shaping factors and mutual relationships, need further examination. To address this, we analyzed APMs collected from 13 cities within four clusters (North and South China, Inner Mongolia, and Tibet). Significant regionalization was found for both the microbiomes (P < 0.001) and core resistomes (P < 0.001) for APMs, with statistical analyses showing significant differences in different regions. Principal coordinate analysis (PCoA) and accompanying ANOSIM analyses showed that microbiomes and core resistomes followed the same regional subclustering hierarchy patterns. This finding, together with response analysis of APM microbiomes and core resistomes to environmental parameters that showed similar response patterns, as well as Procrustes analysis (M² = 0.963, P < 0.05) between APM microbiomes and core resistomes, strongly suggested that APM microbiomes and core resistomes are correlated. Co-occurrence network analysis further revealed key taxa and antimicrobial resistance determinants in the interactions between APM microbiomes and core resistomes. Thus, it was concluded that APM microbiome and resistome compositions were highly regional, that environmental pollutants and APM levels impacted APM microbiomes and resistomes, and that microbiomes and resistomes in APMs are significantly correlated (P < 0.05). IMPORTANCE Bacteria associated with atmospheric particulate matter (APMs) can transmit over long distances. A large portion of these bacteria can potentially threaten human health. The antimicrobial resistance (AMR) of pathogenic bacteria carried by APMs prevents curing from infections. Therefore, both the pathogenic bacteria in APMs and their AMR are receiving more attention. The literature suggests a knowledge gap that exists for bacterial AMR and bacterial pathogenesis in APMs, including their distribution patterns, mutual relationships, and factors influencing their compositions. This work aimed to bridge this knowledge gap by studying APM samples collected from 13 cities. The results demonstrated that both bacteria and antibiotic resistance determinants were highly regional and that their composition patterns were significantly correlated, and influenced by the same group of environmental factors. This study thus determined the relationship between the two important aspects of bacterial pathogenesis in APMs and represents significant progress in understanding bacterial pathogenesis in APMs.

Vertical distribution of antibiotics and antibiotic resistance genes in a representative municipal solid waste landfill, China

The vertical distribution of sulfonamides (SAs), tetracyclines (TCs), macrolides (MLs), and their related antibiotic resistance genes (ARGs) were comprehensively investigated and characterized in a representative municipal solid waste (MSW) landfill in China. The total concentrations of target antibiotics in the MSW landfill were SAs > TCs > MLs. The abundances of mexF (10.78 ± 0.65 log₁₀copies/g) and sul genes (9.15 ± 0.54 log₁₀copies/g) were relatively high, while the tet genes (7.19 ± 0.77 log₁₀copies/g) were the lowest. Both the abundance of antibiotics and genes fluctuated with landfill depth, and the ARGs of the same antibiotics were consistent with depth change. Intl1 and sul genes (sul1, sul2) were tightly connected, and a close relationship also existed between tet genes (tetM, tetQ) and MLs resistance genes (ermB, mefA). High-throughput sequencing showed the dominant genera were Sporosarcina (38%) and Thiobacillus (17%) at sampling points A and C, while the microbial community varied with depth increase at point B were Brevundimonas (20%), Sporosarcina (20%), Pseudomonas (24%), Lysobacter (28%), and Thioalkalimicrobium (14%), respectively. Network analysis further visualized the relationship among antibiotics, genes, and microbial communities and the results indicated the non-random connection among them and the possible host of the target gene. Even at 12.0 m below the landfill surface, the pollution of antibiotics resistance was still serious, which posed difficulties for subsequent landfill remediation and pollution control.

Distribution Pattern and Influencing Factors of Heavy Metal Resistance Genes in the Yellow River Sediments of Henan Section

The transformation of heavy metal resistance genes (MRGs) in the environment has attracted increasing attention in recent years. However, few studies have reported the MRG content in the Yellow River, one of the main irrigation water sources in the North China Plain. In this study, we quantified MRG abundance by a metagenomic approach, and assessed the influence on MRGs of both bioavailable and total heavy metal (HM) content. The results indicate that Cu-resistant genes are the most common genes, and the prevalence of arsM needs more attention. Comamonadaceae is the dominant family in the Yellow River, and the presence of organic pollutants may contribute to the prevalence of Vicinamibacteraceae, Nocardioidaceae, and Flavobacteriacea. The results of the Mantel test and Spearman analysis indicate that both the bioavailable fractions and total content of HMs could have little influence on MRGs. Network analysis results indicate that some dominant bacteria could be the potential hosts of some prevalent MRGs, which may exert an adverse impact on human health.

The elimination of cell-associated and non-cell-associated antibiotic resistance genes during membrane filtration processes: A review

With increasing water reuse as a sustainable water management strategy, antibiotic resistance genes (ARGs) which have been identified as emerging contaminants in wastewater are attracting global attentions. Given that wastewater treatment plants are now well-established as a sink and source of ARGs in both cell-associated and non-cell-associated forms, a need is acknowledged to reduce their proliferation and protect public health. Due to their different characteristics, cell-associated and non-cell-associated ARGs may have distinct responses to membrane filtration processes which are widely used as advanced treatment to the secondary effluent. This review improves the understanding of the abundance of cell-associated and non-cell-associated ARGs in wastewaters and the secondary effluents and compares the elimination of ARGs in cell-associated and non-cell-associated forms by low-pressure and high-pressure membrane filtration processes. The former process reduces the concentration of cell-associated ARGs by more than 2-logs on average. An increase of the retention efficiency of non-cell-associated ARGs is observed with decreasing molecular weight cut-offs in ultrafiltration. The high-pressure membrane filtration (i.e., nanofiltration and reverse osmosis) can effectively eliminate both cell-associated and non-cell-associated ARGs, with averagely more than 4.6-log reduction. In general, the two forms of ARGs can be removed from water by the membrane filtration processes via the effects of size exclusion, adsorption, and electrostatic repulsion. The size and conformation of cell-associated and non-cell-associated ARGs, characteristics of membranes, coexisting substances, and biofilm formation influence ARG retention. Accumulation and potential proliferation of cell-associated and non-cell-associated ARGs in foulants and concentrate and corresponding control strategies warrant future research.

Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches

Driven by anthropogenic pressure, Antibiotic resistance genes (ARGs) could transfer from the environmental resistome into human commensals or even pathogens. The transport of ARGs through aquatic ecosystems is crucial and has attracted attention. Here, we employed metagenomic and binning to compare ARGs profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their hosts between pristine and anthropogenic influenced rivers and explore the ecological mechanisms underlying the dissemination of ARGs induced by anthropogenic activities. The significantly increased relative abundance of macrolide-lincosamide-streptogramins, vancomycin, β-lactam and sulfonamide resistance genes along the environmental gradient from pristine to polluted sediments implied that anthropogenic impact aided the emergence and dissemination of certain ARGs. At the lower reach of the Ba River, the higher ratios for contigs carrying more than one ARG suggested that anthropogenic pollution favored the co-occurrence of multiple ARGs. Anthropogenic pressures also increased the relative abundance of advantaged hosts, including Chloroflexi, Firmicutes and Euryarchaeota. At the lower reach of Ba River, Romboutsia timonensis carrying multiple ARGs and ICEs were successfully recovered, posing a serious threat to human health by affecting the metabolism of gut microbiomes. And Methanothrix soehngenii affiliated to archaea carrying multiple ARGs, MRGs and ICEs were also recovered from the lower Ba River. The partial least squares path modeling revealed that MGEs were the most predominant factors inducing the ARG profiles, and the antibiotic resistance could be enriched by co-transfer with MRGs. Furthermore, environmental factors could impact the ARG profiles indirectly by first influencing the ARGs' hosts.

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

In the One Health context, wastewater treatment plants (WWTPs) are central to safeguarding water resources. Nonetheless, many questions remain about their effectiveness in preventing antimicrobial resistance (AMR) dissemination. Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in intracellular DNA (iDNA) extracted from WWTP influents and effluents. The role of extracellular free DNA (exDNA) in wastewater is mostly overlooked. This study analyzed the transfer of ARGs and MGEs in a full-scale Nereda® reactor removing nutrients with aerobic granular sludge. We tracked the composition and fate of the iDNA and exDNA pools of influent, sludge, and effluent samples. Metagenomics was used to profile the microbiome, resistome, and mobilome signatures of iDNA and exDNA extracts. Selected ARGs and MGEs were analyzed by qPCR. From 2,840 ARGs identified, the genes arr-3 (2%), tetC (1.6%), sul1 (1.5%), oqxB (1.2%), and aph(3")-Ib (1.2%) were the most abundant among all sampling points and bioaggregates. Pseudomonas, Acinetobacter, Aeromonas, Acidovorax, Rhodoferax, and Streptomyces populations were the main potential hosts of ARGs in the sludge. In the effluent, 478 resistance determinants were detected, of which 89% were from exDNA potentially released by cell lysis during aeration in the reactor. MGEs and multiple ARGs were co-localized on the same extracellular genetic contigs. Total intracellular ARGs decreased 3-42% due to wastewater treatment. However, the ermB and sul1 genes increased by 2 and 1 log gene copies mL^-1, respectively, in exDNA from influent to effluent. The exDNA fractions need to be considered in AMR surveillance, risk assessment, and mitigation strategies.

Drivers of microbial beta-diversity in wastewater treatment plants in China

As one of the most well-documented biogeographic patterns, the distance-decay relationship provides insights into the underlying mechanisms driving biodiversity distribution. Although wastewater treatment plants (WWTPs) are well-controlled engineered ecosystems, this pattern has been seen among microbial communities in activated sludge (AS). However, little is known about the relative importance of environmental heterogeneity and dispersal limitation in shaping AS microbial community across China; especially they are related to spatial scale and organism types. Here, we assessed the distance-decay relationship based on different spatial scales and microbial phylogenetic groups by analyzing 132 activated sludge (AS) samples across China comprising 3,379,200 16S rRNA sequences. Our results indicated that the drivers of distance-decay pattern in China were scale-dependent. Microbial biogeographic patterns in WWTPs were mainly driven by dispersal limitation at both local and national scales. In contrast, conductivity, SRT, and pH played dominant roles in shaping AS microbial community compositions at the regional scale. Turnover rates and the drivers of beta-diversity also varied with microorganism populations. Moreover, a quantitative relationship between dispersal limitation ratio and AS microbial turnover rate was generated. Collectively, these results highlighted the importance of considering multiple spatial scales and micro-organism types for understanding microbial biogeography in WWTPs and provided new insights into predicting variations in AS community structure in response to environmental disturbance.

Risk of horizontal transfer of intracellular, extracellular, and bacteriophage antibiotic resistance genes during anaerobic digestion of cow manure

The fate of intracellular antibiotic resistance genes (iARGs), extracellular ARGs (eARGs) and bacteriophage ARGs (bARGs) during anaerobic digestion (AD) of cow manure is unclear. Thus, the characteristics of iARGs, eARGs and bARGs during mesophilic AD (MAD) and thermophilic AD (TAD) of cow manure were investigated. The absolute abundances of iARGs decreased by 69.82% after TAD. After MAD and TAD, the total absolute abundances of eARGs increased by 63.5 times and 67.6 times, respectively, whereas those of the bARGs increased by 47.60% and 59.22%. eARGs were mainly derived from the non-specific lysis of Firmicutes, Bacteroidetes, while bacteriophages had a wide range of hosts. The variations in iARGs, eARGs and bARGs were affected by the microbial hosts but also directly driven by physicochemical factors (e.g., pH). Overall, the findings of this study revealed that there may be a risk of eARGs and bARGs disseminating during the AD of cow manure.

Liming mitigates the spread of antibiotic resistance genes in an acid black soil

The threat of antibiotic resistance genes (ARGs) caused by animal manure application to human health has been the focus of attention in agriculture. Applying lime to acid soil for the amelioration of soil acidity is a prevailing agricultural practice. However, the role of lime on the spread of antibiotic resistome from soil to plant is unknown. In this study, a pot experiment of lettuce was established in the acid black soil with lime addition at the rate (w/w) of 0%, 0.08%, 0.16%, and 0.32% of the total soil mass to explore the transmission of ARGs introduced by the fresh poultry manure in the soil-plant system. The bulk and rhizosphere soils as well as the leaf samples were collected after lettuce was cultivated for 60 days, the bacterial community and antibiotic resistome in these samples were determined by using Illumina sequencing and high-throughput quantitative PCR (HT-qPCR) methods, respectively. Results showed that lime application decreased the number and abundance of ARGs and slowed down the spread of manure-derived ARGs in the soil-plant system. The ARGs and bacterial community composition were significantly varied among bulk soils, rhizosphere soils and leaf endophyte, and also influenced by lime within the same sampling types. The structural equation model further demonstrated that the lime addition had a negative effect on ARG diversity, which was also indirectly regulated by bacterial community diversity. These findings suggest that lime addition can alleviate the level and dissemination of ARGs in soils and provide a potential measure to control the spread of ARGs derived from animal manure.

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River

Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.

Impacts of combined pollution under gradient increasing and gradient decreasing exposure modes on activated sludge: Microbial communities and antibiotic resistance genes

The responses of microbial communities and antibiotic resistance genes (ARGs) to azithromycin and copper combined pollution under gradient increasing (from 0.5 to 10 mg/L) and decreasing exposure (from 10 to 0.5 mg/L) modes were investigated. Nitrification was inhibited more obviously under gradient increasing exposure mode. Responses of archaeal community and function structure were more obvious than bacteria under both exposure modes. The dominant bacterial and archaeal compositions (Hyphomicrobium, Euryarchaeota, etc.) were affected by two exposure modes, except some rare archaea (Methanoregula and Methanosarcina). There were more positive correlations between bacteria and archaea, and Nitrospira was keystone genus. Ammonia-oxidizing archaea (0.37-3.06%) and complete ammonia oxidizers (Nitrospira_ENR4) were enriched, and Nitrososphaera_viennensis was closely related to denitrifying genes (napA/B, nosZ, etc.). 50 ARG subtypes were detected and specific ARG subtypes (aac, ImrA, etc.) proliferated in two exposure modes. Bacteria and archaea were common hosts for 24 ARGs and contributed to their shifts.

Fate, mobility, and pathogenicity of drinking water treatment plant resistomes deciphered by metagenomic assembly and network analyses

Antibiotic resistance genes (ARGs) have been regarded as emerging environmental contaminants. The profile of resistome (collection of all ARGs) in drinking water and its fate during drinking water treatment remain unclear. This study applied metagenomic assembly combined with network analysis to decipher the profile, mobility, host, and pathogenicity of resistomes in two full-scale drinking water treatment plants (DWTPs), each applying conventional treatment and advanced treatment of ozonation followed by biological activated carbon filtration. In source waters and effluents of each treatment process collected from both DWTPs, 215 ARGs belonging to 20 types were detected with total concentration ranging from 6.30 ± 1.83 to 5.20 ± 0.26 × 10⁴ copies/mL. Both the conventional and advanced DWTPs were revealed to effectively reduce the concentration of total ARGs, with the average removal efficiency of 3.61-log₁₀ and 2.21-log₁₀, respectively. Multiple statistical analyses (including network analysis) indicated drinking water resistome correlated tightly with mobile gene elements (MGEs) and bacterial community, with the latter acting as the premier driver of resistome alteration in DWTPs. Further analysis of ARG-carrying contigs (ACCs) assembled from drinking water metagenomes (i) tracked down potential bacterial hosts of ARGs (e.g., Proteobacteria phylum as the major pool of resistome), (ii) provided co-localization information of ARGs and MGEs (e.g., MacB-E7196 plasmid1), and (iii) identified ARG-carrying human pathogens (e.g., Enterococcus faecium and Ralstonia pickettii). This work firstly determined the concentration, mobility incidence, and pathogenicity incidence of DWTP resistomes, based on which the actual health risk regarding antibiotic resistance could be quantitatively assessed in further study, providing a useful direction for decision-making concerning the risk control of ARGs in DWTPs.

Diversity, abundance and expression of the antibiotic resistance genes in a Chinese landfill: Effect of deposit age

Landfills are the hotspots for the occurrence of antibiotic resistance genes (ARGs) in the environment. However, limited information is available on the profile of ARGs in response to the varying age of refuse in landfills. In this study, the diversity, abundance and expression of ARGs in a Chinese landfill were assessed by high-throughput quantitative PCR. A total of 154 ARGs were detected and 66% of them were transcriptionally active. The total abundance of ARG transcripts was one magnitude lower than that of ARGs. The ermT-01, tetX, sul2, aadA-02 and aadA2-03 genes were found to be the most abundant ARGs (ARG transcripts) and their sum abundance showed a linear relation with the total abundance of ARGs (ARG transcripts). The total abundance of ARGs (ARG transcripts) in young refuse was significantly higher than that in old refuse (p < 0.01) and the profile of ARGs (ARG transcripts) between the old and young refuse was distinct as revealed by the principal coordinates analysis. The variation partitioning analysis showed heavy metals (mainly Cr and Zn) were the major drivers that affect the profile of ARGs (ARG transcripts). These findings provided new insights into the ARGs in landfills and indicated their potential threats should not be neglected.

The Effect of the Effluent from a Small-Scale Conventional Wastewater Treatment Plant Treating Municipal Wastewater on the Composition and Abundance of the Microbial Community, Antibiotic Resistome, and Pathogens in the Sediment and Water of a Receiving Stream

The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of the microbial community as well as the antibiotic resistome and pathogens in the sediment and water of the receiving stream and river was studied using metagenome sequencing and a quantitative approach. Elevated Bacteroidetes proportions in the prokaryotic community, heightened sulfonamide and aminoglycoside resistance determinants proportions, and an increase of up to three orders of magnitude of sul1–sul2–aadA–blaOXA2 gene cluster abundances were recorded in stream water and sediments 0.3 km downstream of a WWTP discharge point. Further downstream, a gradual recovery of affected microbial communities along a distance gradient from WWTP was recorded, culminating in the mostly comparable state of river water and sediment parameters 3.7 km downstream of WWTP and stream water and sediments upstream of the WWTP discharge point. Archaea, especially Methanosarcina, Methanothrix, and Methanoregula, formed a substantial proportion of the microbial community of WWTP effluent as well as receiving stream water and sediment, and were linked to the spread of ARGs. Opportunistic environmental-origin pathogens were predominant in WWTP effluent and receiving stream bacterial communities, with Citrobacter freundii proportion being especially elevated in the close vicinity downstream of the WWTP discharge point.

Potential of coagulation to remove particle-associated and free-living antibiotic resistome from wastewater

Coagulation has been accepted as a cost-effective and environmental-friendly method to remove pollutants. In our recent work, two coagulants of polyaluminum chloride (PAC) and polyaluminum ferric chloride (PAFC) with dosage gradients, and one coagulant aid of anionic polyacrylamide (PAM) were used to investigate their potential to remove particle-associated (PA) and free-living (FL) ARGs and MGEs detected by high throughput qPCR (HT-qPCR) method. The results indicated that the maximum removal efficiencies of PA- and FL-ARGs (4.67- and 3.18-logs) were obtained at the PAFC dosage of 50.0 mg/L. Excessive PAFC dosage can hamper the removal of size-fractionated ARGs. As PAC aid, anionic PAM (1.0 mg/L) had limited effects to promote the removal of PA-ARG, while FL-ARG removal was enhanced by 0.34 log at the PAC dosage of 50.0 mg/L. The fitted curves suggested that the optimal chemical dosages of PAC, PAFC and PAC coupled with PAM in the removal of total ARGs and MGEs were 40.5, 64.7 and 50.0 mg/L, respectively. In addition, we found that much more coagulants were needed to remove FL-ARGs compared to that of PA-ARGs. The removal efficiencies of size-fractionated ARGs by flocculation can be affected by coagulant type, dosage, coagulant aid, Zeta potential and microorganism lifestyle (PA or FL).