New insights into antibiotic resistome in drinking water and management perspectives: A metagenomic based study of small-sized microbes

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

Antibiotic resistance genes risks in relation to host pathogenicity and mobility in a typical hospital wastewater treatment process

Hospital wastewaters (HWWs) serve as critical reservoirs for disseminating antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, the dynamics and noteworthy shifts of ARGs and their associated pathogenicity, mobility, and resistome risks during HWWs treatment processes remain poorly understood. Utilizing metagenomic sequencing and assembly, we identified 817 ARG subtypes conferring resistance to 20 classes of antibiotics across 18 HWW samples from influent to effluent. Genes encoding resistance to multidrug, aminoglycoside and beta_lactam were the most prevalent ARG types, reflecting patterns observed in clinical settings. On-site treatment efforts decreased the relative abundance of ARGs by 77.4% from influent to secondary sedimentation, whereas chlorine disinfection significantly increased their abundance in the final effluent. Deterministic processes primarily drove the taxonomic assembly, with Proteobacteria being the most abundant phylum and serving as the primary host for 15 ARG types. Contig-based analysis further revealed 114 pathogenic ARB, with Escherichia coli, Pseudomonas alcaligenes, and Pseudomonas aeruginosa exhibiting multidrug-resistant. The contributions of host bacteria and pathogenic ARB varied throughout wastewater treatment. In addition, 7.10%-31.0 % ARGs were flanked by mobile genetic elements (MGEs), predominantly mediated by transposase (74.1%). Notably, tnpA exhibited the highest potential for ARG dissemination, frequently co-occurring with beta-lactam resistance genes (35.2%). Considering ARG profiles, pathogenic hosts, and transferability, raw influent exhibited the highest antibiotic resistome risk index (ARRI), followed by the final effluent. Chlorine disinfection exacerbated resistome risks by inducing potential pathogenic ARB and mobile ARGs, posing threats to the receiving environment. This study delineates ARG occurrence patterns, highlights mechanisms of ARG carriage and horizontal gene transfer, and provides insights for assessing resistance risks and prioritizing interventions in clinical settings.

Effects of wastewater treatment plant effluent on microbial risks of pathogens and their antibiotic resistance in the receiving river

The increase in effluent discharge from wastewater treatment plants (WWTPs) into urban rivers has raised concerns about the potential effects on pathogen risks. This study utilized metagenomic sequencing combined with flow cytometry to analyze pathogen concentrations and antibiotic resistance in a typical effluent-receiving river. Quantitative microbial risk assessment (QMRA) was employed to assess the microbial risks of pathogens. The results indicated obvious spatial-temporal differences (i.e., summer vs. winter and effluent vs. river) in microbial composition. Microcystis emerged as a crucial species contributing to these variations. Pathogen concentrations were found to be higher in the river than in the effluent, with the winter exhibiting higher concentrations compared to the summer. The effluent discharge slightly increased the pathogen concentrations in the river in summer but dramatically reduced them in winter. The combined effects of cyanobacterial bloom and high temperature were considered key factors suppressing pathogen concentrations in summer. Moreover, the prevalence of antibiotic resistance of pathogens in the river was inferior to that in the effluent, with higher levels in winter than in summer. Three high-concentration pathogens (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were selected for QMRA. The results showed that the risks of pathogens exceeded the recommended threshold value. Escherichia coli posed the highest risks. And the fishing scenario posed significantly higher risks than the walking scenario. Importantly, the effluent discharge helped reduce the microbial risks in the receiving river in winter. The study contributes to the management and decision-making regarding microbial risks in the effluent-receiving river.

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.

Potential environmental risks of field bio/non-degradable microplastic from mulching residues in farmland: Evidence from metagenomic analysis of plastisphere

The plastisphere may act as reservoir of antibiotic resistome, accelerating global antimicrobial resistance dissemination. However, the environmental risks in the plastisphere of field microplastics (MPs) in farmland remain largely unknown. Here, antibiotic resistance genes (ARGs) and virulence factors (VFs) on polyethylene microplastics (PE-MPs) and polybutylene adipate terephthalate and polylactic acid microplastics (PBAT/PLA-MPs) from residues were investigated using metagenomic analysis. The results suggested that the profiles of ARG and VF in the plastisphere of PBAT/PLA-MPs had greater number of detected genes with statistically higher values of diversity and abundance than soil and PE-MP. Procrustes analysis indicated a good fitting correlation between ARG/VF profiles and bacterial community composition. Actinobacteria was the major host for tetracycline and glycopeptide resistance genes in the soil and PE-MP plastisphere, whereas the primary host for multidrug resistance genes changed to Proteobacteria in PBAT/PLA-MP plastisphere. Besides, three human pathogens, Sphingomonas paucimobilis, Lactobacillus plantarum and Pseudomonas aeruginosa were identified in the plastisphere. The PE-MP plastisphere exhibited a higher transfer potential of ARGs than PBAT/PLA-MP plastisphere. This work enhances our knowledge of potential environmental risks posed by microplastic in farmland and provides valuable insights for risk assessment and management of agricultural mulching applications.

Free-living lifestyle preferences drive the antibiotic resistance promotion during drinking water chlorination

The risk associated with antibiotic resistance genes (ARGs) in size-fractionated bacterial community during drinking water chlorination remains unclear, and is of paramount importance for risk mitigation through process selection and optimization. This study employed metagenomic approaches to reveal the alterations of ARGs, their potential functions and hosts within the free-living and particle-associated fractions. The total relative abundance of ARGs, mobile genetic elements (MGEs), and virulence factor genes (VFGs) significantly increased in the free-living fraction after chlorination. The contribution of the free-living fraction to the ARG relative abundance rose from 16.40 ± 1.31 % to 93.62 ± 0.47 % after chlorination. Multidrug resistance genes (e.g. mexF and mexW) were major contributors, and their co-occurrence with MGEs in the free-living fraction was enhanced after chlorination. Considering multiple perspectives, including presence, mobility, and pathogenicity, chlorination led to a significant risk of the antibiotic resistome in the free-living fraction. Moreover, potential functions of ARGs, such as cell wall/membrane/envelope biogenesis, defense mechanisms, and transcription in the free-living fraction, were intensified following chlorination. Potential pathogens, including Pseudomonas aeruginosa, Pseudomonas alcaligenes, and Acinetobacter junii, were identified as the predominant hosts of multidrug resistance genes, with their increased abundances primarily contributing to the rise of the corresponding ARGs. Overall, alterations of hosts as well as enhancing mobility and biological functions could collectively aid the proliferation and spread of ARGs in the free-living fraction after chlorination. This study provides novel insights into antibiotic resistance evolution in size-fractionated bacteria community and offers a management strategy for microbiological safety in drinking water.

Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly

Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.

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.

Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective

Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.

Parabens as environmental contaminants of aquatic systems affecting water quality and microbial dynamics

Among different pollutants of emerging concern, parabens have gained rising interest due to their widespread detection in water sources worldwide. This occurs because parabens are used in personal care products, pharmaceuticals, and food, in which residues are generated and released into aquatic environments. The regulation of the use of parabens varies across different geographic regions, resulting in diverse concentrations observed globally. Concentrations of parabens exceeding 100 μg/L have been found in wastewater treatment plants and surface waters while drinking water (DW) sources typically exhibit concentrations below 6 μg/L. Despite their low levels, the presence of parabens in DW is a potential exposure route for humans, raising concerns for both human health and environmental microbiota. Although a few studies have reported alterations in the functions and characteristics of microbial communities following exposure to emerging contaminants, the impact of the exposure to parabens by microbial communities, particularly biofilm colonizers, remains largely understudied. This review gathers the most recent information on the occurrence of parabens in water sources, as well as their effects on human health and aquatic organisms. The interactions of parabens with microbial communities are reviewed for the first time, filling the knowledge gaps on the effects of paraben exposure on microbial ecosystems and their impact on disinfection tolerance and antimicrobial resistance, with potential implications for public health.

Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement

The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.

Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater

Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.

Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking

Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10-4 to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.

Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions

Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.

Distribution and relationship of antibiotics, heavy metals and resistance genes in the upstream of Hanjiang River Basin in Shiyan, China

The upstream basin of Hanjiang River is an important water source for the middle route of China's South-to-North Water Diversion Project. The quality of water and soil in the Hanjiang River have enormous biological and environmental impacts, and resistant genetic contamination has emerged, but only few studies are concerned the correlation between heavy metals and metal resistance genes (MRGs). In this study, 8 antibiotics and 19 heavy metals were analyzed, the results showed that the highest antibiotic content was tetracycline, with mean concentrations of 43.201 µg/kg and 0.022 µg/L. Mn was the highest heavy metal in soil with a content of 1408.284 µg/kg, and in water was Zn with a content of 10.611 µg/L. We found that the most abundant antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the study area were bacA and arsT genes, coding for resistance mechanisms to bacitracin and arsenic, respectively. The data showed that heavy metals had a greater impact on antibiotic resistance genes than antibiotics, and the correlation between resistance genes was significantly positive. This work expands our understanding of the correlations of antibiotics, heavy metals, and resistance genes in the Hanjiang River, indicating that more attention should be paid to the effects of resistance genes and the quality of water.

Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly

Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.

Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses

The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.

Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial community and antibiotic resistome varied with sampling season and site. Temperature, ammonia, chlorite and total plate count (TPC) drove the variations of microbial community structure. Moreover, environmental parameters (total organic carbon (TOC), chlorite, TPC and hardness) shifted antibiotic resistome. ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn, which might be attributed to detached pipe biofilm. In particular, ARG-bacitracin and plasmid were the predominant ARG and MGE, respectively. ARG hosts changed with season and site and were more diverse in summer and autumn. In winter and spring, Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community. In addition, in summer and autumn, high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone (0.4 km from the water treatment plant). Compared with MGEs, microbial community had a greater contribution to the variation of antibiotic resistome. This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.

Insight into the dynamics of drinking water resistome in China

Antibiotic resistance (AR) is a serious environmental hazard of the current age. Antibiotic resistance genes (ARGs) are the fundamental entities that spread AR in the environment. ARGs are likely to be transferred from the non-pathogenic to pathogenic microbes that might ultimately be responsible for the AR in humans and other organisms. Drinking water (DW) is the primary interaction route between ARGs and humans. Being the highest producer and consumer of antibiotics China poses a potential threat to developing superbugs and ARGs dissemination. Herein, we comprehensively seek to review the ARGs from dominant DW sources in China. Furthermore, the origin and influencing factors of the ARGs to the DW in China have been evaluated. Commonly used methods, both classical and modern, are being compiled. In addition, the risk posed and mitigation strategies of DW ARGs in China have been outlined. Overall, we believe this review would contribute to the assessment of ARGs in DW of China and their dissemination to humans and other animals and ultimately help the policymakers and scientists in the field to counteract this problem on an emergency basis.

Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes

The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members' presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types.

Multi-omics methods reveal that putrescine and cadaverine cause different degrees of enrichment of high-risk resistomes and opportunistic pathogens in the water and sediment of the Yellow River

Contamination of antibiotic resistomes due to animal carcass decay has become a serious environmental concern. However, the relationship between main metabolite compounds of corpse decomposition (i.e., putrescine and cadaverine) and antibiotic resistomes remains unclear. To tackle this issue, the response of antibiotic resistance genes (ARGs) and microbiome in aquatic environment to excess putrescine, cadaverine and a mixture of both based on laboratory simulation experiment was investigated by high-throughput quantitative PCR and amplicon sequencing methods. Our results showed putrescine and cadaverine led to the increasing of TC (total carbon) and TN (total nitrogen) both in water and sediment. Under the exposure of putrescine and cadaverine, the total abundance of mobile genetic elements (MGEs) and most ARGs in water was higher than in sediment. In particular, putrescine and cadaverine caused significantly different decreases in alpha diversity of microbial community in water and sediment compared with the control group. Microbial community structures both in water and sediment were also significantly affected by cadaverine and putrescine. Furthermore, putrescine and cadaverine led to different degrees of increases of high-risk ARGs (like mecA) and opportunistic pathogens (like Delftia) in sediment, promoting the prevalence of antibiotic resistant bacteria. In conclusion, our findings revealed the influences of main metabolites of carcass decay on microbiome and resistomes, providing references for risk assessment and pollution management.

Lightning-Rod Effect on Nanowire Tips Reinforces Electroporation and Electrochemical Oxidation: An Efficient Strategy for Eliminating Intracellular Antibiotic Resistance Genes

Conventional oxidative disinfection methods are usually inefficient to eliminate intracellular antibiotic resistance genes (i-ARGs) due to competitive oxidation of cellular components of antibiotic-resistant bacteria (ARB), resulting in the ubiquitous occurrence of ARGs in drinking water systems. Herein, we developed the strategy of coupling electroporation and electrochemical oxidation on a Co₃O₄-nanowires-modified electrode to destroy the multiresistant Escherichia coli cells and promote subsequent i-ARG (bla_TEM-1 and aac(3)-II) degradation. The lightning-rod effect over nanowire tips can form finite regions with a locally enhanced electric field and highly concentrated charge density, in turn facilitating the electroporation for ARB cell damage and electrochemical reactivity for reactive chlorine/oxygen species generation. Characterization of the ARB membrane integrity and morphology revealed that electroporation-induced cell pores were further enlarged by the oxidation of reactive species, resulting in i-ARG removal at lower applied voltages and with 6-9 times lower energy consumption than the conventional electrochemical oxidation approach with a Co₃O₄-film-modified electrode. The satisfactory application and effective inhibition of horizontal gene transfer in tap water further demonstrated the great potential of our strategy in the control of the ARG dissemination risk in drinking water systems.

Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water

Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.

The persistent, bioaccumulative, toxic, and resistance (PBTR) risk assessment framework of antibiotics in the drinking water sources

Antibiotics are emerging pollutants largely considered to have a lower risk based on persistent, bioaccumulative, toxic (PBT) risk assessments. However, an increasing number of studies have illustrated that antibiotics are responsible for the global increase in antimicrobial resistance (AMR), which suggests that the risk of antibiotics has been largely underestimated by using PBT risk assessment. Here, we designed an integrated innovation risk assessment framework of persistent, bioaccumulative, toxic, and resistance (PBTR) that accounts for antibiotic resistance to better represent the antibiotic environmental risk. This novel antibiotic risk assessment framework was further verified via application to 39 target antibiotics in the 23 drinking water sources of the lower Yangtze River (LYR), China, during the normal and flood seasons. In contrast with the PBT assessment, single toxicity assessment and single resistance assessment, in the PBTR assessment, 7 of 39 target antibiotics with bacterial insensitivity were observed to represent a more prominent risk, as were the sites sampled during the flood season with low concentrations but high pollution loads, which confirmed that the sensitivity of PBTR risk assessment was instructive. The PBTR risk assessment for the screened priority antibiotics contributes not only representative data but also an innovative approach for identifying resistance risks. Using the positive matrix factorization (PMF) model, the sources of priority antibiotics can be predicted and thus supported the corresponding policy. Overall, this study first constructed a PBTR risk assessment framework, then applied it to facilitate the accurate management of antibiotic pollution at the basin level.

Industrial effluents boosted antibiotic resistome risk in coastal environments

Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.

Airborne bacterial communities in the poultry farm and their relevance with environmental factors and antibiotic resistance genes

The accelerating occurrence and environmental dissemination of bacteria, gas pollutants and antibiotic resistance genes (ARGs) in aerosols of poultry farms have become emerging environmental issues due to their potential threat to animals, workers, and the communities located near such farms. Here, aerosol samples were gathered from inside and outside of the chicken house in winter with a transportable high-flow bioaerosol sampler. Then, 16S rRNA gene amplicon sequencing was used to categorize the bacteria in air samples, and the abundance of 12 ARG subtypes was researched via the real-time quantitative polymerase chain reaction (qPCR). Results indicated that the bacterial richness and diversity and total absolute abundance of ARGs were similar in the bioaerosols from indoor and downwind site of the poultry farm. The zoonotic pathogens, Staphylococcus and Corynebacterium, were detected both inside and outside of the chicken house, and the four most abundant target genes were bla_TEM, tetQ, ermB and sul1 in aerosols. Moreover, the correlation between the bacterial communities and environmental factors, such as NH₃ and H₂S concentrations, wind speed, temperature and relative humidity, was analyzed. The result revealed that the indoor bacteria community was positively associated with temperature and concentrations of air pollutants (NH₃ and H₂S), and could spread from confinement buildings to the ambient atmosphere through wind. In addition, the network analysis result showed that the airborne bacteria might significantly contribute in shaping the ARGs' profiles in bioaerosol from inside and outside of the poultry house. Overall, our results revealed the airborne bacterial communities and their associated influencing factors in the micro-environment (inside of the chicken house and nearby the boundary of the farm), and brought a new perspective for studying the gas pollutants and bioaerosol from poultry farms in winter.

A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use

Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.

It’s a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality

Microbial communities interact with us and affect our health in ways that are only beginning to be understood. Microorganisms have been detected in every ecosystem on Earth, as well as in any built environment that has been investigated. Drinking water sources, drinking water treatment plants and distribution systems provide peculiar microbial ecological niches, dismantling the belief of the “biological simplicity” of drinking water. Nevertheless, drinking water microbiomes are understudied compared to other microbiomes. Recent DNA sequencing and meta-omics advancements allow a deeper understanding of drinking water microbiota. Thus, moving beyond the limits of day-to-day testing for specific pathogenic microbes, new approaches aim at predicting microbiome changes driven by disturbances at the macro-scale and overtime. This will foster an effective and proactive management of water sources, improving the drinking water supply system and the monitoring activities to lower public health risk. Here, we want to give a new angle on drinking water microbiome research. Starting from a selection of 231 scientific publications on this topic, we emphasize the value of biodiversity in drinking water ecosystems and how it can be related with industrialization. We then discuss how microbiome research can support sustainable drinking water management, encouraging collaborations across sectors and involving the society through responsible research and innovation.

Characteristics, Biodiversity, and Cultivation Strategy of Low Nucleic Acid Content Bacteria

Low nucleic acid content (LNA) bacteria are ubiquitous and estimated to constitute 20%–90% of the total bacterial community in marine and freshwater environment. LNA bacteria with unique physiological characteristics, including small cell size and small genomes, can pass through 0.45-μm filtration. The researchers came up with different terminologies for low nucleic acid content bacteria based on different research backgrounds, such as: filterable bacteria, oligotrophic bacteria, and low-DNA bacteria. LNA bacteria have an extremely high level of genetic diversity and play an important role in material circulation in oligotrophic environment. However, the majority of LNA bacteria in the environment remain uncultivated. Thus, an important challenge now is to isolate more LNA bacteria from oligotrophic environments and gain insights into their unique metabolic mechanisms and ecological functions. Here, we reviewed LNA bacteria in aquatic environments, focusing on their characteristics, community structure and diversity, functions, and cultivation strategies. Exciting future prospects for LNA bacteria are also discussed.

A review of the global climate change impacts, adaptation, and sustainable mitigation measures

Climate change is a long-lasting change in the weather arrays across tropics to polls. It is a global threat that has embarked on to put stress on various sectors. This study is aimed to conceptually engineer how climate variability is deteriorating the sustainability of diverse sectors worldwide. Specifically, the agricultural sector's vulnerability is a globally concerning scenario, as sufficient production and food supplies are threatened due to irreversible weather fluctuations. In turn, it is challenging the global feeding patterns, particularly in countries with agriculture as an integral part of their economy and total productivity. Climate change has also put the integrity and survival of many species at stake due to shifts in optimum temperature ranges, thereby accelerating biodiversity loss by progressively changing the ecosystem structures. Climate variations increase the likelihood of particular food and waterborne and vector-borne diseases, and a recent example is a coronavirus pandemic. Climate change also accelerates the enigma of antimicrobial resistance, another threat to human health due to the increasing incidence of resistant pathogenic infections. Besides, the global tourism industry is devastated as climate change impacts unfavorable tourism spots. The methodology investigates hypothetical scenarios of climate variability and attempts to describe the quality of evidence to facilitate readers' careful, critical engagement. Secondary data is used to identify sustainability issues such as environmental, social, and economic viability. To better understand the problem, gathered the information in this report from various media outlets, research agencies, policy papers, newspapers, and other sources. This review is a sectorial assessment of climate change mitigation and adaptation approaches worldwide in the aforementioned sectors and the associated economic costs. According to the findings, government involvement is necessary for the country's long-term development through strict accountability of resources and regulations implemented in the past to generate cutting-edge climate policy. Therefore, mitigating the impacts of climate change must be of the utmost importance, and hence, this global threat requires global commitment to address its dreadful implications to ensure global sustenance.

Metagenomic Analysis Reveals Changes in Bacterial Communities and Antibiotic Resistance Genes in an Eye Specialty Hospital and a General Hospital Before and After Wastewater Treatment

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in hospital wastewater poses a great threat to public health, and wastewater treatment plants (WWTPs) play an important role in reducing the levels of ARB and ARGs. In this study, high-throughput metagenomic sequencing was used to analyze the bacterial community composition and ARGs in two hospitals exposed to different antibiotic use conditions (an eye specialty hospital and a general hospital) before and after wastewater treatment. The results showed that there were various potential pathogenic bacteria in the hospital wastewater, and the abundance and diversity of the influent ARGs in the general hospital were higher than those in the eye hospital. The influent of the eye hospital was mainly composed of Thauera and Pseudomonas, and sul1 (sulfonamide) was the most abundant ARG. The influent of the general hospital contained mainly Aeromonas and Acinetobacter, and tet39 (tetracycline) was the most abundant ARG. Furthermore, co-occurrence network analysis showed that the main bacteria carrying ARGs in hospital wastewater varied with hospital type; the same bacteria in wastewater from different hospitals could carry different ARGs, and the same ARG could also be carried by different bacteria. The changes in the bacterial community and ARG abundance in the effluent from the two hospitals showed that the activated sludge treatment and the direct chlorination disinfection can effectively remove some bacteria and ARGs in wastewater but have limitations. The species diversity increased significantly after the activated sludge treatment, while the direct chlorination disinfection did not increase the diversity. The activated sludge treatment has a better effect on the elimination of ARGs than the direct chlorination disinfection. In summary, we investigated the differences in bacterial communities and ARGs in wastewater from two hospitals exposed to different antibiotic usage conditions, evaluated the effects of different wastewater treatment methods on the bacterial communities and ARGs in hospital wastewater, and recommended appropriate methods for certain clinical environments.

Antibiotic resistomes in water supply reservoirs sediments of central China: main biotic drivers and distribution pattern

Water supply reservoirs form one of the critical drinking water resources. Their water quality directly affects human health. However, reservoir sediments have not received adequate attention in antibiotic resistance genes (ARGs) dissemination, though they reflect long-term ARGs contamination of water supply reservoirs. Moreover, the physicochemical parameters in water supply reservoir sediments are generally better than those in the other media. Thus, the main ARGs biotic drivers of the media would demonstrate their unique characteristics. In this study, sediment samples were collected from 10 water supply reservoirs in central China, and the antibiotic resistomes were determined with the metagenomic method. As revealed from the results, 174 ARGs (18 ARG types) were detected in the reservoir sediment. Besides, multidrug-, sulfonamide-, and vancomycin-ARGs were the dominant ARGs in the sediment samples. The macrolide-resistant Microcystis was prevalent (100% detection frequency with 0.35% average percentage) in reservoir sediments and posed potential risks to human health. Furthermore, the results of the Mantel test and VPA demonstrated that mobile genetic elements (MGEs) were the more essential biotic drivers in ARG contents of reservoir sediments rather than the bacteria community.

Lilium spp., as unnoticed environmental vector, spreading OptrA-carrying Enterococcus spp

Flower is an essential element in the human lifestyle but its role in disseminating antimicrobial resistance (AMR) between the environment and humans is unclear. In this study, we screened fresh flowers (Lilium spp.) collected from planting bases, market and florists in Guangzhou China aiming to investigate the prevalence of AMR genes, particularly cfr, optrA and poxtA mediating resistance to linezolid, a first-line drug for the treatment of different Gram-positive bacterial infections. We found 223 Enterococcus isolates consisting of Enterococcus faecalis, Enterococcus faecium and Enterococcus mundtii, and >50% of these isolates exhibited multiple-drug resistance. Additionally, 31 optrA-positive Enterococcus including 22 E. faecalis and 9 E. mundtii strains were recovered, however cfr and poxtA were not detected. The 22 E. faecalis strains were belonged to 7 Multilocus sequence types in which ST202 and ST376 were predominant and 9 E. mundtii strains from the same plantation bases were divided into three PFGE groups. Genetically, the majority of optrA were located on the chromosome and shared similar insertion sites and transpositions mediated by Tn554 family members. Plasmid-bearing optrA were identified in 6 E. faecalis strains where IS1216 family played key roles in horizontal transfer of optrA. These findings emphasize that the prevalence of drug resistant Enterococcus in fresh flowers is a latent danger and increases the risk of AMR dissemination to humans from the environment.

The Presence of Opportunistic Premise Plumbing Pathogens in Residential Buildings: A Literature Review

Opportunistic premise plumbing pathogens (OPPP) are microorganisms that are native to the plumbing environment and that present an emerging infectious disease problem. They share characteristics, such as disinfectant resistance, thermal tolerance, and biofilm formation. The colonisation of domestic water systems presents an elevated health risk for immune-compromised individuals who receive healthcare at home. The literature that has identified the previously described OPPPs (Aeromonas spp., Acinetobacter spp., Helicobacter spp., Legionella spp., Methylobacterium spp., Mycobacteria spp., Pseudomonas spp., and Stenotrophomonas spp.) in residential drinking water systems were systematically reviewed. By applying the Preferred reporting items for systematic reviews and meta-analyses guidelines, 214 studies were identified from the Scopus and Web of Science databases, which included 30 clinical case investigations. Tap components and showerheads were the most frequently identified sources of OPPPs. Sixty-four of these studies detected additional clinically relevant pathogens that are not classified as OPPPs in these reservoirs. There was considerable variation in the detection methods, which included traditional culturing and molecular approaches. These identified studies demonstrate that the current drinking water treatment methods are ineffective against many waterborne pathogens. It is critical that, as at-home healthcare services continue to be promoted, we understand the emergent risks that are posed by OPPPs in residential drinking water. Future research is needed in order to provide consistent data on the prevalence of OPPPs in residential water, and on the incidence of waterborne homecare-associated infections. This will enable the identification of the contributing risk factors, and the development of effective controls.

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.

Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing

The contamination of antibiotic resistance genes (ARGs) may directly threaten human health. This study used a metagenomic approach to investigate the ARG profile in a drinking water treatment system (DWTS) in south China. In total, 317 ARG subtypes were detected; specifically, genes encoding bacitracin, multidrug, and sulfonamide were widely detected in the DWTS. Putative ARG hosts included Acidovorax (6.0%), Polynucleobacter (4.3%), Pseudomonas (3.4%), Escherichia (1.7%), and Klebsiella (1.5%) as the enriched biomarkers in the DWTS, which mainly carried bacitracin, beta-lactam, and aminoglycoside ARGs. From a further analysis of ARG-carrying contigs (ACCs), Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens among the 49 ACC pathogens in the DWTS. The metagenomic binning results demonstrated that 33 high-quality metagenome-assembled genomes (MAGs) were discovered in the DWTS; particularly, the MAG identified as S. maltophilia-like (bin.195) harbored the greatest number of ARG subtypes (n = 8), namely, multidrug (n = 6; smeD, semE, multidrug_transporter, mexE, semB, and smeC), beta-lactam (n = 1; metallo-beta-lactamase), and aminoglycoside [n = 1; aph(3’)-IIb]. The strong positive correlation between MGEs and ARG subtypes revealed a high ARG dissemination risk in the DWTS. Based on the pure-culture method, 93 isolates that belong to 30 genera were recovered from the DWTS. Specifically, multidrug-resistant pathogens and opportunistic pathogens such as P. aeruginosa, Bacillus cereus, and S. maltophilia were detected in the DWTS. These insights into the DWTS’s antibiotic resistome indicated the need for more comprehensive ARG monitoring and management in the DWTS. Furthermore, more effective disinfection methods need to be developed to remove ARGs in DWTSs, and these findings could assist governing bodies in the surveillance of antibiotic resistance in DWTSs.

One-step synthesis of natural montmorillonite/hematite composites with enhanced persulfate catalytic activity for sulfamethoxazole degradation: Efficiency, kinetics, and mechanism

Along with rapid development of sulfate radicals-based advanced oxidation process, efficient, alternatively eco-friendly and cost-effective catalyst is of uppermost priority. However, expensive chemicals are used as source of metal in most of these catalysts, and lose sight of the abundant natural mineral resources on immediate surroundings. In this work, montmorillonite and hematite, two of abundantly natural minerals were utilized to prepare a persulfate catalyst (TMH@M) for sulfamethoxazole (SMX) degradation. The results indicated more than 91% of SMX was removed within 60 min in TMH@M/PS system. The degradation efficiency of SMX of TMH@M/PS combined system was impacted by SMX concentration, PS dosage and natural organic matters, and can remain stable in a certain concentration of HA/chelating agent and a wide pH range (3.01-9.06). Radical scavenging and EPR tests demonstrated ¹O₂, OH, and SO₄^- were major reactive oxygen species in the TMH@M/PS system, while the latter seems more important for degradation of SMX. The results of SEM-EDS, XRD and XPS conformed that low valence iron species (Fe⁰, Fe²⁺ and Fe₃O₄) on TMH@M surface are the main driving force behind PS activation to generate reactive species. Furthermore, the iron species on TMH@M surface were transformed during reaction, that in favor of mitigating metal leaching. This work presented a method based on ubiquitous natural minerals to prepare catalyst with excellent PS activate performance for organic wastewater treatment implying a new strategy in minerals utilization deeply and a promisingly alternative process for organic wastewater treatment based on mineral materials.

Rapid absolute quantification of pathogens and ARGs by nanopore sequencing

Compositional nature of relative abundance data in the current standard microbiome studies limits microbial dynamics interpretations and cross-sample comparisons. Here, we demonstrate the first rapid (1-h sequencing) method coupling Nanopore metagenomic sequencing with cellular spike-in to facilitate the absolute quantification and removal assessment of pathogens and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Nanopore sequencing-based quantification results for both simple mock community and complex real environmental samples showed a high consistency with those from the widely-used Illumina and culture-based approaches. Implementing such method, we quantified 46 predominant putative pathogenic species, and 361 ARGs in three WWTP sample sets. Though high log removals of dominant pathogens (2.23 logs) and ARGs (1.98 logs) were achieved, complete removal of all pathogens and ARGs were not achieved. Noticeably, Mycobacterium spp., Clostridium_P perfringens, and Borrelia hermsii exhibited low removal, and 13 ARGs even increased in absolute abundance after the treatment. Our proposed approach manifested its profound ability in providing absolute quantitation information guiding wastewater-based epidemiological surveillance and quantitative risk assessment facilitating microbial hazards management.

A TbPO4-based capturer for environmental extracellular antibiotic genes by interrogating lanthanide phosphates nanoneedles

Accurate determination of antibiotic resistance genes (ARGs) in environmental DNA molecules (eDNA) is challenging owing to its low abundance in the aquatic environment. Here we report a facile and cost-efficient approach to extract trace amount of eDNAs in the aquatic environment using LnPO₄ nanomaterials. Among the nanomaterials, less crystalline TbPO₄ nanoneedles was identified as the most prominent candidate for long stranded DNA and short stranded DNA with adsorption efficiency above 97%. The adsorbed DNA was washed off from TbPO₄ nanoneedles by optimized eluant (85% PBS, 15% EtOH, 4 g/L glycine, pH 10.0) with an optimal DNA recovery of 78.83%. Our approach showed a comparable or better eDNA extraction efficiency than a commercial extraction method for different environmental samples, but 89% less cost. The high purity of the extracted eDNA was demonstrated by a high A_260/280 ratio. Using qPCR experiment, the occurrence of six common ARGs in the eDNA were detected with abundance ranging from 4.06 × 10³ to 3.51 × 10⁹ copies/L in river samples. This specific DNA capturer is valuable for the evaluation of spatial and temporal dynamic of ARGs pollution to provide insight into the potential risk with regard to the human health.

Association of cooking water with the health of middle-aged and elderly Chinese individuals: evidence from a national household longitudinal survey

Little evidence has demonstrated the association between health conditions and cooking water. The purpose of this study was to explore the relationship, using a representative sample of 10,531 subjects selected from the China Family Panel Study (CFPS). The usage rate of surface-exposed water showed a slight upward trend from 2010 to 2018. The adjusted odds ratio (OR) of chronic diseases with surface-exposed and well water was 1.140 (95% CI: 0.989-1.315) and 0.902 (95% CI: 0.839-0.969), respectively, with reference to tap/purified water. Surface-exposed water increased the likelihood of a worsening health change by 25.5% (OR: 1.255; 95% CI: 1.123-1.411), while well water was associated with poor self-rated health (OR: 1.169; 95% CI: 1.094-1.249). As such, surface-exposed water was associated with chronic diseases and worsening changes in health, and well water was negatively associated with chronic diseases. Although efforts to improve quality of drinking water have been made in China for decades, our conclusions reveal that water quality still remains a critical public livelihood issue among middle-aged and elderly populations. More in-depth research is required on whether the disinfection ingredients of tap water may increase the risk for chronic disease.

Estuarine salinity gradient governs sedimentary bacterial community but not antibiotic resistance gene profile

Antibiotic resistance gene (ARG) pollution in estuarine environment has drawn great attention, and it is not clear if the physical and chemical parameters such as salinity, total organic carbon, total nitrogen, total phosphorus and antibiotics affects the distribution of ARGs. Herein, we deciphered the ARG profiles and microbial community compositions in sediments from Jiulong River Estuary (JRE) and Min River Estuary (MRE) of China using high-throughput sequencing-based metagenomics analysis. Furthermore, we explored the influence of salinity on bacterial community and ARG profiles. The results showed that Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these two estuaries. The abundance of ARGs ranged from 1.05 × 10^-1 to 2.93 × 10^-1 copy of ARG per copy of 16S rRNA gene in all the sediment samples and the profiles of ARGs presented similar patterns in two estuaries. Multidrug resistance genes were the dominant ARG types in both estuaries, with an overall abundance of 2.39 × 10^-2-1.07 × 10^-1 copy of ARG per copy of 16S rRNA gene, followed by genes conferring resistance to bacitracin and macrolide-lincosamide-streptogramin. Salinity was an important influencing factor on the bacterial community but not on the ARG profiles. Instead, stochastic processes exerted the main influence on the distribution of ARGs. The comparison of ARG profiles among estuary sediments, marine sediments, and samples from anthropogenic pollution environments revealed remarkable similarity of ARG profiles between samples from estuary sediments and those from municipal wastewater treatment plants. These results suggested that the complex emission of anthropogenic pollution could cause the stochastic ecological pattern of ARGs.

Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off

Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR. In stage two, pathogens were isolated and genotyped with multi-locus sequence typing (MLST) or conventional PCR. Finally, virulence genes from metagenomic data were assessed for pathogenicity. Two regions (Donggang and Zhanjiang) with potential public health concerns were selected for evaluation, each of which comprised of one urban and one farming wastewater sampling location. Overall, metagenomic sequencing reflected the variation in the relative abundance of medically important bacteria. Over 90 bacterial pathogens were monitored in the metagenomic dataset, of which 56 species harbored virulence genes. In Donggang, a pathogenic Acinetobacter sp. reached high abundances in 2018 and 2020, whereas all pathogenic Vibrio spp. peaked in October 2019. In Zhanjiang, A. baumanni, and other Enterobacteriaceae species were abundantly present in 2019 and 2020, whereas Aeromonas and Vibrio spp. peaked in November-2017. Forty species were subsequently isolated and subtyped by MLST, half of which were prevalent genotypes in clinical data. Additionally, we identified the African Swine Fever Virus (ASFV) in water samples collected in 2017, ahead of the first reported ASFV outbreak in 2018 in China. RNA viruses like Hepatitis A virus (HAV) and Enterovirus 71 (EV71) were also detected, with concentrations peaking in April 2020 and April 2018, respectively. The dynamics of HAV and EV71 were consistent with local epidemic trends. Finally, based on the virulence gene profiles, our study identified the risk level in wastewater of two cities. This workflow illustrates the potential for an early warning of local epidemics, which helps to prioritize the preparedness for specific pathogens locally.

An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis

Wastewater treatment plants (WWTPs) are regarded as critical points in disseminating antibiotic resistance genes (ARGs). In particular, the discharging effluents from WWTPs generally bring downstream catchment areas exogenous ARGs and resistant bacteria. However, there lacks a sufficient assessment of the resistome and mobilome in effluents. In this study, a consecutive monthly sampling was conducted over 13 months in three Hong Kong (HK) WWTPs for metagenomic sequencing. Prevalence information of ARGs and mobile genetic elements (MGEs) was compared with counterparts in effluents from cities of North America, South America, Europe, and Asia. Moreover, a publicly accessible platform integrating the exposure ranking scheme, which was based on the global archive of ARG abundance, and a readily implementable online pipeline was developed to benefit communication in academia and government consultancy. Results demonstrated HK WWTPs were featured high ARG removal efficiency of 2.34-2.43 log reduction rate, and effluents were ranked in moderate levels of Level 2 and Level 3 in the exposure prioritizing scheme based on total ARG abundance. Moreover, absolute quantification of temporal variations of effluent resistome disclosed distinct changes over time among varied ARG types which were associated with prevalently used antibiotics, including quinolone and sulfonamide. This reinforces the need for real-time management of WWTP systems. Notably, ARGs of anthropogenic prevalence, high mobility, and potential pathogenicity were found to be present in HK effluents, drawing attention to the necessity for improved risk management. In addition, source tracking of effluent resistome and structural equation model analysis was conducted to explore the disparity in ARG abundance and diversity in different samples. The discovery of this study and the recommendation of a comprehensive exposure assessment will facilitate decision-making in resistome management in WWTPs to reduce the ARG and antibiotic resistant bacteria (ARB) contamination in the receiving environments.

Risk assessment of antibiotic resistance genes in the drinking water system

Antibiotic resistance genes (ARGs) are extensively detected in various environmental media, whose risk assessment in the drinking water systems has not been comprehensive. This study established a new risk assessment of ARGs in the drinking water systems, considering the chlorine-resistance ability, transferability, and ARGs harboring potential of pathogens. The risk of ARGs in a typical drinking water reservoir was also evaluated based on the detection of ARGs and antibiotic-resistant bacteria (ARB). Fourteen ARGs were detected with a relative concentration range of 10^-4-10^-3 (ARGs/16S rRNA gene). Five isolated ARB were identified as human opportunistic pathogens, one of which (Pseudomonas aeruginosa HLS-6, CCTCC AB 2017269) is resistant to hundreds of milligrams per liter levels of antibiotics and low-level chlorine. This result indicated that ARB tolerant to high-levels of antibiotics could be isolated from environments containing trace levels of antibiotics. Moreover, complete genome sequencing confirmed the inclusion of ARGs (sul1, aadA2) on the class I integron in HLS-6, indicating that the risk of ARGs in this drinking water reservoir could be classified as resistance risk ranking in drinking water system 1 (R³DW 1). The risk assessment of ARGs in this study provides a clear understanding of ARG risk in drinking water systems. The results reveal that the ARGs and ARB contamination of drinking water reservoirs pose significant challenges for drinking water treatment efficiency and affect drinking water safety.

Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria

Loss of basic utilities, such as drinking water and electricity distribution, were sustained for months in the aftermath of Hurricane Maria's (HM) landfall in Puerto Rico (PR) in September 2017. The goal of this study was to assess if there was deterioration in biological quality of drinking water due to these disruptions. This study characterized the microbial composition of drinking water following HM across nine drinking water systems (DWSs) in PR and utilized an extended temporal sampling campaign to determine if changes in the drinking water microbiome were indicative of HM associated disturbance followed by recovery. In addition to monitoring water chemistry, the samples were subjected to culture independent targeted and non-targeted microbial analysis including quantitative PCR (qPCR) and genome-resolved metagenomics. The qPCR results showed that residual disinfectant was the major driver of bacterial concentrations in tap water with marked decrease in concentrations from early to late sampling timepoints. While Mycobacterium avium and Pseudomonas aeruginosa were not detected in any sampling locations and timepoints, genetic material from Leptospira and Legionella pneumophila were transiently detected in a few sampling locations. The majority of metagenome assembled genomes (MAGs) recovered from these samples were not associated with pathogens and were consistent with bacterial community members routinely detected in DWSs. Further, whole metagenome-level comparisons between drinking water samples collected in this study with samples from other full-scale DWS indicated no significant deviation from expected community membership of the drinking water microbiome. Overall, our results suggest that disruptions due to HM did not result in significant and sustained deterioration of biological quality of drinking water at our study sites.

Burkholderiaceae and Multidrug Resistance Genes Are Key Players in Resistome Development in a Germfree Soil Model

Assembly of a resistome in parallel with the establishment of a microbial community is not well understood. Germfree models can reveal microbiota interactions and shed light on bacterial colonization and resistance development under antibiotic pressure. In this study, we exposed germfree soil (GS), GS with diluted nontreated soil (DS), and nontreated soil (NS) to various concentrations of tetracycline (TET) in a nongermfree environment for 10 weeks, followed by 2 weeks of exposure to water. High-throughput sequencing was used to profile bacterial communities and antibiotic resistance genes (ARGs) in the soils. The initial bacterial loads were found to shape the profiles of bacterial communities and the resistomes. GS and DS treated with TET and the same soils left untreated had similar profiles, whereas NS showed different profiles. Soils with the same initial bacterial loads had their profiles shifted by TET treatment. Multidrug resistance (MDR) genes were the most abundant ARG types in all soils, with multidrug efflux pump genes being the discriminatory ARGs in GS regardless of different TET treatments and in GS, DS, and NS after TET. Furthermore, MDR genes were significantly enriched by TET treatment. In contrast, tetracycline resistance genes were either absent or low in relative abundance. The family Burkholderiaceae was predominant in all soils (except in NS treated with water) and was positively selected for by TET treatment. Most importantly, Burkholderiaceae were the primary carrier of ARGs, including MDR genes. IMPORTANCE This is the first study to examine how resistomes develop and evolve using GS. GS can be used to study the colonization and establishment of bacterial communities under antibiotic selection. Surprisingly, MDR genes were the main ARGs detected in GS, and TET treatments did not positively select for specific tetracycline resistance genes. Additionally, Burkholderiaceae were the key bacterial hosts for MDR genes in the current GS model under the conditions investigated. These results show that the family Burkholderiaceae underpins the development of resistome and serves as a source of ARGs. The ease of establishment of Burkholderiaceae and MDR genes in soils has serious implications for human health, since these bacteria are versatile and ubiquitous in the environment.

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.

Water volume influences antibiotic resistomes and microbiomes during fish corpse decomposition

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.

Anthropogenic disturbances on antibiotic resistome along the Yarlung Tsangpo River on the Tibetan Plateau: Ecological dissemination mechanisms of antibiotic resistance genes to bacterial pathogens

Human activities can accelerate the antibiotic resistome prevalence and pose threats to ecological safety and public health globally. However, antibiotic resistance gene (ARG) mobility and dissemination into bacterial pathogens under anthropogenic disturbances are still poorly understood. Here, we used a metagenomic approach to profile the biogeography of ARGs and pathogenic antibiotic resistant bacteria (PARB) under anthropogenic disturbances along the Yarlung Tsangpo River. Results showed the ARGs was dominated by bacA gene along the Yarlung Tsangpo River on the Tibetan Plateau. The ARG composition was differently impacted by rapid urbanization and dam construction, which urbanization could promote ARGs resistant to sulfonamide and tetracycline, whereas dam construction could elevate the resistance to chloramphenicol and aminoglycoside. Land use pattern was identified as a critical factor influencing ARG composition under anthropogenic disturbances, as it could directly reflect the land degradation level and indicate the inputs of ARG-selective chemicals of different human activities. Moreover, despite of the lack of variation in ARG relative abundance, PARB were highly promoted by anthropogenic activities, indicating increasing ARG dissemination to pathogen. We found that human-impacted environments harbored high proportion of mobile genetic elements (MGEs), and the MGE carrying ARGs also increased under anthropogenic disturbances in the pathogenic hosts, which confirmed that anthropogenic activities could promote ARG horizontal gene transfer. Furthermore, anthropogenic activities could influence PARB assembly processes. Basically, stochastic processes dominated PARB assembly along the river, and with increasing level of anthropogenic activities, these processes shifted from undominated stochastic processes to dispersal limitation. In summary, this study provides useful strategies in watershed resistome management and reduction of ARG dissemination to pathogens, which should consider the mode and intensity of human activity and its potential influence on horizontal gene transfer and assembly processes.

Analysis of Antibiotic Resistance Genes, Environmental Factors, and Microbial Community From Aquaculture Farms in Five Provinces, China

The excessive use of antibiotics speeds up the dissemination and aggregation of antibiotic resistance genes (ARGs) in the environment. The ARGs have been regarded as a contaminant of serious environmental threats on a global scale. The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat bacterial infections; there is a universal concern about the environmental risk of ARGs in the aquaculture environment. In this study, a survey was conducted to evaluate the abundance and distributions of 10 ARGs, bacterial community, and environmental factors in sediment samples from aquatic farms distributed in Anhui (AP1, AP2, and AP3), Fujian (FP1, FP2, and FP3), Guangxi (GP1, GP2, and GP3), Hainan (HP1, HP2, and HP3), and Shaanxi (SP1, SP2, and SP3) Province in China. The results showed that the relative abundance of total ARGs was higher in AP1, AP2, AP3, FP3, GP3, HP1, HP2, and HP3 than that in FP1, FP2, GP1, GP2, SP1, SP2, and SP3. The sul1 and tetW genes of all sediment samples had the highest abundance. The class 1 integron (intl1) was detected in all samples, and the result of Pearson correlation analysis showed that the intl1 has a positive correlation with the sul1, sul2, sul3, bla_OXA, qnrS, tetM, tetQ, and tetW genes. Correlation analysis of the bacterial community diversity and environmental factors showed that the Ca²⁺ concentration has a negative correlation with richness and diversity of the bacterial community in these samples. Of the identified bacterial community, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the predominant phyla in these samples. Redundancy analysis showed that environmental factors (TN, TP, Cl^–, and Ca²⁺) have a positive correlation with the bacterial community (AP1, GP1, GP2, GP3, SP1, SP2, and SP3), and the abundance of ARGs (sul1, tetW, qnrS, and intl1) has a positive correlation with the bacterial community (AP2, AP3, HP1, HP2, and HP3). Based on the network analysis, the ARGs (sul1, sul2, bla_CMY, bla_OXA, qnrS, tetW, tetQ, tetM, and intl1) were found to co-occur with bacterial taxa from the phyla Chloroflexi, Euryarchaeota, Firmicutes, Halobacterota, and Proteobacteria. In conclusion, this study provides an important reference for understanding the environmental risk associated with aquaculture activities in China.