Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system

Nature-based bioreactors: Tackling antibiotic resistance in urban wastewater treatment

The overuse and misuse of antibiotics have accelerated the selection of antibiotic-resistant bacteria, significantly impacting human, animal, and environmental health. As aquatic environments are vulnerable to antibiotic resistance, suitable management practices should be adopted to tackle this phenomenon. Here we show an effective, nature-based solution for reducing antibiotic resistance from actual wastewater. We utilize a bioreactor that relies on benthic (biofilms) and planktonic microbial communities to treat secondary effluent from a small urban wastewater treatment plant (<10,000 population equivalent). This treated effluent is eventually released into the local aquatic ecosystem. We observe high removal efficiency for genes that provide resistance to commonly used antibiotic families, as well as for mobile genetic elements that could potentially aid in their spread. Importantly, we notice a buildup of sulfonamide (sul1 and sul2) and tetracycline (tet(C), tet(G), and tetR) resistance genes specifically in biofilms. This advancement marks the initial step in considering this bioreactor as a nature-based, cost-effective tertiary treatment option for small UWWTPs facing antibiotic resistance challenges.

Novel visible-light activated photocatalytic ultrafiltration membrane for simultaneous separation and degradation of emerging contaminants

Emerging contaminants (ECs) in secondary effluent of wastewater treatment plants (WWTPs) have received increasing attention due to their adverse effects on aquatic ecosystems and human health. Herein, visible-light responsive photocatalyst TM (TiO2 @NH2-MIL-101(Fe)) and resultant photocatalytic ultrafiltration (PUF, PVDF/TM) membrane were prepared to remove 32 typical compounds of antibiotics, 296 compounds of antibiotic resistance genes (ARGs), and their corresponding bacterial hosts. The construction of heterojunction photocatalyst promoted the electron transfer from NH2-MIL-101(Fe) to TiO2 and the formation of N-TiO2, enhancing visible-light (λ ≥ 420 nm) photocatalytic activity. With highly-hydrophilic surface and delicately-regulated pore structure, the initial water permeance of optimal PUF membrane significantly increased to 3912.2 L/m2/h at 1.0 bar. Meanwhile, membrane retention (via adsorption, electrostatic interaction, and steric hindrance) was improved due to the narrowed pore size, highly-negative surface charge and abundant functional groups. Additionally, hydroxyl radical (•OH) was the dominant active reactive oxygen species (ROS) for ECs degradation, and the narrowed pore structure could serve as microreactors to increase ROS concentration and reduce migration distance. Consequently, the removal efficiencies of antibiotics, bacteria and ARGs were 86.5 %, 91.4 % and 91.8 %, respectively. Overall, this novel visible-light-activated PUF membrane expands membrane application, and has great potential in ECs treatment.

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

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

Body size: A hidden trait of the organisms that influences the distribution of antibiotic resistance genes in soil

Body size is a key life-history trait of organisms, which has important ecological functions. However, the relationship between soil antibiotic resistance gene (ARG) distribution and organisms' body size has not been systematically reported so far. Herein, the impact of organic fertilizer on the soil ARGs and organisms (bacteria, fungi, and nematode) at the aggregate level was analyzed. The results showed that the smaller the soil aggregate size, the greater the abundance of ARGs, and the larger the body size of bacteria and nematodes. Further analysis revealed significant positive correlations of ARG abundance with the body sizes of bacteria, fungi, and nematodes, respectively. Additionally, the structural equation model demonstrated that changes in soil fertility mainly regulate the ARG abundance by affecting bacterial body size. The random forest model revealed that total phosphorus was the primary soil fertility factor influencing the body size of organisms. Therefore, these findings proposed that excessive application of phosphate fertilizers could increase the risk of soil ARG transmission by increasing the body size of soil organisms. This study highlights the significance of organisms' body size in determining the distribution of soil ARGs and proposes a new disadvantage of excessive fertilization from the perspective of ARGs.

Metagenomic profiling of antibiotic resistance genes/bacteria removal in urban water: Algal-bacterial consortium treatment system

Antibiotic resistance genes (ARGs) have exhibited significant ecological concerns, especially in the urban water that are closely associated with human health. In this study, with presence of exogenous Chlorella vulgaris-Bacillus licheniformis consortium, most of the typical ARGs and MGEs were removed. Furthermore, the relative abundance of potential ARGs hosts has generally decreased by 1-4 orders of magnitude, revealing the role of algal-bacterial consortium in cutting the spread of ARGs in urban water. While some of ARGs such as macB increased, which may be due to the negative impact of algicidal bacteria and algal viruses in urban water on exogenous C. vulgaris and the suppression of exogenous B. licheniformis by indigenous microorganisms. A new algal-bacterial interaction might form between C. vulgaris and indigenous microorganisms. The interplay between C. vulgaris and bacteria has a significant impact on the fate of ARGs removal in urban water.

Food waste compost and digestate as novel fertilizers: Impacts on antibiotic resistome and potential risks in a soil-vegetable system

As a novel agricultural practice, the reuse of food waste compost and digestate as fertilizers leads to a circular economy, but inevitably introduces bio-contaminants such as antibiotic resistance genes (ARGs) into the agroecosystem. Moreover, heavy metal and antibiotic contamination in farmland soil may exert selective pressures on the evolution of ARGs, posing threats to human health. This study investigated the fate, influencing mechanisms and potential risks of ARGs in a soil-vegetable system under different food waste fertilization and remediation treatments and soil contamination conditions. Application of food waste fertilizers significantly promoted the pakchoi growth, but resulted in the spread of ARGs from fertilizers to pakchoi. A total of 56, 80, 84, 41, and 73 ARGs, mobile genetic elements (MGEs) and metal resistance genes (MRGs) were detected in the rhizosphere soil (RS), bulk soil (BS), control soil (CS), root endophytes (RE), and leaf endophytes (LE), respectively. Notably, 7 genes were shared in the above five subgroups, indicating a specific soil-root-endophytes transmission pathway. 36 genes were uniquely detected in the LE, which may originate from airborne ARGs. The combined application of biochar and fertilizers reduced the occurrence of ARGs and MGEs to some extent, showing the remediation effect of biochar. The average abundance of ARGs in the RS, BS and CS was 3.15 × 10-2, 1.31 × 10-2 and 2.35 × 10-1, respectively. Rhizosphere effects may reduce the abundance of ARGs in soil. The distribution pattern of ARGs was influenced by the types of soil, endophyte and contaminant. MGEs is the key driver shaping ARGs dynamics. Soil properties and pakchoi growth status may affect the bacterial composition, and consequently regulate ARGs fate, while endophytic ARGs were more impacted by biotic factors. Moreover, the average daily doses of ARGs from pakchoi consumption is 107-109 copies/d/kg, and its potential health risks should be emphasized.

Prevalence of antibiotics, antibiotic resistance genes, and their associations in municipal wastewater treatment plants along the Yangtze River basin, China

The overuse and misuse of antibiotics have resulted in the pollution of antibiotics and antibiotic resistance genes (ARGs) in municipal wastewater treatment plants (WWTPs), posing threats to ecological security and human health. Thus, a comprehensive investigation was conducted to assess the occurrence, removal efficiency, and ecological risk of antibiotics, along with the diversity, abundance, and co-occurrence of ARGs, and their correlations in 13 WWTPs along the Yangtze River Basin. Among 35 target antibiotics, 23 antibiotics within 6 categories were detected in all the samples. Amoxicillin (AMO), ofloxacin (OFL), and pefloxacin (PEF) were predominant in influents, while AMO exhibited dominance with the highest concentration of 1409 ng/L in effluents. Although antibiotic removal performance varied among different WWTPs, a significant decrease in each antibiotic category and overall antibiotics was observed in effluents compared with that in influents (p < 0.05). Remarkably, ecological risk assessment revealed high risks associated with AMO and ciprofloxacin (CIP) and medium risks linked to several antibiotics, notably including OFL, roxithromycin (ROX), clarithromycin (CLA), and tetracycline (TC). Furthermore, 96 ARG subtypes within 12 resistance types were detected in this study, and the total absolute abundance and diversity of ARGs were significantly decreased from influents to effluents (p < 0.05). Enrichment of 38 ARGs (e.g., blaNDM, ermA, vatA, mexA, and dfrA25) in effluents indicated potential health risks. Various mobile genetic elements (MGEs), exhibited significant correlations with a majority of ARGs in both influents and effluents, such as intⅠ1, tnpA1, tnpA5, and tp614, underscoring the important role of MGEs in contributing to the ARG dissemination. Many antibiotics displayed lower correlations with corresponding ARGs, but exhibited higher correlations with other ARGs, suggesting complex selective pressures influencing ARG propagation. Overall, the incomplete elimination of antibiotics and ARGs in WWTPs is likely to pose adverse impacts on aquatic ecosystems in the Yangtze River Basin.

Horizontal transfer potential of antibiotic resistance genes in wastewater treatment plants unraveled by microfluidic-based mini-metagenomics

Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs), which can potentially spread to the environment and human populations. However, the extent and mechanisms of ARG transfer in WWTPs are not well understood due to the high microbial diversity and limitations of molecular techniques. In this study, we used a microfluidic-based mini-metagenomics approach to investigate the transfer potential and mechanisms of ARGs in activated sludge from WWTPs. Our results show that while diverse ARGs are present in activated sludge, only a few highly similar ARGs are observed across different taxa, indicating limited transfer potential. We identified two ARGs, ermF and tla-1, which occur in a variety of bacterial taxa and may have high transfer potential facilitated by mobile genetic elements. Interestingly, genes that are highly similar to the sequences of these two ARGs, as identified in this study, display varying patterns of abundance across geographic regions. Genes similar to ermF found are widely found in Asia and the Americas, while genes resembling tla-1 are primarily detected in Asia. Genes similar to both genes are barely detected in European WWTPs. These findings shed light on the limited horizontal transfer potential of ARGs in WWTPs and highlight the importance of monitoring specific ARGs in different regions to mitigate the spread of antibiotic resistance.

Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.

Elucidating applied voltage on the fate of antibiotic resistance genes in microbial electrolysis cell: Focusing on its transmission between anolyte and biofilm microbes

Microbial electrolysis cell (MEC) system to treat wastewater containing antibiotics has been researched actively in past years. However, the fate of antibiotic resistant genes (ARGs) in MEC is not fully revealed. The effect of applied voltage on the migration of ARGs between anolyte and biofilm microbes via examining the microbial physiology and abundances of macrolide resistance genes (MRGs) and mobile genetic elements (MGEs) was elucidated in this research. Results showed that the abundance of MRGs and MGEs was decreased in the anolyte, but their abundances were increased on the electrode biofilm, indicating their transmission from anolyte to biofilm microbes. Increased applied voltage enhanced adenosine triphosphate (ATP), reactive oxygen species (ROS), and cell membrane permeability of electrode microorganisms. The structure of the electrode microbial community was shifted through applied voltage, and the abundance of electroactive microorganisms (Geobacter, Azospirillum and Dechlorobacter) was significantly improved. Network analysis revealed that Geobacter and Geothrix were potential hosts for MRGs. Therefore, the horizontal and vertical gene transfer of ARGs could be increased by the applied voltage, leading to the enriched ARGs at the electrode biofilm. This study provides evidence and insights into the transmission of ARGs between anolyte and biofilm microbes in MEC system. SYNOPSIS: This study revealed the effect of applied voltage on ARGs in MEC and the potential migration mechanism of ARGs.

Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes

Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.

Removal of intI1, ARGs, and SARS-CoV-2 and changes in bacterial communities in four sewage treatment facilities

Currently, discharge regulations for wastewater treatment plants (WWTPs) are based on conventional parameters, but more is needed to ensure safe water reuse. In particular, emerging pollutants, as antimicrobials and antibiotic resistance genes (ARGs), are not considered. This research focuses on the fate of emerging biological contaminants during wastewater treatment in Mexico City. intI1 and the ARGs cphA-02, OXA-10 and sul1 were analyzed by qPCR; pathogenic bacteria species were characterized by high throughput sequencing of complete 16S rRNA gene, and fragments of SARS-CoV-2 were quantified by RT-qPCR. Conventional parameters (chemical oxygen demand and coliform bacteria) were also determined. Two sampling campaigns (rainy and dry seasons) were carried out in four municipal WWTPs in Mexico City, representing five biological treatment processes: conventional activated sludge, extended aeration activated sludge, membrane bioreactor, direct anaerobic digestion, and constructed wetland, followed by ultraviolet light or chlorine disinfection. In most cases, gene fragments of SARS-CoV-2 were eliminated below the detection limit of RT-qPCR. The abundance of intI1 positively correlated with the sul1, OXA-10, and cphA-02 abundances; intI1 and the ARGs here studied were partially removed in the WWTPs, and in most cases, the number of copies per second discarded in the sludge were higher those in the effluent. The treatment processes decreased the abundance of dominant bacterial groups in the raw wastewater, while enriching bacterial groups in the effluent and the biological sludge, with possible pollutant removal capabilities. Bacterial communities in the raw wastewater showed the predominance of the genus Arcobacter (from 62.4 to 86.0 %) containing potentially pathogenic species. Additionally, DNA of some species persisted after the treatment processes: A. johnsonii, A. junii, A. caviae, A. hydrophila, A. veronii, A. butzleri, A. cryaerophilus, Chryseobacterium indologenes, Hafnia paralvei, M. osloensis, Pseudomonas putida and Vibrio cholerae, which deserves special attention in future regulation for safe water reuse.

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations

BACKGROUND

Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails.

RESULTS

We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments.

CONCLUSIONS

Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.

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

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

Size-dependent promotion of micro(nano)plastics on the horizontal gene transfer of antibiotic resistance genes in constructed wetlands

Constructed wetlands (CWs) have been identified as significant sources of micro(nano)plastics (MPs/NPs) and antibiotic resistance genes (ARGs) in aquatic environments. However, little is known about the impact of MPs/NPs exposure on horizontal gene transfer (HGT) of ARGs and shaping the corresponding ARG hosts' community. Herein, the contribution of polystyrene (PS) particles (control, 4 mm, 100 μm, and 100 nm) to ARG transfer was investigated by adding an engineered fluorescent Escherichia coli harboring RP4 plasmid-encoded ARGs into CWs. It was found MPs/NPs significantly promoted ARG transfer in a size-dependent manner in each CW medium (p < 0.05). The 100 μm-sized PS exhibited the most significant promotion of ARG transfer (p < 0.05), whereas 100 nm-sized PS induced limited promotion due to its inhibitory activity on microbes. The altered RP4-carrying bacterial communities suggested that MPs/NPs, especially 100 µm-PS, could recruit pathogenic and nitrifying bacteria to acquire ARGs. The increased sharing of RP4-carrying core bacteria in CW medium further suggested that ARGs can spread into CW microbiome using MPs/NPs as carriers. Overall, our results highlight the high risks of ARG dissemination induced by MPs/NPs exposure and emphasize the need for better control of plastic disposal to prevent the potential health threats.

Exploring resistomes and microbiomes in pilot-scale microalgae-bacteria wastewater treatment systems for use in low-resource settings

Antibiotic resistance genes (ARGs) released into the environment are an emerging human and environmental health concern, including ARGs spread in wastewater treatment effluents. In low-to-middle income countries (LMICs), an alternate wastewater treatment option instead of conventional systems are low-energy, high-rate algal ponds (HRAP) that use microalgae-bacteria aggregates (MABA) for waste degradation. Here we studied the robustness of ARG removal in MABA-based pilot-scale outdoor systems for 140 days of continuous operation. The HRAP system successfully removed 73 to 88 % chemical oxygen demand and up to 97.4 % ammonia, with aggregate size increasing over operating time. Fourteen ARG classes were identified in the HRAP influent, MABA, and effluent using metagenomics, with the HRAP process reducing total ARG abundances by up to 5-fold from influent to effluent. Parallel qPCR analyses showed the HRAP system significantly reduced exemplar ARGs (p < 0.05), with 1.2 to 4.9, 2.7 to 6.3, 0 to 1.5, and 1.2 to 4.8 log-removals for sul1, tetQ, blaKPC, and intl1 genes, respectively. Sequencing of influent, effluent and MABAs samples showed associated microbial communities differed significantly, with influent communities by Enterobacteriales (clinically relevant ARGs carrying bacteria), which were less evident in MABA and effluent. In this sense, such bacteria might be excluded from MABA due to their good settling properties and the presence of antimicrobial peptides. Microalgae-bacteria treatment systems steadily reduced ARGs from wastewater during operation time, using sunlight as the energetic driver, making them ideal for use in LMIC wastewater treatment applications.

Metagenomic evidence for antibiotics-driven co-evolution of microbial community, resistome and mobilome in hospital sewage

Overconsumption of antibiotics is an immediate cause for the emergence of antimicrobial resistance (AMR) and antibiotic resistant bacteria (ARB), though its environmental impact remains inadequately clarified. There is an urgent need to dissect the complex links underpinning the dynamic co-evolution of ARB and their resistome and mobilome in hospital sewage. Metagenomic and bioinformatic methods were employed to analyze the microbial community, resistome and mobilome in hospital sewage, in relation to data on clinical antibiotic use collected from a tertiary-care hospital. In this study, resistome (1,568 antibiotic resistance genes, ARGs, corresponding to 29 antibiotic types/subtypes) and mobilome (247 types of mobile genetic elements, MGEs) were identified. Networks connecting co-occurring ARGs with MGEs encompass 176 nodes and 578 edges, in which over 19 types of ARGs had significant correlations with MGEs. Prescribed dosage and time-dependent antibiotic consumption were associated with the abundance and distributions of ARGs, and conjugative transfer of ARGs via MGEs. Variation partitioning analyses show that effects of conjugative transfer were most likely the main contributors to transient propagation and persistence of AMR. We have presented the first evidence supporting idea that use of clinical antibiotics is a potent driving force for the development of co-evolving resistome and mobilome, which in turn supports the growth and evolution of ARB in hospital sewage. The use of clinical antibiotics calls for greater attention in antibiotic stewardship and management.

Transfer route and driving forces of antibiotic resistance genes from reclaimed water to groundwater

The infiltration of reclaimed water has created a significant environmental risk due to the spread of antibiotic resistance genes (ARGs) in riparian groundwater. Reclaimed water from wastewater treatment plants (WWTPs) had been identified as a source of both antibiotics and ARGs in groundwater, based on their spatial and temporal distribution. The assembly process of microbial communities in the groundwater of the infiltration zone was more influenced by deterministic processes. Co-occurrence network analysis revealed that Thermotoga, Desulfotomaculum, Methanobacterium, and other such genera were dominant shared genera. These were considered core genera and hosts of ARGs for transport from reclaimed water to groundwater. The most abundant ARG in these shared genera was MacB, enriched in groundwater point G3 and potentially transferred from reclaimed water to groundwater by Acidovorax, Hydrogenophaga, Methylotenera, Dechloromonas, and Nitrospira. During the infiltration process, environmental factors and the tradeoff between energy metabolism and antibiotic defense strategy may have affected ARG transfer. Understanding the transfer route and driving forces of ARGs from reclaimed water to groundwater provided a new perspective for evaluating the spread risk of ARGs in reclaimed water infiltration.

Understanding the distribution of antibiotic resistance genes in an urban community using wastewater-based epidemiological approach

The study aimed to evaluate the community-wide antimicrobial resistance (AMR) profile of an urban setting using the culture-independent wastewater-based epidemiological surveillance (WBE) approach. The domestic wastewater sample was collected at the converging point of the drain connecting the Sewage Treatment Plant (STP). The collected water sample was evaluated for the presence of 125 antibiotic resistance genes (ARGs) and 13 mobile genetic elements (MGEs, 5 integrons and 8 transposons). Antibiotic residues and the composition of bacterial communities were also examined. Community's sewage showed a diverse resistance pattern, with the positive detection of targeted ARGs, notably aph, aadA1, and strB being particularly abundant. Resistance to aminoglycoside and trimethoprim classes was prevalent, followed by chloramphenicol, sulfonamide, and β-lactams. According to the microbial diversity assessment, Proteobacteria, Bacteroidetes, Firmicutes, and Chloroflexi were abundant phyla observed, while Helicobacteraceae, Pseudomonadaceae, and Moraxellaceae were prevalent families. The study provided comprehensive baseline information of ARGs on a community scale and will be of use for ARG prevention and management.

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

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

Metagenomic analysis revealed sources, transmission, and health risk of antibiotic resistance genes in confluence of Fenhe, Weihe, and Yellow Rivers

Rivers are important vectors and reservoirs of antibiotics resistance genes (ARGs). Information regarding transmission and health risk of ARGs in river confluence is still lacking. In this study, metagenomics was used to distinguish contributions of human activities on ARGs and human pathogenic bacteria (HPB) in confluence of Fenhe, Weihe, and Yellow Rivers. Bacitracin resistance gene and bacA were the highest in all rivers, with 1.86 × 10^-2-7.26 × 10^-2 and 1.79 × 10^-2-9.12 × 10^-2 copies/16S rRNA copies, respectively. River confluence significantly increased the abundance of ARGs, especially at the confluence of three rivers with the highest 1.53 × 10^-1 copies/16S rRNA copies. Antibiotic efflux and antibiotic target alteration were the dominant resistant mechanisms in three rivers. ARGs profiles were influenced by multiple factors, with the contributions of various factors ranked as microbial communities > physicochemical factors > human activities > mobile genetic elements (MGEs). Notably, human activities and animal feces were important potential contributors of ARGs in the Weihe River and Yellow River. Transposons, as the main MGEs in three rivers, played important roles in ARGs transfer. The confluence of three rivers had the highest abundance of MGEs with the greatest transfer potentials, and therefore exhibiting the largest exposure risk of ARGs with 232.4 copies/cap·d. Furthermore, correlations of ARGs, MGEs, and HPB in different rivers were constructed via co-occurrence modes to systematically illustrate the health risks of ARGs. This study firstly unveiled the transmission and health risk of ARGs in river confluence, providing supports for ARGs control in watershed.

Cyanobacterial blooms: A player in the freshwater environmental resistome with public health relevance?

Cyanobacterial harmful algal blooms (cyanoHABs) are an ecological concern because of large ecosystem-disrupting blooms and a global public health concern because of the cyanotoxins produced by certain bloom-forming species. Another threat to global public health is the dissemination of antibiotic resistance (AR) in freshwater environmental reservoirs from anthropogenic sources, such as wastewater discharge and urban and agricultural runoff. In this study, cyanobacteria are now hypothesized to play a role in the environmental resistome. A non-systematic literature review of studies using molecular techniques (such as PCR and metagenomic sequencing) was conducted to explore indirect and direct ways cyanobacteria might contribute to environmental AR. Results show cyanobacteria can host antibiotic resistance genes (ARGs) and might promote the spread of ARGs in bacteria due to the significant contribution of mobile genetic elements (MGEs) located in genera such as Microcystis. However, cyanobacteria may promote or inhibit the spread of ARGs in environmental freshwater bacteria due to other factors as well. The purpose of this review is to 1) consider the role of cyanobacteria as AR hosts, since cyanoHABs are historically considered to be a separate problem from AR, and 2) to identify the knowledge gap in understanding cyanobacteria as ARG reservoirs. Cyanobacterial blooms, as well as other biotic (e.g. interactions with protists or cyanophages) and abiotic factors, should be studied further using advanced methods such as shotgun metagenomic and long read sequencing to clarify the extent of their functional ARGs/MGEs and influences on environmental AR.

New insight into the microbiome, resistome, and mobilome on the dental waste water in the context of heavy metal environment

Object

Hospital sewage have been associated with incorporation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into microbes, which is considered as a key indicator for the spread of antimicrobial resistance (AMR). The compositions of dental waste water (DWW) contain heavy metals, the evolution of AMR and its effects on the water environment in the context of heavy metal environment have not been seriously investigated. Thus, our major aims were to elucidate the evolution of AMR in DWW.

Methods

DWW samples were collected from a major dental department. The presence of microbial communities, ARGs, and MGEs in untreated and treated (by filter membrane and ozone) samples were analyzed using metagenomics and bioinformatic methods.

Results

DWW-associated resistomes included 1,208 types of ARGs, belonging to 29 antibiotic types/subtypes. The most abundant types/subtypes were ARGs of multidrug resistance and of antibiotics that were frequently used in the clinical practice. Pseudomonas putida, Pseudomonas aeruginosa, Chryseobacterium indologenes, Sphingomonas laterariae were the main bacteria which hosted these ARGs. Mobilomes in DWW consisted of 93 MGE subtypes which belonged to 8 MGE types. Transposases were the most frequently detected MGEs which formed networks of communications. For example, ISCrsp1 and tnpA.5/4/11 were the main transposases located in the central hubs of a network. These significant associations between ARGs and MGEs revealed the strong potential of ARGs transmission towards development of antimicrobial-resistant (AMR) bacteria. On the other hand, treatment of DWW using membranes and ozone was only effective in removing minor species of bacteria and types of ARGs and MGEs.

Conclusion

DWW contained abundant ARGs, and MGEs, which contributed to the occurrence and spread of AMR bacteria. Consequently, DWW would seriously increase environmental health concerns which may be different but have been well-documented from hospital waste waters.

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

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

Fate of resistome components and characteristics of microbial communities in constructed wetlands and their receiving river

Currently, most researches focus on that constructed wetlands (CWs) achieve desirable removal of antibiotics, antibiotic resistance genes (ARGs) and human pathogens. However, few studies have assessed the fate of resistome components, especially the behavior and cooccurrence of ARGs, mobile genetic elements (MGEs) and virulence factors (VFs). Therefore, characteristics of microbial communities (MCs) in CWs and their receiving rivers also deserve attention. These factors are critical to water ecological security. This study used two CWs to explore the fate of resistome components and characteristics of MCs in the CWs and their receiving river. Eleven samples were collected from the two CWs and their receiving river. High-throughput profiles of ARGs and microbial taxa in the samples were characterized. 31 ARG types consisting of 400 subtypes with total relative abundance 42.63-84.94× /Gb of sequence were detected in CWs, and 62.07-88.08× /Gb of sequence in river, evidencing that ARG pollution covered CWs and the river, and implying huge potential risks from ARGs. MGEs and VFs were detected, and tnpA, IS91 and intI1 were the three dominant MGEs, while Flagella. Type IV pili and peritrichous flagella were main VFs. Both CWs can remove ARGs, MGEs and VFs efficiently. However, some ARGs were difficult to remove, such as sul1 and sul2, and certain ARGs remained in the effluent of the CWs. The co-occurrence of ARGs, MGEs, and VFs implies the risk of antibiotic resistance and dissemination of ARGs. Eighty-five types of human pathogen were detected in the river samples, particularly Pseudomonas aeruginosa, Bordetella bronchiseptica, Aeromonas hydrophila and Helicobacter pylori. Correlation analysis indicated that MCs had significant effects on the profiles of ARGs in the water environment. This study reveals potential risks of the reuse of reclaimed water, and illustrates the removal ability of ARGs and related elements by CWs. This study will be helpful for monitoring and managing resistomes in water environments.

Dynamic distribution and driving mechanisms of antibiotic resistance genes in a human-intensive watershed

Accelerated urbanization has promoted urban watersheds as important reservoirs of antibiotic resistance genes (ARGs); yet the biogeographical patterns and driving mechanisms of ARGs at the watershed scale remain unclear. Here, we examined the dynamic distribution of ARGs in a human-intensive watershed (including city, river and lake systems) over different seasons in a temperate region, as well as revealed the key factors shaping ARGs dynamics through structural equation models (SEMs). High diversity and abundance of ARGs were detected in sediments and surface water, with aminoglycoside, beta-lactamase and multidrug resistance genes dominating. PCoA showed distinct ARGs variations between the two phases. Seasonal changes and regional functions had significant impacts on the distribution patterns of ARGs. More diverse ARGs were detected in winter, while higher ARGs abundances were observed in spring and summer. The city system showed the highest level of ARGs contamination and was mainly derived from wastewater and human/animal feces based on SourceTracker analysis and ARGs indicators. Notably, watershed restoration could significantly mitigate the ARGs pollution status and improve biodiversity in the aquatic environment. Network analysis identified several hub ARGs and bacterial genera, which helped to infer potential bacterial hosts carrying ARGs. Furthermore, ARGs indicators provided insights to trace ARGs sources. SEMs indicated that bioavailable heavy metals and nutrients can greatly shape ARGs dynamics in regions with high-intensity human activities, while the microbial community and MGEs dominate the fate of ARGs in less human-impacted regions. More attention should be given to control heavy metals and nutrients to curb the spread of ARGs. Overall, this study highlights the environmental fate of ARGs and provides novel strategies to mitigate ARGs pollution in the human-intensive watershed.

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

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

Dormancy induced by oxidative damage during disinfection facilitates conjugation of ARGs through enhancing efflux and oxidative stress: A lagging response

Disinfection is known to greatly alter bacterial characteristics in water, and high horizontal gene transfer (HGT) frequency occurs in eutrophic conditions. Interestingly, these two seemingly irrelevant phenomena were closely linked by a lagging response of the increased conjugation frequency probably via daily water disinfection in this study. Three disinfection methods (UV, chlorine, and UV/chlorine) were selected to investigate the increased frequency of conjugation of ARGs during the stage of continuing culture after disinfection. The results showed that the conjugative transfer frequency was inhibited for all disinfection treatments after 24 h of co-incubation. Unexpectedly, after 3-7 days of co-cultivation, the HGT frequencies were increased by 2.71-5.61-fold and 5.46-13.96-fold in chlorine (30 min) and UV/chlorine (1 min) groups compared to the control, but not in UV-irradiated groups. A neglected lagging response was found for the first time, i.e., oxidative disinfection-induced dormancy promotes conjugative transfer of ARGs. Furthermore, mechanistic insights were gained from (1) membrane permeability, (2) conjugation-regulated system, (3) efflux pump system, and (4) oxidative stress system, suggesting the critical role of enhancing efflux and oxidative stress in the propagation of ARGs. Finally, the known instantaneous effect of oxidation disinfection was compared to address the controversial debate in this research field, proposing that the dormancy level of donor bacteria is the key to evaluating whether it can promote the HGT process. This study has important environmental implications for elucidating the transmission of ARGs after oxidation disinfection.

Conurbation size drives antibiotic resistance along the river

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

The fate and behavior mechanism of antibiotic resistance genes and microbial communities in anaerobic reactors treating oxytetracycline manufacturing wastewater

In this study, two parallel-operated expanded granular sludge bed (EGSB) reactors, one used to treat oxytetracycline (OTC) manufacturing wastewater with gradual increase of OTC concentration as experimental reactor and the other fed with the same wastewater without OTC as control reactor, were operated to investigate the behavior of antibiotics resistance genes (ARGs) and mobile genetic elements (MGEs) and their possible relationships with bacterial community among influent, sludge and effluent environments. Though the average absolute abundance of ARGs slightly decreased (0.26 - log), the ARGs' relative abundance normalized to 16S-rRNA gene copy numbers showed a significant upward trend in effluent (2 multiples - increase) and the absolute and relative abundances both extremely increased in anaerobic sludge, indicating that anaerobic treatment process cannot reduce ARGs efficiently, inversely can increase the risk of ARGs through the proliferation of antibiotics resistance bacteria (ARB) under the suppression of OTC. MGEs, bacterial communities and OTC concentration mainly impacted the ARGs profiles, which contributed 88.4% to the variation of ARGs. The differences and correlations of hosts in influent, effluent and sludge were further confirmed by network analysis. Overall, this study enhanced the understanding of the prevalence and transfer of ARGs in OTC production effluents during anaerobic treatment.

Heavy metals in a typical city-river-reservoir system of East China: Multi-phase distribution, microbial response and ecological risk

The rapid construction of artificial reservoirs in metropolises has promoted the emergence of city-river-reservoir systems worldwide. This study investigated the environmental behaviors and risks of heavy metals in the aquatic environment of a typical system composed of main watersheds in Suzhou and Jinze Reservoir in Shanghai. Results shown that Mn, Zn and Cu were the dominant metals detected in multiple phases. Cd, Mn and Zn were mainly presented in exchangeable fraction and exhibited high bioavailability. Great proportion and high mobility of metals were found in suspended particulate matter (SPM), suggesting that SPM can greatly affect metal multi-phase distribution process. Spatially, city system (CiS) exhibited more serious metal pollution and higher ecological risk than river system (RiS) and reservoir system (ReS) owing to the diverse emission sources. CiS and ReS were regarded as critical pollution source and sink, respectively, while RiS was a vital transportation aisle. Microbial community in sediments exhibited evident spatial variation and obviously modified by exchangeable metals and nutrients. In particular, Bacteroidetes and Firmicutes presented significant positive correlations with most exchangeable metals. Risk assessment implied that As, Sb and Ni in water may pose potential carcinogenic risk to human health. Nevertheless, ReS was in a fairly safe state. Hg was the main risk contributor in SPM, while Cu, Zn, Ni and Sb showed moderate risk in sediments. Overall, Hg, Sb and CiS were screened out as priority metals and system, respectively. More attention should be paid to these priority issues to promote the sustainable development of the watershed.

What's the cost-effective pattern for rural wastewater treatment?

Inadequate sanitation infrastructure is a global problem that is particularly impacting rural areas. And decentralized wastewater management system is considered as the feasible solution for rural sewage treatment (RuST). However, determining the cost-effective (CE) pattern for decentralized RuST is methodologically challenging because of scarce decision-support tools. In this research, a RuST optimization model (RuST-OM) was developed to gain an insight into the CE pattern of RuST based on the greedy algorithm. This model involves tradeoffs in the economy-of-scale and technology of wastewater treatment system versus the cost and energy consumption of the sewage collection system. The investment associated with the CE pattern for RuST is closely linked to the environmental demand, RuST coverage, topographic complexity, and degree of household dispersion. The cost of the CE pattern falls between the onsite-B and community-based pattern, and this range represents the optimized interval for RuST planning. Nature-based technology is a sustainable alternative for RuST in areas characterized by low or moderate environmental demand. To ensure applicability of the RuST-OM in other countries/regions, built-in datasets (e.g., technology and pipeline design parameters) are designed based on rural area features that can be modified as necessary. This research highlights the utility of the CE pattern for RuST planning, and can serve as a reference for RuST planning around the world.

Towards risk assessment for antibiotic resistant pathogens in recycled water: a systematic review and summary of research needs

Risk assessment is critical for identifying target concentrations of antibiotic resistant pathogens necessary for mitigating potential harmful exposures associated with water reuse. However, there is currently limited available data characterizing the concentrations of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in recycled water to support robust efforts at risk assessment. The objective of this systematic review was to identify and synthesize the existing literature documenting the presence and abundance of ARB and ARGs in recycled water. In addition, this review identifies best practices and explores monitoring targets for studying ARB and ARGs in recycled water to guide future work and identifies key research needs aimed at better supporting quantitative microbial risk assessment focused on recycled water and antibiotic resistance. Future efforts to collect data about ARB and ARG prevalence in recycled water should report concentration data per unit volume. Sample metadata should also be provided, including a description of treatment approach, a description of planned water uses (e.g., potable, irrigation), methods for conveyance to the point of use, and available physicochemical water quality data. Additional research is needed aimed at identifying recommended ARB and ARG monitoring targets and for developing approaches to incorporate metagenomic data into risk assessment.

Mechanistic insight of simultaneous removal of tetracycline and its related antibiotic resistance bacteria and genes by ferrate(VI)

The emergence of antibiotics and their corresponding antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have posed great challenges to the public health. The paper demonstrates the removal of co-existing tetracycline (TC), its resistant Escherichia coli (E. coli), and ARGs (tetA and tetR) in a mixed system by applying ferrate(VI) (Fe^VIO₄^2-, Fe(VI)) at pH 7.0. TC was efficiently degraded by Fe(VI), and the rapid inactivation of the resistant E. coli was found with the complete loss of culturability. The results of flow cytometry suggested that the damage of membrane integrity and respiratory activity were highly correlated with the Fe(VI) dosages. Moreover, high-dose Fe(VI) eliminates 6 log₁₀ viable but non-culturable (VBNC) cells and even breaks the cells into fragments. ARGs in extracellular form (e-ARGs) exhibited a high sensitivity of 4.44 log₁₀ removal to Fe(VI). Comparatively, no removal of intracellular ARGs (i-ARGs) was observed due to the multi-protection of cellular structure and rapid decay of Fe(VI). The oxidized products of TC were assessed to be less toxic than the parent compound. Overall, this study demonstrated the superior efficiency and great promise of Fe(VI) on simultaneous removal of antibiotics and their related ARB and ARGs in water.

The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes

The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. High ARGs abundances (absolute: 1.03 × 10⁷-2.82 × 10⁹copies/mL; relative: 0.076-2.778copies/16S rRNA) were observed across all samples. Although biotreatment effectively reduced absolute abundance of ARGs, additional bacteria acquiring ARGs caused an increase in their relative abundance, which further increased the transmission risk of ARGs. mexF, blaCTX-M, sul1 played crucial roles and sul1 might be considered as an indicator for the prediction of total ARGs. It is worrying that the discharge (effluent and sludge) included highly abundant ARGs (5.09 × 10¹⁴-4.83 × 10¹⁵copies/d), integrons (1.11 × 10¹⁴-6.04 × 10¹⁴copies/d) and potential pathogens (such as Pseudomonas and Streptococcus), which should be given more attentions. blaCTX-M and tetQ possessed most potential hosts, Proteobacteria-L and Firmicutes-W were predominant contributors of ARGs-hosts at genus level. This study suggested FW leachate biotreatment systems could be reservoirs of ARGs and facilitated the proliferation of them. The exploration of effective removal methods and formulation of emission standard are necessary for future ARGs mitigation.

On-site chlorination responsible for effective disinfection of wastewater from hospital

Both hospital effluent and a model sewage treatment plant (STP) wastewater prepared by mixing STP influent and STP secondary effluent at a volume ratio of 1:9 were directly treated with chlorine for investigation of their effects on disinfection of antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB). The overall results indicate that the chlorine disinfection effectively inactivated the majority of AMRB and AMSB, expect for MRSA and Staphylococcus aureus in both wastewaters. No significant differences could further be observed in the taxonomic diversity of micro-organisms after the treatment. The degrees of disinfection given by the direct chlorination were comparable to those attained by combination of conventional activated sludge process and additional chlorine treatment at the STP. The results of this study evoked a recommendation to operate local chlorination treatment directly for the wastewater from medicinal facilities prior to its flow into the STP as sewage. Although additional disinfection treatment at the STP seems necessary to remove the recalcitrant MRSA and Staphylococcus aureus, the present study desirably contributes to a great reduction of the loads of STP and urgent prevention of spreading of infectious diseases in the present state.

Distribution of antibiotic resistance genes and their association with bacteria and viruses in decentralized sewage treatment facilities

The distribution of antibiotic resistance genes (ARGs) has been intensively studied in large-scale wastewater treatment plants and livestock sources. However, small-scale decentralized sewage treatment facilities must also be explored due to their possible direct exposure to residents. In this study, six wastewater treatment facilities in developed rural areas in eastern China were investigated to understand their risks of spreading ARGs. Using metagenomics and network analysis tools, ARGs and bacterial and viral communities were identified in the influent (INF) and effluent (EFF) samples. The dominant ARGs belonged to the bacitracin class, which are different from most of municipal wastewater treatment plants (WWTPs). The dominant hosts of ARGs are Acidovorax in bacterial communities and Prymnesiovirus in viral communities. Furthermore, a positive relationship was found between ARGs and phages. The ARGs significantly correlated with phages were all hosted by specific genera of bacteria, indicating that phages had contributed to the ARG's proliferation in sewage treatment facilities. Paying significant concern on the possible enhanced risks caused by bacteria, viruses and their related ARGs in decentralized sewage treatment facilities is necessary.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material is available in the online version of this article at 10.1007/s11783-021-1469-4 and is accessible for authorized users.

Fate of antibiotic resistance genes during temperature-changed psychrophilic anaerobic digestion of municipal sludge

The effects of anaerobic digestion (AD) on the abundance of antibiotic resistance genes (ARGs) are highly related to operational temperature. However, the removal performance of ARGs in psychrophilic AD and changed temperatures simulating variable seasonal temperatures is poorly understood. Herein, we investigated the fate of ARGs, correlated bacterial communities and physicochemical properties of AD operation at psychrophilic (15 ℃), mesophilic (35 ℃), and temperature changed conditions (15 to 35 ℃ and 35 to 15 ℃). The results indicated that ammonia release was positively correlated with temperature. The mesophilic AD facilitated phosphorous intake and ARGs proliferation and selection with oxytetracycline (OTC), while psychrophilic AD was conducive to the removal and control of ARGs if no OTC existed. The diversity and composition of AD bacterial communities were influenced more by temperature than OTC. The dominant genera like Candidatus_Microthrix and Acinetobacter had dramatical abundance discrepancies at different temperatures and were obviously positively correlated with ARGs (tet39, tetC and mexD), mobile genetic elements (MGEs) intI, insert sequences (IS) and plasmid. The physicochemical properties of AD influenced the bacterial richness, which in turn significantly correlated with the ARGs abundances. Therefore, ARGs removal could be potentially optimized by eliminating bacterial hosts with deteriorated living conditions and decreased nutrients. This study clarified the response of antibiotic resistome to different temperature variation and highlighted the potential strategies for improved ARGs removal in AD.

Simultaneous elimination of amoxicillin and antibiotic resistance genes in activated sludge process: Contributions of easy-to-biodegrade food

Antibiotics are continuously released into aquatic environments and ecosystems where they accumulate, which increases risks from the transmission of antibiotic resistance genes (ARGs). However, it is difficult to completely remove antibiotics by conventional biological methods, and during such treatment, ARGs may spread via the activated sludge process. Easy-to-biodegrade food have been reported to improve the removal of toxic pollutants, and therefore, this study investigated whether such co-substrates may also decrease the abundance of ARGs and their transferal. This study investigated amoxicillin (AMO) degradation using 0-100 mg/L acetate sodium as co-substrate in a sequencing biological reactor. Proteobacteria, Bacteroidetes, and Actinobacteria were identified as dominant phyla for AMO removal and mineralization. Furthermore, acetate addition increased the abundances of adeF and mdsC as efflux resistance genes, which improved microbial resistance, the coping ability of AMO toxicity, and the repair of the damage from AMO. As a result, acetate addition contributed to almost 100% AMO removal and stabilized the chemical oxygen demand (~20 mg/L) in effluents when the influent AMO fluctuated from 20 to 100 mg/L. Moreover, the total abundance of ARGs decreased by approximately ~30%, and the proportion of the most dominant antibiotic resistance bacteria Proteobacteria decreased by ~9%. The total abundance of plasmids that encode ARGs decreased by as much as ~30%, implying that the ARG spreading risks were alleviated. In summary, easy-to-biodegrade food contributed to the simultaneous elimination of antibiotics and ARGs in an activated sludge process.

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

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

Profiles of antibiotic resistome and microbial community in groundwater of CKDu prevalence zones in Sri Lanka

The chronic kidney disease of unknown etiology (CKDu) prevalent in certain regions of Sri Lanka poses a serious threat to human health. Previous epidemiological studies focused on the search of causative agents for CKDu etiology from the viewpoint of groundwater composition, but how CKDu prevalence affected the groundwater microbial composition, especially the antibiotic resistome, has never been illuminated. This study investigated the response of microbial community and antibiotic resistome to CKDu prevalence in the groundwater through the high throughput sequencing and qPCR (HT-qPCR), respectively. Results showed that CKDu prevalence significantly influenced the distribution of antibiotic resistome and microbial community composition. The mexF dominated in all the groundwater samples and could be considered as an intrinsic ARG, and the β-lactamase cphA was specially enriched and closely associated with the antibiotics used for CKDu patients. The Acinetobacter was a potential human pathogen common in the groundwater of CKDu affected regions, while CKDu prevalence specially enriched the Aeromonas. Statistical analysis indicated that CKDu prevalence impacted antibiotic resistome through the microbial community as a whole, and MGEs contributed to the occurrence of mexF, while the enrichment of cphA could be attributed to the increase of Aeromonas.

Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview

Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.

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

Serious concerns have been raised regarding antibiotic resistance genes (ARGs) with respect to their potential threat to human health. Wastewater treatment plants (WWTPs) have been considered to be hotspots for ARGs. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) was used to profile size-dependent ARGs and mobile genetic elements (MGEs) divided by particle-associated (PA) assemblages (>3.0-μm), free-living (FL) bacteria (0.2 - 3.0-μm) and cell-free (CF) DNA (< 0.2-μm) in two full-scale WWTPs (plants A and B) and a receiving stream. The results revealed that FL-ARGs were predominant in WWTPs and the receiving stream, especially in the final effluent of both plants. More than 40 types of CF-ARGs and CF-MGEs were detected with absolute abundances ranging from 6.0 ± 0.7 × 10⁵ to 1.0 ± 0.2 × 10⁸ copies/mL in wastewater, and relatively high abundances were also detected in the final effluent of the two plants, suggesting that CF-ARGs were important sources spreading from the WWTPs to the receiving environment. Plant A exhibited higher log-removal of size-fractionated ARGs and MGEs than was observed for plant B, which was attributed to the enhanced settleability of PA assemblages and FL bacteria by additional macrophytes and chemical coagulants. Ultraviolet disinfection had limited effects on ARGs and MGEs of the PA and FL fractions, which was probably ascribed to the protective matrices of the particles and cell walls. The bacterial communities of the two plants were significantly different among the size fractions (p < 0.01). The variation partitioning analysis (VPA) indicated that the microbial community structures and MGEs contributed a variation of 68.2% in total to the relative abundance changes of size-fractionated ARGs. Procrustes analyses and Mantel tests showed that the relative abundances of ARGs were significantly correlated with bacterial community structures. These results suggested that the bacterial community structures and MGEs might have been the main drivers of the size-fractionated ARG disseminations. This study provides novel insights into size-fractionated ARGs and MGEs in full-scale WWTPs and may lead to the identification of key targets to control the spread of ARGs.