Metagenomics shows that low-energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene levels from domestic wastewater

The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater

Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.

Assembling bacterial puzzles: piecing together functions into microbial pathways

Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in the KEGG database. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.

Performance of pharmaceutical products removal in a bioelectrochemical system at low temperatures and changes in microbial communities and antibiotic resistance genes

Biological methods do not effectively remove pharmaceutical products (PPs) and antibiotic resistance genes (ARGs) from wastewater at low temperatures, leading to environmental pollution. Therefore, anaerobic-aerobic-coupled upflow bioelectrochemical reactors (AO-UBERs) were designed to improve the removal of PPs at low temperatures (10 ± 2 °C). The result shows that diclofenac (DIC) and ibuprofen (IBU) removals in the system with aerobic anodic and anaerobic cathodic chambers were 91.7% and 94.7%, higher than that in the control system (12.2 ± 1.5%, 36.5 ± 5.9%), and aerobic zone favors DIC and IBU removal; fluoroquinolone antibiotics (FQs) removals in the system with aerobic cathodic and anaerobic anodic chambers were 17.5-22.4% higher than that in the control system (9.1-22.4%), and anaerobic zone favors FQs removal. Analysis of microbial community structure and ARGs showed that different electrotrophic microbes (Flavobacterium, Acinetobacter, and Delftia) with cold-resistant ability to degrade PPs were enriched in different electrode combinations, and the aerobic cathodic chambers could remove certain ARGs. These results showed that AO-UBERs under intermittent electrical stimulation mode are an alternative method for the effective removal of PPs and ARGs at low temperatures.

Computer-Aided Assessment of Repigmentation Rates in Vitiligo Patients: Implications for Treatment Efficacy - A Retrospective Study

Precise evaluation of repigmentation in vitiligo patients is crucial for monitoring treatment efficacy and enhancing patient satisfaction. This study aimed to develop a computer-aided system for assessing repigmentation rates in vitiligo patients, providing valuable insights for clinical practice. A retrospective study was conducted at the Dermatology Department of Shenzhen People's Hospital between June 2019 and November 2022. Pre- and post-treatment images of vitiligo lesions under Wood's lamp were collected, involving 833 participants stratified by sex, age, and pigmentation patterns. Our results demonstrated that the marginal pigmentation pattern exhibited a higher repigmentation rate of 72% compared with the central non-follicular pattern at 45%. Males had a slightly higher average repigmentation rate of 0.37 in comparison to females at 0.33. Among age groups, individuals aged 0-20 years showed the highest average repigmentation rate at 0.41, while the oldest age group (61-80 years) displayed the lowest rate at 0.25. Analysis of multiple visits identified the marginal pattern as the most prevalent (60%), with a mean repigmentation rate of 40%. This study introduced a computational system for evaluating vitiligo repigmentation rates, enhancing our comprehension of patient responses, and ultimately contributing to enhanced clinical care.

The fate of antibiotic resistance genes in wastewater containing microalgae treated by chlorination, ultra-violet, and Fenton reaction

Antibiotic resistance genes (ARGs) and bacteria (ARBs) in the effluent of wastewater treatment plants (WWTPs) are of utmost importance for the dissemination of ARGs in natural aquatic environments. Therefore, there is an urgent need for effective technologies to eliminate WWTP ARGs/ARBs and mitigate the associated risks posed by the discharged ARG in aquatic environments. To test the effective technology for eliminating ARGs/ARBs, we compared the removal of ARGs and ARBs by three different tertiary treatments, namely ultra-violet (UV) disinfection, chlorination disinfection, and Fenton oxidation. Then, the treated wastewater was co-cultured with Chlorella vulgaris (representative of aquatic biota) to investigate the fate of discharged ARGs into the aquatic environment. The results demonstrated that chlorination (at a chlorine concentration of 15 mg/L) and Fenton (at pH 2.73, with 0.005 mol/L Fe2+ and 0.0025 mol/L H2O2) treatment showed higher efficacy in ARG removal (1.8 - 4.17 logs) than UV treatment (15 min) (1.29 - 3.87 logs). Moreover, chlorine at 15 mg/L and Fenton treatment effectively suppressed ARB regeneration while UV treatment for 15 min could not. Regardless of treatments tested in this study, the input of treated wastewater to the Chlorella system increased the number of ARGs and mobile genetic elements (MGEs), indicating the potential risk of ARG dissemination associated with WWTP discharge. Among the wastewater-Chlorella co-culture systems, chlorination resulted in less of an increase in the number of ARGs and MGEs compared to Fenton and UV treatment. When comparing the wastewater systems to the co-culture systems, it was observed that Chlorella vulgaris reduced the number of ARGs and MGEs in chlorination and UV-treated wastewater; however, Chlorella vulgaris promoted ARG survival in Fenton-treated water, suggesting that aquatic microalgae might act as a barrier to ARG dissemination. Overall, chlorination treatment not only effectively removes ARGs and inhibits ARB regeneration but also shows a lower risk of ARG dissemination. Therefore, chlorination is recommended for practical application in controlling the spread of discharged ARGs from WWTP effluent in natural aquatic environments.

Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants

Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.

Tetracycline hydrochloride degradation in polarity inverted microbial fuel cells: Performance, mechanisms and microbiology

Tetracycline antibiotics are widely used in veterinary medicine, human therapy and agriculture, and their presence in natural water raises environmental concerns. In this study, more than 94% of tetracycline hydrochloride (TCH) could be rapidly degraded within 48 h in polarity-inverted microbial fuel cells. The electrochemically active bacteria had the best electrochemical performance at 1 mg/L of TCH with the minimum internal resistance of 77.38 Ω. The electron-rich functional groups of TCH were continuously attacked and finally degradated into small molecules in three possible degradation pathways. Microbial community structure analysis showed that Comamonas and Shinella were enriched at the electrode as polarity-inverted bacteria. Genomic analysis showed that both direct and indirect electron transfer participated in the degradation of TCH in polarity-inverted microbial fuel cell (MFC) and the functional genes related to electrical conductivity in polarity-inverted MFC were more enriched on the electrode surface than non-polarity-inverted MFC. This study can facilitate further investigations about the biodegradation of TCH in polarity-inverted microbial fuel cell.

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.

Portable biosensor combining CRISPR/Cas12a and loop-mediated isothermal amplification for antibiotic resistance gene ermB in wastewater

Wastewater is among the main sources of antibiotic resistance genes (ARGs) in the environment, but effective methods to quickly assess ARGs on-site in wastewater are lacking. Here, using the typical ARG ermB as the target, we report a portable biosensor combining CRISPR/Cas12a and loop-mediated isothermal amplification (LAMP) for the detection of ARGs. Six primers of LAMP and the crRNA of CRISPR/Cas12a were first designed to be preamplification with LAMP and lead Cas12a to recognize the ermB via base pairing. Due to the trans-cleavage activity of CRISPR/Cas12a after amplicon recognition, ssDNA probes modified with reporter molecules were used to implement a visual assay with lateral flow test strips and fluorescence. After a simple nucleic acid extraction with magnetic beads, the constructed biosensor possesses excellent sensitivity and selectivity as low as 2.75 × 103 copies/μL using fluorescence and later flow strips in wastewater. We further evaluated the community-wide prevalence of ermB in wastewater influent and found high mass loads of ermB during different months. This user-friendly and low-cost biosensor is applicable for rapid on-site ARG detection, providing a potential point-of-use method for rapid assessments of ARG abundance in wastewater from large city areas with many wastewater treatment plants and in resource-limited rural areas.

Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities

Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.

Comprehensive assessment of toxicity and environmental risk associated with sulfamethoxazole biodegradation in sulfur-mediated biological wastewater treatment

Incomplete mineralization of sulfamethoxazole (SMX) in wastewater treatment systems poses a threat to ecological health. The toxicity and environmental risk associated with SMX biodegradation in the sulfur-mediated biological process were examined for the first time through a long-term (180 days) bioreactor study and a series of bioassays. The results indicated that the sulfur-mediated biological system was highly resistant and tolerant to SMX toxicity, as evidenced by the enrichment of sulfate-reducing bacteria (SRB), the improved microbial metabolic activity, and the excellent performance on pollutants removal under long-term SMX exposure. SMX can be effectively biodegraded by the cleavage and rearrangement of the isoxazole ring, hydrogenation and hydroxylation reactions in sulfur-mediated biological wastewater system. These biodegradation pathways effectively reduced the acute toxicity, antibacterial activity, and ecotoxicities of SMX and its biotransformation products (TPs) in the effluent of the sulfur-mediated biological system. The TPs produced via hydrogenation (TP1), hydroxylation, and isoxazole ring cleavage (TP3, TP4, TP5, TP8, and TP9) exhibited lower toxicity than SMX. Under SMX stress, although the abundance of sulfonamide resistance genes increased, the total abundance of ARGs decreased due to the extrusion of some intracellular SMX by the efflux pump genes and the inactivation of some SMX through the biodegradation process. Efflux pump and inactivation, as the main resistance mechanisms of antibiotics in the sulfur-mediated biological system, play a crucial role in microbial self-defense. The findings of this study demonstrate the great potential of the sulfur-mediated biological system in SMX removal, detoxication, and ARGs environmental risk reduction.

Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer

Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.

Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent

The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.

Occurrence of antibiotics in wastewater: Potential ecological risk and removal through anaerobic-aerobic systems

Antibiotics are intensively used to improve public health, prevent diseases and enhance productivity in animal farms. Contrarily, when released, the antibiotics laden wastewater produced from pharmaceutical industries and their application sources poses a potential ecological risk to the environment. This study provides a discussion on the occurrence of various antibiotics in wastewater and their potential ecological risk in the environment. Further, a critical review of anaerobic-aerobic processes based on three major systems (such as constructed wetland, high-rate bioreactor, and integrated treatment technologies) applied for antibiotics removal from wastewater is performed. The review also explores microbial dynamics responsible for antibiotic biodegradation in anaerobic-aerobic systems and its economic feasibility at wider-scale applications. The operational problems and prospective modifications are discussed to define key future research directions. The appropriate selection of treatment processes, sources control, understanding of antibiotic fate, and adopting precise monitoring strategies could eliminate the potential ecological risks of antibiotics. Integrated bio-electrochemical systems exhibit antibiotics removal ≥95% by dominant Geobacter sp. at short HRT ∼4-10 h. Major process factors like organic loading rate, hydraulic loading rate (HRT), and solid retention time significantly affect the system performance. This review will be beneficial to the researchers by providing in-depth understanding of antibiotic pollution and its abatement via anaerobic-aerobic processes to develop sustainable wastewater treatment technology in the future.

Metagenomic insights into the distribution, mobility, and hosts of extracellular antibiotic resistance genes in activated sludge under starvation stress

Extracellular antibiotic resistance genes (eARGs) are important emerging environmental pollutants in wastewater treatment plants (WWTPs). Nutritional substrate deficiency (i.e., starvation) frequently occurs in WWTPs owing to annual maintenance, water quality fluctuation, and sludge storage; and it can greatly alter the antibiotic resistance and extracellular DNA content of bacteria. However, the fate and corresponding transmission risk of eARGs in activated sludge under starvation stress remain largely unknown. Herein, we used metagenomic sequencing to explore the effects of starvation scenarios (carbon, nitrogen, and/or phosphorus deficiency) and environmental conditions (alternating anaerobic-aerobic, anaerobic, anoxic, and aerobic) on the distribution, mobility, and hosts of eARGs in activated sludge. The results showed that 30 days of starvation reduced the absolute abundances of eARGs by 40.9%-88.2%, but high-risk dual and multidrug resistance genes persisted. Starvation, particularly the simultaneous lack of carbon, nitrogen, and phosphorus under aerobic conditions, effectively alleviated eARGs by reducing the abundance of extracellular mobile genetic elements (eMGEs). Starvation also altered the profile of bacterial hosts of eARGs and the bacterial community composition, the latter of which had an indirect positive effect on eARGs via changing eMGEs. Our findings shed light on the response patterns and mechanisms of eARGs in activated sludge under starvation conditions and highlight starvation as a potential strategy to mitigate the risk of previously neglected eARGs in WWTPs.

Effects of micron-scale zero valent iron on behaviors of antibiotic resistance genes and pathogens in thermophilic anaerobic digestion of waste activated sludge

This work investigated the metagenomics-based behavior and risk of antibiotic resistance genes (ARGs), and their potential hosts during thermophilic anaerobic digestion (TAD) of waste activated sludge, enhanced by micron-scale zero valent iron (mZVI). Tests were conducted with 0, 25, 100, and 250 mg mZVI/g total solids (TS). Results showed that up to 7.3% and 4.8% decrease in ARGs' abundance and diversity, respectively, were achieved with 100 mg mZVI/g TS. At these conditions, ARGs with health risk in abundance and human pathogenic bacteria (HPB) diversity were also decreased by 8.3% and 3.6%, respectively. Additionally, mZVI reduced abundance of 72 potential pathogenic supercarriers for ARGs with high health risk by 2.5%, 5.0%, and 6.1%, as its dosage increased. Overall, mZVI, especially at 100 mg/g TS, can mitigate antibiotic resistance risk in TAD. These findings are important for better understanding risks of ARGs and their pathogenic hosts in ZVI-enhanced TAD of solid wastes.

Enhanced biodegradation of fluoroquinolones and the changes of bacterial communities and antibiotic-resistant genes under intermittent electrical stimulation

In this study, an anaerobic-aerobic coupling system under intermittent electrical stimulation was used to improve the biodegradation of synthetic wastewater containing fluoroquinolones (FQs). The effect of electrical stimulation on FQ removal performance is more pronounced with appropriate voltage and hydraulic retention time. In addition, the combination of anaerobic-anodic and aerobic-cathodic chambers is more conducive to improving the removal efficiency of FQs. Under 0.9 V, the removal efficiencies of ofloxacin, norfloxacin, ciprofloxacin, and enrofloxacin were significantly improved in the anaerobic-anodic and aerobic-cathodic system. The contribution of the anaerobic/aerobic anodic chambers to FQ removal was greater than that of the anaerobic/aerobic cathodic chambers. Electrical stimulation selectively enriched electroactive bacteria related to biodegradation (Desulfovibrio and Terrimonas), antibiotic-resistant bacteria (Atopobium and Neochlamydia), and nitrifying bacteria (SM1A02 and Reyranella). This study indicated the potential effectiveness of intermittent electrical stimulation in treating fluoroquinolone-containing wastewater in a biofilm reactor. However, electrical stimulation led to an increase in mobile genetic elements , induced horizontal gene transfer and enriched resistant bacteria, which accelerated the spread of antibiotic-resistant genes (ARGs) in the system, indicating that the diffusion of ARGs remains a challenge.

Performance assessment of a modified trickling filter and conventional activated sludge process along with tertiary treatment in removing emerging pollutants from urban sewage

The absence of effective wastewater treatment technology to eliminate emerging pollutants from municipal sewage has become a pressing issue. In this study, the efficacy of a novel modified trickling filter (MTF), conventional activated sludge process (ASP) and two tertiary systems (UV and ozonation) were compared in eliminating antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs) and pharmaceuticals and personal care products (PPCPs) from urban sewage. MTF and ASP resulted in >1 log unit reduction in the abundance of ARB, while for ARGs, the removal was observed in the range of 0.1 to 1.7 log units. In MTF, ARGs were substantially removed in the aerobic zone compared to the anoxic zone. The relative abundance of most of the ARGs either decreased or remained unchanged during MTF and ASP operations. However, the relative abundance of most of the ARGs increased in the secondary sludge generated from ASP. The concentration of PPCPs such as atenolol, sulfamethazine, triclosan, and ranitidine was reduced by MTF by >80 %. Overall, the results indicated that MTF followed by ozonation is the most effective combination for removing emerging contaminants from municipal sewage.

Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community

The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.

Responses of microbial community and antibiotic resistance genes to co-existence of chloramphenicol and salinity

In recent years, the risk from environmental pollution caused by chloramphenicol (CAP) has emerged as a serious concern worldwide, especially for the co-selection of antibiotic resistance microorganisms simultaneously exposed to CAP and salts. In this study, the multistage contact oxidation reactor (MCOR) was employed for the first time to treat the CAP wastewater under the co-existence of CAP (10-80 mg/L) and salinity (0-30 g/L NaCl). The CAP removal efficiency reached 91.7% under the co-existence of 30 mg/L CAP and 10 g/L NaCl in the influent, but it fluctuated around 60% with the increase of CAP concentration and salinity. Trichococcus and Lactococcus were the major contributors to the CAP and salinity shock loads. Furthermore, the elevated CAP and salinity selection pressures inhibited the spread of CAP efflux pump genes, including cmlA, tetC, and floR, and significantly affected the composition and abundance of antibiotic resistance genes (ARGs). As the potential hosts of CAP resistance genes, Acinetobacter, Enterococcus, and unclassified_d_Bacteria developed resistance against high osmotic pressure and antibiotic environment using the efflux pump mechanism. The results also revealed that shifting of potential host bacteria significantly contributed to the change in ARGs. Overall, the co-existence of CAP and salinity promoted the enrichment of core genera Trichococcus and Lactococcus; however, they inhibited the proliferation of ARGs. KEY POINTS: • Trichococcus and Lactococcus were the core bacteria related to CAP biodegradation • Co-existence of CAP and salinity inhibited proliferation of cmlA, tetC, and floR • The microorganism resisted the CAP using the efflux pump mechanism.

A review on antibiotics removal: Leveraging the combination of grey and green techniques

Antibiotics are currently a major source of concern around the world due to the serious risks posed to human health and the environment. The performance of the secondary wastewater treatment processes/technologies (representing grey process) and constructed wetlands (CWs) (typical green process) in removing antibiotics and antibiotic resistance genes (ARG) was reviewed. The result showed that the grey process mainly removes antibiotics, but does not significantly remove ARG, and some processes may even cause ARG enrichment. The overall treatment in CWs is better than WWTPs, especially for ARG. Vertical subsurface flow CWs (VFCWs) are more conductive to antibiotics removal, while horizontal subsurface flow CWs (HFCWs) have a better ARG removal. More importantly, this review admits and suggests that the combination of grey process with green process is an effective strategy to remove antibiotics and ARG. The most advantage of the combination lies in realizing complementary advantages, i.e. the grey process as the primary treatment while CWs as the polishing stage. The efficiency of such the hybrid system is much higher than either single treatment process.

Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies

This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.

Antibiotics and antibiotic resistant bacteria/genes in urban wastewater: A comparison of their fate in conventional treatment systems and constructed wetlands

There is a growing concern that the use and misuse of antibiotics can increase the detection of antibiotic resistant genes (ARGs) in wastewater. Conventional wastewater treatment plants provide a pathway for ARGs and antibiotic resistant bacteria (ARB) to be released into natural water bodies. Research has indicated that conventional primary and secondary treatment systems can reduce ARGs/ARB to varying degrees. However, in developing/low-income countries, only 8-28% of wastewater is treated via conventional treatment processes, resulting in the environment being exposed to high levels of ARGs, ARB and pharmaceuticals in raw sewage. The use of constructed wetlands (CWs) has the potential to provide a low-cost solution for wastewater treatment, with respect to removal of nutrients, pathogens, ARB/ARGs either as a standalone treatment process or when integrated with conventional treatment systems. Recently, CWs have also been employed for the reduction of antibiotic residues, pharmaceuticals, and emerging contaminants. Given the benefits of ARG removal, low cost of construction, maintenance, energy requirement, and performance efficiencies, CWs offer a promising solution for developing/low-income countries. This review promotes a better understanding of the performance efficiency of treatment technologies (both conventional systems and CWs) for the reduction of antibiotics and ARGs/ARB from wastewater and explores workable alternatives.

Effects of heavy metals on the development and proliferation of antibiotic resistance in urban sewage treatment plants

Sewage treatment plants (STPs) are considered as "hotspots" for the emergence and proliferation of antibiotic resistance. However, the impact of heavy metals contamination on dispersal of antibiotic resistance in STPs is poorly understood. This study simultaneously investigated the effect of removal of metal and antibiotic resistance as well as mobile elements at different treatment units of STPs in Delhi, India. Results showed that treatment technologies used in STPs were inefficient for the complete removal of metal and antibiotic resistance, posing an ecological risk of co-selection of antibiotic resistance. The strong correlations were observed between heavy metals, metal and antibiotic resistance, and integrons, implying that antibiotic resistance may be exacerbated in the presence of heavy metals via integrons, and that metal and antibiotic resistance share a common or closely associated mechanism. We quantified an MRG rcnA, conferring resistance to Co and Ni, and identified that it was more abundant than all MRGs, ARGs, integrons, and 16S rRNA, suggesting rcnA could be important in antibiotic resistance dissemination in the environment. The associations between heavy metals, metal and antibiotic resistance, and integrons highlight the need for additional research to better understand the mechanism of co-selection as well as to improve the removal efficacy of current treatment systems.

Fate of antibiotic resistant genes in wastewater environments and treatment strategies - A review

Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have emerged in aquatic environments through the discharge of large amounts of antibiotics into wastewater. Well-designed wastewater treatment plants (WWTPs) with effective treatment processes are essential to prevent the release of ARGs directly into the environment. Although some systematic sequential treatment methods are used to remove ARGs, considerable gaps in removal mechanisms will be discussed. Therefore, deep analysis and discussion of various treatment methods are required to understand the ARGs removal mechanisms. In this manuscript, the role of antibiotics and the resistance mechanism of ARB are discussed in depth. In addition, the fate of ARGs in an aquatic environment and detection methods are compared comprehensively and discussed. In particular, the advantages and disadvantages of various methods are summarized and reviewed critically. Finally, combined technologies, such as advanced oxidation process (AOP) with biochemical systems, membrane separation with electrochemical AOP, ultrafiltration (UF) membrane coupled with photocatalytic treatment, and UF membrane separation coupled with sonication, are introduced. Overall, low-energy anaerobic treatment reactors with any of the above combined treatments might reduce the discharge of large quantities of ARGs into the environment. Finally, this review provides valuable insights for better ARG removal technologies by introducing combined effective treatment strategies used in real WWTPs.

The reduction and fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in microbial fuel cell (MFC) during treatment of livestock wastewater

The fate and removal efficiency of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in livestock wastewater by microbial fuel cell (MFC) was evaluated by High-throughput quantitative PCR. The results showed that 137 ARGs and 9 MGEs were detected in untreated livestock wastewater. The ARG number of macrolide-lincosamide-streptogramin group B (MLSB), tetracycline and sulfonamide were relatively higher. Throughout the treatment process, the number and abundance of ARGs and MGEs significantly decreased. The relative abundance of tetracycline, sulfonamide and chloramphenicol resistance genes showed the most obvious decreasing trend, and the relative abundance of MGEs decreased by 75% (from 0.012 copies/16S rRNA copies to 0.003 copies/16S rRNA copies). However, the absolute abundance of beta-lactamase resistance genes slightly increased. The operation process of MFC produces selective pressure on microorganisms, and Actinobacteria were predominant and had the ability to decompose antibiotics. The COD removal rate and TN removal rate of livestock wastewater were 67.81% and 62.09%, and the maximum power density and coulomb efficiency (CE) reached 11.49% and 38.40% respectively. This study demonstrated that although the removal of COD and TN by MFC was limited, MFC was quite effective in reducing the risk of antibiotic toxicity and horizontal gene transfer.

Effects of different oxygen conditions on pollutants removal and the abundances of tetracycline resistance genes in activated sludge systems

The individual and combined effects of tetracycline (TC) and divalent copper (Cu²⁺) on the performance of activated sludge systems and the abundances of tetracycline resistance genes (TRGs) in activated sludge, under both aerobic and anaerobic conditions, were studied. Activated sludge systems received TC (0.2 mg L^-1) and Cu²⁺ (5 mg L^-1) separately or jointly under either aerobic or anaerobic conditions. The addition of TC did not affect the performance of activated sludge systems and the addition of Cu²⁺ and mixed TC/Cu²⁺ inhibited biological phosphorus removal. The TC removal efficiencies in systems under aerobic and anaerobic conditions were 98.4%-99.7% and 96.8%-99.9%, respectively, and Cu²⁺ promoted TC removal in activated sludge systems. The TC degradation product was 4-epitetracycline (ETC) in activated sludge systems under both aerobic and anaerobic conditions. The total relative abundances of TRGs (tetA, tetC, tetE, tetM, tetO, tetW, tetX and tetB(P)) in activated sludge showed opposite development trends under the two oxygen conditions and aerobic condition was beneficial to the attenuation of high-risk TRGs. The results of this study might improve evaluation of the combined effects of antibiotics and heavy metals on wastewater biological treatment systems.

Individual and synergic effect of carbamazepine and diclofenac in the removal of organic matter from an expanded granular bed anaerobic reactor

Due to the negative effects caused to the natural environment by the presence of pharmaceutical-type traces and other pollutants in wastewater, it is necessary to develop and optimize efficient treatment systems. This study evaluated the effect of carbamazepine (CBZ) and diclofenac (DCF) on the behavior of seven EGSB (expanded granular sludge bed) anaerobic reactors at laboratory scale, using chromatographic and physicochemical analyses of the influent, effluent, and the biomass contained in the reactors. The results showed that CBZ had a greater effect on the removal and behavior of microorganisms than DCF, with average efficiencies of 34.04 ± 18.58%, 20.76 ± 8.51% and 16.29 ± 11.08% during stage II, III and IV, respectively, for CBZ, and 92.37 ± 12.74%, 26.77 ± 5.90% and 22.28 ± 9.60% during stage II, III and IV, respectively, for DCF. Additionally, it was found that the interaction of the co-substrate used (sodium acetate) in conjunction with the pharmaceutical compounds decreased the efficiency of the system in terms of the removal of analytes.

Occurrence of Antibiotic-Resistant Genes and Bacteria in Household Greywater Treated in Constructed Wetlands

There is a growing body of knowledge on the persistence of antibiotic-resistant genes (ARGs) and antibiotic-resistant bacteria (ARB) in greywater and greywater treatment systems such as constructed wetlands (CWs). Our research quantified ARGs (sul1, qnrS, and blaCTXM32), class one integron (intI1), and bacterial marker (16S) in four recirculating vertical flow CWs in a small community in the Negev desert, Israel, using quantitative polymerase chain reaction (qPCR). The greywater microbial community was characterized using 16S rRNA amplicon sequencing. Results show that CWs can reduce ARG in greywater by 1–3 log, depending on the gene and the quality of the raw greywater. Community sequencing results showed that the bacterial community composition was not significantly altered after treatment and that Proteobacteria, Epsilonbacteraeota, and Bacteroidetes were the most dominant phyla before and after treatment. Pseudomonas, Citrobacter, Enterobacter, and Aeromonas were the most commonly identified genera of the extended spectrum beta lactamase (ESBL) colonies. Some of the ESBL bacteria identified have been linked to clinical infections (Acinetobacter nosocomialis, Pseudomonas fulva, Pseudomonas putida, Pseudomonas monteilii, and Roseomonas cervicalis). It is important to monitor intI1 for the potential transfer of ARGs to pathogenic bacteria.

Antibiotics and antibiotic resistance genes in landfills: A review

Landfill are important reservoirs of antibiotics and antibiotic resistance genes (ARGs). They harbor diverse contaminants, such as heavy metals and persistent organic chemicals, complex microbial consortia, and anaerobic degradation processes, which facilitate the occurrence, development, and transfer of ARGs and antibiotic resistant bacteria (ARB). The main concern is that antibiotics and developed ARGs and ARB may transfer to the local environment via leachate and landfill leakage. In this paper, we provide an overview of established studies on antibiotics and ARGs in landfills, summarize the origins and distribution of antibiotics and ARGs, discuss the linkages among various antibiotics, ARGs, and bacterial communities as well as the influencing factors of ARGs, and evaluate the current treatment processes of antibiotics and ARGs. Finally, future research is proposed to fill the current knowledge gaps, which include mechanisms for the development and transmission of antibiotic resistance, as well as efficient treatment approaches for antibiotic resistance.

Higher abundance of core antimicrobial resistant genes in effluent from wastewater treatment plants

Wastewater treatment plants (WWTPs) receive sewage water from a variety of sources, including livestock farms, hospitals, industries, and households, that contain antimicrobial resistant bacteria (ARB) and antimicrobial resistant genes (ARGs). Current treatment technologies are unable to completely remove ARB and ARGs, which are eventually released into the aquatic environment. This study focused on the core resistome of urban WWTPs that are persistent through wastewater treatment processes. We adopted the Hiseq-based metagenomic sequencing approach to identify the core resistome, their genetic context, and pathogenic potential of core ARGs in the influent (IN) and effluent (EF) samples of 12 urban WWTPs in South Korea. In this study, the abundance of ARGs ranged from 0.32 to 3.5 copies of ARGs per copy of the 16S rRNA gene, where the IN samples were relatively higher than the EF samples, especially for the macrolide-lincosamide-streptogramin (MLS)- and tetracycline- resistant genes. On the other hand, there were 43 core ARGs sharing up to 90% of the total, among which the relative abundance of sul1, APH(3'')-lb, and RbpA was higher in EF than in IN (p < 0.05). Moreover, tetracycline and sulfonamide-related core ARGs in both EF and IN were significantly more abundant on plasmids than on chromosomes (p < 0.05). We also found that the majority of core ARGs were carried by opportunistic pathogens such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa in both IN and EF. In addition, phages were the only mobile elements whose abundance correlated with that of core ARGs in EF, suggesting that transduction may play a major role in disseminating ARGs in the receiving water environment of the urban WWTP. The persistent release of core ARGs with pathogenic potential into environmental water is of immediate concern. The mobility of ARGs and ARBs in the environment is a major public health concern. These results should be taken into consideration when developing policy to mitigate environmental dissemination of ARG by WWTPs.

Changes of antibiotic resistance genes and bacterial communities in the advanced biological wastewater treatment system under low selective pressure of tetracycline

Effluents of conventional wastewater treatment systems contain antibiotic residues at concentrations below the minimal inhibitory concentrations (MIC), which nevertheless could still select for antibiotic-resistant bacteria. This work focuses on evaluating the changes of antibiotic resistance genes (ARGs) and bacterial communities in a planted advanced biological wastewater treatment system (ABWWTS) under long-term exposure to sub-MIC tetracycline. In the ABWWTS, the removal rates of tetracycline ranged from 97.9% to 99.9%, and a 17.2% decrease in the average removal rates of NH₄⁺-N was observed after the addition of tetracycline. Although the background of ABWWTS contributed to the ARGs in effluents, the concentration of 283 targeted ARGs (ΣARGs) was 83.5% lower in effluents than in influents after sub-MIC tetracycline exposure, and the concentrations of ΣARGs in the ABWWTS were, on average, 30.0% lower than those in an unplanted biological wastewater treatment system (UBWWTS) after a performance of 130 days. The relative abundance of tetracycline resistance genes increased within ABWWTS and UBWWTS under tetracycline exposure. After tetracycline exposure, bacterial diversity in ABWWTS and UBWWTS increased on average by 36.2% and 42.7%, respectively, and the abundances of Nitrosomonas and Nitrospira in the aerobic zone were more than 10-times higher in the ABWWTS than in the UBWWTS. Sub-MIC tetracycline concentrations were linearly correlated with the relative abundance of tetracycline resistance genes in Escherichia coli (E. coli). Long-term exposure to tetracycline at the same concentration increased abundances of the same ARGs (i.e., tetR-02 and tetM-01) in E. coli and the microflora of the ABWWTS, revealing that sub-MIC tetracycline could increase the abundance of ARGs in the ABWWTS by facilitating the vertical transfer of tetracycline resistance genes. These findings demonstrated that planted ABWWTS played a positive role in removing ARGs under low antibiotic selective pressure, which was in accompany with increasing levels of corresponding ARGs within the system.

A Review on Occurrence and Spread of Antibiotic Resistance in Wastewaters and in Wastewater Treatment Plants: Mechanisms and Perspectives

This paper reviews current knowledge on sources, spread and removal mechanisms of antibiotic resistance genes (ARGs) in microbial communities of wastewaters, treatment plants and downstream recipients. Antibiotic is the most important tool to cure bacterial infections in humans and animals. The over- and misuse of antibiotics have played a major role in the development, spread, and prevalence of antibiotic resistance (AR) in the microbiomes of humans and animals, and microbial ecosystems worldwide. AR can be transferred and spread amongst bacteria via intra- and interspecies horizontal gene transfer (HGT). Wastewater treatment plants (WWTPs) receive wastewater containing an enormous variety of pollutants, including antibiotics, and chemicals from different sources. They contain large and diverse communities of microorganisms and provide a favorable environment for the spread and reproduction of AR. Existing WWTPs are not designed to remove micropollutants, antibiotic resistant bacteria (ARB) and ARGs, which therefore remain present in the effluent. Studies have shown that raw and treated wastewaters carry a higher amount of ARB in comparison to surface water, and such reports have led to further studies on more advanced treatment processes. This review summarizes what is known about AR removal efficiencies of different wastewater treatment methods, and it shows the variations among different methods. Results vary, but the trend is that conventional activated sludge treatment, with aerobic and/or anaerobic reactors alone or in series, followed by advanced post treatment methods like UV, ozonation, and oxidation removes considerably more ARGs and ARB than activated sludge treatment alone. In addition to AR levels in treated wastewater, it examines AR levels in biosolids, settled by-product from wastewater treatment, and discusses AR removal efficiency of different biosolids treatment procedures. Finally, it puts forward key-points and suggestions for dealing with and preventing further increase of AR in WWTPs and other aquatic environments, together with a discussion on the use of mathematical models to quantify and simulate the spread of ARGs in WWTPs. Mathematical models already play a role in the analysis and development of WWTPs, but they do not consider AR and challenges remain before models can be used to reliably study the dynamics and reduction of AR in such systems.

Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt

Wastewater treatment plants (WWTPs) are recognized as hotspots for the dissemination of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in the environment. Our study utilized a high-throughput sequencing-based metagenomic analysis approach to compare the ARG abundance profiles of the raw sewage, treated effluent and activated sludge samples from a full-scale WWTP in Egypt. In addition, the difference in microbial community composition due to the treatment process was assessed. As a result, 578 ARG subtypes (resistance genes) belonging to 18 ARG types (antibiotic resistance classes) were identified. ARGs encoding for resistance against multidrug, aminoglycoside, bacitracin, beta-lactam, sulfonamide, and tetracycline antibiotics were the most abundant types. The total removal efficiency percentage of ARGs in the WWTP was found to be 98% however, the ARG persistence results indicated that around 68% of the ARGs in the influent could be found in the treated effluent. This finding suggests that the treated wastewater poses a potential risk for the ARG dissemination in bacterial communities of the receiving water bodies via horizontal gene transfer (HGT). The community composition at phylum level showed that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant phyla in all datasets. Although the relative abundance of several pathogenic bacteria in the influent declined to less than 1% in the effluent, the taxonomic assignments at species level for the effluent and sludge metagenomes demonstrated that clinically important pathogens such as Escherichia coli, Klebsiella pneumonia, and Aeromonas caviae were present. Overall, the results of this study would hopefully enhance our knowledge about the abundance profiles of ARGs and their fate in different wastewater treatment compartments that have never been examined before.

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning

While the microbiome of activated sludge (AS) in wastewater treatment plants (WWTPs) plays a vital role in shaping the resistome, identifying the potential bacterial hosts of antibiotic resistance genes (ARGs) in WWTPs remains challenging. The objective of this study is to explore the feasibility of using a machine learning approach, random forests (RF's), to identify the strength of associations between ARGs and bacterial taxa in metagenomic datasets from the activated sludge of WWTPs. Our results show that the abundance of select ARGs can be predicted by RF's using abundant genera (Candidatus Accumulibacter, Dechloromonas, Pesudomonas, and Thauera, etc.), (opportunistic) pathogens and indicators (Bacteroides, Clostridium, and Streptococcus, etc.), and nitrifiers (Nitrosomonas and Nitrospira, etc.) as explanatory variables. The correlations between predicted and observed abundance of ARGs (erm(B), tet(O), tet(Q), etc.) ranged from medium (0.400 < R² < 0.600) to strong (R² > 0.600) when validated on testing datasets. Compared to those belonging to the other two groups, individual genera in the group of (opportunistic) pathogens and indicator bacteria had more positive functional relationships with select ARGs, suggesting genera in this group (e.g., Bacteroides, Clostridium, and Streptococcus) may be hosts of select ARGs. Furthermore, RF's with (opportunistic) pathogens and indicators as explanatory variables were used to predict the abundance of select ARGs in a full-scale WWTP successfully. Machine learning approaches such as RF's can potentially identify bacterial hosts of ARGs and reveal possible functional relationships between the ARGs and microbial community in the AS of WWTPs.

Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges

Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pathogen host relationship and risk management. These research gaps need to be addressed and research findings need to be transformed into practical guidance for WWTP operators to enable effective progress towards mitigating the evolution and spread of AMR.

Role of anaerobic sludge digestion in handling antibiotic resistant bacteria and antibiotic resistance genes - A review

Currently, anaerobic sludge digestion (ASD) is considered not only for treating residual sewage sludge and energy recovery but also for the reduction of antibiotic resistance genes (ARGs). The current review highlights the reasons why antibiotic resistant bacteria (ARB) and ARGs exist in ASD and how ASD performs in the reduction of ARB and ARGs. ARGs and ARB have been detected in ASD with some reports indicating some of the ARGs can be completely removed during the ASD process, while other studies reported the enrichment of ARB and ARGs after ASD. This paper reviews the performance of ASD based on operational parameters as well as environmental chemistry. More studies are needed to improve the performance of ASD in reducing ARGs that are difficult to handle and also differentiate between extracellular (eARGs) and intracellular ARGs (iARGs) to achieve more accurate quantification of the ARGs.

Variation of Metagenome From Feedstock to Digestate in Full-Scale Biogas Plants

Anaerobic digestion (AD) has been widely used to resolve the problem of organic wastes worldwide. Previous studies showed that the types of feedstock have a great influence on the AD microbiome, and a huge number of AD populations are migrated from upstream feedstocks. However, the changes of microbial compositions from feedstock to AD digestate are still less understood. We collected feedstock samples from 56 full-scale biogas plants, generated 1,716 Gb feedstock metagenomic data in total, and constructed the first comprehensive microbial gene catalog of feedstock containing 25.2 million genes. Our result indicated that the predominant phyla in feedstock are Firmicutes, Bacteroidetes, and Proteobacteria, which is similar to that in AD digestate, and the microbial diversity of feedstock samples is higher than that of AD digestate samples. In addition, the relative abundance of most genes involved in methanogenesis increase from feedstock to AD digestate. Besides, the amount of antibiotic resistance genes (ARGs) and pathogenic bacteria in AD are effectively reduced compared to feedstocks. This study provides a comprehensive microbial gene catalog of feedstock, and deepens the understanding of variation of microbial communities from feedstock to AD digestate of full-scale AD. The results also suggest the potential of AD to reduce the level of ARGs and pathogens in animal manure.

Effects of micro-aeration on microbial niches and antimicrobial resistances in blackwater anaerobic digesters

Anaerobic digestion (AD) of source-diverted blackwater (toilet flush) at ambient room temperature presents challenges for fast hydrolysis of particulate matters. This study investigated the effect of different micro-aeration dosages for blackwater AD. Sequencing batch reactors were operated at ambient room temperature (22 ± 1°C) with micro-aeration (0, 5, 10, 50, and 150 mg O₂ g^-1 COD_feed per cycle) and gradually reduced hydraulic retention times from 5 d to 2 d. The methanogenesis efficiencies were greater at low oxygen dosages (i.e., 0, 5, 10) while the volatile fatty acids (VFAs) accumulated more at high oxygen dosages (i.e., 50, 150). Microbial communities were significantly different under different oxygen dosages (p<0.05), with segregation of microbial ecological niches in low and high oxygen dosage communities. The low-oxygen-dosage niche (0, 5, and 10 mg g^-1 COD_feed) was inhabited by fermenting and syntrophic bacteria (e.g., Cytophaga, Syntrophomonas) and methanogens (e.g., Methanobacterium, Methanolinea, Methanosaeta). The high-oxygen-dosage niche (50 and 150 mg g^-1 COD_feed) had significantly (p<0.05) more facultative anaerobic bacteria (Ignavibacteriales and Cloacamonales), and aerobic bacteria (Rhodocyclales). Moreover, blackwater can be a source of antimicrobial resistance genes (ARGs), which are affected by different oxygen dosages. The ARG variation correlated with the microbial community composition (p<0.05). Low-oxygen-dosage communities contained a higher prevalence of mobile gene elements (intI1 and korB) and tetM, ermB, sul1, sul2, and blaCTX-M than the high-oxygen-dosage communities, indicating that oxygen dosage influenced the prevalence of populations carrying ARGs. These findings suggest that application of micro-aeration to AD can be used to control ARG profiles.

Electrolysis-sulfate-reducing up-flow sludge bed-biological contact oxidation reactor for Norfloxacin removal from wastewater with high sulfate content

This study investigated the treatment of 100-mg/L Norfloxacin (NOR) wastewater containing high concentrations of sulfate through a combination of electrolysis, sulfate-reducing up-flow sludge bed (SRUSB), and biological contact oxidation reactor (BCOR) treatments. Results revealed that after 62 h, the reaction system had processed over 97% of the NOR. Additionally, electrolysis with sodium sulfate as the electrolyte transformed 87.8% of the NOR but only 33.5% of the total organic carbon (TOC). In the SRUSB, the TOC and SO₄^2- contents were simultaneously reduced by 87.4% and 95.6%, respectively, providing a stable environment to the BCOR. In the BCOR, 36.3% and 85.9% of the NOR and TOC were degraded. High-performance liquid chromatography-tandem mass spectrometry analysis identified three possible degradation pathways under the attack of -OH during electrolysis, including defluorination, piperazinyl ring transformation, and quinolone ring transformation. Furthermore, the Illumina HiSeq sequencing results demonstrated that the sulfate-reducing bacteria (represented by Desulfobacter and Desulfobulbus) in the SRUSB and the sulfate-oxidizing bacteria (mainly consisting of Gammaproteobacteria and Alphaproteobacteria) in the BCOR played important roles in carbon chain oxidation and benzene ring opening and thoroughly degraded the electrolysis products. Thus, this method effectively overcomes the incomplete degradation and low removal efficiency issues associated with single electrolysis or biological methods in traditional processes.

Antibiotic resistance in the environment: a critical insight on its occurrence, fate, and eco-toxicity

The overuse, misuse, and underuse of antibiotics tend to increase the antibiotic burden in the environment resulting into the evolution in microbial community to possess resistance that renders antibiotics ineffective against them. The current review recapitulates the present state of knowledge about the occurrence and fate of antibiotics in various environmental matrices. Also, the prevalence of antibiotic-resistant bacteria/antibiotic-resistant genes (ARB/ARGs) in various biological and non-biological systems, eco-toxicity of antibiotics on non-target organisms, and remediation methods for antibiotics and ARB/ARGs removal were critically reviewed. Furthermore, a comparison of various technologies for their efficiency to eliminate antibiotic residues and ARB/ARGs is made. The study identified gaps in the investigation of toxic effects of low concentration of antibiotics and the mixture of multiple antibiotics on non-target organisms. The study of antibiotics' phytotoxicity and toxicity towards sediment and soil-dwelling organisms are also recognized as a knowledge gap. The review also details policies implemented across the globe to fight against antibiotic resistance, and the scarcity of data on lab to land transferred remediation technology was identified. The present study entails a critical review of literature providing guidelines for the articulation of policies for prudent use of antibiotics, limits on the amount of antibiotics in pharmaceutical formulations, and regular surveillance in the Indian context.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Metagenomic analysis reveals the fate of antibiotic resistance genes in two-stage and one-stage anaerobic digestion of waste activated sludge

Waste activated sludge (WAS) from wastewater treatment plants is an important reservoir of antibiotic resistance genes (ARGs). The fate of ARGs in this process was not revealed previously. The present study applied metagenomic approach to examine the occurrence and fate of ARGs in thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM), by comparison with mesophilic alkaline fermentation followed by mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The removal efficiency of two-stage anaerobic digestion (AD) to total ARGs is higher than that of one-stage AD. The hydrogen and methane production stages of two-stage AD processes have dissimilar impact on the fate of ARGs. Macrolide, lincosamide, and streptogramin (MLS) resistance genes were enriched, especially in the hydrogen production reactors of TM and MM processes. Statistical analysis of metagenomic profiles analysis suggested that bacA may be the differential ARG subtype of two-stage AD process. ARG-like sequences encoding antibiotic efflux pump, antibiotic inactivation and antibiotic target alteration mechanisms were identified as the dominant ARGs resistance mechanisms in all samples. Procrustes analysis showed that microbial community composition structured the resistome. Co-occurrence patterns between ARGs and microbial phylogeny revealed that 26 bacterial species might be potential hosts of 94 ARG subtypes.

Nanotechnology as a viable alternative for the removal of antimicrobial resistance determinants from discharged municipal effluents and associated watersheds: A review

Effective and efficient utilization of antimicrobial drugs has been one of the important cornerstone of modern medicine. However, since antibiotics were first discovered by Alexander Fleming about a century ago, the time clock of antimicrobial resistance (AMR) started ticking somewhat leading to a global fear of a possible "post-antimicrobial era". Antibiotic resistance (AR) remains a serious challenge causing global outcry in both the clinical setting and the environment. The huge influence of municipal wastewater effluent discharges on the aquatic environment has made the niche a hotspot of research interest in the study of emergence and spread of AMR microbes and their resistance determinants/genes. The current review adopted a holistic approach in studying the proliferation of antibiotic resistance determinants (ARDs) as well as their impacts and fate in municipal wastewater effluents and the receiving aquatic environments. The various strategies deployed hitherto for the removal of resistance determinants in municipal effluents were carefully reviewed, while the potential for the use of nanotechnology as a viable alternative is explicitly explored. Also, highlighted in this review are the knowledge gaps to be filled in order to curtail the spread of AMR in aquatic environment and lastly, suggestions on the applicability of nanotechnology in eliminating AMR determinants in municipal wastewater treatment facilities are proffered.

Analysis of microbial community structure and degradation of ammonia nitrogen in groundwater in cold regions

Nitrogen pollution exceeding the standard because of intensive farming and cropping systems has been a widespread problem in Northeast China. This study investigated the characteristics of functional microorganisms in groundwater in the Bang River farming area. Metagenomic sequencing was used to analyze microbial community structures and Canoco was applied to reveal the response relationship between the microbial community and water environmental factors and to identify changes in the microbial population in response to the addition of electronic donors NH₄⁺-N, NO₂^--N, and NO₃^--N. The results showed that the dominant microorganisms in groundwater belong to the genera Exiguobacterium, Citrobacter, Acinetobacter, and Pseudomonas, which accounted for more than 40% of the total microbes in the study area. When combined with the results of a water chemical factor test, the dominant bacteria were found to be correlated with Fe²⁺, Mn²⁺, NH₄⁺, NO₃^-, NO₂^-, HCO₃^-, DOC, and pH in the water. However, the microbial population changed after the addition of the electron donor, with the genera Pseudomonas, Serratia, Enterobacter, Azomonas, and Ewingella accounting for 97.06% of the total sequences. Indigenous nitrogen-degrading bacteria suitable for low temperature, low oxygen, and oligotrophic groundwater were screened out. The total removal efficiency of NH₄⁺-N, NO₂^--N, and NO₃^--N in 120 h was 90.83%, 75.04%, and 73.35%, respectively. According to the experimental results, the degradation reaction kinetics followed a pseudo-second-order equation. The results presented herein provide an important scientific basis for the microbial remediation of groundwater contaminated by ammonia.

Impact of Redox Conditions on Antibiotic Resistance Conjugative Gene Transfer Frequency and Plasmid Fate in Wastewater Ecosystems

Wastewater is a common pathway for the spread of antibiotic resistance (AR) genes and bacteria into the environment. Biological treatment can mitigate this path, but horizontal gene transfer (HGT) between bacteria also occurs in such processes, although the influence of bioreactor habitat and ecology on HGT frequency is not well understood. Here, we quantified how oxidation-reduction (redox) conditions impact the fate of a Green fluorescent protein (Gfp)-tagged AR plasmid (pRP4-gfp) within an E. coli host (EcoFJ1) in the liquid phase and biofilms in bioreactors. Replicate reactors treating domestic wastewater were operated under stable aerobic (+195 ± 25 mV), anoxic (-15 ± 50 mV), and anaerobic (-195 ± 15 mV) conditions, and flow cytometry and selective plating were used to quantify donor strain, EcoFJ1(pRP4-gfp), and putative transconjugants over time. Plasmid pRP4-gfp-bearing cells disappeared rapidly in aerobic ecosystems (∼2.0 log reduction after 72 h), especially in the liquid phase. In contrast, EcoFJ1(pRP4-gfp) and putative transconjugants persisted much longer in anaerobic biofilms (∼1.0 log reduction, after 72 h). Plasmid transfer frequencies were also higher under anaerobic conditions. In parallel, protozoan abundances were over 20 times higher in aerobic reactors relative to anaerobic reactors, and protozoa numbers significantly inversely correlated with pRP4-gfp signals across all reactors (p < 0.05). Taken together, observed HGT frequency and plasmid retention are impacted by habitat conditions and trophic effects, especially oxygen conditions and apparent predation. New aerobic bioreactor designs are needed, ideally employing passive aeration to save energy, to minimize resistance HGT in biological wastewater treatment processes.

Dynamic characteristics of immobilized microorganisms for remediation of nitrogen-contaminated groundwater and high-throughput sequencing analysis of the microbial community

The aim of this study was to investigate the effect of adsorption by a composite active medium (nitrogen-degrading bacteria immobilized on scoria) on the removal of ammonium nitrogen (NH₄⁺-N), nitrite nitrogen (NO₂^-N) and nitrate nitrogen (NO₃^-N). Transport of these three forms of nitrogen was investigated using columns with different flow rates, initial concentrations and depths. Immobilization of the bacteria on the scoria significantly enhanced the ability of the composite active medium to remove nitrogen during the remediation process. As the flow rate increased, the shear force increased and solute diffusion decreased, thereby improving the tolerance of the bacteria for the three forms of nitrogen and reducing the penetration time. Increasing the initial nitrogen concentration resulted in a decrease in the adsorption rate constant (K_Th). The nitrogen-degrading bacteria immobilized on scoria rapidly reached saturation with regards to their nitrogen adsorption capacity. The initial nitrogen concentration of each media layer was different, and the composite active medium had a certain blocking effect, which resulted in a slow increase in the concentration of nitrogen in the deeper media layer. The transport experiments showed that the process accords with the thomas model and the Bohart-Adams model. The contents of the three forms of nitrogen were within acceptable standards for drinking water after 2 months of a column containing the composite active medium. The composite active medium can be used for in situ and ex situ remediation of groundwater containing excessive nitrogen. High-throughput sequencing analysis was used to monitor the composition of the bacterial community present within the composite active medium. During the remediation process, there were only slight changes in the structure and composition of the nitrogen-degrading bacterial community, although there were clear differences in abundance. Pseudomonas, Stenotrophomonas and Serratia were the three bacterial genera that were effective removal of all three forms of nitrogen.

Antibiotic resistance in wastewater treatment plants: understanding the problem and future perspectives

Antibiotics residues (AR), antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) are a new class of water contaminants, due to their adverse effects on aquatic ecosystems and human health. Contamination of water bodies occurs mainly by the excretion of antibiotics incompletely metabolized by humans and animals and is considered the main source of contamination of antibiotics in the environment. Given the imminent threat, the World Health Organization (WHO) has categorized the spread of antibiotics as one of the top three threats to public health in the twenty-first century. The Urban Wastewater Treatment Plants (UWWTP) bring together AR, ARB, ARG, making the understanding of this peculiar environment fundamental for the investigation of technologies aimed at combating the spread of bacterial resistance. Several methodologies have been employed focusing on reducing the ARB and ARG loads of the effluents, however the reactivation of these microorganisms after the treatment is widely reported. This work aims to elucidate the role of UWWTPs in the spread of bacterial resistance, as well as to report the efforts that have been made so far and future perspectives to combat this important global problem.

Ozone pretreatment of wastewater containing aromatics reduces antibiotic resistance genes in bioreactors: The example of p-aminophenol

Aromatic matters are widely present in wastewater, especially industrial wastewater, and may lead to a high abundance of antibiotic resistance genes (ARGs) in wastewater treatment bioreactors and stimulate horizontal transfers of ARGs. Here, we investigated a practical approach that applying ozone pretreatment to mitigate ARGs in bioreactors treating wastewater containing a typical aromatic pollutant, p-aminophenol (PAP). The results showed that ozone pretreatment could effectively reduce the aromaticity of wastewater, and the relative abundance of ARGs in the bioreactor fed with ozone treated wastewater decreased by over 70% compared to the control reactor. Multidrug, quinolone, mupirocin, polymyxin, aminoglycoside, glycopeptide, beta-lactam, and trimethoprim resistance genes were all reduced in the bioreactors receiving wastewater pretreated by ozone. Metagenomic analysis suggested that the reduction of ARGs could be attributed to the co-occurrence of ARGs and aromatic degradation genes in bacteria. Furthermore, we expanded our analysis to investigate 71 metagenomes from different environments, and the results indicated that the impact of aromatics on ARG abundance widely occurs in various ecosystems and confirmed that high levels of aromatics could lead to high abundance of ARGs. Taken together, our work confirmed that the aromatics played critical roles in selecting ARGs and proposed a feasible approach to reduce ARGs in wastewater treatment bioreactors.