Effects of emerging pollutants on the occurrence and transfer of antibiotic resistance genes: A review

A state-of-art-review on emerging contaminants: Environmental chemistry, health effect, and modern treatment methods

Pollution problems are increasingly becoming e a priority issue from both scientific and technological points of view. The dispersion and frequency of pollutants in the environment are on the rise, leading to the emergence have been increasing, including of a new class of contaminants that not only impact the environment but also pose risks to people's health. Therefore, developing new methods for identifying and quantifying these pollutants classified as emerging contaminants is imperative. These methods enable regulatory actions that effectively minimize their adverse effects to take steps to regulate and reduce their impact. On the other hand, these new contaminants represent a challenge for current technologies to be adapted to control and remove emerging contaminants and involve innovative, eco-friendly, and sustainable remediation technologies. There is a vast amount of information collected in this review on emerging pollutants, comparing the identification and quantification methods, the technologies applied for their control and remediation, and the policies and regulations necessary for their operation and application. In addition, This review will deal with different aspects of emerging contaminants, their origin, nature, detection, and treatment concerning water and wastewater.

Advances, challenges, and prospects in microalgal-bacterial symbiosis system treating heavy metal wastewater

Heavy metal (HM) pollution, particularly in its ionic form in water bodies, is a chronic issue threatening environmental security and human health. The microalgal-bacterial symbiosis (MABS) system, as the basis of water ecosystems, has the potential to treat HM wastewater in a sustainable manner, with the advantages of environmental friendliness and carbon sequestration. However, the differences between laboratory studies and engineering practices, including the complexity of pollutant compositions and extreme environmental conditions, limit the applications of the MABS system. Additionally, the biomass from the MABS system containing HMs requires further disposal or recycling. This review summarized the recent advances of the MABS system treating HM wastewater, including key mechanisms, influence factors related to HM removal, and the tolerance threshold values of the MABS system to HM toxicity. Furthermore, the challenges and prospects of the MABS system in treating actual HM wastewater are analyzed and discussed, and suggestions for biochar preparation from the MABS biomass containing HMs are provided. This review provides a reference point for the MABS system treating HM wastewater and the corresponding challenges faced by future engineering practices.

The perfluoroalkyl substances influenced the distribution of bacterial communities and their functions from source water to tap water

Perfluoroalkyl substances (PFASs) and antibiotic resistance genes (ARGs) in drinking water are environmental issues that require special attention. The objective of this study was to know the effects of PFASs on microbial communities and their functional genes from source water to tap water. PFASs were detected by mass-labeled internal standards method, and the microbial communities and functional genes were analyzed by metagenomics. Our results indicated that the concentration of total PFASs in the water ranged from 47.7 to 171.4 ng/L, with perfluorobutanoic acid (PFBA) and perfluorooctanoic acid (PFOA) being the dominant types. The PFASs concentration decreased slowly from source to tap water in some months. PFBA, PFOA, perfluorooctane sulfonic acid (PFOS) and perfluorohexanoic acid (PFHxA) influenced the functional genes related to two-component system, bacterial secretion system and flagellar assembly of Aquabacterium, Methylobacterium, and Curvibacter, which contributed significantly to macB and evgS. Therefore, the bacterial communities enhanced adaptation to fluctuating environments by upregulating some functional genes under the PFASs stress, with concomitant changes in the expression of ARGs. Moreover, PFASs also promoted the expression of functional genes associated with human diseases, such as shigellosis and tuberculosis, which increased the risk of human pathogenicity. The bench scale experiment results also suggested that PFOA and PFOS in drinking water can promote the ARGs proliferation and induce microbial risk. Therefore, it is necessary to take measures to prevent the risks caused by PFASs and ARGs in drinking water.

ZnO nanostructured matrix as nexus catalysts for the removal of emerging pollutants

Water pollution stands as a pressing global environmental concern, elevating the significance of innovative, dependable, and sustainable solutions. This study represents an extensive review of the use of photocatalytic zinc oxide nanoparticles (ZnO NPs) for the removal of emerging pollutants from water and wastewater. The study examines ZnO NPs' different preparation methods, including physical, chemical, and green synthesis, and emphasizes on advantages, disadvantages, preparation factors, and investigation methods for the structural and morphological properties. ZnO NPs demonstrate remarkable properties as photocatalysts; however, their small dimensions pose an issue, leading to potential post-use environmental losses. A strategy to overcome this challenge is scaling up ZnO NP matrices for enhanced stability and efficiency. The paper introduces novel ZnO NP composites, by incorporating supports like carbon and clay that serve as photocatalysts in the removal of emerging pollutants from water and wastewater. In essence, this research underscores the urgency of finding innovative, efficient, and eco-friendly solutions for the removal of emerging pollutants from wastewater and highlights the high removal efficiencies obtained when using ZnO NPs obtained from green synthesis as a photocatalyst. Future research should be developed on the cost-benefit analysis regarding the preparation methods, treatment processes, and value-added product regeneration efficiency.

Occurrence and risk assessment of pharmaceuticals in hospital wastewater in Costa Rica

This work aims to determine the occurrence, hazard and prioritization of pharmaceuticals from hospital wastewater in Costa Rica through the monitoring of 70 compounds and assessing their environmental risk through a hazard quotient approach (HQ). Moreover, the quantification of selected antibiotic resistance genes (ARGs) was conducted for the first time in this matrix in this geographical location. Thirty-four pharmaceuticals were detected, being caffeine, 1,7-dimethylxanthine, acetaminophen, ibuprofen, naproxen, ciprofloxacin and ketoprofen the most frequent (>50% of the samples). Eighteen pharmaceuticals exhibited high hazard (HQ ≥ 1), while five more showed medium hazard (1 > HQ ≥ 0.1). Prioritization, which also included frequency parameters, revealed caffeine, lovastatin, diphenhydramine, acetaminophen, ibuprofen, ciprofloxacin, and sildenafil as the compounds of major concern. Similarly, cumulative hazard per sample (ΣHQ) estimated high hazard towards aquatic organisms in every sample. All selected ARGs, except mcr-1 (polymyxin resistance), were detected. Among genes conferring resistance to beta-lactams, blaCTX-M and blaKPC were the most abundant, related to resistance to cephalosporins and carbapenems. Ecotoxicological evaluation showed mostly low toxicity towards Daphnia magna and Vibrio fischeri, contrary to the marked effect observed towards Lactuca sativa. These findings provide relevant and novel information on the risk posed by hospital wastewater and their pharmaceutical content in the Latin American environmental context.

Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure

Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.

Promoted dissipation and detoxification of atrazine by graphene oxide coexisting in water

The herbicide atrazine (ATZ) has a detrimental effect on the health of aquatic ecosystems and has become a global concern in recent years. But the understanding of its persistence and potential toxicity under combined pollution, especially in the coexistence of other emerging pollutants, remains limited. In this work, the dissipation and transformation of ATZ in combination with graphene oxide (GO) in water were investigated. Results showed that dissipation rates of ATZ dramatically increased by 15-95% with half-lives shortened by 15-40% depending on initial concentrations of ATZ, and the products were mainly toxic chloro-dealkylated intermediates (deethylatrazine (DEA) and deisopropylatrazine (DIA)), but their contents were significantly lower under the coexistence of GO compared to ATZ alone. In the presence of GO, the nontoxic dechlorinated metabolite hydroxyatrazine (HYA) was detected earlier than 2-9 days, and ATZ transformation into HYA was increased by 6-18% during 21-day incubation periods. This study indicated that the coexistence of GO enhanced the dissipation and detoxification of ATZ. From a remediation standpoint, GO-induced hydrolytic dechlorination of ATZ can reduce its ecological toxicity. But the environmental risks of ATZ for aquatic ecosystem under the coexistence of GO should still be given the necessary prominence due to the potential hazard of ATZ adsorbed on GO and the predominant degradation products (DEA and DIA).

A review of Spaulding's classification system for effective cleaning, disinfection and sterilization of reusable medical devices: Viewed through a modern-day lens that will inform and enable future sustainability

Despite advances in medicine and innovations in many underpinning fields including disease prevention and control, the Spaulding classification system, originally proposed in 1957, remains widely used for defining the disinfection and sterilization of contaminated re-usable medical devices and surgical instruments. Screening PubMed and Scopus databases using a PRISMA guiding framework generated 272 relevant publications that were used in this review. Findings revealed that there is a need to evolve how medical devices are designed, and processed by cleaning, disinfection (and/or sterilization) to mitigate patient risks, including acquiring an infection. This Spaulding Classification remains in use as it is logical, easily applied and understood by users (microbiologists, epidemiologists, manufacturers, industry) and by regulators. However, substantial changes have occurred over the past 65 years that challenge interpretation and application of this system that includes inter alia emergence of new pathogens (viruses, mycobacteria, protozoa, fungi), a greater understanding of innate and adaptive microbial tolerance to disinfection, toxicity risks, increased number of vulnerable patients and associated patient procedures, and greater complexity in design and use of medical devices. Common cited examples include endoscopes that enable non- or minimal invasive procedures but are highly sophisticated with various types of materials (polymers, electronic components etc), long narrow channels, right angle and heat-sensitive components and various accessories (e.g., values) that can be contaminated with high levels of microbial bioburden and patient tissues after use. Contaminated flexible duodenoscopes have been a source of several significant infection outbreaks, where at least 9 reported cases were caused by multidrug resistant organisms [MDROs] with no obvious breach in processing detected. Despite this, there is evidence of the lack of attention to cleaning and maintenance of these devices and associated equipment. Over the last few decades there is increasing genomic evidence of innate and adaptive resistance to chemical disinfectant methods along with adaptive tolerance to environmental stresses. To reduce these risks, it has been proposed to elevate classification of higher-risk flexible endoscopes (such as duodenoscopes) from semi-critical [contact with mucous membrane and intact skin] to critical use [contact with sterile tissue and blood] that entails a transition to using low-temperature sterilization modalities instead of routinely using high-level disinfection; thus, increasing the margin of safety for endoscope processing. This timely review addresses important issues surrounding use of the Spaulding classification system to meet modern-day needs. It specifically addresses the need for automated, robust cleaning and drying methods combined with using real-time monitoring of device processing. There is a need to understand entire end-to-end processing of devices instead of adopting silo approaches that in the future will be informed by artificial intelligence and deep-learning/machine learning. For example, combinational solutions that address the formation of complex biofilms that harbour pathogenic and opportunistic microorganisms on the surfaces of processed devices. Emerging trends are addressed including future sustainability for the medical devices sector that can be enabled via a new Quintuple Helix Hub approach that combines academia, industry, healthcare, regulators, and society to unlock real world solutions.

Simultaneous removal of antibiotics and antibiotic resistance genes in wastewater by a novel nonthermal plasma/peracetic acid combination system: Synergistic performance and mechanism

In this study, a novel and green method combining plasma with peracetic acid (plasma/PAA) was developed to simultaneously remove antibiotics and antibiotic resistance genes (ARGs) in wastewater, which achieves significant synergistic effects in the removal efficiencies and energy yield. At a plasma current of 2.6 A and PAA dosage of 10 mg/L, the removal efficiencies of most detected antibiotics in real wastewater exceeded 90 % in 2 min, with the ARG removal efficiencies ranging from 6.3 % to 75.2 %. The synergistic effects of plasma and PAA could be associated with the motivated production of reactive species (including •OH, •CH₃, ¹O₂, ONOO^-, •O₂^- and NO•), which decomposed antibiotics, killed host bacteria, and inhibited ARG conjugative transfer. In addition, plasma/PAA also changed the contributions and abundances of ARG host bacteria and downregulated the corresponding genes of two-component regulatory systems, thus reducing ARG propagation. Moreover, the weak correlations between the removal of antibiotics and ARGs highlights the commendable performance of plasma/PAA in the simultaneous removal of antibiotics and ARGs. Therefore, this study affords an innovative and effective avenue to remove antibiotics and ARGs, which relies on the synergistic mechanisms of plasma and PAA and the simultaneous removal mechanisms of antibiotics and ARGs in wastewater.

Iron-modified biochar boosts anaerobic digestion of sulfamethoxazole pharmaceutical wastewater: Performance and microbial mechanism

The accumulation of volatile fatty acids (VFAs) caused by antibiotic inhibition significantly reduces the treatment efficiency of sulfamethoxazole (SMX) wastewater. Few studies have been conducted to study the VFAs gradient metabolism of extracellular respiratory bacteria (ERB) and hydrogenotrophic methanogen (HM) under high-concentration sulfonamide antibiotics (SAs). And the effects of iron-modified biochar on antibiotics are unknown. Here, the iron-modified biochar was added to an anaerobic baffled reactor (ABR) to intensify the anaerobic digestion of SMX pharmaceutical wastewater. The results demonstrated that ERB and HM were developed after adding iron-modified biochar, promoting the degradation of butyric, propionic and acetic acids. The content of VFAs reduced from 1166.0 mg L^-1 to 291.5 mg L^-1. Therefore, chemical oxygen demand (COD) and SMX removal efficiency were improved by 22.76% and 36.51%, and methane production was enhanced by 6.19 times. Furthermore, the antibiotic resistance genes (ARGs) such as sul1, sul2, intl1 in effluent were decreased by 39.31%, 43.33%, 44.11%. AUTHM297 (18.07%), Methanobacterium (16.05%), Geobacter (6.05%) were enriched after enhancement. The net energy after enhancement was 0.7122 kWh m^-3. These results confirmed that ERB and HM were enriched via iron-modified biochar to achieve high efficiency of SMX wastewater treatment.

Microplastics exacerbate co-occurrence and horizontal transfer of antibiotic resistance genes

Microplastic pollution is a rising environmental issue worldwide. Microplastics can provide a niche for the microbiome, especially for antibiotic-resistant bacteria, which could increase the transmission of antibiotic resistance genes (ARGs). However, the interactions between microplastics and ARGs are still indistinct in environmental settings. Microplastics were found to be significantly correlated with ARGs (p < 0.001), based on the analysis of samples taken from a chicken farm and its surrounding farmlands. Analysis of chicken feces revealed the highest abundance of microplastics (14.9 items/g) and ARGs (6.24 ×10⁸ copies/g), suggesting that chicken farms could be the hotspot for the co-spread of microplastics and ARGs. Conjugative transfer experiments were performed to investigate the effects of microplastic exposure for different concentrations and sizes on the horizontal gene transfer (HGT) of ARGs between bacteria. Results showed that the microplastics significantly enhanced the bacterial conjugative transfer frequency by 1.4-1.7 folds indicating that microplastics could aggravate ARG dissemination in the environment. Potential mechanisms related to the up-regulation of rpoS, ompA, ompC, ompF, trbBp, traF, trfAp, traJ, and down-regulation of korA, korB, and trbA were induced by microplastics. These findings highlighted the co-occurrence of microplastics and ARGs in the agricultural environment and the exacerbation of ARGs' prevalence via rising the HGT derived from microplastics.

Environmental concentrations of surfactants as a trigger for climax of horizonal gene transfer of antibiotic resistance

Ubiquitous antibiotic resistance genes (ARGs) is a significant global human health concern. Surfactants have been extensively used worldwide, and the consumption of surfactants containing hygiene, cleaning agents and disinfectants was multiplied during COVID-19 pandemic, which have caused significantly increased pollution of surfactants in aquatic environment. Whether such ever-increasing surfactant concentration boost dissemination risk of ARGs still remains unknown. Here the effects of three typical surfactants such as sodium dodecyl sulfate, cetyltrimethylammonium bromide and benzalkonium chloride on the transformation of pUC19 plasmid (2686 bp)-borne ARGs to recipient bacteria E. coli DH5ɑ were investigated. It was found that these surfactants at environmental concentrations facilitated horizonal gene transfer (HGT) via transformation. The transformation triggering concentrations for the three surfactants were 0.25-0.34 mg/L with a maximum increased transformation frequency of 13.51-22.93-fold. The mechanisms involved in activated HGT of ARGs via transformation triggered by surfactants could be mainly attributed to the increased production of reactive oxygen species, which further enhanced cell membrane permeability. These findings provide new sights for understanding of ARG propagation and also imply that the drastic rise of surfactant concentration in aquatic environment may significantly increase the dissemination risk of antibiotic resistance.

Transmission mechanisms of antibiotic resistance genes in arsenic-contaminated soil under sulfamethoxazole stress

Numerous studies have revealed the spread mechanism of antibiotic resistance genes (ARGs) in single antibiotic-contaminated soils. However, the comprehensive impacts of heavy metals and antibiotics on ARGs and the underlying mechanisms are still unknown. Here, high-throughput quantitative PCR and high-throughput sequencing were used to investigate changes in ARGs and bacterial communities under various sulfamethoxazole (SMX) regimes (0, 1, 10, 50 mg kg^-1) in arsenic (As) contaminated soils. The study found that the abundances of ARGs, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) significantly increased in the soil fortified at 10 and 50 mg kg^-1 SMX concentrations. The ARGs abundance increased with the increase in the MGEs abundance. Many significant positive correlations between various ARGs subtypes and HMRGs subtypes were found. These results indicate that the HMRGs and MGEs positively contributed to the enrichment of ARGs in As-contaminated soils under SMX stress. Meanwhile, the abundance of copiotrophic (Actinobacteriota) reduced and oligotrophic (Gemmatimonadota) increased, indicating that the life history strategy of the community changed. In addition, Gemmatimonadota was positively correlated to ARGs, HMRGs, and MGEs, suggesting that Gemmatimonadota, which can cope with As and SMX stress, was the host for resistance genes in the soil. Finally, the study found that MGEs play a determinant role in ARGs proliferation due to the direct utilization of HGT, and the indirect effect for ARGs spread under a co-selection mechanism of ARGs and HMRGs, while the bacterial community showed indirect influences by altering environmental factors to act on MGEs. Collectively, this study revealed new insights into the mechanisms of resistance gene transmission under combined SMX and As contamination in soil ecosystems.

Metal-based nanomaterials as antimicrobial agents: A novel driveway to accelerate the aggravation of antibiotic resistance

The consequences of antibiotic tolerance directly affect human health and result in socioeconomic loss. Nanomaterials as antimicrobial agents are considered a promising alternative to antibiotics and have been blended with various medical applications. However, with increasing evidence that metal-based nanomaterials may induce antibiotic tolerance, there is an urgent need to scrutinize how nanomaterial-induced microbial adaption affects the evolution and spread of antibiotic tolerance. Accordingly, within this investigation, we summarized the principal factors influencing the resistance development exposed to metal-based nanomaterials, including physicochemical properties, exposure scenario, as well as bacterial response. Furthermore, the mechanisms of metal-based nanomaterial-induced antibiotic resistance development were comprehensively elucidated from acquired resistance by horizontal transfer of antibiotic resistance genes (ARGs), intrinsic resistance by genetic mutation or upregulated resistance-related gene expression, and adaptive resistance by global evolution. Overall, our review raises concerns about the safety of nanomaterials as antimicrobial agents, which will facilitate assistance in the safe development of antibiotic-free antibacterial strategies.

A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance

The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Removal of antibiotic resistant bacteria and plasmid-encoded antibiotic resistance genes in water by ozonation and electro-peroxone process

The electro-peroxone (EP) process is an electricity-based oxidation process enabled by electrochemically generating hydrogen peroxide (H₂O₂) from cathodic oxygen (O₂) reduction during ozonation. In this study, the removal of antibiotic resistant bacteria (ARB) and plasmid-encoded antibiotic resistance genes (ARGs) during groundwater treatment by ozonation alone and the EP process was compared. Owing to the H₂O₂-promoted ozone (O₃) conversion to hydroxyl radicals (•OH), higher •OH exposures, but lower O₃ exposures were obtained during the EP process than ozonation alone. This opposite change of O₃ and •OH exposures decreases the efficiency of ARB inactivation and ARG degradation moderately during the EP process compared with ozonation alone. These results suggest that regarding ARB inactivation and ARG degradation, the reduction of O₃ exposures may not be fully counterbalanced by the rise of •OH exposures when changing ozonation to the EP process. However, due to the rise of •OH exposure, plasmid DNA was more effectively cleaved to shorter fragments during the EP process than ozonation alone, which may decrease the risks of natural transformation of ARGs. These findings highlight that the influence of the EP process on ARB and ARG inactivation needs to be considered when implementing this process in water treatment.

Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review

The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.

A review of the impact of conductive materials on antibiotic resistance genes during the anaerobic digestion of sewage sludge and animal manure

The urgent need to reduce the environmental burden of antibiotic resistance genes (ARGs) has become even more apparent as concerted efforts are made globally to tackle the dissemination of antimicrobial resistance. Concerning levels of ARGs abound in sewage sludge and animal manure, and their inadequate attenuation during conventional anaerobic digestion (AD) compromises the safety of the digestate, a nutrient-rich by-product of AD commonly recycled to agricultural land for improvement of soil quality. Exogenous ARGs introduced into the natural environment via the land application of digestate can be transferred from innocuous environmental bacteria to clinically relevant bacteria by horizontal gene transfer (HGT) and may eventually reach humans through food, water, and air. This review, therefore, discusses the prospects of using carbon- and iron-based conductive materials (CMs) as additives to mitigate the proliferation of ARGs during the AD of sewage sludge and animal manure. The review spotlights the core mechanisms underpinning the influence of CMs on the resistome profile, the steps to maximize ARG attenuation using CMs, and the current knowledge gaps. Data and information gathered indicate that CMs can profoundly reduce the abundance of ARGs in the digestate by easing selective pressure on ARGs, altering microbial community structure, and diminishing HGT.

Distribution and drivers of antibiotic resistance genes in brackish water aquaculture sediment

Brackish water aquaculture has brought numerous economic benefits, whereas anthropogenic activities in aquaculture may cause the dissemination of antibiotic resistance genes (ARGs) in brackish water sediments. The intricate relationships between environmental factors and microbial communities as well as their role in ARGs dissemination in brackish water aquaculture remain unclear. This study applied PCR and 16S sequencing to identify the variations in ARGs, class 1 integron gene (intI1) and microbial communities in brackish water aquaculture sediment. The distribution of ARGs in brackish water aquaculture sediment was similar to that in freshwater aquaculture, and the sulfonamide resistance gene sul1 was the indicator of ARGs. Proteobacteria and Firmicutes were the dominant phyla, and Paenisporosarcina (p_ Firmicutes) was the dominant genus. The results of correlation, network and redundancy analysis indicated that the microbial community in the brackish water aquaculture sediment was function-driven. The neutral model and variation partitioning analysis were used to verify the ecological processes of the bacterial community. The normalized stochasticity ratio showed that pond bacteria community was dominated by determinacy, which was affected by aquaculture activities. The total nitrogen and organic matter influenced the abundance of ARGs, while Proteobacteria and Thiobacillus (p_Proteobacteria) were the key antibiotic-resistant hosts. Our study provides insight into the prevalence of ARGs in brackish water aquaculture sediments, and indicates that brackish water aquaculture is a reservoir of ARGs.

Antimicrobial and the Resistances in the Environment: Ecological and Health Risks, Influencing Factors, and Mitigation Strategies

Antimicrobial contamination and antimicrobial resistance have become global environmental and health problems. A large number of antimicrobials are used in medical and animal husbandry, leading to the continuous release of residual antimicrobials into the environment. It not only causes ecological harm, but also promotes the occurrence and spread of antimicrobial resistance. The role of environmental factors in antimicrobial contamination and the spread of antimicrobial resistance is often overlooked. There are a large number of antimicrobial-resistant bacteria and antimicrobial resistance genes in human beings, which increases the likelihood that pathogenic bacteria acquire resistance, and also adds opportunities for human contact with antimicrobial-resistant pathogens. In this paper, we review the fate of antimicrobials and antimicrobial resistance in the environment, including the occurrence, spread, and impact on ecological and human health. More importantly, this review emphasizes a number of environmental factors that can exacerbate antimicrobial contamination and the spread of antimicrobial resistance. In the future, the timely removal of antimicrobials and antimicrobial resistance genes in the environment will be more effective in alleviating antimicrobial contamination and antimicrobial resistance.

Transmission of antibiotic resistance genes through mobile genetic elements in Acinetobacter baumannii and gene-transfer prevention

Antibiotic resistance is a major global public health concern. Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of its high levels of resistance to many antibiotics, particularly those considered as last-resort antibiotics, such as carbapenems. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antibiotic resistance genes (ARGs), including the mobilization of ARGs within and between species. We conducted an in-depth, systematic investigation of the occurrence and dissemination of ARGs associated with MGEs in A. baumannii. We focused on a cross-sectoral approach that integrates humans, animals, and environments. Four strategies for the prevention of ARG dissemination through MGEs have been discussed: prevention of airborne transmission of ARGs using semi-permeable membrane-covered thermophilic composting; application of nanomaterials for the removal of emerging pollutants (antibiotics) and pathogens; tertiary treatment technologies for controlling ARGs and MGEs in wastewater treatment plants; and the removal of ARGs by advanced oxidation techniques. This review contemplates and evaluates the major drivers involved in the transmission of ARGs from the cross-sectoral perspective and ARG-transfer prevention processes.

Host species and microplastics differentiate the crop root endophytic antibiotic resistome

The increasing One-Health concept calls for a more in-depth understanding of the dissemination of antibiotic resistance in plant microbiomes. While there is considerable published evidence that microplastics can promote the spread of antibiotic resistance genes (ARGs) in the environment, whether and how microplastics impact the plant endophytic resistome are largely unknown. Here we examined the ARGs along the soil-root continuum of maize and wheat under the pressure of microplastics. Amendment with heavy metals was also included as they can apply the selective pressure for ARG spread as well. The crop species and genotypes had significant effects on the root endophytic ARG abundance and diversity. The greatest ARG abundance was observed in the maize ZD958 endophytes (0.215 copies per 16S rRNA gene), followed by the maize XY335 (0.092 copies per 16S rRNA gene). For each crop genotype, amendment with microplastics and heavy metals significantly increased the ARG abundances and changed their profiles in root endophytes. The endophytic ARG variances were closely associated with the endophytic microbiome, the rhizosphere bacterial communities and resistome. Additionally, the level of endophytic ARGs was positively relevant to the abundance of mobile genetic elements (MGEs). These findings suggested that the root endophytic resistome was primarily affected by the crop species, and microplastics might show enhancement effects on the endophytic resistome via changing the root-associated microbiome and facilitating the MGE mediation. Overall, this study, for the first time, highlights the root endophytic ARG emergence and dissemination induced by microplastics.

Industrial effluents boosted antibiotic resistome risk in coastal environments

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

Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes

Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.

Antibiotic-Resistant Escherichia coli Strains Isolated from Captive Giant Pandas: A Reservoir of Antibiotic Resistance Genes and Virulence-Associated Genes

Recent studies showed that Escherichia coli (E. coli) strains isolated from captive giant pandas have serious resistance to antibiotics and carry various antibiotic resistance genes (ARGs). ARGs or virulence-associated genes (VAGs) carried by antibiotic-resistant E. coli are considered as a potential health threat to giant pandas, humans, other animals and the environment. In this study, we screened ARGs and VAGs in 84 antibiotic-resistant E. coli strains isolated from clinically healthy captive giant pandas, identified the association between ARGs and VAGs and analyzed the phylogenetic clustering of E. coli isolates. Our results showed that the most prevalent ARG in E. coli strains isolated from giant pandas is bla_TEM (100.00%, 84/84), while the most prevalent VAG is fimC (91.67%, 77/84). There was a significant positive association among 30 pairs of ARGs, of which the strongest was observed for sul1/tetC (OR, 133.33). A significant positive association was demonstrated among 14 pairs of VAGs, and the strongest was observed for fyuA/iroN (OR, 294.40). A positive association was also observed among 45 pairs of ARGs and VAGs, of which the strongest was sul1/eaeA (OR, 23.06). The association of ARGs and mobile gene elements (MGEs) was further analyzed, and the strongest was found for flor and intI1 (OR, 79.86). The result of phylogenetic clustering showed that the most prevalent group was group B2 (67.86%, 57/84), followed by group A (16.67%, 14/84), group D (9.52%, 8/84) and group B1 (5.95%, 5/84). This study implied that antibiotic-resistant E. coli isolated from captive giant pandas is a reservoir of ARGs and VAGs, and significant associations exist among ARGs, VAGs and MGEs. Monitoring ARGs, VAGs and MGEs carried by E. coli from giant pandas is beneficial for controlling the development of antimicrobial resistance.

Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain

Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.

Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum

The dissemination of plasmid-borne antibiotic resistance genes (ARGs) among bacteria is becoming a global challenge to the "One Health" concept. During conjugation, the donor/recipient usually encounter diverse stresses induced by the surrounding environment. Previous studies mainly focused on the effects of oxidative stress on plasmid conjugation, but ignored the potential contribution of reductive stress (RS), the other side of the intracellular redox spectrum. Herein, we demonstrated for the first time that RS induced by dithiothreitol could significantly boost the horizontal transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella Typhimurium, and Pseudomonas putida KT2440). Phenotypic and genotypic tests confirmed that RS upregulated genes encoding the transfer apparatus of plasmid RP4, which was attributed to the promoted consumption of intracellular glutamine in the donor rather than the widely reported SOS response. Moreover, RS was verified to benefit ATP supply by activating glycolysis (e.g., GAPDH) and the respiratory chain (e.g., appBC), triggering the deficiency of intracellular free Mg²⁺ by promoting its binding, and reducing membrane permeability by stimulating cardiolipin biosynthesis, all of which were beneficial to the functioning of transfer apparatus. Overall, our findings uncovered the neglected risks of RS in ARG spreading and updated the regulatory mechanism of plasmid conjugation.

Chronic effects of benzalkonium chlorides on short chain fatty acids and methane production in semi-continuous anaerobic digestion of waste activated sludge

As an emerging pollutant, benzalkonium chlorides (BACs) potentially enriched in waste activated sludge (WAS). However, the microbial response mechanism under chronic effects of BACs on acidogenesis and methanogenesis in anaerobic digestion (AD) has not been clearly disclosed. This study investigated the AD (by-)products and microbial evolution under low to high BACs concentrations from bioreactor startup to steady running. It was found that BACs can lead to an increase of WAS hydrolysis and fermentation, but a disturbance to acidogenic bacteria also occurred at low BACs concentration. A noticeable inhibition to methanogenesis occurred when BAC concentration was up to 15 mg/g TSS. Metagenomic analysis revealed the key genes involved in acetic acid (HAc) biosynthesis (i.e. phosphate acetyltransferase, PTA), β-oxidation pathway (acetyl-CoA C-acetyltransferase) and propionic acid (HPr) conversion was slightly promoted compared with control. Furthermore, BACs inhibited the acetotrophic methanogenesis (i.e. acetyl-CoA synthetase), especially BAC concentration was up to 15 mg/g TSS, thereby enhanced short chain fatty acids (SCFAs) accumulation. Overall, chronic stimulation of functional microorganisms with increasing concentrations of BACs impact WAS fermentation.

Effects of trace PFOA on microbial community and metabolisms: Microbial selectivity, regulations and risks

Perfluorooctanoic acid (PFOA), a "forever chemical", is continuously discharged and mitigated in the environment despite its production and use being severely restricted globally. Due to the transformation, attachment, and adsorption of PFOA in aquatic environments, PFOA accumulates in the porous media of sediments, soils, and vadose regions. However, the impact of trace PFOA in the porous media on interstitial water and water safety is not clear. In this work, we simulated a porous media layer using a sand column and explored the effects of µg-level PFOA migration on microbial community alternation, microbial function regulation, and the generation and spread of microbial risks. After 60 days of PFOA stimulation, Proteobacteria became the dominant phylum with an abundance of 91.8%, since it carried 71% of the antibiotic resistance genes (ARGs). Meanwhile, the halogen-related Dechloromonas abundance increased from 0.4% to 10.6%. In addition, PFOA significantly stimulated protein (more than 1288%) and polysaccharides (more than 4417%) production by up-regulating amino acid metabolism (p< 0.001) and membrane transport (p < 0.001) to accelerate the microbial aggregation. More importantly, the rapidly forming biofilm immobilized and blocked PFOA. The more active antioxidant system repaired the damaged cell membrane by significantly up-regulating glycerophospholipid metabolism and peptidoglycan biosynthesis. It is worth noting that PFOA increased the abundance of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in porous media by 30% and 106%. PFOA increased the proportion of vertical transmission ARGs (vARGs), and co-occurrence network analysis (r ≥ 0.8, p ≤ 0.01) verified that vARGs were mainly mediated by HBPs. A comprehensive understanding of PFOA interactions with its microecological environment is provided.

Triclosan Promotes Conjugative Transfer of Antibiotic Resistance Genes to Opportunistic Pathogens in Environmental Microbiome

Although triclosan, as a widely used antiseptic chemical, is known to promote the transmission of antibiotic resistance to diverse hosts in pure culture, it is still unclear whether and how triclosan could affect the transmission of broad-host-range plasmids among complex microbial communities. Here, bacterial culturing, fluorescence-based cell sorting, and high-throughput 16S rRNA gene amplicon sequencing were combined to investigate contributions of triclosan on the transfer rate and range of an IncP-type plasmid from a proteobacterial donor to an activated sludge microbiome. Our results demonstrate that triclosan significantly enhances the conjugative transfer of the RP4 plasmid among activated sludge communities at environmentally relevant concentrations. High-throughput 16S rRNA gene sequencing on sorted transconjugants demonstrates that triclosan not only promoted the intergenera transfer but also the intragenera transfer of the RP4 plasmid among activated sludge communities. Moreover, triclosan mediated the transfer of the RP4 plasmid to opportunistic human pathogens, for example, Legionella spp. The mechanism of triclosan-mediated conjugative transfer is primarily associated with excessive oxidative stress, followed by increased membrane permeability and provoked SOS response. Our findings offer insights into the impacts of triclosan on the dissemination of antibiotic resistance in the aquatic environmental microbiome.

A pencil graphite-based disposable device for electrochemical monitoring of sulfanilamide in honey and water samples

The present paper reports a simple, fast, and inexpensive process of manufacturing a disposable pencil graphite electrode (PGE) from widely available materials, which showed a reproducibility of at least 7.5%. The electrode was compared to the commercial glassy carbon electrode (GCE) and showed superior electroanalytical performance for sulfanilamide (SFA) with approximately 3.9-fold higher current density. Additionally, a displacement of the oxidation peak from approximately 80 mV to more cathodic regions was observed. Therefore, a method based on square wave voltammetry (SWV) was developed for the determination of the antimicrobial SFA in honey and tap water samples using the proposed sensor. The optimized method presented good detectability (LOD = 2.37 μmol L^-1), with excellent precision and accuracy (relative standard deviation < 4.2%) and percent recovery from spiked samples ranging from 92 to 97%. In addition, the sensor did not suffer significant interference from sample matrix components and other commonly evaluated antimicrobials, which demonstrates the potential of these electrodes for implementation in routine analysis and quality control.

Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria

Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.

Effects of iron mineral adhesion on bacterial conjugation: Interfering the transmission of antibiotic resistance genes through an interfacial process

Bacterial conjugation is one of the most prominent ways for antibiotic resistance genes (ARGs) transmission in the environment. Interfacial interactions between natural colloidal minerals and bacteria can alter the effective contact of bacteria, thereby affecting ARGs conjugation. Understanding the impact of iron minerals, a core component of colloidal minerals, on ARGs conjugation can help assess and intervene in the risk of ARGs transmission. With three selected iron minerals perturbation experiments, it was found that the conjugative transfer of plasmid that carried kanamycin resistance gene was 1.35 - 3.91-fold promoted by low concentrations of iron minerals (i.e., 5 - 100 mg L^-1), but inhibited at high concentrations (i.e., 1000 - 2000 mg L^-1) as 0.10 - 0.22-fold. Conjugation occurrence was highly relevant to the number of bacteria adhering per unit mass of mineral, thus switch in the adhesion modes of mineral-bacterial determined whether the conjugate transfer of ARGs was facilitated or inhibited. In addition, a unified model was formularized upon the physicochemical and physiological effects of adhesion on conjugation, and it can be used in estimating the critical inhibitory concentration of different iron minerals on conjugation. Our findings indicate natural colloidal minerals have great potential for applications in preventing the environmental propagation of ARGs through interfacial interactions.

The Dual Roles of Nano Zero-Valent Iron and Zinc Oxide in Antibiotics Resistance Genes (ARGs) SPREAD in Sediment

Nanoparticles (NPs) are widely used and ubiquitous in the environment, but the consequences of their release into the environment on antibiotics resistance genes (ARGs), microbial abundance, and community, are largely unknown. Therefore, this study examined the effect of nano zero-valent iron (nZVI) and zinc oxide (nZnO) on tetracycline resistance genes (tet-ARGs) and class 1 integron (intI1) in sediment under laboratory incubation. The coexistence of NPs and tetracycline (TC) on tet-ARGs/intI1 was also investigated. It was found that nZVI and nZnO promoted tet-ARGs/intI1 abundance in sediment without TC but reduced the inducing effect of TC on tet-ARGs/intI1 in sediment overlaid with TC solution. Without TC, nZVI, intI1, and the bacterial community could directly promote tet-ARGs spread in nZVI sediment, while intI1 and bacterial abundance were the most directly important reasons for tet-ARGs spread in nZnO sediment. With TC, nZVI and bacterial community could reduce tet-ARGs abundance in nZVI sediment, while nZnO and bacterial community could directly promote tet-ARGs in nZnO sediment. Finally, these findings provided valuable information for understanding the role of NPs in promoting and reducing ARGs in the environment.

Antibiotics and microbial community-induced antibiotic-resistant genes distribution in soil and sediment in the eastern coastline of China

The health risk of antibiotic-resistant genes (ARGs) has been a global concern, while the report on occurrence and prevalence of ARGs in coastal zone is relatively scarce. This study investigated typical ARGs in soil and sediment in coastal line of eastern China and assessed its relationship with antibiotics and heavy metals as well as microbial community. Results showed that eight ARGs were all detected in the samples, and β-lactam resistance gene blaTEM reached the highest absolute abundance (6.28 × 10⁷ ~ 6.48 × 10⁸ copies/g) and relative abundance (2.3 × 10^-2 copies/16S rRNA) among samples. Amoxicillin and tetracycline were most frequently detected with the average concentration of 2.28 μg/kg and 3.48 μg/kg, respectively. Cr and Zn were found to be most abundant heavy metals with average value of 82.1 and 59.1 mg/kg, respectively. Proteobacteria, Campilobacterota, Bacteroidota, and Firmicutes were dominant phyla in most samples, while bacterial community varied significantly among samples. Redundancy analyses (RDA) showed that microbial community and antibiotics (amoxicillin and tetracycline) were driving factors of ARGs distribution, while heavy metals were not significantly correlated with ARGs. This study is helpful to understand the fate of ARGs in coastal zone.

Intracellular and extracellular protective mechanisms of the anammox consortia against exogenous sulfadimidine

Antibiotics and antibiotic resistance genes (ARGs) have been recognized as emerging high-risk pollutants for human and animal health. This study systematically investigated the comprehensive effects of a typical antibiotic (sulfadimidine, SDM) in livestock and poultry breeding wastewater on the anammox process, with the aim of elucidating the intracellular and extracellular protective mechanisms of the anammox consortia to the antibiotic stress. Results revealed that the high-concentration SDM significantly reduced the specific anammox activity (SAA) by 37.8%. Changes in the abundance of Candidatus Kuenenia showed a similar trend with that of SAA, while other nitrogen-related microorganisms (e.g., Nitrosomonas and Nitrospira) contributed to the nitrogen removal especially during the inhibitory period. Resistance of the anammox consortia to SDM mainly depended on the protection of ARGs and EPS. Network analysis revealed the host range of eARGs was relatively larger than that of iARGs, and intI1 was closely associated with representative denitrifiers. In addition, metaproteomic analysis and molecular docking results indicated that abundant proteins in EPS could detain SDM in the extracellular matrix through forming complex via hydrogen bond. These findings provide a guidance for the stable operation of anammox process and ARGs transfer controlling.

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.

Nitric Oxide: A Neglected Driver for the Conjugative Transfer of Antibiotic Resistance Genes among Wastewater Microbiota

The dissemination of plasmid-borne antibiotic resistance genes (ARGs) in wastewater is becoming an urgent concern. Previous studies mainly focused on the effects of coexisting contaminants on plasmid conjugation, but ignored the potential contribution of some byproducts inevitably released from wastewater treatment processes. Herein, we demonstrate for the first time that nitric oxide (NO), an intermediate of the wastewater nitrogen cycle, can significantly boost the conjugative transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella typhimurium, and wastewater microbiota). Phenotypic and genotypic tests confirmed that NO-induced promotion was not attributed to the SOS response, a well-recognized driver for horizontal gene transfer. Instead, NO exposure increased the outer membrane permeability of both the donor and recipient by inhibiting the expression of key genes involved in lipopolysaccharide biosynthesis (such as waaJ), thereby lowering the membrane barrier for conjugation. On the other hand, NO exposure not only resulted in the accumulation of intracellular tryptophan but also triggered the deficiency of intracellular methionine, both of which were validated to play key roles in regulating the global regulatory genes (korA, korB, and trbA) of plasmid RP4, activating its encoding transfer apparatus (represented by trfAp and trbBp). Overall, our findings highlighted the risks of NO in spreading ARGs among wastewater microbiota and updated the regulation mechanism of plasmid conjugation.

Efficient removal of antibiotic-resistant bacteria and intracellular antibiotic resistance genes by heterogeneous activation of peroxymonosulfate on hierarchical macro-mesoporous Co3O4-SiO2 with enhanced photogenerated charges

Antibiotic resistance genes (ARGs) and their host antibiotic-resistant bacteria (ARB) are widely detected in the environment and pose a threat to human health. Traditional disinfection in water treatment plants cannot effectively remove ARGs and ARB. This study explored the potential of a heterogeneous photo-Fenton-like process utilizing a hierarchical macro-mesoporous Co₃O₄-SiO₂ (MM CS) catalyst for activation of peroxymonosulfate (PMS) to inactivate ARB and degrade the intracellular ARGs. A typical gram-negative antibiotic-resistant bacteria called Pseudomonas sp. HLS-6 was used as a model ARB. A completed inactivation of ARB at ∼10⁷ CFU/mL was achieved in 30 s, and an efficient removal rate of more than 4.0 log for specific ARGs (sul1 and intI1) was achieved within 60 min by the MM CS-based heterogeneous photo-Fenton-like process under visible light and neutral pH conditions. Mechanism investigation revealed that •O₂^- and ¹O₂ were the vital reactive species for ARB inactivation and ARG degradation. The formation and transformation of the active species were proposed. Furthermore, the hierarchical macro-mesoporous structure of MM CS provided excellent optical and photoelectrochemical properties that promoted the cycle of Co³⁺/Co²⁺ and the effective utilization of PMS. This process was validated to be effective in various water matrices, including deionized water, underground water, source water, and secondary effluent wastewater. Collectively, this work demonstrated that the MM CS-based heterogeneous photo-Fenton-like process is a promising technology for controlling the spread of antibiotic resistance in aquatic environments.

The plant microbiota signature of the Anthropocene as a challenge for microbiome research

BACKGROUND

One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

RESULTS

Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.

CONCLUSIONS

Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. Video abstract.

Characteristics and removal of antibiotics and antibiotic resistance genes in a constructed wetland from a drinking water source in the Yangtze River Delta

Safe drinking water is crucial to public health. However, approximately one-third of the world's population lacks access to clean drinking water. The presence of antibiotics and antibiotic resistance genes (ARGs) in drinking water sources has become a severe problem worldwide due to its potential threat to human health. We monitored the occurrence and variations of 23 antibiotics and 9 ARGs in different treatment processes in a constructed wetland serving as drinking water source in the Yangtze River Delta, China. The studied wetland is consisted of four treatment processes: pretreatment area, pump station lifting, root-channel ecological purification area and deep purification area. Except for sulfapyridine and roxithromycin, 21 antibiotics were detected at concentrations ranging from 0.15 to 59.52 ng/L. The concentration of macrolides was the highest in this wetland, especially tylosin (42.86-59.52 ng/L). TetG, tetX and sul2 were the dominant ARGs in both water (2.41 × 10^-4-1.87 × 10^-2) and sediment (6.65 × 10^-5-4.92 × 10^-3). In addition, a strong correlation between ARGs in water and ARGs in sediment (Pearson, R² > 0.9, p < 0.05) indicated an exchange between the two phases. Moreover, the significantly positive correlation of ARGs between the inlet and outlet of each subsystem illustrated that upstream pollution was the primary source for downstream processes. In general, the wetland system could efficiently eliminate antibiotics (9.0-53.8%) and ARGs (14.5-94.1%), with the deep purification area having the highest removal efficiency. Overall, our results provide important insights into the occurrence, abundance and removal of antibiotics and ARGs in the constructed wetland serving as drinking water sources.

Photocatalytic degradation of cefixime in aqueous solutions using functionalized SWCNT/ZnO/Fe3O4 under UV-A irradiation

In this study, SWCNT/ZnO/Fe₃O₄ heterojunction composite was prepared for enhancing the degradation of β-lactam drugs such as cefixime (CFX) from an aqueous solution. The effects of several factors such as pH, initial concentration of CFX, and photocatalyst dose were investigated. Among them, pH was the most effective parameter for the degradation of CFX. Pareto graph revealed that the degradation process was accelerated at acidic conditions. The surface morphology test such as scanning electron microscopy (SEM) was applied to enlighten the surface of the functionalized SWCNT/ZnO/Fe₃O₄ photocatalyst. Highly advanced analyzes such as X-ray Photoelectron Spectroscopy (XPS), Energy Dispersive Spectrometry (EDX), Fourier-Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD), and point of zero charge were included to explain the structure of the photocatalyst. The response surface methodology's results show that the optimum CFX efficiency was fully achieved at 94.19%. The optimal conditions with lower standard error (2.08) were given as pH of 5.93, 22.76 ppm of CFX, and 0.46 g L^-1 of the amount of photocatalyst. Besides, the obtained photocatalyst can be easily used many times owing to its high reusability. SWCNT/ZnO/Fe₃O₄ photocatalyst might be recommended to be used for the mineralizing of drug compounds such as antibiotics in water. Moreover, thiazol-2-ol, N-(dihydroxymethyl)-2-(2-hydroxythiazol-4-yl)acetamide,(S)-N-(2-amino-1-hydroxy-2-oxoethyl)-2-(2 hydroxythiazol-4-yl), and 2-(2-hydroxythiazol-4-yl)-N-((2R,3R)-2-mercapto-4-oxoazetidin-3-yl)acetamide were among the detected intermediates products from the cefixime degradation in the process.

Efficient degradation of various emerging pollutants by wild type and evolved fungal DyP4 peroxidases

The accumulation of emerging pollutants in the environment remains a major concern as evidenced by the increasing number of reports citing their potential risk on environment and health. Hence, removal strategies of such pollutants remain an active area of investigation. One way through which emerging pollutants can be eliminated from the environment is by enzyme-mediated bioremediation. Enzyme-based degradation can be further enhanced via advanced protein engineering approaches. In the present study a sensitive and robust bioanalytical liquid chromatography-tandem mass spectrometry (LCMSMS)-based approach was used to investigate the ability of a fungal dye decolorizing peroxidase 4 (DyP4) and two of its evolved variants—that were previously shown to be H₂O₂ tolerant—to degrade a panel of 15 different emerging pollutants. Additionally, the role of a redox mediator was examined in these enzymatic degradation reactions. Our results show that three emerging pollutants (2-mercaptobenzothiazole (MBT), paracetamol, and furosemide) were efficiently degraded by DyP4. Addition of the redox mediator had a synergistic effect as it enabled complete degradation of three more emerging pollutants (methyl paraben, sulfamethoxazole and salicylic acid) and dramatically reduced the time needed for the complete degradation of MBT, paracetamol, and furosemide. Further investigation was carried out using pure MBT to study its degradation by DyP4. Five potential transformation products were generated during the enzymatic degradation of MBT, which were previously reported to be produced during different bioremediation approaches. The current study provides the first instance of the application of fungal DyP4 peroxidases in bioremediation of emerging pollutants.

Insight into using a novel ultraviolet/peracetic acid combination disinfection process to simultaneously remove antibiotics and antibiotic resistance genes in wastewater: Mechanism and comparison with conventional processes

In this study, the simultaneous removal mechanism of antibiotics and antibiotic resistance genes (ARGs) was investigated using the novel ultraviolet/peracetic acid (UV/PAA) combination disinfection process and conventional disinfection processes were also applied for comparison. The results showed that UV/PAA disinfection with a high UV dosage (UV/PAA-H) was most effective for the removal of tetracyclines, quinolones, macrolides and β-lactams; their average removal efficiencies ranged from 25.7% to 100%, while NaClO disinfection was effective for the removal of sulfonamides (∼81.6%). The majority of ARGs were well removed after the UV/PAA-H disinfection, while specific genes including tetB, tetC, ermA and bla_TEM significantly increased after NaClO disinfection. In addition, β-lactam resistance genes (-35.9%) and macrolides resistance genes (-12.0%) remarkably augmented after UV/NaClO disinfection. The highly reactive oxidation species generated from UV/PAA process including hydroxyl radicals (•OH) and carbon-centered organic radicals (R-C•), were responsible for the elimination of antibiotics and ARGs. Correlation analysis showed that tetracycline, sulfonamide and macrolide antibiotics removal showed a positive correlation with the corresponding ARGs, and a low dose of antibiotic residues played an important role in the distribution of ARGs. Metagenomic sequencing analysis showed that UV/PAA disinfection could not only greatly decrease the abundance of resistant bacteria but also downregulate the expression of key functional genes involved in ARGs propagation and inhibit the signal transduction of the host bacteria, underlying that its removal mechanism was quite different from that of NaClO-based disinfection processes. Our study provides valuable information for understanding the simultaneous removal mechanism of antibiotics and ARGs in wastewater during the disinfection processes, especially for the novel UV/PAA combination process.

Effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of antibiotic resistance genes in water environments: A review

Antibiotic resistance has created obstacles in the treatment of infectious diseases with antibiotics. The horizontal transfer of antibiotic resistance genes (ARGs) can exacerbate the dissemination of antibiotic resistance in water environments. In addition to antibiotic selective pressure, multiple non-antibiotic factors can affect the horizontal transfer of ARGs. Herein, we seek to comprehensively review the effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of ARGs in water environments, especially contaminants from human activities and water treatment processes. Four pathways have been identified to accomplish horizontal gene transfer (HGT), i.e., conjugation, transformation, transduction, and vesiduction. Changes in conjugative frequencies by non-antibiotic factors are mainly related to their concentrations, which conform to hormesis. Relevant mechanisms involve the alteration in cell membrane permeability, reactive oxygen species, SOS response, pilus, and mRNA expression of relevant genes. Transformation induced by extracellular DNA may be more vulnerable to non-antibiotic factors than other pathways. Except bacteriophage infection, the effects of non-antibiotic factors on transduction exhibit many similarities with that of conjugation. Given the secretion of membrane vesicles stimulated by non-antibiotic factors, their effects on vesiduction can be inferred. Furthermore, contaminants from human activities at sub-inhibitory or environmentally relevant concentrations usually promote HGT, resulting in further dissemination of antibiotic resistance. The horizontal transfer of ARGs is difficult to be inhibited by individual water treatment processes (e.g., chlorination, UV treatment, and photocatalysis) unless they attain sufficient intensity. Accordingly, the synergistic application containing two or more water treatment processes is recommended. Overall, we believe this review can elucidate the significance for risk assessments of contaminants from human activities and provide insights into the development of environment-friendly and cost-efficient water treatment processes to inhibit the horizontal transfer of ARGs.

Phenolic compounds promote the horizontal transfer of antibiotic resistance genes in activated sludge

Phenolic compounds are common organic pollutants in wastewater. During the wastewater treatment process, these compounds may influence the microbial community structure and functions. However, the impact of the phenolic compounds in the wastewater treatment plants on the horizontal transfer of antibiotic resistance genes (ARGs) has not been well assessed. In this study, we investigated the horizontal transfer of ARGs under the stress of phenolic compounds. The results showed that in pure culture bacteria system, p-nitrophenol (PNP), p-aminophenol (PAP) and phenol (PhOH) (10-100 mg/L) can significantly increase the horizontal transfer frequency of ARGs by 2.2-4.6, 3.6-9.4 and 1.9-9.0 fold, respectively. And, the RP4 plasmid transfer from Escherichia coli HB101 (E. coli HB101) to the bacteria in activated sludge increased obviously under the stress of phenolic compounds. Further investigation revealed that the PNP and PhOH at the concentration of 10-100 mg/L increased the production of reactive oxygen species and the permeability of cell membrane in the donor and recipient, which could be the causes of horizontal transfer of RP4 plasmid. In addition, it was also found that PNP, PAP and PhOH stress inhibit the expression of the global regulatory genes korB and trbA in the RP4 plasmid, and increase the expression level of the traF gene, thereby promoting the conjugative transfer of the RP4 plasmid. Taken together, these results improved our understanding of the horizontal transfer of ARGs under the stress of phenolic compounds and provided basic information for management of the systems that treat wastewater containing phenolic compounds.

Legacy and Emerging Pollutants in an Urban River Stretch and Effects on the Bacterioplankton Community

River contamination is due to a chemical mixture of point and diffuse pollution, which can compromise water quality. Polycyclic Aromatic Hydrocarbons (PAHs) and emerging compounds such as pharmaceuticals and antibiotics are frequently found in rivers flowing through big cities. This work evaluated the presence of fifteen priority PAHs, eight pharmaceuticals including the antibiotics ciprofloxacin (CIP) and sulfamethoxazole (SMX), together with their main antibiotic resistant genes (ARGs) and the structure of the natural bacterioplankton community, in an urbanized stretch of the river Danube. SMX and diclofenac were the most abundant chemicals found (up to 20 ng/L). ARGs were also found to be detected as ubiquitous contaminants. A principal component analysis of the overall microbiological and chemical data revealed which contaminants were correlated with the presence of certain bacterial groups. The highest concentrations of naphthalene were associated with Deltaproteobacteria and intI1 gene. Overall, the most contaminated site was inside the city and located immediately downstream of a wastewater treatment plant. However, both the sampling points before the river reached the city and in its southern suburban area were still affected by emerging and legacy contamination. The diffuse presence of antibiotics and ARGs causes particular concern because the river water is used for drinking purposes.

Metagenomic approach reveals the fates and mechanisms of antibiotic resistance genes exposed to allicins during waste activated sludge fermentation: Insight of the microbial community, cellular status and gene regulation

This work revealed the impacts of exogeneous allicins on the antibiotic resistance genes (ARGs) variations during waste activated sludge (WAS) fermentation process. The overall abundance of ARGs was respectively reduced by 4.84 and 9.42% in presence of 0.01 and 0.05 g allicin/g TSS. Allicins disrupted the EPS structure and increased the permeability of cell membranes, which resulted in the release of ARGs for subsequent removal. Allicins also reduced intracellular ATP levels, which was disadvantageous to ARGs dissemination. Besides, allicins affected the microbial community and decreased the abundance of potential hosts based on bacterial taxa-ARGs network analysis. Moreover, the metabolic pathways and genetic expressions (i.e., two-component system, quorum sensing, and SOS response) involved in ARGs propagation were down-regulated, which caused the ARGs alleviation in allicins-stressed reactors. Overall, the simultaneous responses of cellular status, bacterial host, and genetic regulation accounted for the effective ARGs reduction induced by allicins during WAS fermentation.