Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors

Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.

Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions

Anaerobic digestion (AD) systems are vital for converting organic waste to green bioenergy but also serve as a non-negligible environmental reservoir for antibiotic-resistance genes (ARGs) and resistant bacteria of environmental and human health concerns. This study profiles the antibiotic resistome of 90 full-scale biogas reactors and reveals that AD microbiomes harbor at least 30 types and 1257 subtypes of ARGs, of which 16% are located on plasmids showing potential mobility. The total abundance of AD-ARGs ranges widely from 0.13 to 7.81 copies per cell and is distributed into 42-739 subtypes, significantly influenced (P < 0.05) by operational conditions like digestion temperature and substrate types. Compared with the ambient and mesophilic digesters, the thermophilic digesters harbor a significantly lower abundance and diversity as well as greatly reduced mobility and host pathogenicity levels (all P < 0.05) of ARGs, revealing that a higher digestion temperature mitigates the overall resistome risks. The comprehensive analysis of basic traits and key traits of the AD resistome is demonstrated to provide crucial quantitative and qualitative insights into the diversity, distribution pattern, and health risks of ARGs in full-scale AD systems. The revealed knowledge offers new guidance for improving environmental resistome management and developing oriented mitigation strategies to minimize the unwanted spread of clinically important antimicrobial resistance from AD systems.

Antibiotic resistance reduction mechanisms during thermophilic anaerobic digestion of microalgae-bacteria aggregates

Microalgae-bacteria-based systems are an emerging and promising approach for wastewater treatment plants (WWTP), having nutrient and antibiotic resistance removal comparable to conventional technologies. Still, antibiotic-resistance genes and bacteria (ARG and ARB) can proliferate in microalga-bacteria aggregates (MABA), a concern to control. Different temperature regimes of MABA continuous anaerobic digestion (AD), thermophilic (55 °C), and mesophilic (35 °C) were evaluated in this study as a strategy to eliminate ARB and ARGs. Plate counting techniques and metagenomic-based analysis revealed that thermophilic temperature had a better performance, achieving ARB log reductions of 1.1 to 1.7 for various antibiotics and significantly reduced ARG abundance up to 19.5 ± 0.8 ppm. The microbiome selection, the mobilome restriction, and directed functionality to thermal stress resistance were the main mechanisms responsible for resistome reduction at thermophilic conditions. Thermophilic AD effectively manages antibiotic resistance in microalgae-bacteria aggregates, which has important implications for wastewater treatment and reduces environmental risks.

Different combinations of operating temperature and solids retention time during two-phase anaerobic digestion impacts removal of antibiotic resistance genes

Two-phase anaerobic digestion (AD) performance is significantly influenced by operating parameters such as temperature and solids retention time (SRT), while their impact on antibiotic resistance genes (ARGs) during the acidogenic (AP) and methanogenic (MP) phases remains unclear. This study assessed the abundance of eight ARGs in full-scale two-phase AD, then operated lab-scale two-phase AD systems to evaluate temperature combinations (thermophilic-thermophilic, thermophilic-mesophilic, mesophilic-thermophilic, and mesophilic-mesophilic) at a constant SRT (AP = 2/MP = 13d) and to further assess different SRTs (AP = 2/MP = 13d and AP = 4/MP = 11d). qPCR results revealed that full-scale two-phase AD reduced total ARGs abundance by 87.70 ± 0.50 %. In lab-scale tests, the thermophilic-thermophilic configuration achieved nearly complete ARGs removal (97.61 ± 0.21 %), while the combination of AP = 4/MP = 11d had the highest removal efficiency (83.39 ± 1.17 %). Network analysis indicated that Firmicutes, Bacteroidota, and Proteobacteria were the primary ARG hosts, with Firmicutes dominant. These findings highlight the optimal operating parameters in two-phase AD for maximizing ARGs removal.

Occurrence and dissipation mechanisms of organic contaminants during sewage sludge anaerobic digestion: A critical review

Sewage sludge, a complex mixture of contaminants and pathogenic agents, necessitates treatment or stabilization like anaerobic digestion (AD) before safe disposal. AD-derived products (solid digestate and liquid fraction) can be used as fertilizers. During AD, biogas is also produced, and used for energy purposes. All these fractions can be contaminated with various compounds, whose amount depends on the feedstocks used in AD (and their mutual proportions). This paper reviews studies on the distribution of organic contaminants across AD fractions (solid digestate, liquid fraction, and biogas), delving into the mechanisms behind contaminant dissipation and proposing future research directions. AD proves to be a relatively effective method for removing polychlorinated biphenyls, polycyclic aromatic hydrocarbons, pharmaceuticals, antibiotic resistance genes and hydrocarbons. Contaminants are predominantly removed through biodegradation, but many compounds, especially hydrophobic (e.g. per- and polyfluoroalkyl substances), are also sorbed onto digestate particles. The process of sorption is suggested to reduce the bioavailability of contaminants. As a result of sorption, contaminants accumulate in the largest amount in the solid digestate, whereas in smaller amounts in the other AD products. Polar pharmaceuticals (e.g. metformin) are particularly leached, while volatile methylsiloxanes and polycyclic aromatic hydrocarbons, characterized by a high Henry's law constant, are volatilized into the biogas. The removal of compounds can be affected by AD operational parameters, the type of sludge, physicochemical properties of contaminants, and the sludge pretreatment used.

Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste

Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic

Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.

Temperature-phased anaerobic sludge digestion effectively removes antibiotic resistance genes in a full-scale wastewater treatment plant

Sludge is a major by-product and the final reservoir of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Temperature-phased anaerobic digestion (TPAD), consisting of thermophilic anaerobic digestion (AD) (55 °C) and mesophilic AD processes (37 °C), has been implemented in WWTPs for sludge reduction while improving the biomethane production. However, the impact of TPAD on the ARGs' fate is still undiscovered in lab-scale experiments and full-scale WWTPs. This study, for the first time, investigated the fate of ARGs during the TPAD process across three seasons in a full-size WWTP. Ten typical ARGs and one integrase gene of class 1 integron (intI1) involving ARGs horizontal gene transfer were examined in sludge before and after each step of the TPAD process. TPAD reduced aac(6')-Ib-cr, blaTEM, drfA1, sul1, sul2, ermb, mefA, tetA, tetB and tetX by 87.3-100.0 %. TPAD reduced the overall average absolute abundance of targeted ARGs and intI1 by 92.39 % and 92.50 %, respectively. The abundance of targeted ARGs in sludge was higher in winter than in summer and autumn before and after TPAD. During the TPAD processes, thermophilic AD played a major role in the removal of ARGs, contributing to >60 % removal of ARGs, while the subsequent mesophilic AD contributed to a further 31 % removal of ARGs. The microbial community analysis revealed that thermophilic AD reduced the absolute abundance of ARGs hosts, antibiotic resistant bacteria. In addition, thermophilic AD reduced the abundance of the intI1, while the intI1 did not reproduce during the mesophilic AD, also contributing to a decline in the absolute abundance of ARGs in TPAD. This study demonstrates that TPAD can effectively reduce the abundance of ARGs in sludge, which will suppress the transmission of ARGs from sludge into the natural environment and deliver environmental and health benefits to our society.

Leveraging machine learning for prediction of antibiotic resistance genes post thermal hydrolysis-anaerobic digestion in dairy waste

Anaerobic digestion holds promise as a method for removing antibiotic resistance genes (ARGs) from dairy waste. However, accurately predicting the efficiency of ARG removal remains a challenge. This study introduces a novel appproach utilizing machine learning to forecast changes in ARG abundances following thermal hydrolysis-anaerobic digestion (TH-AD) treatment. Through network analysis and redundancy analyses, key determinants of affect ARG fluctuations were identified, facilitating the development of machine learning models capable of accurately predicting ARG changes during TH-AD processes. The decision tree model demonstrated impressive predictive power, achieving an impessive R2 value of 87% against validation data. Feature analysis revealed that the genes intI2 and intI1 had a critical impact on the absolute abundance of ARGs. The predictive model developed in this study offers valuable insights for improving operational and managerial practices in dairy waste treatment facilities, with the ultimate goal of mitigating the spread of antibiotic resistance.

Pivotal role of intracellular oxidation by HOCl in simultaneously removing antibiotic resistance genes and enhancing dewaterability during conditioning of sewage sludge using Fe2+/Ca(ClO)2

Pre-acidification has been shown to be crucial in attenuating antibiotic resistance genes (ARGs) during the conditioning of sewage sludge. However, it is of great significance to develop alternative conditioning approaches that can effectively eliminate sludge-borne ARGs without relying on pre-acidification. This is due to the high investment costs and operational complexities associated with sludge pre-acidification. In this study, the effects of Fe2+/Ca(ClO)2 conditioning treatment on the enhancement of sludge dewaterability and the removal of ARGs were compared with other conditioning technologies. The dose effect and the associated mechanisms were also investigated. The findings revealed that Fe2+/Ca(ClO)2 conditioning treatment had the highest potential, even surpassing Fenton treatment with pre-acidification, in terms of eliminating the total ARGs. Moreover, the effectiveness of the treatment was found to be dose-dependent. This study also identified that the •OH radical reacted with extracellular polymeric substance (EPS) and extracellular ARGs, and the HOCl, the production of which was positively correlated with the dose of Fe2+/Ca(ClO)2, could infiltrate the EPS layer and diffuse into the cell of sludge flocs, inducing the oxidation of intracellular ARGs. Furthermore, this study observed a significant decrease in the predicted hosts of ARGs and MGEs in sludge conditioned with Fe2+/Ca(ClO)2, accompanied by a significant downregulation of metabolic pathways associated with ARG propagation, thereby contributing to the attenuation of sludge-borne ARGs. Based on these findings, it can be concluded that Fe2+/Ca(ClO)2 conditioning treatment holds great potential for the removal of sludge-borne ARGs while also enhancing sludge dewaterability, which mainly relies on the intracellular oxidation by HOCl.

Assessing impacts of municipal wastewater treatment plant upgrades on bacterial hazard contributions to the receiving urban river using SourceTracker

Upgrading municipal wastewater treatment plants (MWTPs) has been implemented in many megacities of China to reduce the discharges of nutrients and other pollutants and improve water quality of highly urbanized rivers. However, the contribution of MWTP discharge to bacterial hazards in the receiving rivers after upgrades has been largely unknown. In this study, high-throughput sequencing and shotgun metagenomics were applied to investigate the changes in the abundance, composition, potential risks, and contributions of bacteria and antibiotic resistance genes (ARGs) from effluent to receiving river after upgrading the third-largest MWTP in China with denitrification biofilters, ultrafiltration, ozonation, and disinfection processes. The annual loadings of total nitrogen and 27 types of pharmaceuticals were reduced by 42.4% ± 13.2% and 46.2% ± 15.4%, respectively. Bacterial biomass decreased from (3.58 ± 0.49) to (1.23 ± 0.27) × 107 16S rRNA gene copies/mL, and identified biomarkers in effluent and downstream shifted due to the adopted processes. Opportunistic pathogen bacteria downstream were also reduced. Although the relative abundance of total ARGs in MWTP effluent increased from 1.10 ± 0.02 to 2.19 ± 0.03 copies/16S rRNA gene after upgrades, that of total and high-risk ARGs downstream showed no significant difference. More importantly, the Bayesian-based SourceTracker method provided valuable insight by revealing that the contributions of MWTP discharge to downstream bacteria (from 44.2% ± 1.5%-31.4% ± 0.9%) and ARGs (from 61.2% ± 5.3%-47.6% ± 4.1%) were significantly reduced following the upgrades, indicating upgrading MWTP showed integrated benefits to the bacterial hazards in the receiving river. This study provides useful information for better control of bacterial hazard risks and operational strategy for the improvement of the urban aquatic ecosystem.

Promising bioprocesses for the efficient removal of antibiotics and antibiotic-resistance genes from urban and hospital wastewaters: Potentialities of aerobic granular systems

The use, overuse, and improper use of antibiotics have resulted in higher levels of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs), which have profoundly disturbed the equilibrium of the environment. Furthermore, once antibiotic agents are excreted in urine and feces, these substances often can reach wastewater treatment plants (WWTPs), in which improper treatments have been highlighted as the main reason for stronger dissemination of antibiotics, ARB, and ARGs to the receiving bodies. Hence, achieving better antibiotic removal capacities in WWTPs is proposed as an adequate approach to limit the spread of antibiotics, ARB, and ARGs into the environment. In this review, we highlight hospital wastewater (WW) as a critical hotspot for the dissemination of antibiotic resistance due to its high level of antibiotics and pathogens. Hence, monitoring the composition and structure of the bacterial communities related to hospital WW is a key factor in controlling the spread of ARGs. In addition, we discuss the advantages and drawbacks of the current biological WW treatments regarding the antibiotic-resistance phenomenon. Widely used conventional activated sludge technology has proved to be ineffective in mitigating the dissemination of ARB and ARGs to the environment. However, aerobic granular sludge (AGS) technology is a promising technology-with broad adaptability and excellent performance-that could successfully reduce antibiotics, ARB, and ARGs in the generated effluents. We also outline the main operational parameters involved in mitigating antibiotics, ARB, and ARGs in WWTPs. In this regard, WW operation under long hydraulic and solid retention times allows better removal of antibiotics, ARB, and ARGs independently of the WW technology employed. Finally, we address the current knowledge of the adsorption and degradation of antibiotics and their importance in removing ARB and ARGs. Notably, AGS can enhance the removal of antibiotics, ARB, and ARGs due to the complex microbial metabolism within the granular biomass.

Impacts of electric field-magnetic powder coupled membrane bioreactor on phenol wastewater treatment: Performance, synergistic mechanism, antibiotic resistance genes, and eco-environmental benefit evaluation

A novel electric field-magnetic powder coupled membrane bioreactor (EM-MBR) was constructed, which was superior on improvement of phenol treatment performance and sludge characteristics, and mitigation of membrane fouling. EM-MBR enhanced the phenol degradation via the improvement activity of phenol degrading enzymes. The EPS contents and SVI of EM-MBR were significantly reduced by 49.3 % and 58.7 % than that of the conventional MBR, respectively. Moreover, EM-MBR successfully reduced fouling rate by 57.0 %, delaying the membrane resistance. The EPS contents were positively correlated with the SVI and fouling rate, implying that the sludge settleability was strengthened by improving the properties of EPS with the assistance of electromagnetic, thus mitigating the membrane fouling. Microbial co-occurrence network demonstrated that EM-MBR enriched phenol-degrading and EPS-degrading genera correlated to Fe redox cycle. Furthermore, the activation of the antioxidant system in the EM-MBR resulted in the suppression of reactive oxygen species (ROS) generation, consequently impeding the dissemination of antibiotic resistance genes (ARGs). Co-occurrence patterns of MGEs and ARGs revealed that intercellular binding facilitated by ist and Integrase may account for the horizontal transfer of ARGs. The reduction of unit capital costs (15.63 %), running costs (53.00 %), and total average carbon emissions (15.18 %) indicated that EM-MBR was environmentally beneficial.

Performance of sewage sludge treatment for the removal of antibiotic resistance genes: Status and prospects

Wastewater treatment plants (WWTPs) receive wastewater containing antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), which are predominant contributors to environmental pollution in water and soil. Of these sources, sludge is a more significant contributor than effluent. Knowing how sludge treatment affects the fate of ARGs is vital for managing the risk of these genes in both human and natural environments. This review therefore discusses the sources and transmission of ARGs in the environment and highlights the risks of ARGs in sludge. The effects of co-existing constituents (heavy metals, microplastics, etc.) on sludge and ARGs during treatment are collated to highlight the difficulty of treating sludge with complex constituents in ARGs. The effects of various sludge treatment methods on the abundances of ARGs in sludge and in soil from land application of treated sludge are discussed, pointing out that the choice of sludge treatment method should take into account various potential factors, such as soil and soil biology in subsequent land application. This review offers significant insights and explores the abundances of ARGs throughout the process of sludge treatment and disposal. Unintentional addition of antibiotic residues, heavy metals, microplastics and organic matter in sludge could significantly increase the abundance and reduce the removal efficiency of ARGs during treatment, which undoubtedly adds a barrier to the removal of ARGs from sludge treatment. The complexity of the sludge composition and the diversities of ARGs have led to the fact that no effective sludge treatment method has so far been able to completely eliminate the ecological risk of ARGs. In order to reduce risks resulting by transmission of ARGs, technical and management measures need to be implemented.

Antibiotic resistance genes fate during food waste management - Comparison between thermal treatment, hyperthermophilic composting, and anaerobic membrane bioreactor

The fate of eight different antibiotic resistance genes (ARGs) in food waste (sul1, sul2, tetO, tetW, ermF, ermB, ampC, oxa-1), intI1, and rpoB were monitored during thermal treatment (pyrolysis and incineration), hyperthermophilic composting, and anaerobic membrane bioreactor (AnMBR) treatment. ARGs in food waste ranged from 2.9 × 106 to 3.5 × 109 copies/kg with ampC being the least abundant and sul1 being the most abundant. Thermal treatment achieved removal below detection limits of all ARGs. Only two ARGs (sul1 and ampC) persisted in hyperthermophilic composting. While all genes except for ermB decreased in the AnMBR effluent relative to the food waste feed, sul1 remained at relatively high abundance. Biosolids on the contrary, accumulated tetO, ampC and sul2 in all tested operating conditions. Thermal treatment, despite limited resource recovery, provides the most effective mitigation of ARG risk in food waste.

Antibiotic resistance genes and the association with bacterial community in biofilms occurring during the drinking water granular activated carbon (GAC) sandwich biofiltration

The granular activated carbon (GAC) sandwich modification to slow sand filtration could be considered as a promising technology for improved drinking water quality. Biofilms developed on sand and GAC surfaces are expected to show a functional diversity during the biofiltration. Bench-scale GAC sandwich biofilters were set-up and run continuously with and without antibiotic exposure. Surface sand (the schmutzdecke) and GAC biofilms were sampled and subject to high-throughput qPCR for antibiotic resistance gene (ARG) analysis and 16 S rRNA amplicon sequencing. Similar diversity of ARG profile was found in both types of biofilms, suggesting that all ARG categories decreased in richness along the filter bed. In general, surface sand biofilm remained the most active layer with regards to the richness and abundance of ARGs, where GAC biofilms showed slightly lower ARG risks. Network analysis suggested that 10 taxonomic genera were implicated as possible ARG hosts, among which Nitrospira, Methyloversatilis and Methylotenera showed the highest correlation. Overall, this study was the first attempt to consider the whole structure of the GAC sandwich biofilter and results from this study could help to further understand the persistence of ARGs and their association with the microbial community in drinking water biofiltration system.

Impact of soil supplemented with pig manure on the abundance of antibiotic resistant bacteria and their associated genes

This study was conducted to evaluate the abundance of antibiotic resistant bacteria and their resistance genes from agriculture soil supplemented with pig manure. Uncultivable soil sample was supplemented with pig manure samples under microcosm experimental conditions and plated on Luria-Bertani (LB) agar incorporated with commercial antibiotics. The supplementation of soil with 15% pig manure resulted in the highest increase in the population of antibiotic resistant bacteria (ARB)/multiple antibiotic resistant bacteria (MARB). Seven genera that included Pseudomonas, Escherichia, Providencia, Salmonella, Bacillus, Alcaligenes and Paenalcaligenes were the cultivable ARB identified. A total of ten antibiotic resistant bacteria genes (ARGs) frequently used in clinical or veterinary settings and two mobile genetic elements (MGEs) (Class 1 and Class 2 integrons) were detected. Eight heavy metal, copper, cadmium, chromium, manganese, lead, zinc, iron, and cobalt were found in all of the manure samples at different concentrations. Tetracycline resistance genes were widely distributed with prevalence of 50%, while aminoglycoside and quinolone-resistance gene had 16% and 13%, respectively. Eighteen ARB isolates carried more than two ARGs in their genome. Class 1 integron was detected among all the 18 ARB with prevalence of 90-100%, while Class 2 integron was detected among 11 ARB. The two classes of integron were found among 10 ARB. Undoubtedly, pig manure collected from farms in Akure metropolis are rich in ARB and their abundance might play a vital role in the dissemination of resistance genes among clinically-relevant pathogens.

Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau

Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 105 to 6.22 × 107 copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.

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

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

Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review

Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.

Simultaneous Removal of Sulfamethoxazole during Fermentative Production of Short-Chain Fatty Acids

This study explores the simultaneous sulfamethoxazole (SMX) removal and short-chain fatty acids (SCFAs) production by a Clostridium sensu stricto-dominated microbial consortium. SMX is a commonly prescribed and persistent antimicrobial agent frequently detected in aquatic environments, while the prevalence of antibiotic-resistant genes limits the biological removal of SMX. Under strictly anaerobic conditions, sequencing batch cultivation coupled with co-metabolism resulted in the production of butyric acid, valeric acid, succinic acid, and caproic acid. Continuous cultivation in a CSTR achieved a maximum butyric acid production rate and yield of 0.167 g/L/h and 9.56 mg/g COD, respectively, while achieving a maximum SMX degradation rate and removal capacity of 116.06 mg/L/h and 55.8 g SMX/g biomass. Furthermore, continuous anaerobic fermentation reduced sul genes prevalence, thus limiting the transmission of antibiotic resistance genes during antibiotic degradation. These findings suggest a promising approach for efficient antibiotic elimination while simultaneously producing valuable products (e.g., SCFAs).

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.

Hyper-thermophilic anaerobic pretreatment enhances the removal of transferable oxazolidinone and phenicol cross-resistance gene optrA in enterococci

The extensive use of florfenicol in poultry industry results in the emergence of optrA gene, which also confers resistance to clinically important antibiotic linezolid. This study investigated the occurrence, genetic environments, and removal of optrA in enterococci in mesophilic (37 °C) and thermophilic (55 °C) anaerobic digestion systems, and a hyper-thermophilic (70 °C) anaerobic pretreatment system for chicken waste. A total of 331 enterococci were isolated and analyzed for antibiotic resistance against linezolid and florfenicol. The optrA gene was frequently detected in enterococci from chicken waste (42.7%) and effluents from mesophilic (72%) and thermophilic (56.8%) reactors, but rarely detected in the hyper-thermophilic (5.8%) effluent. Whole-genome sequencing revealed that optrA-carrying Enterococcus faecalis sequence type (ST) 368 and ST631 were the dominant clones in chicken waste, and they remained dominant in mesophilic and thermophilic effluents, respectively. The plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E was the core genetic element for optrA in ST368, whereas chromosomal Tn554-fexA-optrA was the key one in ST631. IS1216E might play a key role in horizontal transfer of optrA due to its presence in different clones. Hyper-thermophilic pretreatment removed enterococci with plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E. A hyper-thermophilic pretreatment is recommended for chicken waste to mitigate dissemination of optrA from animal waste to the environment.

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.

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC-MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.

The role of pretreatments in handling antibiotic resistance genes in anaerobic sludge digestion - A review

Sludge is among the most important reservoirs of antibiotic resistance genes (ARGs), which would cause potential environmental risks with the sludge utilization. Currently, anaerobic digestion (AD) is effective to simultaneously realize the resource recovery and pollutants removal, including antibiotic resistance genes (ARGs), and various pretreatments are used to enhance the performance. Recently, plentiful publications have focused on the effects of pretreatment on ARGs removal, but the contradictory results are often obtained, and a comprehensive understanding of the research progress and mechanisms is essential. This study summarizes various pretreatment techniques for improving AD efficiency and ARGs reduction, investigates promising performance in ARGs removal when pretreatments combined with AD, and analyzes the potential mechanisms accounting for ARGs fates. The results showed that although thermal hydrolysis pretreatment showed the best performance in ARGs reduction during the pretreatment process, the significant rebound of ARGs would occur in the subsequent AD process. Conversely, ozone pretreatment and alkali pretreatment had no significant effect on ARGs abundance in the pretreatment stage, but could enhance ARGs removal by 15.6-24.3 % in the subsequent AD. Considering the efficiency and economic effectiveness, free nitrous acid pretreatment would be a promising and feasible option, which could enhance methane yield and ARGs removal by up to 27 % and 74.5 %, respectively. Currently, the factors determining ARGs fates during pretreatment and AD processes included the shift of microbial community, mobile genetic elements (MGEs), and environmental factors. A comprehensive understanding of the relationship between the fate of ARGs and pretreatment technologies could be helpful for systematically evaluating various pretreatments and facilitating the development of emerging and effective pretreatment techniques. Moreover, given the effectiveness, economic efficiency and environmental safety, we called for the applications of modern analysis approaches such as metagenomic and machine learning on the optimization of pretreatment conditions and revealing underlying mechanisms.

Occurrence and prevalence of antibiotic resistance genes in apple orchard after continual application of anaerobic fermentation residues of pig manure

Fermented organic fertilizers made from pig manure contaminated with antibiotics are widely used in fruit tree production. However, their effects on the residual antibiotics and the spread of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in apple orchards are still largely unknown. In the present study, we detected 100 ARGs and 10 MGEs that were transferred from pig manure to an apple orchard. Compared with the original pig manure, significantly greater concentrations of tetracycline, chlortetracycline, oxytetracycline, sulfadiazine, and salfamethyldiazine were observed in anaerobic fermentation residues of the pig manure. The total relative abundance levels of ARGs on the apple pericarp surface, in the orchard soil treated with biogas slurry, and in the orchard soil treated with biogas residue were 122.5, 5.2, 1.4 times higher than those in pristine soil, respectively, which were primarily attributed to the increase in the relative abundance of some ARG subtypes, including blaCTX-M, blaTEM, ermC, sul2, tetO, vgaB, and vgb. Long-term biogas slurry and biogas residue applications to orchard soil enriched bioaccumulation of 10 ARGs and 1 MGEs on the apple pericarp surface with 67.98 the highest factor. This research indicates that the application of anaerobic fermentation residues of pig manure promoted the spread of ARGs in the soil and fruits and increased the level of ARG pollution in the orchard. Results of this study highlight the importance of assessing the ecological safety of organic fertilizers from the perspective of ARGs and indicate that efforts should be devoted to further reducing ARG levels in pig manure before its application to farmland.

Metagenomic analysis of microbiological risk in bioaerosols during biowaste valorization using Musca domestica

Bioconversion using insects has gradually become a promising technology for biowaste management and protein production. However, knowledge about microbiological risk of insect related bioaerosols is sparse and conventional methods failed to provide higher resolved information of environmental microbe. In this study, a metagenomic analysis including microorganisms, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile gene elements (MGEs), and endotoxin distribution in bioaerosols during biowaste conversion via Musca domestica revealed that bioaerosols in Fly rearing room possess the highest ARGs abundances and MGEs diversity. Through a metagenome-assembled genomes (MAGs)-based pipeline, compelling evidence of ARGs/VFGs host assignment and ARG-VFG co-occurrence pattern were provided from metagenomic perspective. Bioaerosols in Bioconversion and Maggot separation zone were identified to own high density of MAGs carrying both ARGs and VFGs. Bacteria in Proteobacteria, Actinobacteriota, and Firmicutes phyla were predominate hosts of ARGs and VFGs. Multidrug-Motility, Multidrug-Adherence, and Beta lactam-Motility pairs were the most common ARG-VFG co-occurrence pattern in this study. Results obtained are of great significance for microbiological risk assessment during housefly biowaste conversion process.

Deciphering basic and key traits of antibiotic resistome in influent and effluent of hospital wastewater treatment systems

Hospital wastewater treatment system (HWTS) is an important source and environmental reservoir of clinically relevant antibiotic resistance genes (ARGs). However, how antibiotic resistome of clinical wastewater changed in HWTS is poorly understood. Herein, the basic quantitative traits (i.e., diversity and abundance) of ARGs in three HWTSs were profiled by metagenomics. In total, 709 ARG subtypes belonging to 20 ARG types were detected with relative abundance ranging from 1.12 × 10^-5 to 7.33 × 10^-1 copies/cell. Notably, most ARGs could not be significantly removed by chlorination treatment in the HWTS. These ARGs were identified to confer resistance to almost all major classes of antibiotics and include ARGs of last-resort antibiotics, such as bla_NDM, mcr and tet(X) which were abundantly occurred in HWTS with 19, 5 and 7 variants, respectively. Moreover, qualitative analysis based on metagenome-assembled genome (MAG) analysis revealed that the putative hosts of the identified ARGs were broadly distributed into at least 8 dominant bacterial phyla. Of the 107 ARG-carrying MAGs recovered, 39 encoded multi-antibiotic resistance and 16 belonged to antibiotic resistant pathogens. Further analysis of co-occurrence patterns of ARGs with mobile genetic elements suggested their potential mobility. These key qualitative traits of ARGs provided further information about their phylogeny and genetic context. This study sheds light on the key traits of ARGs associated with resistance dissemination and pathogenicity and health risks of clinical wastewater.

Bacillus subtilis reduces antibiotic resistance genes of animal sludge in vermicomposting by improving heat stress tolerance of Eisenia foetida and bacterial community adjustment

Antibiotic resistance genes (ARGs) in livestock industry have been recognized as a kind of pollutant. The effect of Bacillus subtilis (B. subtilis) as an additive for the reduction of ARGs in animal sludge from livestock and poultry wastewater treatment plant during vermicomposting was investigated. We also evaluated the oxidative stress level and growth of earthworms, Eisenia foetida, bacterial community succession, and the quality of the end products. Two treatments were conducted using B. subtilis, one at 18 °C and another at 28 °C. Controls were setup without the bacteria. The results showed that inoculation of B. subtilis promoted the degradation of organics at 28 °C and increased the germination index to 236%. The increased activities of the superoxide dismutase (1.69 U/mg pr) and catalase (8.05 U/mg pr) and the decreased activity of malondialdehyde (0.02 nmol/mg pr) by B. subtilis at 28 °C showed that the earthworms were relieved of heat stress. The addition of B. subtilis reduced the abundance of 32 target ARGs, including integron (intI-1), transposase (IS613) and resistant genes, such as sulfonamide (sul2), quinolone (oprJ), macrolide-lincosamide-streptogramin group B (ermF, ermB), tetracycline (tetL-02, tetX), β-lactama (blaOXA10-01) and aminoglycoside [strB, aac(6')-Ib(aka aacA4)-01, aac(6')-Ib(aka aacA4)-02]. Organic matter degrading Membranicola, Paludisphaera, Sphingorhabdus and uncultured bacterium belonging to the order Chitinophagales, nitrifying and nitrogen-fixing Singulisphaera and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, soil remediating Achromobacter, and plant growth promoting Kaistia, Galbibacter and Ilumatobacter were increased significantly (P < 0.05). However, the growth of harmful bacteria such as Burkholderiaceae was inhibited in the vermicompost. In earthworm guts, the probiotic Mesorhizobium was promoted, while the pathogenic uncultured bacterium belonging to the family Enterobacteriaceae was reduced. Besides, B. subtilis enhanced the host relationships between bacteria and ARGs. These findings might be helpful in the removal of ARGs in animal wastes and in understanding the synergy between earthworms and microorganisms.

Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment

Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.

Investigating changes in the characteristics of antibiotic resistance genes at different reaction stages of high solid anaerobic digestion with pig manure

Contamination of antibiotic resistance genes (ARGs) from animals is a serious issue as they may spread to human pathogenic bacteria. The reduction of ARG contamination from livestock waste is thus essential. High solid anaerobic digestion (HSAD) is a new and effective technology although some aspects, such as change characteristics of ARGs at different reaction stages, have not been fully investigated. This study focused firstly on the variations in ARGs at different reaction stages in HSAD systems with five different starting methods: 1 natural start (the control) and 4 rapid starts by changing leachate reflux forms. The results showed that the rapid starting methods could accelerate start-up and increase biogas production by 312.5%. The starting and acidification stages showed higher microbial richness and diversity compared with the other stages. ARGs found to be reduced at acidification stage. Variation in ARGs at the starting and acidification stages was mainly driven by a combination of microbial community, mobile genetic elements (MGEs), and environmental factors; while the main contributory factors at the gas production stage were biomass and several unexplained factors. At the ending stage, the main driving factors were biomass and microbial communities. Most of the potential hosts (16/20) of the ARGs belonged to the Firmicutes phylum, which showed the lowest connections with the ARGs at the gas production stage.

Short-Term Benzalkonium Chloride (C12) Exposure Induced the Occurrence of Wide-Spectrum Antibiotic Resistance in Agricultural Soils

Antibiotic resistance genes (ARGs) are global pollutants that pose a potential risk to human health. Benzalkonium chloride (C₁₂) (BC) disinfectants are thought to exert selection pressure on antibiotic resistance. However, evidence of BC-induced changes in antibiotic resistance in the soil environment is lacking. Here, we established short-term soil microcosms to investigate ARG profile dynamics in agricultural soils amended with sulfamethazine (SMZ, 10 mg kg^-1) and gradient concentrations of BC (0-100 mg kg^-1), using high-throughput quantitative PCR and Illumina sequencing. With the increase in BC concentration, the number of ARGs detected in the soil increased, but the normalized ARG abundance decreased. The added SMZ had a limited impact on ARG profiles. Compared to broad-spectrum fungicidal BC, the specificity of SMZ significantly affected the microbial community. Network analysis found that low-medium BC exposure concentrations resulted in the formation of small but strong ARG co-occurrence clusters in the soil, while high BC exposure concentration led to a higher incidence of ARGs. Variation partitioning analysis suggested that BC stress was the major driver shaping the ARG profile. Overall, this study highlighted the emergence and spread of BC-induced ARGs, potentially leading to the antimicrobial resistance problem in agricultural soils.

Effects of antibiotics on anaerobic digestion of sewage sludge: Performance of anaerobic digestion and structure of the microbial community

As a common biological engineering technology, anaerobic digestion can stabilize sewage sludge and convert the carbon compounds into renewable energy (i.e., methane). However, anaerobic digestion of sewage sludge is severely affected by antibiotics. This review summarizes the effects of different antibiotics on anaerobic digestion of sewage sludge, including production of methane and volatile fatty acids (VFAs), and discusses the impact of antibiotics on biotransformation processes (solubilization, hydrolysis, acidification, acetogenesis and methanogenesis). Moreover, the effects of different antibiotics on microbial community structure (bacteria and archaea) were determined. Most of the research results showed that antibiotics at environmentally relevant concentrations can reduce biogas production mainly by inhibiting methanogenic processes, that is, methanogenic archaea activity, while a few antibiotics can improve biogas production. Moreover, the combination of multiple environmental concentrations of antibiotics inhibited the efficiency of methane production from sludge anaerobic digestion. In addition, some lab-scale pretreatment methods (e.g., ozone, ultrasonic combined ozone, zero-valent iron, Fe³⁺ and magnetite) can promote the performance of anaerobic digestion of sewage sludge inhibited by antibiotics.

Electroactive Ultrafiltration Membrane for Simultaneous Removal of Antibiotic, Antibiotic Resistant Bacteria, and Antibiotic Resistance Genes from Wastewater Effluent

To combat the spread of antibiotic resistance into the environment, we should adequately manage wastewater effluent treatment to achieve simultaneous removal of antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). Herein, we fabricate a multifunctional electroactive poly(vinylidene fluoride) ultrafiltration membrane (C/PVDF) by phase inversion on conductive carbon cloth. The membrane possesses not only excellent retention toward ARB and ARGs but also exhibits high oxidation capacity as an electrode. Notably, sulfamethoxazole degradation involving hydroxylation and hydrolysis by the anode membrane is predominant, and the degradation efficiency is up to 81.5% at +4 V. Both electro-filtration processes exhibit significant ARB inactivation, anode filtration is superior to cathode filtration. Moreover, the degradation of intracellular ARGs (iARGs) located in the genome is more efficient than those located in the plasmid, and these degradation efficiencies at -2 V are higher than +2 V. The degradation efficiencies of extracellular ARGs (eARGs) are opposite and are lower than iARGs. Compared with regular filtration, the normalized flux of electroactive ultrafiltration membrane is improved by 18.0% at -2 V, 15.9% at +2 V, and 30.4% at +4 V during treating wastewater effluent, confirming its antifouling properties and feasibility for practical application.

Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review

Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.

Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms

The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.

Dissecting the roles of conductive materials in attenuating antibiotic resistance genes: Evolution of physiological features and bacterial community

Supplying conductive materials (CMs) into anaerobic bioreactors is considered as a promising technology for antibiotic wastewater treatment. However, whether and how CMs influence antibiotic resistance genes (ARGs) spread remains poorly known. Here, we investigated the effects of three CMs, i.e., magnetite, activated carbon (AC), and zero valent iron (ZVI), on ARGs dissemination during treating sulfamethoxazole wastewater, by dissecting the shifts of physiological features and microbial community. With the addition of magnetite, AC, and ZVI, the SMX removal was improved from 49.05 to 71.56-92.27 %, while the absolute abundance of ARGs reducing by 26.48 %, 61.95 %, 48.45 %, respectively. The reduced mobile genetic elements and antibiotic resistant bacteria suggested the inhibition of horizontal and vertical transfer of ARGs. The physiological features, including oxidative stress response, quorum sensing, and secretion system may regulate horizontal transfer of ARGs. The addition of all CMs relieved oxidative stress compared with no CMs, but ZVI may cause additional free radicals that needs to be concerned. Further, ZVI and AC also interfered with cell communication and secretion system. This research deepens the insights about the underlying mechanisms of CMs in regulating ARGs, and is expected to propose practical ways for mitigating ARGs proliferation.

The Resistome of ESKAPEE Pathogens in Untreated and Treated Wastewater: A Polish Case Study

The aim of this study was to quantify ESKAPEE bacteria, genes encoding resistance to antibiotics targeting this group of pathogens, as well as integrase genes in municipal wastewater and river water. Environmental DNA was extracted from the collected samples and used in deep sequencing with the Illumina TruSeq kit. The abundance of bacterial genera and species belonging to the ESKAPEE group, 400 ARGs associated with this microbial group, and three classes of integrase genes were determined. A taxonomic analysis revealed that Acinetobacter was the dominant bacterial genus, whereas Acinetobacter baumannii and Escherichia coli were the dominant bacterial species. The analyzed samples were characterized by the highest concentrations of the following ARGs: bla_GES, bla_OXA-58, bla_TEM, qnrB, and qnrS. Acinetobacter baumannii, E. coli, and genes encoding resistance to β-lactams (bla_VEB-1, bla_IMP-1, bla_GES, bla_OXA-58, bla_CTX-M, and bla_TEM) and fluoroquinolones (qnrS) were detected in samples of river water collected downstream from the wastewater discharge point. The correlation analysis revealed a strong relationship between A. baumannii (bacterial species regarded as an emerging human pathogen) and genes encoding resistance to all tested groups of antimicrobials. The transmission of the studied bacteria (in particular A. baumannii) and ARGs to the aquatic environment poses a public health risk.

Differential variations of intracellular and extracellular antibiotic resistance genes between treatment units in centralized sewage sludge treatment plants

Centralized sludge treatment plants (CSTPs) are implicated as strong hotspots of antibiotic resistance genes (ARGs). However, the knowledge gap on the fate of intracellular and extracellular ARGs (iARGs and eARGs), and the functionality of resistant hosts limit risk assessment and management of CSTP resistome. Here, the flow of iARGs and eARGs across treatment units and analyses of ARG hosts were systematically explored in three full-scale CSTPs using quantitative metagenomic approaches. We found that 29% of sludge ARGs could be removed, with iARGs being dominant in the produced biosolids. The treatment process significantly affected the variations of iARG and eARG abundance while no significant difference in composition between iARGs and eARGs was observed in CSTPs. 15% of 295 recovered genomes were identified as antibiotic-resistant hosts, among which Actinobacteriota tended to encode multiple resistance. The key functions of ARG hosts were relative to the biological organic removal (e.g., carbohydrates). There also existed relationships between certain resistance mechanisms and functional traits, indicating that ARGs might take part in the physiological process of microorganisms in the sludge treatment. These findings provide important insight into the differential resistome variations and host functionality, which would be crucial in the management of antibiotic resistance in CSTPs.

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

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

Anaerobic electrochemical membrane bioreactor effectively mitigates antibiotic resistance genes proliferation under high antibiotic selection pressure

The spread of antibiotics and antibiotic resistance genes (ARGs) in environments has posed potential threats to public health. Unfortunately, conventional biological wastewater treatment technologies generally show insufficient removal of antibiotics and ARGs. Bioelectrochemical systems, which can effectively degrade refractory organic pollutants via enhancing microbial metabolisms through electrochemical redox reaction, may provide an alternative for the control of antibiotics and ARGs. Herein, an anaerobic electrochemical membrane bioreactor (AnEMBR) was conducted by combining bioelectrochemical system and anaerobic membrane bioreactor to treat antibiotic-containing wastewater. The AnEMBR at open circuit showed stable CH4 production and high removal of COD and chlortetracycline (CTC) in treating 2.5-15 mg/L CTC. However, increasing CTC to 45 mg/L completely inhibited the methanogenesis of AnEMBR at open circuit. After applying external voltage in AnEMBR, the performances of AnEMBR were significantly improved (e.g., increased CH4 production and CTC removal). Moreover, CTC exposure significantly increased the relative abundances of ARGs in sludge, supernatant, and effluent in AnEMBR at open circuit. Applying voltage greatly attenuated the total relative abundances of ARGs in the supernatant and effluent of AnEMBR compared to those at open circuit. This could be attributed to the enrichment of tetracycline degradation gene tetX, which greatly enhanced the removal of CTC by the AnEMBR and thus reduced the selective pressure of CTC on the microorganisms in supernatant and effluent for ARGs proliferation. These results would provide an effective wastewater treatment technology for treating high-level antibiotic-containing wastewater to mitigate the potential risk of ARGs and antibiotics spread in receiving water body.

Effects of Pyroligneous Acid on Diversity and Dynamics of Antibiotic Resistance Genes in Alfalfa Silage

Antibiotic resistance genes (ARGs) are recognized as contaminants due to their potential risk for human and environment. The aim of the present study is to investigate the effects of pyroligneous acid (PA), a waste of biochar production, on fermentation characteristics, diversity, and dynamics of ARGs during ensiling of alfalfa using metagenomic analysis. The results indicated that PA decreased (P < 0.05) dry matter loss, pH value, gas production, coliform bacteria count, protease activity, and nonprotein-N, ammonia-N, and butyric acid contents and increased (P < 0.05) lactic acid content during ensiling. During fermentation, Bacteria, Firmicutes, and Lactobacillus were the most abundant at kingdom, phylum, and genus levels, respectively. Pyroligneous acid reduced the relative abundance of Bacteria and Firmicutes and increased that of Lactobacillus. The detected ARGs belonged to 36 drug classes, including mainly macrolides, tetracycline, lincosamides, and phenicol. These types of ARGs decreased during fermentation and were further reduced by PA. These types of ARGs were positively correlated (P < 0.05) with fermentation parameters like pH value and ammonia-N content and with bacterial communities. At the genus level, the top several drug classes, including macrolide, tetracycline, lincosamide, phenicol, oxazolidinone, streptogramin, pleuromutilin, and glycopeptide, were positively correlated with Staphylococcus, Streptococcus, Listeria, Bacillus, Klebsiella, Clostridium, and Enterobacter, the potential hosts of ARGs. Overall, ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community composition. Ensiling could be a feasible way to mitigate ARGs in forages. The addition of PA could not only improve fermentation quality but also reduce ARG pollution of alfalfa silage.

IMPORTANCE Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ARGs in silages might influence the diversity and distribution of ARGs in animal intestinal and feces and then the manure and the manured soil. However, the diversity and dynamics of ARGs in silage during fermentation are still unknown. We ensiled alfalfa, one of the most widely used forages, with or without pyroligneous acid (PA), which was proved to have the ability to reduce ARGs in soils. The results showed that ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community. The majority of ARGs in alfalfa silage reduced during fermentation. The addition of PA could improve silage quality and reduce ARG pollution in alfalfa silage. This study can provide useful information for understanding and controlling ARG pollution in animal production.

Intensified inactivation of model and environmental bacteria by an atmospheric-pressure air-liquid discharge plasma compared with chlorination

Water-borne pathogenic bacteria are always the top priority to be removed through disinfection process in water treatment due to their threat to human health. It was necessary to develop novel disinfection methods since the conventional chlorine disinfection was inefficient in inactivating chlorine-resistant bacteria, inducing the viable but non-culturable (VBNC) bacteria and forming disinfection by-products (DBPs). In this study, the inactivation of four model strains including Gram-negative (G^-), Gram-positive (G⁺) and environmental samples by atmospheric-pressure air-liquid discharge plasma (ALDP) was assessed systematically. The results showed that ALDP was superior in inactivating all of the samples compared with chlorination. During 10 min ALDP treatment, the G^- bacteria were completely inactivated, and the G⁺ one was inactivated by more than 4.61 logs. The inactivation of bacteria from a campus lake and a wastewater treatment plant effluent exceeded 99.82% and 97.78%, respectively. For G^- bacteria, ALDP resulted in a much lower (10²∼10³ times) levels of VBNC cells than chlorination. ALDP could effectively remove the chlorine-resistant bacteria. More than 96.41% of the intracellular DNA and 99.99% of the extracellular DNA were removed, whereas it was only 56.35% and 12.82% for chlorination. ALDP had a stronger ability to destroy cell structure than chlorination, presumably due to the existence of ROS (·OH, ¹O₂ and O₂^-). GC-MS analysis showed that ALDP produced less DBPs than chlorination. These findings provided new insights for the application of discharge plasma in water disinfection, which could be complemental or alternative to the conventional disinfection methods.

Dynamics and key drivers of antibiotic resistance genes during aerobic composting amended with plant-derived and animal manure-derived biochars

Plant-derived and animal manure-derived biochars have been used to improve the quality of compost but the differences in their effects on antibiotic resistance genes (ARGs) during composting are unclear. This study selected two types of biochar (RB and PB) produced from abundant agricultural waste to be added to the compost. Adding plant-derived RB performed better in ARGs, mobile genetic elements, and human pathogenic bacteria removal during aerobic composting, whereas adding manure-derived PB even increased ARGs abundance. Vertical gene transfer was possibly the key mechanism for persistent ARGs, and easily removed ARGs were regulated by horizontal and vertical gene transfer. Adding plant-derived RB reduced the abundances of persistent ARG hosts (e.g., Pseudomonas and Longispora) and ARG-related metabolic pathways and genes. The higher nitrogen content of manure-derived PB may have promoted the proliferation of ARG hosts. Overall, adding manure-derived biochar during composting may not be the optimal option for eliminating ARGs.

Removal of Diverse and Abundant ARGs by MF-NF Process from Pig Manure and Digestate

Antimicrobial resistances are emerging as one main threat to worldwide human health and are expected to kill 10 million people by 2050. Intensive livestock husbandry, along with biogas digestate, are considered as one of the biggest ARG reservoirs. Despite major concerns, little information is available on the diversity and abundance of various ARGs in small to large scale pig farms and biogas digestate slurry in Germany, followed by their consequent removal using microfiltration (MF)-nanofiltration (NF) process. Here, we report the identification and quantification of 189 ARGs in raw manure and digestate samples, out of which 66 ARGs were shared among manures and 53 ARGs were shared among both manure and digestate samples. The highest reported total ARG copy numbers in a single manure sampling site was 1.15 × 10⁸ copies/100 µL. In addition, we found the absolute concentrations of 37 ARGs were above 10⁵ copies/100 μL. Filtration results showed that the highly concentrated ARGs (except aminoglycoside resistance ARGs) in feed presented high log retention value (LRV) from 3 to as high as 5 after the MF-NF process. Additionally, LRV below 2 was noticed where the initial absolute ARG concentrations were ≤10³ copies/100 μL. Therefore, ARG removal was found to be directly proportional to its initial concentration in the raw manure and in digestate samples. Consequently, some ARGs (tetH, strB) can still be found within the permeate of NF with up to 10⁴ copies/100 μL.

A critical review of process parameters influencing the fate of antibiotic resistance genes in the anaerobic digestion of organic waste

The overuse and inappropriate disposal of antibiotics raised severe public health risks worldwide. Specifically, the incomplete antibiotics metabolism in human and animal bodies contributes to the significant release of antibiotics into the natural ecosystems and the proliferation of antibiotic-resistant bacteria carrying antibiotic-resistant genes. Moreover, the organic feedstocks used for anaerobic digestion are often highly-rich in residual antibiotics and antibiotic-resistant genes. Hence, understanding their fate during anaerobic digestion has become a significant research focus recently. Previous studies demonstrated that various process parameters could considerably influence the propagation of the antibiotic-resistant genes during anaerobic digestion and their transmission via land application of digestate. This review article scrutinizes the influences of process parameters on antibiotic-resistant genes propagation in anaerobic digestion and the inherent fundamentals behind their effects. Based on the literature review, critical research gaps and challenges are summarized to guide the prospects for future studies.

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

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

A meta-analysis reveals that operational parameters influence levels of antibiotic resistance genes during anaerobic digestion of animal manures

Anaerobic digestion (AD) has shown the potential to reduce the numbers and types of antibiotic-resistance genes (ARG) present in animal manures. However, the variability of the results has limited the ability to draw solid conclusions. To address this issue, we performed a series of meta-analyses to evaluate how AD of pig, cattle, and dairy manures affects ARG levels and how different parameters, such as temperature, pH, digestion times, and the addition of other substances (e.g., solids, antibiotics) influence ARG changes. Twenty studies with enough details on changes in ARG levels during the AD process were identified and used for the meta-analyses. The results suggested that AD could significantly reduce ARG levels regardless of the conditions of the process. Also, thermophilic AD was more effective than mesophilic AD at reducing ARGs, although this difference was only significant for pig manures. The results also suggested that long digestion times (>50 days) yielded better ARG reduction rates, and that the addition of solids from an external source (co-digestion) negatively affected the efficiency of ARG reduction. In general, the results suggested that ARG changes during AD could be linked to the abundance and activity of hydrolytic communities.