Determining the composition of bacterial community and relative abundance of specific antibiotics resistance genes via thermophilic anaerobic digestion of sewage sludge

The fate of antibiotic resistance genes during anaerobic digestion of sewage sludge with ultrasonic pretreatment

This study investigated the effect of ultrasonic (US) pretreatment at three different contact times (30, 45, and 60 min) with a power of 240 W and frequency of 40 kHz on the fate of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and enteric pathogens during anaerobic digestion (AD) of sludge. By using real time-qPCR, three MGEs (int1, int2, and tnpA) and seven ARGs (sul1, sul2, tetW, tetA, tetO, ermF, and aac(6')-lb) were quantified that have serious human health impacts and represent the most widely used antibiotics (tetracycline, sulfonamide, macrolide, and aminoglycoside). Results indicated that US pretreatment under different contact times improved the removal of ARGs and MGEs. Compared to 30 and 45 min of US pretreatment, 60 min of US pretreatment resulted in a higher reduction of ARGs with total ARG reduction of 41.70 ± 1.13%. Furthermore, the relative abundance of ARGs and MGEs after US pretreatment was reduced more effectively in anaerobic reactors than in a control AD without US pretreatment. The total ARGs and MGEs removal efficiency of control AD was 44.07 ± 0.72% and 63.69 ± 1.43%, and if US pretreatment at different times were applied, the total ARGs and MGEs removal efficiency of the whole pretreatment AD process improved to 59.71 ± 2.76-68.54 ± 1.58% and 69.82 ± 2.15-76.84 ± 0.22%. The highest removal of total ARGs (68.54 ± 1.58%) and MGEs (76.84 ± 0.22%) was achieved after AD with US pretreatment at 45 min. However, US pretreatment and AD with US pretreatment were not effective in inactivation of enteric pathogens (total coliforms and E. coli), suggesting that posttreatment is needed prior to land application of sludge to reduce the level of enteric pathogens. There was no detection of the studied ARGs and MGEs in the enteric pathogens after US pretreatment in subsequent AD. According to this study, long contact times of US pretreatment can mitigate ARGs and MGEs in AD processes, offering valuable insight into improving environmental safety and sustainable waste management. Additionally, the study highlights the need to investigate posttreatment techniques for reducing enteric pathogens in AD effluent, a crucial consideration for agricultural use and environmental protection.

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.

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.

Data-driven discoveries on widespread contamination of freshwater reservoirs by dominant antibiotic resistance genes

The propagation of antibiotic resistance genes (ARGs) in freshwater reservoirs threatens ecosystem security and human health, and has attracted increasing attention. A series of recent research articles on ARGs provides a unique opportunity for data-driven discoveries in this emerging field. Here, we mined data from a total of 290 samples from 60 reservoirs worldwide with a data-driven framework (DD) developed to discover geographical distribution, influencing factors and pollution hotspots of ARGs in freshwater reservoirs. Most data came from Asia and Europe where nine classes of ARGs were most frequently detected in reservoirs with multi-drug resistance and sulfonamide resistance genes prevailing. Factors driving distribution of reservoir ARGs differed between reservoir waters and sediments, and interactions among these factors had linear or nonlinear enhancement effects on the explanatory power of ARG distribution. During the cold season, small-sized reservoir waters rich in organic carbon, mobile genetic elements (MGEs) and antibiotics had a higher pollution potential of ARGs; during the spring drought, sediments in large reservoirs located in densely populated areas were more conducive to dissemination of ARGs due to their richness in antibiotics and MGEs. Thus, distribution pattern of ARG pollution hotspots in reservoir waters and sediments varies greatly depending on the differences of internal and external factors. From the "One Health" perspective, this widespread contamination of freshwater reservoirs by ARGs we discovered through the DD framework should be a push to promote integrated research across regions and disciplines. Especially the human - food-chain - ecosystem interface needs an improved understanding of ARG contamination mechanisms and targeted monitoring and evaluation systems should be developed to maintain all ecosystem services in freshwater reservoirs as well as to safeguard human health.

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.

Long-Term, Simultaneous Impact of Antimicrobials on the Efficiency of Anaerobic Digestion of Sewage Sludge and Changes in the Microbial Community

The aim of this study was to evaluate the influence of simultaneous, long-term exposure to increasing concentrations of three classes of antimicrobials (β-lactams, fluoroquinolones and nitroimidazoles) on: (1) the efficiency of anaerobic digestion of sewage sludge, (2) qualitative and quantitative changes in microbial consortia that participate in methane fermentation, and (3) fate of antibiotic resistance genes (ARGs). Long-term supplementation of sewage sludge with a combination of metronidazole, amoxicillin and ciprofloxacin applied at different doses did not induce significant changes in process parameters, including the concentrations of volatile fatty acids (VFAs), or the total abundance of ARGs. Exposure to antibiotics significantly decreased methane production and modified microbial composition. The sequencing analysis revealed that the abundance of OTUs characteristic of Archaea was not correlated with the biogas production efficiency. The study also demonstrated that the hydrogen-dependent pathway of methylotrophic methanogenesis could significantly contribute to the stability of anaerobic digestion in the presence of antimicrobials. The greatest changes in microbial biodiversity were noted in substrate samples exposed to the highest dose of the tested antibiotics, relative to control. The widespread use of antimicrobials increases antibiotic concentrations in sewage sludge, which may decrease the efficiency of anaerobic digestion, and contribute to the spread of antibiotic resistance (AR).

Recent advances, current issues and future prospects of bioenergy production: A review

With the immense potential of bioenergy to drive carbon neutrality and achieve the climate targets of the Paris Agreement, this paper aims to present the recent advances in bioenergy production as well as their limitations. The novelty of this review is that it covers a comprehensive range of strategies in bioenergy production and it provides the future prospects for improvement. This paper reviewed more than 200 peer-reviewed scholarly papers mainly published between 2010 and 2021. Bioenergy is derived from biomass, which, through thermochemical and biochemical processes, is converted into various forms of biofuels. This paper reveals that bioenergy production is temperature-dependent and thermochemical processes currently have the advantage of higher efficiency over biochemical processes in terms of lower response time and higher conversion. However, biochemical processes produce more volatile organic compounds and have lower energy and temperature requirements. The combination of the two processes could fill the shortcomings of a single process. The choices of feedstock are diverse as well. In the future, it can be anticipated that continuous technological development to enhance the commercial viability of different processes, as well as approaches of ensuring their sustainability, will be among the main aspects to be studied in greater detail.

Antibiotics and antibiotic resistance genes in landfills: A review

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

Effect of type of coagulants on removal efficiency and removal mechanisms of antibiotic resistance genes in anaerobic digestion of primary sludge produced via a chemically enhanced primary treatment process

The potential impact of the trivalent coagulant cations on the removal mechanisms, removal efficiencies and removal patterns of antibiotic resistance genes (ARGs) during anaerobic digestion (AD) of chemically enhanced primary treatment sludge (CEPTS) was investigated using polyaluminium chloride (PACl), ferric chloride (FeCl₃) and mixed FeCl₃-PACl. The removal efficiency of 23 ARGs and intI1 improved to 72.1% in AD of primary sludge with 100 mg/L FeCl₃ and was lowest (only 54.4 %) in AD of primary sludge with 25 mg/L PACl. The removal of ARGs in AD of CEPTS with addition of single or mixed types of Al-based coagulant began to increase rapidly at the onset of batch operation. On the other hand, both the rapid increase in the removal efficiency of ARGs in AD with FeCl₃ and the maximum removal efficiency were attained later than in the other ADs.

Advancements in detection and removal of antibiotic resistance genes in sludge digestion: A state-of-art review

Sludge from wastewater treatment plants can act as a repository and crucial environmental provider of antibiotic resistance genes (ARGs). Over the past few years, people's knowledge regarding the occurrence and removal of ARGs in sludge has broadened remarkably with advancements in molecular biological techniques. Anaerobic and aerobic digestion were found to effectively achieve sludge reduction and ARGs removal. This review summarized advanced detection and removal techniques of ARGs, in the last decade, in the sludge digestion field. The fate of ARGs due to different sludge digestion strategies (i.e., anaerobic and aerobic digestion under mesophilic or thermophilic conditions, and in combination with relevant pretreatment technologies (e.g., thermal hydrolysis pretreatment, microwave pretreatment and alkaline pretreatment) and additives (e.g., ferric chloride and zero-valent iron) were systematically summarized and compared in this review. To date, this is the first review that provides a comprehensive assessment of the state-of-the-art technologies and future recommendations.

Bioleaching rather than chemical conditioning using Fe[III]/CaO or polyacrylamide mitigates antibiotic resistance in sludge composting via pre-removing antibiotic resistance genes and limiting horizontal gene transfer

Conditioning can drastically improve the dewaterability of sewage sludge and is widely practiced in most wastewater treatment plants (WWTPs). Sludge conditioning was also reported as a crucial step in sludge treatment to attenuate antibiotic resistance, but it remains unclear whether the attenuated antibiotic resistance by conditioning treatments would guarantee low abundance of antibiotic resistance genes (ARGs) in the compost products of municipal sewage sludge. Herein, the impacts of three conditioning treatments, including bioleaching and chemical conditioning using Fe[III]/CaO or polyacrylamide (PAM), on the abundances of 20 ARGs and 4 mobile genetic elements (MGEs) during conventional aerobic composting of dewatered sludge were investigated. It was found that the absolute and relative abundances of total ARGs in compost product of bioleached sludge accounted for only 13.8%-28.8% of that in compost products of un-conditioned, Fe[III]/CaO-conditioned, or PAM-conditioned sludges. Besides, bioleaching conditioning resulted in the lowest abundances of ARG subtypes and ARG-associated bacteria in the sludge compost product. The shift of ARG profiles in the bioleached sludge composting can be mainly ascribed to the ARG-associated bacteria, while the MGEs drove the ARG profiles during conventional composting of un-conditioned sludge and the two chemically conditioned sludge. Thus, bioleaching conditioning is superior to the chemical conditioning using Fe[III]/CaO or PAM in mitigating antibiotic resistance in sludge compost products, which was contributed by the pre-removal of ARGs prior to composting treatment and the potential limitation of ARGs transfer during conventional composting.

Thermophilic rather than mesophilic sludge anaerobic digesters possess lower antibiotic resistant genes abundance

For exploring the impact of temperature on antibiotic resistant genes (ARGs) during sludge anaerobic digestion (AD), the dynamic variations of sludge ARGs, plasmid ARGs, and cell-free ARGs in mesophilic (25 °C and 35 °C) and thermophilic (55 °C) digesters were investigated. The study revealed that the abundance of sludge ARGs and plasmid ARGs in thermophilic sludge AD was significantly lower than that in mesophilic digesters, while the cell-free ARGs abundance of the thermophilic digesters was similar to mesophilic digesters. Higher archaea abundance, lower bacteria abundance, and different microbial community were found in thermophilic digesters compared to that of mesophilic ones. Firmicutes might be a main group of potential hosts of ARGs in sludge AD. The distinct microbial community was the main contributor to the low ARGs abundance in thermophilic sludge AD. Thermophilic operation at 55 °C rather than mesophilic operation is more conducive to control ARGs in sludge anaerobic digestion.

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

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

Behavior of antibiotic resistance genes in a wastewater treatment plant with different upgrading processes

Wastewater treatment plants (WWTPs) in China have been upgraded or renovated with a variety of emerging processes, but a comprehensive understanding of the behavior of antibiotic resistance genes (ARGs) in these WWTPs is still lacking. Here, the distribution of ARGs and bacterial community were investigated in a wastewater treatment plant with upgrading processes (WWTP-UP). 238 unique ARGs were detected in all samples. During the study period, the average ARGs concentration decreased by 98.4% along the entire treatment process. The removal efficiency of A²/O-membrane bioreactor (MBR) process was significantly higher than that of A²/O-high efficiency flocculent settling/cloth media filter (HEFS/CMF) process (p < 0.05), which corresponded to 3.5 and 2.1 log values on average, respectively. Notably, 35 ARGs and 14 mobile genetic elements (MGEs) were persistent in all samples. Based on the co-occurrence pattern revealed by network analysis, persistent ARGs possibly spread through the transfer of persistent MGEs among persistent bacteria. Using multiple linear regression analysis, we obtained 3 to 5 possible indicators for major ARG types, which might be served to evaluate the general distribution of ARGs or even predict the abundance of different ARG types. Our findings provide new insights into the impacts of upgrading process on ARGs and highlight the need for better strategies to improve ARGs elimination in WWTPs.

Improved reduction of antibiotic resistance genes and mobile genetic elements from biowastes in dry anaerobic co-digestion

This study investigated the performance of anaerobic co-digestion (AcoD) of pig manure and food waste on the reduction of antibiotic resistomes under wet and dry AcoD conditions. High-throughput quantitative PCR technology was utilized for a comprehensive assessment of the performances of the two processes. The results show that dry AcoD with a total solids (TS) content of 20% effectively reduced total antibiotic resistance genes (ARGs) by 1.24 log copies/g wet sample, while only 0.54 log copies/g wet sample was reduced in wet AcoD with a TS content of 5%. Dry AcoD was more efficient in reduction of aminoglycosides, multidrug and sulfonamide resistance genes compared with the reduction of other classes of ARGs. Dry AcoD caused a significant reduction of ARGs with resistance mechanisms of efflux pump and antibiotic deactivation. In contrast, there was no obvious difference in reductions of ARGs with different resistance mechanisms in wet AcoD. Network analysis showed that ARGs were significantly correlated with mobile genetic elements (MGEs) (Spearman's r > 0.8, P < 0.05), as well as microbial communities. Enrichment of ARGs and MGEs was found at the early period of AcoD processes, indicating some ARGs and MGEs increased during the hydrolysis and acidogenesis stages. But after a long retention time, their abundances were effectively reduced by dry AcoD in the subsequent stages.

Enhanced control of sulfonamide resistance genes and host bacteria during thermophilic aerobic composting of cow manure

Traditional composting has already shown a certain effect in eliminating antibiotic residues, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs). It is worth noting that the rebounding of ARGs and the succession of the bacterial community during conventional aerobic composting are still serious threats. Considering the probable risk, improved and adaptable technologies are urgently needed to control antibiotic resistance efficiently. This study monitored how thermophilic aerobic composting affected the ARGs, as well as the bacterial diversity during the composting of cow manure spiked with sulfamethoxazole (SMX) at different concentrations. Results showed that the degradation of SMX was enhanced during thermophilic aerobic composting (control > SMX25 > SMX50 > SMX100) and was no longer detected after 20 days of composting. High temperature or heat significantly stimulated the rebounding of certain genes. After 35 days, the abundance of detected genes (sul2, sulA, dfrA7, and dfrA1) significantly decreased (p < 0.05) in control and antibiotic-spiked treatments, except for sul1. The addition of three concentrations of SMX elicited a sharp effect on bacterial diversity, and microbial structure in SMX25 led to significant differences with others (p < 0.05). The network analysis revealed more rigorous interactions among ARGs and abundant genera, suggesting that the host of ARGs potentially increased at low concentrations of SMX. Especially, genera g_norank_f__Beggiatoaceae, Ruminiclostridium, Caldicoprobacter, g_norank_o_MBA03, Hydrogenispora, and Ruminiclostridium_1 were major potential hosts for sul1. In conclusion, the rebounding of ARGs could be intermitted partially, and more efficient control of antibiotic resistance could be achieved in the thermophilic composting compared to conventional methods.

A review of chemical and microbial contamination in food: What are the threats to a circular food system?

A circular food system is one in which food waste is processed to recover plant nutrients and returned to the soil to enable the production of more food, rather than being diverted to landfill or incineration. The approach may be used to reduce energy and water use in food production and contribute to the sustainability of the system. Anaerobic digestion and composting are common food waste treatment technologies used to stabilize waste and produce residual materials that can replenish the soil, thus contributing to a circular food system. This approach can only be deemed safe and feasible, however, if food waste is uncontaminated or any contaminants are destroyed during treatment. This review brings together information on several contaminant classes at different stages of the food supply chain, their possible sources, and their fates during composting and digestion. The main aim is to identify factors that could impede the transition towards a safe, reliable and efficient circular food system. We investigated heavy metals, halogenated organic compounds, foodborne pathogens and antibiotic resistance genes (ARGs) in the food system and their fates during digestion and composting. Production and processing stages were identified as major entry points for these classes of contaminants. Heavy metals and foodborne pathogens pose less risk in a circular system than halogenated organics or antibiotic resistance. Given the diversity of properties among halogenated organic compounds, there is conflicting evidence about their fate during treatment. There are relatively few studies on the fate of ARGs during treatment, and these have produced variable results, indicating a need for more research to clarify their fate in the final products. Repeated land application of contaminated food waste residuals can increase the risk of accumulation and jeopardize the safety of a circular food system. Thus, careful management of the system and research into the fate of the contaminants during treatment is needed.

Effect of Antibiotics on the Microbial Efficiency of Anaerobic Digestion of Wastewater: A Review

Recycling waste into new materials and energy is becoming a major challenge in the context of the future circular economy, calling for advanced methods of waste treatment. For instance, microbially-mediated anaerobic digestion is widely used for conversion of sewage sludge into biomethane, fertilizers and other products, yet the efficiency of microbial digestion is limited by the occurrence of antibiotics in sludges, originating from drug consumption for human and animal health. Here we present antibiotic levels in Chinese wastewater, then we review the effects of antibiotics on hydrolysis, acidogenesis and methanogenesis, with focus on macrolides, tetracyclines, β-lactams and antibiotic mixtures. We detail effects of antibiotics on fermentative bacteria and methanogenic archaea. Most results display adverse effects of antibiotics on anaerobic digestion, yet some antibiotics promote hydrolysis, acidogenesis and methanogenesis.