Increasing the removal efficiency of antibiotic resistance through anaerobic digestion with free nitrous acid pretreatment

Harnessing biotechnology for penicillin production: Opportunities and environmental considerations

Since the discovery of antibiotics, penicillin has remained the top choice in clinical medicine. With continuous advancements in biotechnology, penicillin production has become cost-effective and efficient. Genetic engineering techniques have been employed to enhance biosynthetic pathways, leading to the production of new penicillin derivatives with improved properties and increased efficacy against antibiotic-resistant pathogens. Advances in bioreactor design, media formulation, and process optimization have contributed to higher yields, reduced production costs, and increased penicillin accessibility. While biotechnological advances have clearly benefited the global production of this life-saving drug, they have also created challenges in terms of waste management. Production fermentation broths from industries contain residual antibiotics, by-products, and other contaminants that pose direct environmental threats, while increased global consumption intensifies the risk of antimicrobial resistance in both the environment and living organisms. The current geographical and spatial distribution of antibiotic and penicillin consumption dramatically reveals a worldwide threat. These challenges are being addressed through the development of novel waste management techniques. Efforts are aimed at both upstream and downstream processing of antibiotic and penicillin production to minimize costs and improve yield efficiency while lowering the overall environmental impact. Yield optimization using artificial intelligence (AI), along with biological and chemical treatment of waste, is also being explored to reduce adverse impacts. The implementation of strict regulatory frameworks and guidelines is also essential to ensure proper management and disposal of penicillin production waste. This review is novel because it explores the key remaining challenges in antibiotic development, the scope of machine learning tools such as Quantitative Structure-Activity Relationship (QSAR) in modern biotechnology-driven production, improved waste management for antibiotics, discovering alternative path to reducing antibiotic use in agriculture through alternative meat production, addressing current practices, and offering effective recommendations.

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.

Metagenomic insights into the influence of pH on antibiotic removal and antibiotic resistance during nitritation: Regulations on functional genus and genes

The changes in pH and the resulting presence of free nitrous acid (FNA) or free ammonia (FA) often inhibit antibiotic biodegradation during nitritation. However, the specific mechanisms through which pH, FNA and FA influence antibiotic removal and the fate of antibiotic resistance genes (ARGs) are not yet fully understood. In this study, the effects of pH, FNA, and FA on the removal of cefalexin and amoxicillin during nitritation were investigated. The results revealed that the decreased antibiotic removal under both acidic condition (pH 4.5) and alkaline condition (pH 9.5) was due to the inhibition of the expression of amoA in ammonia-oxidizing bacteria and functional genes (hydrolase-encoding genes, transferase-encoding genes, lyase-encoding genes, and oxidoreductase-encoding genes) in heterotrophs. Furthermore, acidity was the primary inhibitor of antibiotic removal at pH 4.5, followed by FNA. Antibiotic removal was primarily inhibited by alkalinity at pH 9.5, followed by FA. The proliferation of ARGs mediated by mobile genetic element was promoted under both acidic and alkaline conditions, attributed to the promotion of FNA and FA, respectively. Overall, this study highlights the inhibitory effects of acidity and alkalinity on antibiotic removal during nitritation.

Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community

Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.

An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes

Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.

Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

Review in anaerobic digestion of food waste

Due to the special property of food waste (FW), anaerobic digestion of food waste is facing many challenges like foaming, acidification, ammonia nitrogen and (NH4+-N) inhibition which resulted in a low biogas yield. A better understanding on the problems exiting in the FW anaerobic digestion would enhance the bio-energy recovery and increase the stable operation. Meanwhile, to overcome the bottle necks, pretreatment, co-digestion and additives is proposed as well as the solutions to improve biogas yield in FW digestion system. At last, future research directions regarding FW anaerobic digestion were proposed.

Enhanced nutrient recovery from anaerobically digested poultry wastewater through struvite precipitation by organic acid pre-treatment and seeding in a bubble column electrolytic reactor

Limited mineralization of organic phosphorus to phosphate during the anaerobic digestion process poses a significant challenge in the development of cost-effective nutrient recovery strategies from anaerobically digested poultry wastewater (ADPW). This study investigated the influence of organic acids on phosphorus solubilization from ADPW, followed by its recycling in the form of struvite using a bubble column electrolytic reactor (BCER) without adding chemicals. The impact of seeding on the efficiency of PO43- and NH3-N recovery as well as the size distribution of recovered precipitates from the acid pre-treated ADPW was also evaluated. Pre-treatment of the ADPW with oxalic acid achieved complete solubilization of phosphorus, reaching ∼100% extraction efficiency at pH 2.5. The maximum removal efficiency of phosphate and ammonia-nitrogen from the ADPW were 88.9% and 90.1%, respectively, while the addition of 5 and 10 g/L struvite seed to the BCER increased PO43- removal efficiency by 9.6% and 11.5%, respectively. The value of the kinetic rate constant, k, increased from 0.0176 min-1 (unseeded) to 0.0198 min-1, 0.0307 min-1, and 0.0375 min-1 with the seed loading rate of 2, 5, and 10 g/L, respectively. Concurrently, the average particle size rose from 75.3 μm (unseeded) to 82.1 μm, 125.7 μm, and 148.9 μm, respectively. Results from XRD, FTIR, EDS, and dissolved chemical analysis revealed that the solid product obtained from the recovery process was a multi-nutrient fertilizer consisting of 94.7% struvite with negligible levels of heavy metals.

Co-exposure of microplastics and sulfamethoxazole propagated antibiotic resistance genes in sediments by regulating the microbial carbon metabolism

The concerns on the carriers of microplastics (MPs) on co-existing pollutants in aquatic environments are sharply rising in recent years. However, little is known about their interactions on the colonization of microbiota, especially for the spread of pathogens and antibiotic resistance genes (ARGs). Therefore, this study aimed to investigate the influences on the propagation of ARGs in sediments by the co-exposure of different MPs and sulfamethoxazole (SMX). The results showed that the presence of MPs significantly enhanced the contents of total organic carbon, while having no effects on the removal of SMX in sediments. Exposure to SMX and MPs obviously activated the microbial carbon utilization capacities based on the BIOLOG method. The propagation of ARGs in sediments was activated by SMX, which was further promoted by the presence of polylactic acid (PLA) MPs, but significantly lowered by the co-exposed polyethylene (PE) MPs. This apparent difference may be attributed to the distinct influence on the antibiotic efflux pumps of two MPs. Moreover, the propagation of ARGs may be also dominated by microbial carbon metabolism in sediments, especially through regulating the carbon sources of carboxylic acids, carbohydrates, and amino acids. This study provides new insights into the carrier effects of MPs in sediments.

Antibiotics resistance removal from piggery wastewater by an integrated anaerobic-aerobic biofilm reactor: Efficiency and mechanism

Antibiotic resistance residual in piggery wastewater poses serious threat to environment and human health. Biological treatment process is commonly installed to remove nutrient from piggery wastewater and also effective in removing antibiotics to varying degrees. But the specific pathways and mechanisms involved in the removal of antibiotic resistance are not yet well-understood. An integrated anaerobic-aerobic biofilm reactor (IAOBR) has been demonstrated efficient in removing conventional nutrients. It is here shown that the IAOBR effectively removed 79.0% of Sulfonamides, 55.7% of Tetracyclines and 53.6% of Quinones. Antibiotic resistance bacteria (ARB) were simultaneously inactivated by ~0.5 logs. Antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were decreased by 0.51 logs and 0.42 logs, respectively. The antibiotics were mainly removed through aerobic compartments of the IAOBR. The mass loss of antibiotics in the reactor was achieved by biodegradation and adsorption, accounting for 52.1% and 47.9%, respectively. An obvious accumulation of ARGs was observed in the activated sludge. The potential host of ARGs was analyzed via microbial community and network. Partial least squares-structural equation model and correlation analysis revealed that the enrichment of ARGs was positively affected by MGEs, followed by bacterial community and ARBs, but the effect of antibiotics on ARGs was negative. Outcomes of this study provide valuable insights into the mechanisms of antibiotic resistance removal in biological treatment processes.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion

Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.

Fenton oxidation treatment of oxytetracycline fermentation residues: Harmless performance and bioresource properties

The pharmaceutical factories of oxytetracycline (OTC) massively produce OTC fermentation residues (OFRs). The high content of residual OTC and antibiotic resistance genes in OFRs must to be considered and controlled at an acceptable level. This study therefore investigated the applicability of Fenton oxidation in OTC degradation and resistant gene inactivation of OFRs. The results revealed that Fe²⁺ as catalyzer could very rapidly activate H₂O₂ to produce HO^•, leading to instantaneous degradation of OTC. The optimum conditions for OTC removal were 60 mM H₂O₂ and 140 mg/L Fe²⁺ under pH 7. After Fenton oxidation treatment, the release of water-soluble polysaccharides, NO₃-N, and PO₄-P was enhanced, whereas for proteins and NH₃-N were reduced. Three soluble fluorescence components (humic, tryptophan-like, and humic acid-like substances) were identified through fluorescence spectra with parallel factor analysis, and their reduction exceeded 50% after Fenton oxidation. There were twelve intermediates and three degradation pathways of OTC in OFRs during Fenton process. According to toxicity prediction, the comprehensive toxicity of OTC in OFRs was alleviated via Fenton oxidation treatment. In addition, Fenton oxidation showed the ability to reduce antibiotic resistance genes and mobile genetic elements, and even tetO, tetG, intI1, and intI2 were eliminated completely. These results suggested that Fenton oxidation treatment could be an efficient strategy for removing OTC and resistance genes in OFRs.

The advantage of a two-stage nitrification method for fertilizer recovery from human urine

Recycling nutrients (nitrogen, phosphorus, and potassium) from human urine can potentially offset more than 13% of global agricultural fertilizer demand. Biological nitrification is a promising method for converting volatile ammonia in high-strength human urine into stable ammonium nitrate (a typical fertilizer), but it is usually terminated in the intermediate production of nitrite due to the inhibition of nitrite-oxidizing bacteria by free nitrous acid (FNA). This study aimed to develop a stable nitrification process in a unique two-stage bioreactor by removing critical barriers associated with FNA inhibition. Experimental results show that half of the ammonium in high-strength urine was successfully converted into nitrate, forming valuable ammonium nitrate (with a nitrogen concentration greater than 1500 mg N/L). The ammonium nitrate solution could retain most phosphorus (75% ± 3%) and potassium (96% ± 1%) in human urine, resulting in nearly full nutrient recovery. Once concentrated, the liquid compound fertilizer of ammonium nitrate was generated. Based on an assessment of economic and environmental impacts at the urban scale, urine diversion for nutrient recovery using a technical combination of nitrification and reverse osmosis could reduce total energy input by 43%, greenhouse gas emission by 40%, and cost by 33% compared to conventional wastewater management. Further research is needed to optimize the two-stage nitrification method on a larger scale.

Effect of photocatalysis on the physicochemical properties of liquid digestate

Antibiotic residues pose a risk to the agricultural application of liquid digestate. In our previous study, photocatalysis was employed to degrade the antibiotics in liquid digestate and observed that the removal efficiency of TC, OTC, and CTC was up to 94.99%, 88.92%, and 95.52%, respectively, at the optimal experimental level, demonstrating the feasibility of this technology. In this study, the liquid digestate after photocatalysis was analyzed to evaluate the effect of photocatalysis on the nutrients, phytotoxicity, and bacterial community of liquid digestate. The results showed that photocatalysis had little effect on the major nutrients TN, TP, and TK in liquid digestate. However, photocatalysis could cause an increase in tryptophan substances as well as soluble microbial by-products and a decrease in humic acid substances in the liquid digestate. The toxicity of liquid digestate after photocatalysis exhibited an increasing trend followed by a decreasing trend, and the liquid digestate after photocatalysis for 2 h had a promoting effect on seed germination and root growth. The richness, diversity, and evenness of bacterial communities in liquid digestate were decreased as a result of photocatalysis. The dominant species in the liquid digestate was dramatically changed by photocatalysis, and the antibiotic concentration also had a major effect on the dominant species in the liquid digestate after photocatalysis. After photocatalysis for 2 h, the dominant species in the liquid digestate changed from Firmicutes to Proteobacteria.

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.

High-yield production of single-cell protein from starch processing wastewater using co-cultivation of yeasts

Single-cell protein (SCP) from potato starch processing wastewater (PSPW) shows great potential against protein scarcity and unsustainable production of plant and animal proteins. In this study, five yeasts were selected to conduct a series of PSPW fermentation for obtaining high-value SCP by optimizing fermentation conditions. The yeast combination was optimized as Candida utilis, Geotrichum candidum and Candida tropicalis with the volume proportion of 9:5:1. The inoculum size, temperature, rotation speed and initial pH were optimized at 12 %, 24℃, 200 r·min^-1 and ∼ 4.13 (natural pH), respectively. At the optimal conditions, SCP yield of 3.06 g·L^-1 and water-soluble protein of 17.32 % were obtained with the chemical oxygen demand removal of 56.9 %. A resource-recycling process of PSPW was proposed by coupling yeast fermentation and up-flow anaerobic sludge blanket (UASB) treatment to achieve simultaneous high-level organic removal and SCP production, which could be a promising alternative technology for PSPW treatment.